Diff of the two buildlogs: -- --- b1/build.log 2025-02-17 18:52:30.407675014 +0000 +++ b2/build.log 2025-02-17 19:01:25.379723893 +0000 @@ -1,6 +1,7 @@ +W: cgroups are not available on the host, not using them. I: pbuilder: network access will be disabled during build -I: Current time: Sun Mar 22 13:11:36 -12 2026 -I: pbuilder-time-stamp: 1774228296 +I: Current time: Tue Feb 18 08:52:35 +14 2025 +I: pbuilder-time-stamp: 1739818355 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -22,52 +23,83 @@ dpkg-source: info: unpacking diamond-aligner_2.1.9-2.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/414869/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1926292/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Feb 17 18:52 /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/1926292/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1926292/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='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='16b95be0b0f54f8e9b52f891fee4ea78' - 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='414869' - PS1='# ' - PS2='> ' + 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=1926292 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.D2bmhxXd/pbuilderrc_N3zv --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.D2bmhxXd/b1 --logfile b1/build.log diamond-aligner_2.1.9-2.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.D2bmhxXd/pbuilderrc_TNj5 --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.D2bmhxXd/b2 --logfile b2/build.log diamond-aligner_2.1.9-2.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink03-arm64 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/414869/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1926292/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: 59 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.1 [920 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] -Fetched 38.8 MB in 0s (123 MB/s) +Fetched 38.8 MB in 0s (212 MB/s) Preconfiguring packages ... Selecting previously unselected package libproc2-0:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19918 files and directories currently installed.) @@ -429,7 +461,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/diamond-aligner-2.1.9/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../diamond-aligner_2.1.9-2_source.changes +I: user script /srv/workspace/pbuilder/1926292/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/1926292/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/diamond-aligner-2.1.9/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../diamond-aligner_2.1.9-2_source.changes dpkg-buildpackage: info: source package diamond-aligner dpkg-buildpackage: info: source version 2.1.9-2 dpkg-buildpackage: info: source distribution unstable @@ -486,8 +522,8 @@ -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE --- Configuring done (3.2s) --- Generating done (0.1s) +-- Configuring done (2.9s) +-- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -517,64 +553,60 @@ cd /build/reproducible-path/diamond-aligner-2.1.9/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/diamond-aligner-2.1.9 /build/reproducible-path/diamond-aligner-2.1.9 /build/reproducible-path/diamond-aligner-2.1.9/obj-aarch64-linux-gnu /build/reproducible-path/diamond-aligner-2.1.9/obj-aarch64-linux-gnu /build/reproducible-path/diamond-aligner-2.1.9/obj-aarch64-linux-gnu/CMakeFiles/arch_neon.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/diamond-aligner-2.1.9/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-2.1.9/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/diamond-aligner-2.1.9/obj-aarch64-linux-gnu' make -f CMakeFiles/arch_neon.dir/build.make CMakeFiles/arch_neon.dir/build +[ 0%] Building CXX object CMakeFiles/arch_generic.dir/src/dp/swipe/banded_3frame_swipe.cpp.o make[3]: Entering directory '/build/reproducible-path/diamond-aligner-2.1.9/obj-aarch64-linux-gnu' -make[3]: Entering directory '/build/reproducible-path/diamond-aligner-2.1.9/obj-aarch64-linux-gnu' -[ 0%] Building CXX object CMakeFiles/arch_neon.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-2.1.9/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -DDISPATCH_ARCH=ARCH_GENERIC -DARCH_ID=0 -DEigen=Eigen_GENERIC -MD -MT CMakeFiles/arch_generic.dir/src/dp/swipe/banded_3frame_swipe.cpp.o -MF CMakeFiles/arch_generic.dir/src/dp/swipe/banded_3frame_swipe.cpp.o.d -o CMakeFiles/arch_generic.dir/src/dp/swipe/banded_3frame_swipe.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/banded_3frame_swipe.cpp +[ 1%] Building CXX object CMakeFiles/arch_generic.dir/src/search/stage1_2.cpp.o [ 2%] Building CXX object CMakeFiles/arch_neon.dir/src/dp/swipe/banded_3frame_swipe.cpp.o -[ 2%] Building CXX object CMakeFiles/arch_generic.dir/src/dp/swipe/swipe_wrapper.cpp.o -[ 2%] Building CXX object CMakeFiles/arch_generic.dir/src/masking/tantan.cpp.o -[ 3%] 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-2.1.9/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -DDISPATCH_ARCH=ARCH_NEON -DARCH_ID=4 -D__ARM_NEON -D__aarch64__ -DEigen=Eigen_NEON -MD -MT CMakeFiles/arch_neon.dir/src/dp/swipe/banded_3frame_swipe.cpp.o -MF CMakeFiles/arch_neon.dir/src/dp/swipe/banded_3frame_swipe.cpp.o.d -o CMakeFiles/arch_neon.dir/src/dp/swipe/banded_3frame_swipe.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/banded_3frame_swipe.cpp -/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_NEON -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.9/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -DDISPATCH_ARCH=ARCH_GENERIC -DARCH_ID=0 -DEigen=Eigen_GENERIC -MD -MT CMakeFiles/arch_generic.dir/src/dp/swipe/swipe_wrapper.cpp.o -MF CMakeFiles/arch_generic.dir/src/dp/swipe/swipe_wrapper.cpp.o.d -o CMakeFiles/arch_generic.dir/src/dp/swipe/swipe_wrapper.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/swipe_wrapper.cpp -/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_NEON -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.9/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -DDISPATCH_ARCH=ARCH_GENERIC -DARCH_ID=0 -DEigen=Eigen_GENERIC -MD -MT CMakeFiles/arch_generic.dir/src/masking/tantan.cpp.o -MF CMakeFiles/arch_generic.dir/src/masking/tantan.cpp.o.d -o CMakeFiles/arch_generic.dir/src/masking/tantan.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/masking/tantan.cpp -[ 3%] Building CXX object CMakeFiles/arch_generic.dir/src/tools/benchmark.cpp.o -/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_NEON -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.9/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -DDISPATCH_ARCH=ARCH_NEON -DARCH_ID=4 -D__ARM_NEON -D__aarch64__ -DEigen=Eigen_NEON -MD -MT CMakeFiles/arch_neon.dir/src/search/stage1_2.cpp.o -MF CMakeFiles/arch_neon.dir/src/search/stage1_2.cpp.o.d -o CMakeFiles/arch_neon.dir/src/search/stage1_2.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/search/stage1_2.cpp -/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_NEON -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.9/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -DDISPATCH_ARCH=ARCH_GENERIC -DARCH_ID=0 -DEigen=Eigen_GENERIC -MD -MT CMakeFiles/arch_generic.dir/src/dp/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-2.1.9/src/dp/scan_diags.cpp -[ 3%] Building CXX object CMakeFiles/arch_generic.dir/src/dp/swipe/banded_3frame_swipe.cpp.o -[ 4%] Building CXX object CMakeFiles/arch_generic.dir/src/dp/pfscan/pfscan.cpp.o -[ 5%] 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-2.1.9/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -DDISPATCH_ARCH=ARCH_GENERIC -DARCH_ID=0 -DEigen=Eigen_GENERIC -MD -MT CMakeFiles/arch_generic.dir/src/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-2.1.9/src/search/stage1_2.cpp +[ 2%] Building CXX object CMakeFiles/arch_generic.dir/src/tools/benchmark.cpp.o /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_NEON -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.9/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -DDISPATCH_ARCH=ARCH_GENERIC -DARCH_ID=0 -DEigen=Eigen_GENERIC -MD -MT CMakeFiles/arch_generic.dir/src/tools/benchmark.cpp.o -MF CMakeFiles/arch_generic.dir/src/tools/benchmark.cpp.o.d -o CMakeFiles/arch_generic.dir/src/tools/benchmark.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/tools/benchmark.cpp +[ 2%] Building CXX object CMakeFiles/arch_neon.dir/src/search/stage1_2.cpp.o +[ 3%] Building CXX object CMakeFiles/arch_generic.dir/src/dp/swipe/swipe_wrapper.cpp.o +[ 4%] Building CXX object CMakeFiles/arch_neon.dir/src/tools/benchmark.cpp.o +[ 4%] Building CXX object CMakeFiles/arch_generic.dir/src/masking/tantan.cpp.o +/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_NEON -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.9/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -DDISPATCH_ARCH=ARCH_NEON -DARCH_ID=4 -D__ARM_NEON -D__aarch64__ -DEigen=Eigen_NEON -MD -MT CMakeFiles/arch_neon.dir/src/search/stage1_2.cpp.o -MF 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CMakeFiles/arch_generic.dir/src/dp/swipe/swipe_wrapper.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/swipe_wrapper.cpp +[ 5%] Building CXX object CMakeFiles/arch_generic.dir/src/dp/scan_diags.cpp.o [ 5%] 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-2.1.9/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -DDISPATCH_ARCH=ARCH_GENERIC -DARCH_ID=0 -DEigen=Eigen_GENERIC -MD -MT 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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-2.1.9/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -DDISPATCH_ARCH=ARCH_GENERIC -DARCH_ID=0 -DEigen=Eigen_GENERIC -MD -MT CMakeFiles/arch_generic.dir/src/dp/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-2.1.9/src/dp/swipe/anchored_wrapper.cpp -[ 7%] Building CXX object CMakeFiles/arch_generic.dir/src/dp/score_profile.cpp.o -/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_NEON -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.9/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -DDISPATCH_ARCH=ARCH_GENERIC -DARCH_ID=0 -DEigen=Eigen_GENERIC -MD -MT CMakeFiles/arch_generic.dir/src/dp/score_profile.cpp.o -MF CMakeFiles/arch_generic.dir/src/dp/score_profile.cpp.o.d -o CMakeFiles/arch_generic.dir/src/dp/score_profile.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/dp/score_profile.cpp -[ 8%] Building CXX object CMakeFiles/arch_neon.dir/src/masking/tantan.cpp.o +[ 5%] Building CXX object CMakeFiles/arch_neon.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-2.1.9/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -DDISPATCH_ARCH=ARCH_NEON -DARCH_ID=4 -D__ARM_NEON -D__aarch64__ -DEigen=Eigen_NEON -MD -MT CMakeFiles/arch_neon.dir/src/dp/swipe/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-2.1.9/src/dp/swipe/swipe_wrapper.cpp +[ 6%] Building CXX object CMakeFiles/arch_neon.dir/src/masking/tantan.cpp.o /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_NEON -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.9/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -DDISPATCH_ARCH=ARCH_NEON -DARCH_ID=4 -D__ARM_NEON -D__aarch64__ -DEigen=Eigen_NEON -MD -MT CMakeFiles/arch_neon.dir/src/masking/tantan.cpp.o -MF CMakeFiles/arch_neon.dir/src/masking/tantan.cpp.o.d -o CMakeFiles/arch_neon.dir/src/masking/tantan.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/masking/tantan.cpp -[ 8%] Building CXX object CMakeFiles/arch_neon.dir/src/dp/scan_diags.cpp.o +[ 6%] Building CXX object CMakeFiles/arch_neon.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-2.1.9/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 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-DNDEBUG -std=gnu++17 -DDISPATCH_ARCH=ARCH_GENERIC -DARCH_ID=0 -DEigen=Eigen_GENERIC -MD -MT CMakeFiles/arch_generic.dir/src/dp/pfscan/pfscan.cpp.o -MF CMakeFiles/arch_generic.dir/src/dp/pfscan/pfscan.cpp.o.d -o CMakeFiles/arch_generic.dir/src/dp/pfscan/pfscan.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/dp/pfscan/pfscan.cpp In file included from /build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/cell_update.h:23, from /build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/swipe_wrapper.cpp:34: -/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/stat_cell.h: In instantiation of ‘void set_channel(ForwardCell&, int, typename ARCH_NEON::ScoreTraits::Score) [with Sv = int; typename ARCH_NEON::ScoreTraits::Score = int]’: -/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/full_matrix.h:76:15: required from ‘void DP::Swipe::ARCH_NEON::Matrix::set_zero(int) [with Sv = ForwardCell]’ +/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/stat_cell.h: In instantiation of ‘void set_channel(ForwardCell&, int, typename ARCH_GENERIC::ScoreTraits::Score) [with Sv = int; typename ARCH_GENERIC::ScoreTraits::Score = int]’: +/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/full_matrix.h:76:15: required from ‘void DP::Swipe::ARCH_GENERIC::Matrix::set_zero(int) [with Sv = ForwardCell]’ 76 | set_channel(hgap_[i], c, z); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/full_swipe.h:232:17: required from ‘std::__cxx11::list DP::Swipe::ARCH_NEON::swipe(It, It, std::atomic*, _cbs, std::vector&, DP::Params&) [with _sv = int; _cbs = DP::NoCBS; It = __gnu_cxx::__normal_iterator >; Cfg = SwipeConfig, ForwardCell, VectorIdMask >]’ +/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/full_swipe.h:232:17: required from ‘std::__cxx11::list DP::Swipe::ARCH_GENERIC::swipe(It, It, std::atomic*, _cbs, std::vector&, DP::Params&) [with _sv = int; _cbs = DP::NoCBS; It = __gnu_cxx::__normal_iterator >; Cfg = SwipeConfig, ForwardCell, VectorIdMask >]’ 232 | dp.set_zero(c); | ~~~~~~~~~~~^~~ -/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/swipe_wrapper.cpp:141:61: required from ‘std::__cxx11::list DP::BandedSwipe::ARCH_NEON::dispatch_swipe(It, It, std::atomic*, Cbs, std::vector&, DP::Params&) [with Sv = int; Cbs = DP::NoCBS; It = __gnu_cxx::__normal_iterator >; Cfg = SwipeConfig, ForwardCell, VectorIdMask >]’ +/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/swipe_wrapper.cpp:141:61: required from ‘std::__cxx11::list DP::BandedSwipe::ARCH_GENERIC::dispatch_swipe(It, It, std::atomic*, Cbs, std::vector&, DP::Params&) [with Sv = int; Cbs = DP::NoCBS; It = __gnu_cxx::__normal_iterator >; Cfg = SwipeConfig, ForwardCell, VectorIdMask >]’ 141 | return ::DP::Swipe::DISPATCH_ARCH::swipe(begin, end, next, composition_bias, overflow, p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/swipe_wrapper.cpp:154:44: required from ‘std::__cxx11::list DP::BandedSwipe::ARCH_NEON::dispatch_swipe(It, It, std::atomic*, std::vector&, DP::Params&) [with Sv = int; It = __gnu_cxx::__normal_iterator >; Cfg = SwipeConfig, ForwardCell, VectorIdMask >]’ +/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/swipe_wrapper.cpp:154:44: required from ‘std::__cxx11::list DP::BandedSwipe::ARCH_GENERIC::dispatch_swipe(It, It, std::atomic*, std::vector&, DP::Params&) [with Sv = int; It = __gnu_cxx::__normal_iterator >; Cfg = SwipeConfig, ForwardCell, VectorIdMask >]’ 154 | return dispatch_swipe(begin, end, next, NoCBS(), overflow, p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/swipe_wrapper.cpp:177:38: required from ‘std::__cxx11::list DP::BandedSwipe::ARCH_NEON::dispatch_swipe(It, It, std::atomic*, std::vector&, int, int, DP::Params&) [with Sv = int; It = __gnu_cxx::__normal_iterator >]’ +/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/swipe_wrapper.cpp:177:38: required from ‘std::__cxx11::list DP::BandedSwipe::ARCH_GENERIC::dispatch_swipe(It, It, std::atomic*, std::vector&, int, int, DP::Params&) [with Sv = int; It = __gnu_cxx::__normal_iterator >]’ 177 | return dispatch_swipe(begin, end, next, overflow, p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/swipe_wrapper.cpp:277:32: required from ‘std::__cxx11::list DP::BandedSwipe::ARCH_NEON::swipe_threads(It, It, std::vector&, int, int, DP::Params&) [with Sv = int; It = __gnu_cxx::__normal_iterator >]’ +/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/swipe_wrapper.cpp:277:32: required from ‘std::__cxx11::list DP::BandedSwipe::ARCH_GENERIC::swipe_threads(It, It, std::vector&, int, int, DP::Params&) [with Sv = int; It = __gnu_cxx::__normal_iterator >]’ 277 | return dispatch_swipe(begin, end, &next, overflow, round, bin, p); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/swipe_wrapper.cpp:341:35: required from ‘std::pair, std::vector > DP::BandedSwipe::ARCH_NEON::swipe_bin(unsigned int, It, It, int, DP::Params&) [with It = __gnu_cxx::__normal_iterator >]’ +/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/swipe_wrapper.cpp:341:35: required from ‘std::pair, std::vector > DP::BandedSwipe::ARCH_GENERIC::swipe_bin(unsigned int, It, It, int, DP::Params&) [with It = __gnu_cxx::__normal_iterator >]’ 341 | out = swipe_threads(begin, end, overflow, round, bin, p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/swipe_wrapper.cpp:397:21: required from here @@ -583,26 +615,26 @@ /build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/stat_cell.h:100:21: warning: casting ‘ForwardCell’ to ‘int&’ does not use ‘ForwardCell::operator int32_t() const’ [-Wcast-user-defined] 100 | set_channel((Sv&)v, i, x); | ^~~~~~ -/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/stat_cell.h: In instantiation of ‘void set_channel(BackwardCell&, int, typename ARCH_NEON::ScoreTraits::Score) [with Sv = int; typename ARCH_NEON::ScoreTraits::Score = int]’: -/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/full_matrix.h:76:15: required from ‘void DP::Swipe::ARCH_NEON::Matrix::set_zero(int) [with Sv = BackwardCell]’ +/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/stat_cell.h: In instantiation of ‘void set_channel(BackwardCell&, int, typename ARCH_GENERIC::ScoreTraits::Score) [with Sv = int; typename ARCH_GENERIC::ScoreTraits::Score = int]’: +/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/full_matrix.h:76:15: required from ‘void DP::Swipe::ARCH_GENERIC::Matrix::set_zero(int) [with Sv = BackwardCell]’ 76 | set_channel(hgap_[i], c, z); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/full_swipe.h:232:17: required from ‘std::__cxx11::list DP::Swipe::ARCH_NEON::swipe(It, It, std::atomic*, _cbs, std::vector&, DP::Params&) [with _sv = int; _cbs = DP::NoCBS; It = __gnu_cxx::__normal_iterator >; Cfg = SwipeConfig, BackwardCell, VectorIdMask >]’ +/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/full_swipe.h:232:17: required from ‘std::__cxx11::list DP::Swipe::ARCH_GENERIC::swipe(It, It, std::atomic*, _cbs, std::vector&, DP::Params&) [with _sv = int; _cbs = DP::NoCBS; It = __gnu_cxx::__normal_iterator >; Cfg = SwipeConfig, BackwardCell, VectorIdMask >]’ 232 | dp.set_zero(c); | ~~~~~~~~~~~^~~ -/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/swipe_wrapper.cpp:141:61: required from ‘std::__cxx11::list DP::BandedSwipe::ARCH_NEON::dispatch_swipe(It, It, std::atomic*, Cbs, std::vector&, DP::Params&) [with Sv = int; Cbs = DP::NoCBS; It = __gnu_cxx::__normal_iterator >; Cfg = SwipeConfig, BackwardCell, VectorIdMask >]’ +/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/swipe_wrapper.cpp:141:61: required from ‘std::__cxx11::list DP::BandedSwipe::ARCH_GENERIC::dispatch_swipe(It, It, std::atomic*, Cbs, std::vector&, DP::Params&) [with Sv = int; Cbs = DP::NoCBS; It = __gnu_cxx::__normal_iterator >; Cfg = SwipeConfig, BackwardCell, VectorIdMask >]’ 141 | return ::DP::Swipe::DISPATCH_ARCH::swipe(begin, end, next, composition_bias, overflow, p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/swipe_wrapper.cpp:154:44: required from ‘std::__cxx11::list DP::BandedSwipe::ARCH_NEON::dispatch_swipe(It, It, std::atomic*, std::vector&, DP::Params&) [with Sv = int; It = __gnu_cxx::__normal_iterator >; Cfg = SwipeConfig, BackwardCell, VectorIdMask >]’ +/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/swipe_wrapper.cpp:154:44: required from ‘std::__cxx11::list DP::BandedSwipe::ARCH_GENERIC::dispatch_swipe(It, It, std::atomic*, std::vector&, DP::Params&) [with Sv = int; It = __gnu_cxx::__normal_iterator >; Cfg = SwipeConfig, BackwardCell, VectorIdMask >]’ 154 | return dispatch_swipe(begin, end, next, NoCBS(), overflow, p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/swipe_wrapper.cpp:187:38: required from ‘std::__cxx11::list DP::BandedSwipe::ARCH_NEON::dispatch_swipe(It, It, std::atomic*, std::vector&, int, int, DP::Params&) [with Sv = int; It = __gnu_cxx::__normal_iterator >]’ +/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/swipe_wrapper.cpp:187:38: required from ‘std::__cxx11::list DP::BandedSwipe::ARCH_GENERIC::dispatch_swipe(It, It, std::atomic*, std::vector&, int, int, DP::Params&) [with Sv = int; It = __gnu_cxx::__normal_iterator >]’ 187 | return dispatch_swipe(begin, end, next, overflow, p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/swipe_wrapper.cpp:277:32: required from ‘std::__cxx11::list DP::BandedSwipe::ARCH_NEON::swipe_threads(It, It, std::vector&, int, int, DP::Params&) [with Sv = int; It = __gnu_cxx::__normal_iterator >]’ +/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/swipe_wrapper.cpp:277:32: required from ‘std::__cxx11::list DP::BandedSwipe::ARCH_GENERIC::swipe_threads(It, It, std::vector&, int, int, DP::Params&) [with Sv = int; It = __gnu_cxx::__normal_iterator >]’ 277 | return dispatch_swipe(begin, end, &next, overflow, round, bin, p); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/swipe_wrapper.cpp:341:35: required from ‘std::pair, std::vector > DP::BandedSwipe::ARCH_NEON::swipe_bin(unsigned int, It, It, int, DP::Params&) [with It = __gnu_cxx::__normal_iterator >]’ +/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/swipe_wrapper.cpp:341:35: required from ‘std::pair, std::vector > DP::BandedSwipe::ARCH_GENERIC::swipe_bin(unsigned int, It, It, int, DP::Params&) [with It = __gnu_cxx::__normal_iterator >]’ 341 | out = swipe_threads(begin, end, overflow, round, bin, p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/swipe_wrapper.cpp:397:21: required from here @@ -613,26 +645,26 @@ | ^~~~~~ In file included from /build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/cell_update.h:23, from /build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/swipe_wrapper.cpp:34: -/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/stat_cell.h: In instantiation of ‘void set_channel(ForwardCell&, int, typename ARCH_GENERIC::ScoreTraits::Score) [with Sv = int; typename ARCH_GENERIC::ScoreTraits::Score = int]’: -/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/full_matrix.h:76:15: required from ‘void DP::Swipe::ARCH_GENERIC::Matrix::set_zero(int) [with Sv = ForwardCell]’ +/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/stat_cell.h: In instantiation of ‘void set_channel(ForwardCell&, int, typename ARCH_NEON::ScoreTraits::Score) [with Sv = int; typename ARCH_NEON::ScoreTraits::Score = int]’: +/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/full_matrix.h:76:15: required from ‘void DP::Swipe::ARCH_NEON::Matrix::set_zero(int) [with Sv = ForwardCell]’ 76 | set_channel(hgap_[i], c, z); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/full_swipe.h:232:17: required from ‘std::__cxx11::list DP::Swipe::ARCH_GENERIC::swipe(It, It, std::atomic*, _cbs, std::vector&, DP::Params&) [with _sv = int; _cbs = DP::NoCBS; It = __gnu_cxx::__normal_iterator >; Cfg = SwipeConfig, ForwardCell, VectorIdMask >]’ +/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/full_swipe.h:232:17: required from ‘std::__cxx11::list DP::Swipe::ARCH_NEON::swipe(It, It, std::atomic*, _cbs, std::vector&, DP::Params&) [with _sv = int; _cbs = DP::NoCBS; It = __gnu_cxx::__normal_iterator >; Cfg = SwipeConfig, ForwardCell, VectorIdMask >]’ 232 | dp.set_zero(c); | ~~~~~~~~~~~^~~ -/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/swipe_wrapper.cpp:141:61: required from ‘std::__cxx11::list DP::BandedSwipe::ARCH_GENERIC::dispatch_swipe(It, It, std::atomic*, Cbs, std::vector&, DP::Params&) [with Sv = int; Cbs = DP::NoCBS; It = __gnu_cxx::__normal_iterator >; Cfg = SwipeConfig, ForwardCell, VectorIdMask >]’ +/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/swipe_wrapper.cpp:141:61: required from ‘std::__cxx11::list DP::BandedSwipe::ARCH_NEON::dispatch_swipe(It, It, std::atomic*, Cbs, std::vector&, DP::Params&) [with Sv = int; Cbs = DP::NoCBS; It = __gnu_cxx::__normal_iterator >; Cfg = SwipeConfig, ForwardCell, VectorIdMask >]’ 141 | return ::DP::Swipe::DISPATCH_ARCH::swipe(begin, end, next, composition_bias, overflow, p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/swipe_wrapper.cpp:154:44: required from ‘std::__cxx11::list DP::BandedSwipe::ARCH_GENERIC::dispatch_swipe(It, It, std::atomic*, std::vector&, DP::Params&) [with Sv = int; It = __gnu_cxx::__normal_iterator >; Cfg = SwipeConfig, ForwardCell, VectorIdMask >]’ +/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/swipe_wrapper.cpp:154:44: required from ‘std::__cxx11::list DP::BandedSwipe::ARCH_NEON::dispatch_swipe(It, It, std::atomic*, std::vector&, DP::Params&) [with Sv = int; It = __gnu_cxx::__normal_iterator >; Cfg = SwipeConfig, ForwardCell, VectorIdMask >]’ 154 | return dispatch_swipe(begin, end, next, NoCBS(), overflow, p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/swipe_wrapper.cpp:177:38: required from ‘std::__cxx11::list DP::BandedSwipe::ARCH_GENERIC::dispatch_swipe(It, It, std::atomic*, std::vector&, int, int, DP::Params&) [with Sv = int; It = __gnu_cxx::__normal_iterator >]’ +/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/swipe_wrapper.cpp:177:38: required from ‘std::__cxx11::list DP::BandedSwipe::ARCH_NEON::dispatch_swipe(It, It, std::atomic*, std::vector&, int, int, DP::Params&) [with Sv = int; It = __gnu_cxx::__normal_iterator >]’ 177 | return dispatch_swipe(begin, end, next, overflow, p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/swipe_wrapper.cpp:277:32: required from ‘std::__cxx11::list DP::BandedSwipe::ARCH_GENERIC::swipe_threads(It, It, std::vector&, int, int, DP::Params&) [with Sv = int; It = __gnu_cxx::__normal_iterator >]’ +/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/swipe_wrapper.cpp:277:32: required from ‘std::__cxx11::list DP::BandedSwipe::ARCH_NEON::swipe_threads(It, It, std::vector&, int, int, DP::Params&) [with Sv = int; It = __gnu_cxx::__normal_iterator >]’ 277 | return dispatch_swipe(begin, end, &next, overflow, round, bin, p); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/swipe_wrapper.cpp:341:35: required from ‘std::pair, std::vector > DP::BandedSwipe::ARCH_GENERIC::swipe_bin(unsigned int, It, It, int, DP::Params&) [with It = __gnu_cxx::__normal_iterator >]’ +/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/swipe_wrapper.cpp:341:35: required from ‘std::pair, std::vector > DP::BandedSwipe::ARCH_NEON::swipe_bin(unsigned int, It, It, int, DP::Params&) [with It = __gnu_cxx::__normal_iterator >]’ 341 | out = swipe_threads(begin, end, overflow, round, bin, p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/swipe_wrapper.cpp:397:21: required from here @@ -641,26 +673,26 @@ /build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/stat_cell.h:100:21: warning: casting ‘ForwardCell’ to ‘int&’ does not use ‘ForwardCell::operator int32_t() const’ [-Wcast-user-defined] 100 | set_channel((Sv&)v, i, x); | ^~~~~~ -/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/stat_cell.h: In instantiation of ‘void set_channel(BackwardCell&, int, typename ARCH_GENERIC::ScoreTraits::Score) [with Sv = int; typename ARCH_GENERIC::ScoreTraits::Score = int]’: -/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/full_matrix.h:76:15: required from ‘void DP::Swipe::ARCH_GENERIC::Matrix::set_zero(int) [with Sv = BackwardCell]’ +/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/stat_cell.h: In instantiation of ‘void set_channel(BackwardCell&, int, typename ARCH_NEON::ScoreTraits::Score) [with Sv = int; typename ARCH_NEON::ScoreTraits::Score = int]’: +/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/full_matrix.h:76:15: required from ‘void DP::Swipe::ARCH_NEON::Matrix::set_zero(int) [with Sv = BackwardCell]’ 76 | set_channel(hgap_[i], c, z); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/full_swipe.h:232:17: required from ‘std::__cxx11::list DP::Swipe::ARCH_GENERIC::swipe(It, It, std::atomic*, _cbs, std::vector&, DP::Params&) [with _sv = int; _cbs = DP::NoCBS; It = __gnu_cxx::__normal_iterator >; Cfg = SwipeConfig, BackwardCell, VectorIdMask >]’ +/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/full_swipe.h:232:17: required from ‘std::__cxx11::list DP::Swipe::ARCH_NEON::swipe(It, It, std::atomic*, _cbs, std::vector&, DP::Params&) [with _sv = int; _cbs = DP::NoCBS; It = __gnu_cxx::__normal_iterator >; Cfg = SwipeConfig, BackwardCell, VectorIdMask >]’ 232 | dp.set_zero(c); | ~~~~~~~~~~~^~~ -/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/swipe_wrapper.cpp:141:61: required from ‘std::__cxx11::list DP::BandedSwipe::ARCH_GENERIC::dispatch_swipe(It, It, std::atomic*, Cbs, std::vector&, DP::Params&) [with Sv = int; Cbs = DP::NoCBS; It = __gnu_cxx::__normal_iterator >; Cfg = SwipeConfig, BackwardCell, VectorIdMask >]’ +/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/swipe_wrapper.cpp:141:61: required from ‘std::__cxx11::list DP::BandedSwipe::ARCH_NEON::dispatch_swipe(It, It, std::atomic*, Cbs, std::vector&, DP::Params&) [with Sv = int; Cbs = DP::NoCBS; It = __gnu_cxx::__normal_iterator >; Cfg = SwipeConfig, BackwardCell, VectorIdMask >]’ 141 | return ::DP::Swipe::DISPATCH_ARCH::swipe(begin, end, next, composition_bias, overflow, p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/swipe_wrapper.cpp:154:44: required from ‘std::__cxx11::list DP::BandedSwipe::ARCH_GENERIC::dispatch_swipe(It, It, std::atomic*, std::vector&, DP::Params&) [with Sv = int; It = __gnu_cxx::__normal_iterator >; Cfg = SwipeConfig, BackwardCell, VectorIdMask >]’ +/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/swipe_wrapper.cpp:154:44: required from ‘std::__cxx11::list DP::BandedSwipe::ARCH_NEON::dispatch_swipe(It, It, std::atomic*, std::vector&, DP::Params&) [with Sv = int; It = __gnu_cxx::__normal_iterator >; Cfg = SwipeConfig, BackwardCell, VectorIdMask >]’ 154 | return dispatch_swipe(begin, end, next, NoCBS(), overflow, p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/swipe_wrapper.cpp:187:38: required from ‘std::__cxx11::list DP::BandedSwipe::ARCH_GENERIC::dispatch_swipe(It, It, std::atomic*, std::vector&, int, int, DP::Params&) [with Sv = int; It = __gnu_cxx::__normal_iterator >]’ +/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/swipe_wrapper.cpp:187:38: required from ‘std::__cxx11::list DP::BandedSwipe::ARCH_NEON::dispatch_swipe(It, It, std::atomic*, std::vector&, int, int, DP::Params&) [with Sv = int; It = __gnu_cxx::__normal_iterator >]’ 187 | return dispatch_swipe(begin, end, next, overflow, p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/swipe_wrapper.cpp:277:32: required from ‘std::__cxx11::list DP::BandedSwipe::ARCH_GENERIC::swipe_threads(It, It, std::vector&, int, int, DP::Params&) [with Sv = int; It = __gnu_cxx::__normal_iterator >]’ +/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/swipe_wrapper.cpp:277:32: required from ‘std::__cxx11::list DP::BandedSwipe::ARCH_NEON::swipe_threads(It, It, std::vector&, int, int, DP::Params&) [with Sv = int; It = __gnu_cxx::__normal_iterator >]’ 277 | return dispatch_swipe(begin, end, &next, overflow, round, bin, p); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/swipe_wrapper.cpp:341:35: required from ‘std::pair, std::vector > DP::BandedSwipe::ARCH_GENERIC::swipe_bin(unsigned int, It, It, int, DP::Params&) [with It = __gnu_cxx::__normal_iterator >]’ +/build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/swipe_wrapper.cpp:341:35: required from ‘std::pair, std::vector > DP::BandedSwipe::ARCH_NEON::swipe_bin(unsigned int, It, It, int, DP::Params&) [with It = __gnu_cxx::__normal_iterator >]’ 341 | out = swipe_threads(begin, end, overflow, round, bin, p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/swipe_wrapper.cpp:397:21: required from here @@ -669,10 +701,14 @@ /build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/stat_cell.h:158:21: warning: casting ‘BackwardCell’ to ‘int&’ does not use ‘BackwardCell::operator int32_t() const’ [-Wcast-user-defined] 158 | set_channel((Sv&)v, i, x); | ^~~~~~ -[ 9%] Building CXX object CMakeFiles/arch_neon.dir/src/dp/ungapped_simd.cpp.o +[ 7%] 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-2.1.9/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -DDISPATCH_ARCH=ARCH_GENERIC -DARCH_ID=0 -DEigen=Eigen_GENERIC -MD -MT CMakeFiles/arch_generic.dir/src/dp/swipe/anchored_wrapper.cpp.o -MF 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-std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/lib/alp/sls_alp_regression.cpp.o -MF CMakeFiles/diamond.dir/src/lib/alp/sls_alp_regression.cpp.o.d -o CMakeFiles/diamond.dir/src/lib/alp/sls_alp_regression.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/lib/alp/sls_alp_regression.cpp In file included from /build/reproducible-path/diamond-aligner-2.1.9/src/lib/alp/njn_dynprogproblim.hpp:39, - from /build/reproducible-path/diamond-aligner-2.1.9/src/lib/alp/njn_localmaxstat.cpp:39: + from /build/reproducible-path/diamond-aligner-2.1.9/src/lib/alp/njn_localmaxstatutil.cpp:39: /build/reproducible-path/diamond-aligner-2.1.9/src/lib/alp/njn_dynprogprob.hpp:110:37: warning: ‘virtual Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 110 | virtual inline DynProgProb &operator= (const DynProgProb &dynProgProb_) | ^~~~~~~~ @@ -1028,12 +1063,13 @@ /build/reproducible-path/diamond-aligner-2.1.9/src/lib/alp/njn_dynprogproblim.hpp:101:29: note: by ‘Njn::DynProgProbLim::copy’ 101 | virtual inline void copy ( | ^~~~ +[ 62%] Building CXX object CMakeFiles/diamond.dir/src/lib/alp/sls_alp_sim.cpp.o +/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_NEON -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.9/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/lib/alp/sls_alp_sim.cpp.o -MF CMakeFiles/diamond.dir/src/lib/alp/sls_alp_sim.cpp.o.d -o CMakeFiles/diamond.dir/src/lib/alp/sls_alp_sim.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/lib/alp/sls_alp_sim.cpp [ 63%] Building CXX object CMakeFiles/diamond.dir/src/lib/alp/sls_basic.cpp.o /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_NEON -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.9/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/lib/alp/sls_basic.cpp.o -MF CMakeFiles/diamond.dir/src/lib/alp/sls_basic.cpp.o.d -o CMakeFiles/diamond.dir/src/lib/alp/sls_basic.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/lib/alp/sls_basic.cpp cc1plus: note: unrecognized command-line option ‘-Wno-unknown-warning-option’ may have been intended to silence earlier diagnostics [ 63%] Building CXX object CMakeFiles/diamond.dir/src/lib/alp/sls_pvalues.cpp.o /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_NEON -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.9/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/lib/alp/sls_pvalues.cpp.o -MF CMakeFiles/diamond.dir/src/lib/alp/sls_pvalues.cpp.o.d -o CMakeFiles/diamond.dir/src/lib/alp/sls_pvalues.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/lib/alp/sls_pvalues.cpp -cc1plus: note: unrecognized command-line option ‘-Wno-unknown-warning-option’ may have been intended to silence earlier diagnostics [ 64%] Building CXX object CMakeFiles/diamond.dir/src/align/global_ranking/global_ranking.cpp.o /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_NEON -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.9/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/align/global_ranking/global_ranking.cpp.o -MF CMakeFiles/diamond.dir/src/align/global_ranking/global_ranking.cpp.o.d -o CMakeFiles/diamond.dir/src/align/global_ranking/global_ranking.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/align/global_ranking/global_ranking.cpp [ 64%] Building CXX object CMakeFiles/diamond.dir/src/align/global_ranking/extend.cpp.o @@ -1132,10 +1168,10 @@ /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_NEON -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.9/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/dna/smith_watermann.cpp.o -MF CMakeFiles/diamond.dir/src/dna/smith_watermann.cpp.o.d -o CMakeFiles/diamond.dir/src/dna/smith_watermann.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/dna/smith_watermann.cpp [ 90%] Building CXX object CMakeFiles/diamond.dir/src/stats/dna_scoring/build_score.cpp.o /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_NEON -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.9/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/stats/dna_scoring/build_score.cpp.o -MF CMakeFiles/diamond.dir/src/stats/dna_scoring/build_score.cpp.o.d -o CMakeFiles/diamond.dir/src/stats/dna_scoring/build_score.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/stats/dna_scoring/build_score.cpp -[ 90%] Building CXX object CMakeFiles/diamond.dir/src/lib/blast/blast_stat.cpp.o -/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_NEON -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.9/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/lib/blast/blast_stat.cpp.o -MF CMakeFiles/diamond.dir/src/lib/blast/blast_stat.cpp.o.d -o CMakeFiles/diamond.dir/src/lib/blast/blast_stat.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/lib/blast/blast_stat.cpp [ 91%] Building CXX object CMakeFiles/diamond.dir/src/lib/blast/blast_message.cpp.o /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_NEON -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.9/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/lib/blast/blast_message.cpp.o -MF CMakeFiles/diamond.dir/src/lib/blast/blast_message.cpp.o.d -o CMakeFiles/diamond.dir/src/lib/blast/blast_message.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/lib/blast/blast_message.cpp +[ 91%] Building CXX object CMakeFiles/diamond.dir/src/lib/blast/blast_stat.cpp.o +/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_NEON -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.9/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/lib/blast/blast_stat.cpp.o -MF CMakeFiles/diamond.dir/src/lib/blast/blast_stat.cpp.o.d -o CMakeFiles/diamond.dir/src/lib/blast/blast_stat.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/lib/blast/blast_stat.cpp [ 92%] Building CXX object CMakeFiles/diamond.dir/src/lib/blast/blastn_score.cpp.o /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_NEON -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.9/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/lib/blast/blastn_score.cpp.o -MF CMakeFiles/diamond.dir/src/lib/blast/blastn_score.cpp.o.d -o CMakeFiles/diamond.dir/src/lib/blast/blastn_score.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/lib/blast/blastn_score.cpp [ 92%] Building CXX object CMakeFiles/diamond.dir/src/lib/blast/ncbi_std.cpp.o @@ -1174,17 +1210,17 @@ make[1]: Leaving directory '/build/reproducible-path/diamond-aligner-2.1.9/obj-aarch64-linux-gnu' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/diamond-aligner-2.1.9' -cd debian/tests && PATH=/build/reproducible-path/diamond-aligner-2.1.9/obj-aarch64-linux-gnu:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games sh diamond-calls -+ mktemp -d -+ TESTDIR=/tmp/tmp.5NVdiqKBrK -+ diamond blastp --threads 1 --db test/C.faa.diamond --query test/E.faa --out /tmp/tmp.5NVdiqKBrK/E.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive +cd debian/tests && PATH=/build/reproducible-path/diamond-aligner-2.1.9/obj-aarch64-linux-gnu:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path sh diamond-calls +++ mktemp -d ++ TESTDIR=/tmp/tmp.UghWydqRLz ++ diamond blastp --threads 1 --db test/C.faa.diamond --query test/E.faa --out /tmp/tmp.UghWydqRLz/E.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.9.163 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.5NVdiqKBrK +Temporary directory: /tmp/tmp.UghWydqRLz #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C.faa.diamond (type: Diamond database, sequences: 109, letters: 51213) @@ -1192,471 +1228,471 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.015s] +Masking queries... [0.042s] Algorithm: Double-indexed -Building query histograms... [0.026s] +Building query histograms... [0.044s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.008s] +Masking reference... [0.003s] Initializing temporary storage... [0s] -Building reference histograms... [0.022s] +Building reference histograms... [0.03s] 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... [0.005s] -Computing hash join... [0.001s] +Building reference seed array... [0.019s] +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... [0.004s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] +Building reference seed array... [0.038s] +Building query seed array... [0.012s] +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... [0.004s] -Building query seed array... [0.005s] -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 1/16, index chunk 4/4. -Building reference seed array... [0.004s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] +Building reference seed array... [0.016s] +Building query seed array... [0.001s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4. -Building reference seed array... [0.005s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] +Building reference seed array... [0.021s] +Building query seed array... [0.027s] +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 2/16, 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... [0.011s] +Building query seed array... [0.011s] +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... [0.005s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.008s] +Computing hash join... [0s] +Masking low complexity seeds... [0.008s] +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... [0.005s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... 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[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... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building query seed array... [0.02s] +Computing hash join... [0.014s] +Masking low complexity seeds... [0.019s] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 3/4. -Building reference seed array... [0.004s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] +Building reference seed array... [0.031s] +Building query seed array... [0.033s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 4/4. -Building reference seed array... [0.004s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.03s] +Building query seed array... [0.021s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.026s] 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... [0.005s] +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 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 3/4. -Building reference seed array... [0.004s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] +Building reference seed array... [0.039s] +Building query seed array... [0.004s] +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 6/16, index chunk 4/4. -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... [0.015s] +Building query seed array... [0.023s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.02s] 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... [0.005s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.03s] +Building query seed array... [0.015s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.007s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 2/4. -Building reference seed array... [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... [0.007s] +Building query seed array... [0.019s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.004s] +Searching alignments... [0.009s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 3/4. -Building reference seed array... [0.004s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.017s] +Building query seed array... [0.023s] +Computing hash join... [0.008s] +Masking low complexity seeds... [0.007s] +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... [0.004s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.005s] +Building query seed array... [0.013s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.025s] +Searching alignments... [0.026s] 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 reference seed array... [0.005s] Building query seed array... [0.004s] -Computing hash join... [0.001s] +Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.015s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] +Building reference seed array... [0.028s] +Building query seed array... [0.012s] +Computing hash join... [0.011s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 3/4. -Building reference seed array... [0.005s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building reference seed array... [0.003s] +Building query seed array... [0.015s] +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... [0.005s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.012s] +Computing hash join... [0s] +Masking low complexity seeds... [0.013s] 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... [0.005s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.013s] +Building query seed array... [0.027s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.012s] +Searching alignments... [0.015s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] +Building reference seed array... [0.016s] +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 9/16, index chunk 3/4. -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] +Building reference seed array... [0.015s] +Building query seed array... [0.007s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.011s] +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... [0.005s] -Building query seed array... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.002s] +Building query seed array... [0.014s] +Computing hash join... [0.019s] +Masking low complexity seeds... [0.012s] +Searching alignments... [0.03s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 1/4. -Building reference seed array... [0.004s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.016s] +Building query seed array... [0.003s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.01s] 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... [0.005s] -Computing hash join... [0.001s] +Building reference seed array... [0.011s] +Building query seed array... [0.019s] +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 3/4. -Building reference seed array... [0.004s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] +Building reference seed array... [0.022s] +Building query seed array... [0.016s] +Computing hash join... [0.019s] 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... [0.005s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.021s] +Building query seed array... [0.008s] +Computing hash join... [0.007s] +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 reference seed array... [0.006s] Building query seed array... [0.005s] -Computing hash join... [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 11/16, 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... [0.013s] +Building query seed array... [0.016s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.017s] +Searching alignments... [0.024s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 3/4. Building reference seed array... [0.005s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building query seed array... [0.001s] +Computing hash join... [0s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.018s] 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... [0.005s] -Computing hash join... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.03s] +Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.018s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 1/4. -Building reference seed array... [0.004s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.043s] +Building query seed array... [0.019s] +Computing hash join... [0.008s] +Masking low complexity seeds... [0.019s] +Searching alignments... [0.018s] 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] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.002s] +Building query seed array... [0.021s] +Computing hash join... [0.014s] +Masking low complexity seeds... [0.009s] +Searching alignments... [0.015s] 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... [0.004s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.008s] +Building query seed array... [0.008s] +Computing hash join... [0.019s] +Masking low complexity seeds... [0.019s] +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... [0.004s] -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... [0.018s] +Computing hash join... [0.002s] +Masking low complexity seeds... [0.005s] 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... [0.005s] -Computing hash join... [0.001s] +Building reference seed array... [0.014s] +Building query seed array... [0.012s] +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... [0.005s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.003s] +Building query seed array... [0.023s] +Computing hash join... [0.004s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.017s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 3/4. -Building reference seed array... [0.004s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] +Building reference seed array... [0.011s] +Building query seed array... [0.012s] +Computing hash join... [0.019s] 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... [0.008s] +Building query seed array... [0.019s] +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 14/16, index chunk 1/4. -Building reference seed array... [0.004s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building reference seed array... [0.005s] +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 14/16, 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... [0.013s] +Building query seed array... [0.002s] +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 14/16, index chunk 3/4. -Building reference seed array... [0.004s] -Building query seed array... [0.005s] -Computing hash join... [0s] +Building reference seed array... [0.002s] +Building query seed array... [0.02s] +Computing hash join... [0.008s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.017s] 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... [0.008s] +Building query seed array... [0.014s] +Computing hash join... [0.018s] 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 1/4. -Building reference seed array... [0.004s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] +Building reference seed array... [0.023s] +Building query seed array... [0.051s] +Computing hash join... [0.008s] 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... [0.004s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] +Building query seed array... [0.003s] +Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.011s] 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... [0.005s] -Computing hash join... [0.001s] +Building reference seed array... [0.031s] +Building query seed array... [0.02s] +Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.016s] 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... [0.005s] -Computing hash join... [0.001s] +Building reference seed array... [0.02s] +Building query seed array... [0.035s] +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... [0.005s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.015s] +Building query seed array... [0.016s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.001s] +Searching alignments... [0.031s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 2/4. -Building reference seed array... [0.004s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] +Building reference seed array... [0.015s] +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 16/16, index chunk 3/4. -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... [0.016s] +Building query seed array... [0.009s] +Computing hash join... [0.01s] +Masking low complexity seeds... [0.011s] +Searching alignments... [0.021s] 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... [0.005s] -Computing hash join... [0.001s] +Building reference seed array... [0.008s] +Building query seed array... [0.019s] +Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.005s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0.004s] +Computing alignments... Loading trace points... [0.007s] Sorting trace points... [0s] -Computing alignments... [0.241s] +Computing alignments... [0.337s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.246s] + [0.345s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -1666,17 +1702,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 1.346s +Total time = 3.462s 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.5NVdiqKBrK/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.UghWydqRLz/C.faa.vs.E.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.9.163 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.5NVdiqKBrK +Temporary directory: /tmp/tmp.UghWydqRLz #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/E.faa.diamond (type: Diamond database, sequences: 72, letters: 54509) @@ -1684,471 +1720,471 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.028s] +Masking queries... [0.033s] Algorithm: Double-indexed -Building query histograms... [0.025s] +Building query histograms... [0.014s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.008s] +Masking reference... [0.023s] Initializing temporary storage... [0s] -Building reference histograms... [0.026s] +Building reference histograms... [0.056s] 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... [0.005s] -Computing hash join... [0.001s] +Building reference seed array... [0.016s] +Building query seed array... [0.001s] +Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.012s] +Computing hash join... [0s] +Masking low complexity seeds... [0.007s] +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... [0.004s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.023s] +Building query seed array... [0.002s] +Computing hash join... [0.02s] +Masking low complexity seeds... [0.012s] +Searching alignments... [0.015s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 4/4. -Building reference seed array... [0.005s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.044s] +Building query seed array... [0.012s] +Computing hash join... [0s] +Masking low complexity seeds... [0.006s] 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] +Building reference seed array... [0.012s] +Building query seed array... [0.019s] +Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.023s] 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... [0.004s] -Computing hash join... [0.001s] +Building reference seed array... [0.023s] +Building query seed array... [0.043s] +Computing hash join... [0.003s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.023s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 3/4. -Building reference seed array... [0.005s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] +Building reference seed array... [0.031s] +Building query seed array... [0.014s] +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... [0.003s] -Computing hash join... [0.001s] +Building reference seed array... [0.02s] +Building query seed array... [0.035s] +Computing hash join... [0.02s] 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... [0.004s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.002s] +Building query seed array... [0.016s] +Computing hash join... [0s] +Masking low complexity seeds... [0.007s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.018s] +Building query seed array... [0.02s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.009s] 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... [0.004s] -Computing hash join... [0.001s] +Building reference seed array... [0.004s] +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 3/16, 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... [0.033s] +Building query seed array... [0.022s] +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] -Computing hash join... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.022s] +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... [0.005s] -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 3/4. -Building reference seed array... [0.005s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] +Building reference seed array... [0.021s] +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... [0.005s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0.007s] +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 5/16, 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... [0.016s] +Building query seed array... [0.001s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.012s] +Building query seed array... [0.014s] +Computing hash join... [0.024s] +Masking low complexity seeds... [0.006s] +Searching alignments... [0.005s] 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... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.022s] +Building query seed array... [0.009s] +Computing hash join... [0.024s] +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... [0.005s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.039s] +Building query seed array... [0.011s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.019s] +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... [0.005s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building reference seed array... [0.008s] +Building query seed array... [0.003s] +Computing hash join... [0.019s] 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... [0.005s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.023s] +Building query seed array... [0.008s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.011s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 3/4. -Building reference seed array... [0.005s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building reference seed array... [0.007s] +Building query seed array... [0.02s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 4/4. -Building reference seed array... [0.005s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building reference seed array... [0.013s] +Building query seed array... [0.02s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4. -Building reference seed array... [0.005s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] +Building reference seed array... [0.02s] +Building query seed array... [0.001s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] +Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.005s] 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] -Computing hash join... [0.001s] +Building reference seed array... [0.015s] +Building query seed array... [0.052s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 4/4. -Building reference seed array... [0.005s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building reference seed array... [0.009s] +Building query seed array... [0.005s] +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... [0.005s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building reference seed array... [0.011s] +Building query seed array... [0.019s] +Computing hash join... [0.008s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.039s] 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... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.036s] +Building query seed array... [0.032s] +Computing hash join... [0.011s] +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... [0.005s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.035s] +Building query seed array... [0.067s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.011s] 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... [0.034s] +Building query seed array... [0.032s] +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... [0.004s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.021s] +Building query seed array... [0.015s] +Computing hash join... [0.004s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.015s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.011s] +Building query seed array... [0.035s] +Computing hash join... [0.019s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.011s] 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... [0.004s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.031s] +Building query seed array... [0.035s] +Computing hash join... [0.023s] +Masking low complexity seeds... [0.027s] +Searching alignments... [0.011s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 4/4. -Building reference seed array... [0.005s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.05s] +Building query seed array... [0.025s] +Computing hash join... [0.02s] +Masking low complexity seeds... [0.007s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 1/4. -Building reference seed array... [0.005s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building reference seed array... [0.006s] +Building query seed array... [0.02s] +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... [0.005s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.029s] +Building query seed array... [0.004s] +Computing hash join... [0s] +Masking low complexity seeds... [0.01s] 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... [0.004s] -Computing hash join... [0.001s] +Building reference seed array... [0.014s] +Building query seed array... [0.016s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 4/4. -Building reference seed array... [0.005s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] +Building reference seed array... [0.012s] +Building query seed array... [0.014s] +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 1/4. -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... [0.001s] +Building query seed array... [0.02s] +Computing hash join... [0.027s] +Masking low complexity seeds... [0.007s] +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... [0.005s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building reference seed array... [0.008s] +Building query seed array... [0.025s] +Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.018s] 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 reference seed array... [0.052s] +Building query seed array... [0.003s] +Computing hash join... [0.024s] 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... [0.005s] -Computing hash join... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.011s] +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] -Computing hash join... [0.001s] +Building reference seed array... [0.029s] +Building query seed array... [0.019s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building reference seed array... [0.009s] +Building query seed array... [0.023s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 3/4. -Building reference seed array... [0.005s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building reference seed array... [0.008s] +Building query seed array... [0.011s] +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... [0.005s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building query seed array... [0.016s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 1/4. -Building reference seed array... [0.005s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building reference seed array... [0.007s] +Building query seed array... [0.012s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 2/4. Building reference seed array... [0.005s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building query seed array... [0.027s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.011s] +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... [0.005s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] +Building reference seed array... [0.035s] +Building query seed array... [0.027s] +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 13/16, index chunk 4/4. -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... [0.013s] +Building query seed array... [0.009s] +Computing hash join... [0.004s] +Masking low complexity seeds... [0.039s] +Searching alignments... [0.021s] 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... [0.004s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.027s] +Building query seed array... [0.039s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.015s] +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... [0.005s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] +Building reference seed array... [0.008s] +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 14/16, 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... [0.008s] +Building query seed array... [0.008s] +Computing hash join... [0.015s] 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 4/4. -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... [0.015s] +Building query seed array... [0.001s] +Computing hash join... [0.005s] +Masking low complexity seeds... [0.004s] +Searching alignments... [0.005s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 1/4. Building reference seed array... [0.005s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building query seed array... [0.001s] +Computing hash join... [0.004s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.013s] 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... [0.011s] +Building query seed array... [0.02s] +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... [0.005s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.031s] +Building query seed array... [0.032s] +Computing hash join... [0.019s] +Masking low complexity seeds... [0.008s] +Searching alignments... [0.005s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 4/4. -Building reference seed array... [0.005s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building reference seed array... [0.023s] +Building query seed array... [0.039s] +Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.013s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 1/4. -Building reference seed array... [0.005s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building reference seed array... [0.047s] +Building query seed array... [0.027s] +Computing hash join... [0.003s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.017s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 2/4. -Building reference seed array... [0.004s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.031s] +Building query seed array... [0.043s] +Computing hash join... [0.027s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.025s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 3/4. -Building reference seed array... [0.005s] -Building query seed array... [0.004s] +Building reference seed array... [0.003s] +Building query seed array... [0.003s] Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 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... [0.013s] +Building query seed array... [0.003s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.004s] Searching alignments... [0s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0.002s] +Computing alignments... Loading trace points... [0.053s] Sorting trace points... [0s] -Computing alignments... [0.079s] +Computing alignments... [0.141s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.083s] + [0.195s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -2158,17 +2194,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 1.205s +Total time = 3.831s 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.5NVdiqKBrK/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.UghWydqRLz/L.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.9.163 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.5NVdiqKBrK +Temporary directory: /tmp/tmp.UghWydqRLz #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C.faa.diamond (type: Diamond database, sequences: 109, letters: 51213) @@ -2176,471 +2212,471 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.023s] +Masking queries... [0.04s] Algorithm: Double-indexed -Building query histograms... [0.013s] +Building query histograms... [0.043s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.008s] +Masking reference... [0.011s] Initializing temporary storage... [0s] -Building reference histograms... [0.024s] +Building reference histograms... [0.047s] 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... [0.031s] +Building query seed array... [0.019s] +Computing hash join... [0.017s] +Masking low complexity seeds... [0.018s] +Searching alignments... [0.007s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] +Building reference seed array... [0.008s] +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 1/16, 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... [0.015s] +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 1/16, 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... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] +Building reference seed array... [0.008s] +Building query seed array... [0.024s] 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 query seed array... [0.002s] -Computing hash join... [0.001s] +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 3/4. -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... [0.015s] +Computing hash join... [0.002s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 4/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.016s] +Building query seed array... [0.067s] +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 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... [0.029s] +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... [0.004s] -Building query seed array... [0.002s] +Building reference seed array... [0.026s] +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... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.007s] +Building query seed array... [0.015s] +Computing hash join... [0.015s] 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... [0.004s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.035s] +Building query seed array... [0.004s] +Computing hash join... [0.018s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 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... [0.001s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.019s] 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] -Computing hash join... [0s] +Building reference seed array... [0.035s] +Building query seed array... [0.015s] +Computing hash join... [0.008s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.011s] 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... [0.015s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 4/4. -Building reference seed array... [0.004s] -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 5/16, index chunk 1/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.018s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 2/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.007s] +Building query seed array... [0.008s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.019s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 3/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] -Masking low complexity seeds... [0s] +Masking low complexity seeds... [0.019s] 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... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 1/4. -Building reference seed array... [0.005s] -Building 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 2/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 3/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.022s] +Building query seed array... [0.015s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.006s] 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] +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... [0.004s] -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 7/16, index chunk 2/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.013s] +Building query seed array... [0.01s] +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 7/16, index chunk 3/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] +Building reference seed array... [0.006s] +Building query seed array... [0.024s] 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... [0.004s] -Building query seed array... [0.002s] +Building reference seed array... [0.013s] +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 1/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] +Building reference seed array... [0.003s] +Building query seed array... [0.001s] 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 8/16, index chunk 2/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.019s] +Building query seed array... [0.004s] +Computing hash join... [0.004s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.01s] 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... [0.002s] +Building reference seed array... [0.01s] +Building query seed array... [0.007s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.013s] 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] -Computing hash join... [0s] +Building reference seed array... [0.019s] +Building query seed array... [0.008s] +Computing hash join... [0.01s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.011s] 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] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.032s] +Building query seed array... [0.02s] +Computing hash join... [0.018s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.007s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 2/4. -Building reference seed array... [0.004s] -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... [0.004s] +Building reference seed array... [0.003s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 4/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] +Building reference seed array... [0.013s] +Building query seed array... [0.012s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 1/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] +Building reference seed array... [0.006s] +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 2/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] +Building reference seed array... [0.013s] +Building query seed array... [0.004s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.006s] +Searching alignments... [0.014s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 3/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.017s] +Building query seed array... [0.017s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.015s] +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... [0.004s] -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... [0.031s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.014s] 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] +Building reference seed array... [0.001s] +Building query seed array... [0.038s] +Computing hash join... [0.015s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.013s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 2/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.024s] +Building query seed array... [0.01s] +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 11/16, index chunk 3/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] +Building reference seed array... [0.012s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.018s] 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] +Building reference seed array... [0.01s] +Building query seed array... [0.02s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 1/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.02s] +Building query seed array... [0.019s] +Computing hash join... [0.023s] +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 2/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] +Building reference seed array... [0.014s] +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... [0.004s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.024s] +Building query seed array... [0.001s] +Computing hash join... [0.009s] +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 4/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] +Building reference seed array... [0.013s] +Building query seed array... [0.041s] 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] -Computing hash join... [0s] +Building reference seed array... [0.035s] +Building query seed array... [0.008s] +Computing hash join... [0.003s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.021s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.028s] +Building query seed array... [0.013s] +Computing hash join... [0.005s] +Masking low complexity seeds... [0.023s] +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... [0.004s] -Building query seed array... [0.002s] +Building reference seed array... [0.015s] +Building query seed array... [0.029s] 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] +Building reference seed array... [0.001s] +Building query seed array... [0.014s] 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] +Building reference seed array... [0.005s] +Building query seed array... [0.014s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 2/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.016s] +Building query seed array... [0.016s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.023s] +Searching alignments... [0.014s] 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... [0.002s] +Building reference seed array... [0.032s] +Building query seed array... [0.011s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 4/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] +Building reference seed array... [0.005s] +Building query seed array... [0.027s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.013s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 1/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.008s] +Building query seed array... [0.019s] +Computing hash join... [0.019s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.005s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 2/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.012s] +Building query seed array... [0.031s] +Computing hash join... [0.023s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.005s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 3/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.028s] +Building query seed array... [0.023s] +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... [0.003s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.009s] +Building query seed array... [0.014s] +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 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... [0s] +Building reference seed array... [0.019s] +Building query seed array... [0.015s] +Computing hash join... [0.019s] +Masking low complexity seeds... [0.017s] +Searching alignments... [0.015s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 2/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.01s] +Building query seed array... [0.038s] +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 3/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] +Building reference seed array... [0.024s] +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 16/16, 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... [0.043s] +Building query seed array... [0.023s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.001s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0.003s] +Computing alignments... Loading trace points... [0.303s] Sorting trace points... [0s] -Computing alignments... [0.14s] +Computing alignments... [0.218s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.145s] + [0.523s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -2650,17 +2686,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 1.073s +Total time = 3.36s 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.5NVdiqKBrK/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.UghWydqRLz/C.faa.vs.L.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.9.163 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.5NVdiqKBrK +Temporary directory: /tmp/tmp.UghWydqRLz #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/L.faa.diamond (type: Diamond database, sequences: 40, letters: 26652) @@ -2668,471 +2704,471 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.029s] +Masking queries... [0.051s] Algorithm: Double-indexed -Building query histograms... [0.024s] +Building query histograms... [0.022s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.004s] +Masking reference... [0.012s] Initializing temporary storage... [0s] -Building reference histograms... [0.013s] +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... [0.002s] -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 1/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.003s] +Building reference seed array... [0.024s] +Building query seed array... [0.022s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.037s] +Building query seed array... [0.051s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.011s] +Searching alignments... [0.019s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.039s] +Building query seed array... [0.007s] +Computing hash join... [0.023s] +Masking low complexity seeds... [0.023s] +Searching alignments... [0.015s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.036s] +Building query seed array... [0.011s] +Computing hash join... [0.019s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.011s] 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... [0.004s] +Building reference seed array... [0.021s] +Building query seed array... [0.006s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.018s] +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... [0.002s] -Building query seed array... [0.004s] -Computing hash join... [0s] +Building reference seed array... [0.019s] +Building query seed array... [0.031s] +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... [0.004s] -Computing hash join... [0.001s] +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 3/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building reference seed array... [0.014s] +Building query seed array... [0.012s] 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... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.017s] +Computing hash join... [0.008s] +Masking low complexity seeds... [0.018s] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.031s] +Building query seed array... [0.007s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.008s] +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... [0.002s] -Building query seed array... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.007s] +Building query seed array... [0.019s] +Computing hash join... [0.004s] +Masking low complexity seeds... [0.019s] +Searching alignments... [0.019s] 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... [0.004s] -Computing hash join... [0s] +Building reference seed array... [0.012s] +Building query seed array... [0.008s] +Computing hash join... [0.02s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building reference seed array... [0.016s] +Building query seed array... [0.028s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0s] +Building query seed array... [0.005s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.013s] 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 reference seed array... [0.001s] +Building query seed array... [0.009s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, 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... [0.005s] 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 2/4. Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building query seed array... [0.016s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.018s] +Searching alignments... [0.011s] 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] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.011s] +Building query seed array... [0.016s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.015s] +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... [0.004s] +Building reference seed array... [0.004s] +Building query seed array... [0.011s] 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... [0.004s] -Computing hash join... [0s] +Building reference seed array... [0.014s] +Building query seed array... [0.015s] +Computing hash join... [0.011s] 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] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.027s] +Building query seed array... [0.031s] +Computing hash join... [0.008s] +Masking low complexity seeds... [0.012s] +Searching alignments... [0.01s] 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.02s] +Building query seed array... [0.011s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.023s] +Searching alignments... [0.015s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building reference seed array... [0.039s] +Building query seed array... [0.016s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.016s] +Computing hash join... [0.023s] +Masking low complexity seeds... [0.019s] +Searching alignments... [0.011s] 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] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.035s] +Building query seed array... [0.008s] +Computing hash join... [0.023s] +Masking low complexity seeds... [0.011s] +Searching alignments... [0.015s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.012s] +Building query seed array... [0.031s] +Computing hash join... [0.031s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 4/4. -Building reference seed array... [0.002s] -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] 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... [0.007s] +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 8/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.014s] +Computing hash join... [0.031s] +Masking low complexity seeds... [0.015s] 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... [0.01s] Building query seed array... [0.005s] -Computing hash join... [0.001s] -Masking low complexity seeds... [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... [0.002s] -Building query seed array... [0.004s] +Building reference seed array... [0.028s] +Building query seed array... [0.017s] 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... [0.002s] -Building query seed array... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.051s] +Building query seed array... [0.047s] +Computing hash join... [0.023s] +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 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building reference seed array... [0.001s] +Building query seed array... [0.01s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building reference seed array... [0.023s] +Building query seed array... [0.024s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building reference seed array... [0.017s] +Building query seed array... [0.012s] 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] +Building query seed array... [0.008s] 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 10/16, 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... [0.012s] 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... [0.004s] +Building reference seed array... [0.001s] +Building query seed array... [0.005s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.008s] +Searching alignments... [0.012s] 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] -Masking low complexity seeds... [0s] +Building reference seed array... [0.004s] +Building query seed array... [0.016s] +Computing hash join... [0.015s] +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... [0.002s] -Building query seed array... [0.004s] +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 11/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] -Computing hash join... [0s] +Building reference seed array... [0.02s] +Building query seed array... [0.011s] +Computing hash join... [0.011s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.03s] +Building query seed array... [0.026s] +Computing hash join... [0.016s] +Masking low complexity seeds... [0.011s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.021s] +Computing hash join... [0.023s] +Masking low complexity seeds... [0.023s] +Searching alignments... [0.018s] 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.031s] +Building query seed array... [0.035s] +Computing hash join... [0.027s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.014s] 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... [0.027s] +Building query seed array... [0.001s] +Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.015s] 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... [0.039s] +Building query seed array... [0.012s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.004s] +Building query seed array... [0.008s] +Computing hash join... [0.004s] +Masking low complexity seeds... [0.01s] +Searching alignments... [0.017s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building reference seed array... [0.039s] +Building query seed array... [0.067s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.025s] 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] -Computing hash join... [0s] +Building reference seed array... [0.024s] +Building query seed array... [0.011s] +Computing hash join... [0.015s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.025s] 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... [0.035s] Building query seed array... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Computing hash join... [0.01s] +Masking low complexity seeds... [0.007s] +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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.008s] +Building query seed array... [0.008s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.011s] 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... [0.017s] +Building query seed array... [0.024s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building reference seed array... [0.021s] +Building query seed array... [0.021s] 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 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building reference seed array... [0.019s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.022s] +Building query seed array... [0.012s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.005s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building reference seed array... [0.008s] +Building query seed array... [0.027s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.031s] 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 reference seed array... [0.053s] +Building query seed array... [0.012s] 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 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building reference seed array... [0.059s] +Building query seed array... [0.011s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building reference seed array... [0.004s] +Building query seed array... [0.011s] 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 query seed array... [0.004s] +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 16/16, 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] -Searching alignments... [0s] +Building reference seed array... [0.014s] +Building query seed array... [0.01s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.009s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building reference seed array... [0.007s] +Building query seed array... [0.019s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.023s] +Building query seed array... [0.028s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.015s] Searching alignments... [0s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0.004s] +Computing alignments... Loading trace points... [0.177s] Sorting trace points... [0s] -Computing alignments... [0.207s] +Computing alignments... [0.292s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.212s] + [0.47s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -3142,17 +3178,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 1.152s +Total time = 4.058s 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.5NVdiqKBrK/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.UghWydqRLz/M.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.9.163 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.5NVdiqKBrK +Temporary directory: /tmp/tmp.UghWydqRLz #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C.faa.diamond (type: Diamond database, sequences: 109, letters: 51213) @@ -3160,471 +3196,471 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.023s] +Masking queries... [0.042s] Algorithm: Double-indexed -Building query histograms... [0.013s] +Building query histograms... [0.009s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.008s] +Masking reference... [0.002s] Initializing temporary storage... [0s] -Building reference histograms... [0.025s] +Building reference histograms... [0.028s] 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... [0.003s] +Building reference seed array... [0.004s] +Building query seed array... [0.016s] 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 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... [0.008s] +Building query seed array... [0.015s] +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 1/16, index chunk 3/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] +Building reference seed array... [0.011s] +Building query seed array... [0.014s] 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.014s] +Building query seed array... [0.027s] +Computing hash join... [0.004s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.004s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.008s] +Building query seed array... [0.041s] +Computing hash join... [0.01s] 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... [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 query 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... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 4/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] +Building reference seed array... [0.022s] +Building query seed array... [0.02s] 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.023s] +Building query seed array... [0.01s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.031s] +Searching alignments... [0.055s] 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... [0.007s] +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 3/16, index chunk 3/4. -Building reference seed array... [0.003s] -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... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 4/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.006s] +Building query seed array... [0.009s] +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 4/16, index chunk 1/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] +Building reference seed array... [0.019s] +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 query seed array... [0.002s] +Building reference seed array... [0.013s] +Building query seed array... [0.011s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.023s] 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... [0.001s] +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 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... [0.027s] +Building query seed array... [0.009s] +Computing hash join... [0.006s] +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 1/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] +Building reference seed array... [0.007s] +Building query seed array... [0.008s] 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 2/4. -Building reference seed array... [0.004s] -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... [0.031s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.011s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 3/4. Building reference seed array... [0.004s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 4/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.011s] +Building query seed array... [0.019s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.028s] +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... [0.004s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.02s] +Building query seed array... [0.007s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.019s] +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... [0.004s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.007s] +Building query seed array... [0.016s] +Computing hash join... [0.01s] 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... [0.004s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.005s] +Building query seed array... [0.014s] +Computing hash join... [0.004s] 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 4/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] +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 7/16, 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] +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... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [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... [0.001s] 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... [0.003s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0s] +Computing hash join... [0.005s] +Masking low complexity seeds... [0.008s] 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... [0.004s] -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... [0.016s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.012s] +Searching alignments... [0.007s] 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... [0.01s] Computing hash join... [0s] -Masking low complexity seeds... [0s] +Masking low complexity seeds... [0.015s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0s] +Computing hash join... [0.015s] +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... [0.005s] -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 8/16, 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... [0.014s] +Building query seed array... [0.003s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.01s] 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 query seed array... [0.024s] 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... [0.01s] +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... [0.004s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.025s] +Building query seed array... [0.038s] +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 4/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.014s] +Building query seed array... [0.031s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.017s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 1/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] +Building reference seed array... [0.011s] +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 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] +Building reference seed array... [0.007s] +Building query seed array... [0.016s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +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... [0.004s] -Building query seed array... [0.002s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building query seed array... [0.025s] +Computing hash join... [0.005s] +Masking low complexity seeds... [0.009s] +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... [0.004s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.008s] +Building query seed array... [0.016s] +Computing hash join... [0.018s] +Masking low complexity seeds... [0.02s] +Searching alignments... [0.01s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 1/4. Building reference seed array... [0.004s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building query seed array... [0.011s] +Computing hash join... [0.019s] +Masking low complexity seeds... [0.008s] +Searching alignments... [0.013s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 2/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] +Building reference seed array... [0.04s] +Building query seed array... [0.015s] 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... [0.013s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 4/4. -Building reference seed array... [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] +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... [0.004s] -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... [0.01s] +Computing hash join... [0.018s] +Masking low complexity seeds... [0.013s] +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] -Computing hash join... [0s] +Building reference seed array... [0.015s] +Building query seed array... [0.027s] +Computing hash join... [0.008s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.013s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 3/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.007s] +Building query seed array... [0.029s] +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 12/16, 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] +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... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.01s] +Building query seed array... [0.012s] +Computing hash join... [0.012s] +Masking low complexity seeds... [0.011s] 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... [0.002s] +Building query seed array... [0.012s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 3/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 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... [0.026s] +Building query seed array... [0.019s] +Computing hash join... [0.047s] +Masking low complexity seeds... [0.014s] +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... [0.004s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.019s] +Building query seed array... [0.014s] +Computing hash join... [0.017s] +Masking low complexity seeds... [0.011s] 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.005s] +Building query seed array... [0.023s] +Computing hash join... [0.023s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.013s] 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... [0.002s] +Building reference seed array... [0.024s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.018s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 4/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.024s] +Building query seed array... [0.005s] +Computing hash join... [0.002s] +Masking low complexity seeds... [0.013s] +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... [0.005s] -Building query seed array... [0.002s] +Building reference seed array... [0.027s] +Building query seed array... [0.028s] 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... [0.005s] -Building query seed array... [0.002s] +Building query seed array... [0.017s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.013s] +Searching alignments... [0.015s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 3/4. -Building reference seed array... [0.004s] -Building query seed array... [0.003s] +Building reference seed array... [0.012s] +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... [0.004s] -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... [0.004s] +Computing hash join... [0.001s] +Masking low complexity seeds... [0.004s] +Searching alignments... [0.031s] 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] -Masking low complexity seeds... [0s] +Building query seed array... [0.011s] +Computing hash join... [0.019s] +Masking low complexity seeds... [0.027s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.008s] +Building query seed array... [0.008s] +Computing hash join... [0.011s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.005s] 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... [0.015s] 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building query seed array... [0.015s] +Computing hash join... [0.004s] +Masking low complexity seeds... [0.043s] Searching alignments... [0s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0.003s] +Computing alignments... Loading trace points... [0.189s] Sorting trace points... [0s] -Computing alignments... [0.141s] +Computing alignments... [0.194s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.145s] + [0.384s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -3634,17 +3670,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 1.085s +Total time = 3.136s 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.5NVdiqKBrK/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.UghWydqRLz/C.faa.vs.M.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.9.163 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.5NVdiqKBrK +Temporary directory: /tmp/tmp.UghWydqRLz #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/M.faa.diamond (type: Diamond database, sequences: 40, letters: 26963) @@ -3652,471 +3688,471 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.029s] +Masking queries... [0.036s] Algorithm: Double-indexed -Building query histograms... [0.025s] +Building query histograms... [0.013s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.004s] +Masking reference... [0.012s] Initializing temporary storage... [0s] -Building reference histograms... [0.013s] +Building reference histograms... [0.047s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building reference seed array... [0.043s] +Building query seed array... [0.013s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] +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] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building reference seed array... [0.011s] +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 1/16, 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... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building reference seed array... [0.001s] +Building query seed array... [0.014s] 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] -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... [0s] +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... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.006s] +Building query seed array... [0.012s] +Computing hash join... [0.004s] +Masking low complexity seeds... [0.005s] 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... [0.004s] -Computing hash join... [0s] +Building reference seed array... [0.005s] +Building query seed array... [0.015s] +Computing hash join... [0.015s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building reference seed array... [0.011s] +Building query seed array... [0.035s] 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... [0.005s] -Computing hash join... [0s] +Building reference seed array... [0.006s] +Building query seed array... [0.015s] +Computing hash join... [0.015s] 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... [0.004s] -Computing hash join... [0s] +Building reference seed array... [0.026s] +Building query seed array... [0.012s] +Computing hash join... [0.015s] 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... [0.008s] +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 4/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] -Computing hash join... [0s] +Building reference seed array... [0.006s] +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 4/16, 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... [0.01s] +Building query seed array... [0.024s] +Computing hash join... [0.007s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.011s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] -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 4/16, 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] +Building reference seed array... [0.013s] +Building query seed array... [0.028s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.015s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building reference seed array... [0.011s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.015s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.019s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, 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... [0.023s] +Building query seed array... [0.012s] +Computing hash join... [0.013s] +Masking low complexity seeds... [0.013s] +Searching alignments... [0.026s] 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 reference seed array... [0.013s] +Building query seed array... [0.023s] 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... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building query seed array... [0.012s] +Computing hash join... [0.023s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.011s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.023s] +Building query seed array... [0.028s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 3/4. -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... [0.004s] +Building query seed array... [0.043s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.019s] 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.008s] +Building query seed array... [0.023s] +Computing hash join... [0.019s] +Masking low complexity seeds... [0.015s] +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] +Building reference seed array... [0.005s] +Building query seed array... [0.012s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building 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 7/16, 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... [0.015s] +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 7/16, 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... [0s] +Building reference seed array... [0.039s] +Building query seed array... [0.03s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.028s] +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 query seed array... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.029s] +Building query seed array... [0.003s] +Computing hash join... [0.042s] +Masking low complexity seeds... [0.031s] +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... [0.002s] -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] +Masking low complexity seeds... [0.005s] 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 reference seed array... [0.034s] +Building query seed array... [0.032s] Computing hash join... [0s] -Masking low complexity seeds... [0s] +Masking low complexity seeds... [0.038s] 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... [0.005s] +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] Processing query block 1, reference block 1/1, shape 9/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building reference seed array... [0.005s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building reference seed array... [0.001s] +Building query seed array... [0.015s] 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 9/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building reference seed array... [0.004s] +Building query seed array... [0.008s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.022s] +Searching alignments... [0.011s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building reference seed array... [0.012s] +Building query seed array... [0.031s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.019s] +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... [0.002s] -Building query seed array... [0.004s] +Building reference seed array... [0.012s] +Building query seed array... [0.012s] 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 10/16, 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... [0.001s] Computing hash join... [0s] -Masking low complexity seeds... [0s] +Masking low complexity seeds... [0.028s] 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... [0.006s] +Building query seed array... [0.019s] +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 10/16, 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... [0s] +Building reference seed array... [0.005s] +Building query seed array... [0.015s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.004s] +Searching alignments... [0.022s] 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... [0.004s] +Building reference seed array... [0.016s] +Building query seed array... [0.031s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.017s] 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... [0s] +Building reference seed array... [0.004s] +Building query seed array... [0.031s] +Computing hash join... [0.011s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.037s] 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... [0.023s] +Building query seed array... [0.044s] 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... [0.002s] -Building query seed array... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.018s] +Building query seed array... [0.007s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.006s] 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] -Computing hash join... [0s] +Building reference seed array... [0.015s] +Building query seed array... [0.043s] +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 12/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building reference seed array... [0.015s] +Building query seed array... [0.009s] 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 12/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.015s] 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 12/16, 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] +Building reference seed array... [0.013s] +Building query seed array... [0.023s] +Computing hash join... [0.016s] +Masking low complexity seeds... [0.011s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building reference seed array... [0.005s] +Building query seed array... [0.023s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.013s] +Building query seed array... [0.013s] +Computing hash join... [0.006s] +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... [0.004s] -Computing hash join... [0s] +Building reference seed array... [0.029s] +Building query seed array... [0.025s] +Computing hash join... [0.018s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.013s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building reference seed array... [0.005s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building reference seed array... [0.026s] +Building query seed array... [0.003s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.006s] +Searching alignments... [0.013s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.024s] +Building query seed array... [0.008s] +Computing hash join... [0.004s] +Masking low complexity seeds... [0.005s] 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] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.024s] +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 14/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] -Computing hash join... [0s] +Building reference seed array... [0.01s] +Building query seed array... [0.012s] +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 15/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building reference seed array... [0.015s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.019s] 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.008s] +Building query seed array... [0.015s] +Computing hash join... [0.023s] +Masking low complexity seeds... [0.005s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building reference seed array... [0.001s] +Building query seed array... [0.01s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, 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... [0.017s] 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 query seed array... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.017s] +Building query seed array... [0.013s] +Computing hash join... [0.023s] +Masking low complexity seeds... [0.004s] +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... [0.002s] -Building query seed array... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.027s] +Building query seed array... [0.022s] +Computing hash join... [0.018s] +Masking low complexity seeds... [0.019s] +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... [0.002s] -Building query seed array... [0.004s] +Building reference seed array... [0.012s] +Building query seed array... [0.007s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.02s] 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... [0.011s] +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] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0.004s] +Computing alignments... Loading trace points... [0.104s] Sorting trace points... [0s] -Computing alignments... [0.207s] +Computing alignments... [0.222s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.213s] + [0.327s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -4126,17 +4162,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 1.158s +Total time = 3.411s 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.5NVdiqKBrK/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.UghWydqRLz/C2.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.9.163 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.5NVdiqKBrK +Temporary directory: /tmp/tmp.UghWydqRLz #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C.faa.diamond (type: Diamond database, sequences: 109, letters: 51213) @@ -4144,334 +4180,334 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0s] +Masking queries... [0.004s] Algorithm: Double-indexed -Building query histograms... [0s] +Building query histograms... [0.026s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.008s] +Masking reference... [0.007s] Initializing temporary storage... [0s] -Building reference histograms... [0.024s] +Building reference histograms... [0.023s] 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... [0s] +Building reference seed array... [0.006s] +Building query seed array... [0.017s] 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... [0.004s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.009s] +Building query seed array... [0.013s] +Computing hash join... [0.01s] +Masking low complexity seeds... [0.004s] +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... [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 1/16, index chunk 4/4. -Building reference seed array... [0.005s] -Building query seed array... [0s] +Building reference seed array... [0.003s] +Building query seed array... [0.012s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] +Building reference seed array... [0.019s] +Building query seed array... [0.011s] 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 query seed array... [0s] -Computing hash join... [0s] +Building reference seed array... [0.008s] +Building query seed array... [0.006s] +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 3/4. -Building reference seed array... [0.005s] -Building query seed array... [0s] +Building reference seed array... [0.011s] +Building query seed array... [0.013s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.025s] 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... [0s] +Building reference seed array... [0.021s] +Building query seed array... [0.01s] Computing hash join... [0s] -Masking low complexity seeds... [0s] +Masking low complexity seeds... [0.015s] 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... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.019s] +Building query seed array... [0.019s] +Computing hash join... [0.004s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.015s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0s] -Computing hash join... [0s] +Building reference seed array... [0.051s] +Building query seed array... [0.019s] +Computing hash join... [0.005s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.013s] 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... [0s] +Building reference seed array... [0.051s] +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 3/16, index chunk 4/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] +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 4/16, index chunk 1/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] -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... [0s] +Searching alignments... [0.006s] 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... [0s] +Building reference seed array... [0.011s] +Building query seed array... [0.016s] 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 4/16, index chunk 3/4. -Building reference seed array... [0.005s] -Building query seed array... [0s] +Building reference seed array... [0.024s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.01s] 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... [0s] +Building reference seed array... [0.015s] +Building query seed array... [0.004s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.023s] +Searching alignments... [0.019s] 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... [0s] +Building reference seed array... [0.039s] +Building query seed array... [0.016s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 2/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] +Building reference seed array... [0.015s] +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 3/4. -Building reference seed array... [0.005s] -Building query seed array... [0s] +Building reference seed array... [0.02s] +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 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] -Searching alignments... [0s] +Searching alignments... [0.015s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 1/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.019s] +Building query seed array... [0.011s] +Computing hash join... [0.023s] +Masking low complexity seeds... [0.016s] +Searching alignments... [0.023s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 2/4. -Building reference seed array... [0.004s] +Building reference seed array... [0.023s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 3/4. -Building reference seed array... [0.004s] +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 6/16, index chunk 4/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] +Building reference seed array... [0.012s] +Building query seed array... [0.011s] Computing hash join... [0s] -Masking low complexity seeds... [0s] +Masking low complexity seeds... [0.011s] 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... [0s] +Building reference seed array... [0.027s] +Building query seed array... [0.039s] 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 7/16, index chunk 2/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.007s] +Building query seed array... [0.017s] +Computing hash join... [0.023s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.019s] 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] +Building reference seed array... [0.039s] +Building query seed array... [0.011s] 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 7/16, index chunk 4/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] +Building reference seed array... [0.012s] +Building query seed array... [0.023s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 1/4. -Building reference seed array... [0.005s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.018s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 2/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.028s] +Building query seed array... [0.011s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.007s] +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... [0.005s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.012s] +Building query seed array... [0.015s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.019s] +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... [0.004s] +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 9/16, 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] +Searching alignments... [0.006s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0s] +Building reference seed array... [0.019s] +Building query seed array... [0.019s] 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 9/16, index chunk 3/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.008s] +Building query seed array... [0.006s] +Computing hash join... [0.004s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.031s] 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... [0s] -Computing hash join... [0s] +Building reference seed array... [0.008s] +Building query seed array... [0.003s] +Computing hash join... [0.016s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +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... [0.005s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.016s] +Building query seed array... [0.027s] +Computing hash join... [0.023s] +Masking low complexity seeds... [0.004s] 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... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.013s] +Building query seed array... [0.007s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.001s] +Searching alignments... [0.017s] 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... [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 4/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] +Building reference seed array... [0.031s] +Building query seed array... [0.015s] 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 11/16, index chunk 1/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] +Building reference seed array... [0.009s] +Building query seed array... [0.012s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.013s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 2/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] +Building reference seed array... [0.019s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 3/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] +Building reference seed array... [0.006s] +Building query seed array... [0.006s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.037s] 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... [0.012s] +Building query seed array... [0.043s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.017s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 1/4. -Building reference seed array... [0.004s] +Building reference seed array... [0.02s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0s] -Computing hash join... [0s] +Building reference seed array... [0.011s] +Building query seed array... [0.016s] +Computing hash join... [0.003s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] @@ -4483,132 +4519,132 @@ 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 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 13/16, index chunk 1/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] -Computing hash join... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.01s] +Computing hash join... [0.015s] 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 reference seed array... [0.014s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 3/4. -Building reference seed array... [0.004s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.011s] 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... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.023s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 1/4. -Building reference seed array... [0.004s] +Building reference seed array... [0.001s] Building query seed array... [0s] 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... [0.004s] -Building query seed array... [0s] +Building reference seed array... [0.006s] +Building query seed array... [0.012s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.016s] 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... [0.02s] +Building query seed array... [0.003s] +Computing hash join... [0.005s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.023s] 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... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building query seed array... [0.013s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.004s] 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... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.006s] +Building query seed array... [0.014s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.024s] +Searching alignments... [0.013s] 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] -Computing hash join... [0s] +Building reference seed array... [0.027s] +Building query seed array... [0.007s] +Computing hash join... [0.023s] 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... [0.001s] 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... [0.004s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.012s] +Building query seed array... [0.019s] +Computing hash join... [0.021s] +Masking low complexity seeds... [0.018s] 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... [0s] +Building reference seed array... [0.02s] +Building query seed array... [0.016s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 2/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] +Building reference seed array... [0.012s] +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 16/16, index chunk 3/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] +Building reference seed array... [0.036s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.016s] 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... [0.018s] +Building query seed array... [0.007s] Computing hash join... [0s] -Masking low complexity seeds... [0s] +Masking low complexity seeds... [0.023s] Searching alignments... [0s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0.001s] +Computing alignments... Loading trace points... [0s] Sorting trace points... [0s] -Computing alignments... [0.004s] +Computing alignments... [0.001s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.006s] + [0.003s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -4618,17 +4654,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.743s +Total time = 2.69s 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.5NVdiqKBrK/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.UghWydqRLz/C.faa.vs.C2.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.9.163 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.5NVdiqKBrK +Temporary directory: /tmp/tmp.UghWydqRLz #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C2.faa.diamond (type: Diamond database, sequences: 2, letters: 726) @@ -4636,471 +4672,471 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.029s] +Masking queries... [0.123s] Algorithm: Double-indexed -Building query histograms... [0.024s] +Building query histograms... [0.022s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0s] +Masking reference... [0.012s] Initializing temporary storage... [0s] -Building reference histograms... [0s] +Building reference histograms... [0.003s] 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... [0.012s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.011s] 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] -Computing hash join... [0s] +Building reference seed array... [0.019s] +Building query seed array... [0.012s] +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 3/4. Building reference seed array... [0s] -Building query seed array... [0.004s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 4/4. -Building reference seed array... [0s] -Building query seed array... [0.004s] -Computing hash join... [0s] +Building reference seed array... [0.007s] +Building query seed array... [0.011s] +Computing hash join... [0.02s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.013s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4. -Building reference seed array... [0s] -Building query seed array... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.022s] +Building query seed array... [0.035s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.016s] 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building query seed array... [0.001s] +Computing hash join... [0.013s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.008s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 3/4. -Building reference seed array... [0s] +Building reference seed array... [0.015s] Building query seed array... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Computing hash join... [0.019s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.008s] 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 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 1/4. Building reference seed array... [0s] -Building query seed array... [0.005s] -Computing hash join... [0s] +Building query seed array... [0.004s] +Computing hash join... [0.008s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 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 3/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.004s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.004s] -Computing hash join... [0s] +Building query seed array... [0.043s] +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... [0s] -Building query seed array... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.026s] +Building query seed array... [0.031s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.023s] 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.008s] +Building query seed array... [0.015s] +Computing hash join... [0.019s] +Masking low complexity seeds... [0.004s] +Searching alignments... [0.014s] 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.023s] +Building query seed array... [0.023s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.012s] +Searching alignments... [0.019s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 4/4. -Building reference seed array... [0s] -Building query seed array... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.011s] +Building query seed array... [0.016s] +Computing hash join... [0.019s] +Masking low complexity seeds... [0.011s] +Searching alignments... [0.019s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 1/4. -Building reference seed array... [0s] -Building query seed array... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.015s] +Building query seed array... [0.03s] +Computing hash join... [0.029s] +Masking low complexity seeds... [0.024s] +Searching alignments... [0.007s] 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 reference seed array... [0.015s] +Building query seed array... [0.041s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.026s] 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... [0.027s] +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... [0s] -Building query seed array... [0.004s] +Building reference seed array... [0.005s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.004s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.011s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 2/4. -Building reference seed array... [0s] -Building query seed array... [0.004s] +Building reference seed array... [0.051s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.004s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.004s] -Computing hash join... [0s] +Building query seed array... [0.012s] +Computing hash join... [0.002s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.012s] 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 reference seed array... [0.012s] +Building query seed array... [0.016s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.004s] +Building query seed array... [0.009s] 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 7/16, index chunk 3/4. -Building reference seed array... [0s] -Building query seed array... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.043s] +Building query seed array... [0.032s] +Computing hash join... [0.001s] +Masking low complexity seeds... [0.005s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 4/4. -Building reference seed array... [0s] -Building query seed array... [0.004s] +Building reference seed array... [0.022s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 1/4. -Building reference seed array... [0s] -Building query seed array... [0.004s] +Building 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 8/16, 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 8/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.004s] +Building query seed array... [0.02s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.007s] +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... [0s] -Building query seed array... [0.004s] +Building reference seed array... [0.019s] +Building query seed array... [0.045s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 1/4. -Building reference seed array... [0s] -Building query seed array... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.044s] +Building query seed array... [0.011s] +Computing hash join... [0.019s] +Masking low complexity seeds... [0.007s] 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.005s] +Building query seed array... [0.003s] +Computing hash join... [0.023s] +Masking low complexity seeds... [0.019s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.004s] +Building query seed array... [0.001s] 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... [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] +Searching alignments... [0.009s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 1/4. -Building reference seed array... [0s] -Building query seed array... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.011s] +Building query seed array... [0.001s] +Computing hash join... [0.017s] +Masking low complexity seeds... [0.012s] 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] -Computing hash join... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.012s] +Computing hash join... [0.011s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 3/4. -Building reference seed array... [0s] -Building query seed array... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.007s] +Building query seed array... [0.026s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.002s] +Searching alignments... [0.004s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 4/4. -Building reference seed array... [0s] -Building query seed array... [0.004s] +Building reference seed array... [0.011s] +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 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... [0.011s] +Building query seed array... [0.027s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.007s] 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... [0.007s] +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 11/16, index chunk 3/4. -Building reference seed array... [0s] -Building query seed array... [0.004s] +Building reference seed array... [0.016s] +Building query seed array... [0.023s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.011s] +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... [0s] -Building query seed array... [0.004s] -Computing hash join... [0s] +Building query seed array... [0.019s] +Computing hash join... [0.019s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 1/4. -Building reference seed array... [0s] -Building query seed array... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.018s] +Computing hash join... [0.004s] +Masking low complexity seeds... [0.004s] +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... [0s] -Building query seed array... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.015s] +Building query seed array... [0.028s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.017s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 3/4. -Building reference seed array... [0s] +Building reference seed array... [0.004s] Building query seed array... [0.004s] -Computing hash join... [0s] +Computing hash join... [0.003s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.009s] 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 reference seed array... [0.015s] +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 1/4. -Building reference seed array... [0s] -Building query seed array... [0.004s] +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... [0.003s] 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] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.021s] +Building query seed array... [0.028s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.008s] +Searching alignments... [0.009s] 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.011s] +Building query seed array... [0.031s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.004s] +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... [0s] -Building query seed array... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.007s] +Building query seed array... [0.012s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.011s] +Searching alignments... [0.01s] 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... [0.004s] +Building reference seed array... [0.011s] +Building query seed array... [0.012s] 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... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.039s] +Building query seed array... [0.023s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.023s] 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.005s] +Building query seed array... [0.043s] +Computing hash join... [0.004s] +Masking low complexity seeds... [0.015s] +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... [0s] -Building query seed array... [0.004s] +Building reference seed array... [0.021s] +Building query seed array... [0.012s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.024s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 1/4. -Building reference seed array... [0s] -Building query seed array... [0.004s] +Building reference seed array... [0.027s] +Building query seed array... [0.016s] 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... [0.004s] +Building reference seed array... [0.003s] +Building query seed array... [0.016s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 3/4. -Building reference seed array... [0s] -Building query seed array... [0.004s] -Computing hash join... [0s] +Building reference seed array... [0.024s] +Building query seed array... [0.015s] +Computing hash join... [0.023s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.021s] 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.015s] +Building query seed array... [0.035s] +Computing hash join... [0.023s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.021s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 1/4. -Building reference seed array... [0s] -Building query seed array... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.003s] +Building query seed array... [0.021s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.003s] 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... [0.004s] +Building reference seed array... [0.004s] +Building query seed array... [0.016s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 3/4. -Building reference seed array... [0s] -Building query seed array... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.009s] +Building query seed array... [0.025s] +Computing hash join... [0.004s] +Masking low complexity seeds... [0.014s] +Searching alignments... [0.01s] 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] +Building reference seed array... [0.032s] +Building query seed array... [0.008s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.012s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0.001s] +Computing alignments... Loading trace points... [0.019s] Sorting trace points... [0s] Computing alignments... [0.005s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.007s] + [0.025s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -5110,489 +5146,489 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.765s +Total time = 3.178s 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.5NVdiqKBrK/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.UghWydqRLz/L.faa.vs.E.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.9.163 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.5NVdiqKBrK +Temporary directory: /tmp/tmp.UghWydqRLz #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... [0s] -Masking queries... [0.024s] +Loading query sequences... [0.016s] +Masking queries... [0.066s] Algorithm: Double-indexed -Building query histograms... [0.013s] +Building query histograms... [0.027s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.008s] +Masking reference... [0.006s] Initializing temporary storage... [0s] -Building reference histograms... [0.026s] +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... [0.005s] -Building query seed array... [0.003s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Building reference seed array... [0.011s] +Building query seed array... [0.004s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.011s] +Searching alignments... [0.027s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] +Building reference seed array... [0.032s] +Building query seed array... [0.011s] 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] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.02s] +Building query seed array... [0.02s] +Computing hash join... [0.019s] +Masking low complexity seeds... [0.007s] +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... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.031s] +Building query seed array... [0.024s] +Computing hash join... [0.003s] 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 2/16, index chunk 1/4. Building reference seed array... [0.005s] -Building query seed array... [0.002s] +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 2/16, 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... [0.001s] +Building query seed array... [0.004s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 3/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.025s] +Building query seed array... [0.042s] +Computing hash join... [0.004s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 4/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0s] +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 3/16, index chunk 1/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] +Building reference seed array... [0.018s] +Building query seed array... [0.028s] 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 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... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.007s] +Computing hash join... [0.019s] +Masking low complexity seeds... [0.027s] +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... [0.005s] -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 3/16, index chunk 4/4. -Building reference seed array... [0.005s] -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... [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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.021s] +Building query seed array... [0.027s] +Computing hash join... [0.008s] +Masking low complexity seeds... [0.023s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.031s] +Building query seed array... [0.023s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.019s] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 3/4. Building reference seed array... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building query seed array... [0.014s] +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 4/16, index chunk 4/4. -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... [0.012s] +Building query seed array... [0.05s] +Computing hash join... [0.023s] +Masking low complexity seeds... [0.015s] +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... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0.014s] 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... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.027s] +Building query seed array... [0.012s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.019s] +Searching alignments... [0.015s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 3/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] +Building reference seed array... [0.029s] +Building query seed array... [0.012s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 4/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] +Building reference seed array... [0.04s] +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 6/16, index chunk 1/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] +Building reference seed array... [0.007s] +Building query seed array... [0.011s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Masking low complexity seeds... [0.014s] +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... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.024s] +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 6/16, 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... [0.012s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 4/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] +Building reference seed array... [0.006s] +Building query seed array... [0.015s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Masking low complexity seeds... [0.003s] +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... [0.005s] -Building query seed array... [0.002s] +Building reference seed array... [0.011s] +Building query seed array... [0.027s] 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... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.008s] +Building query seed array... [0.021s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.011s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 3/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.021s] +Building query seed array... [0.001s] +Computing hash join... [0.018s] +Masking low complexity seeds... [0.012s] +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... [0.005s] -Building query seed array... [0.002s] +Building reference seed array... [0.031s] +Building query seed array... [0.016s] 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 8/16, 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... [0.001s] +Building reference seed array... [0.026s] +Building query seed array... [0.015s] +Computing hash join... [0.019s] +Masking low complexity seeds... [0.012s] +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] -Computing hash join... [0s] +Building reference seed array... [0.02s] +Building query seed array... [0.019s] +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 4/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] +Building reference seed array... [0.01s] +Building query seed array... [0.008s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Masking low complexity seeds... [0.007s] +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... [0.001s] +Building query seed array... [0s] +Computing hash join... [0.027s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0.022s] 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... [0.001s] +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 3/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.003s] +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... [0.005s] -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... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 1/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] +Building reference seed array... [0.007s] +Building query seed array... [0.018s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Masking low complexity seeds... [0.007s] +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... [0.005s] -Building query seed array... [0.002s] +Building reference seed array... [0.012s] +Building query seed array... [0.009s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0.012s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 3/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] +Building reference seed array... [0.016s] +Building query seed array... [0.023s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0.014s] 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... [0.018s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 1/4. -Building reference seed array... [0.005s] -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... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 2/4. -Building reference seed array... [0.005s] -Building 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... [0.028s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.025s] 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... [0.008s] +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 11/16, 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... [0.001s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Masking low complexity seeds... [0.023s] +Searching alignments... [0.01s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 1/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] +Building reference seed array... [0.051s] +Building query seed array... [0.015s] 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 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] -Searching alignments... [0.001s] +Building reference seed array... [0.009s] +Building query seed array... [0.039s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.009s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 3/4. -Building reference seed array... [0.005s] -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... [0.002s] 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 query seed array... [0.002s] +Building reference seed array... [0.019s] +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 13/16, index chunk 1/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] +Building reference seed array... [0.007s] +Building query seed array... [0.012s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Masking low complexity seeds... [0.006s] +Searching alignments... [0.005s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] +Building reference seed array... [0.01s] +Building query seed array... [0.008s] 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 13/16, index chunk 3/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] +Building reference seed array... [0.017s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0.012s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 4/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.035s] +Building query seed array... [0.008s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.011s] +Searching alignments... [0.007s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 1/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] +Building reference seed array... [0.063s] +Building query seed array... [0.035s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] +Building reference seed array... [0.007s] +Building query seed array... [0.009s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Masking low complexity seeds... [0.002s] +Searching alignments... [0.009s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 3/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] +Building reference seed array... [0.023s] +Building query seed array... [0.008s] 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 14/16, 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... [0.003s] 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 15/16, 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... [0.001s] +Building query seed array... [0.009s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.008s] +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... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.016s] +Building query seed array... [0.027s] +Computing hash join... [0.004s] 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... [0.005s] -Building query seed array... [0.002s] +Building reference seed array... [0.007s] +Building query seed array... [0.015s] 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.023s] +Building query seed array... [0.008s] +Computing hash join... [0.019s] +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 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... [0.008s] +Building query seed array... [0.006s] +Computing hash join... [0.013s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.012s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] +Building reference seed array... [0.004s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0.015s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 3/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.008s] +Building query seed array... [0.039s] +Computing hash join... [0.009s] 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... [0.005s] -Building query seed array... [0.002s] +Building reference seed array... [0.006s] +Building query seed array... [0.014s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Masking low complexity seeds... [0.006s] +Searching alignments... [0.002s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0.003s] +Computing alignments... Loading trace points... [0.056s] Sorting trace points... [0s] -Computing alignments... [0.348s] +Computing alignments... [0.444s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.353s] + [0.501s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -5602,17 +5638,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 1.366s +Total time = 3.575s 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.5NVdiqKBrK/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.UghWydqRLz/E.faa.vs.L.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.9.163 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.5NVdiqKBrK +Temporary directory: /tmp/tmp.UghWydqRLz #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/L.faa.diamond (type: Diamond database, sequences: 40, letters: 26652) @@ -5620,471 +5656,471 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.014s] +Masking queries... [0.01s] Algorithm: Double-indexed -Building query histograms... [0.026s] +Building query histograms... [0.027s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.004s] +Masking reference... [0.007s] Initializing temporary storage... [0s] -Building reference histograms... [0.013s] +Building reference histograms... [0.031s] 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 reference seed array... [0.011s] Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.003s] +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... [0.005s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Building reference seed array... [0.009s] +Building query seed array... [0.002s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.003s] +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... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] +Building reference seed array... [0.016s] +Building query seed array... [0.016s] +Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building reference seed array... [0.021s] +Building query seed array... [0.02s] 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0.004s] +Computing hash join... [0.01s] +Masking low complexity seeds... [0.007s] +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... [0.031s] +Building query seed array... [0.014s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.01s] Building query seed array... [0.005s] -Computing hash join... [0s] +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 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... [0.006s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Masking low complexity seeds... [0.022s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building reference seed array... [0.01s] +Building query seed array... [0.008s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Masking low complexity seeds... [0.002s] +Searching alignments... [0.007s] 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... [0.028s] +Building query seed array... [0.024s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Masking low complexity seeds... [0.01s] +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... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.01s] +Building query seed array... [0.027s] +Computing hash join... [0.039s] +Masking low complexity seeds... [0.007s] +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... [0.005s] -Computing hash join... [0s] +Building reference seed array... [0.014s] +Building query seed array... [0.012s] +Computing hash join... [0.006s] 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... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] +Building reference seed array... [0.031s] +Building query seed array... [0.028s] +Computing hash join... [0.011s] 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... [0.005s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.014s] +Building query seed array... [0.016s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.004s] +Searching alignments... [0.012s] 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] +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... [0.005s] -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] +Searching alignments... [0.011s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.023s] +Building query seed array... [0.015s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.019s] +Searching alignments... [0.012s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [0s] +Building reference seed array... [0.011s] +Building query seed array... [0.018s] +Computing hash join... [0.018s] 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] +Building reference seed array... [0.013s] +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 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... [0.047s] +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 6/16, 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... [0.007s] +Building query seed array... [0.01s] +Computing hash join... [0.023s] +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... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] +Building reference seed array... [0.013s] +Building query seed array... [0.001s] +Computing hash join... [0.016s] 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 6/16, 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... [0.036s] +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 4/4. -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] +Building reference seed array... [0.005s] +Building query seed array... [0.036s] +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 7/16, 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... [0.008s] +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 7/16, 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... [0.001s] +Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0.015s] 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... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.011s] +Building query seed array... [0.007s] +Computing hash join... [0.016s] +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... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.039s] +Building query seed array... [0.007s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.011s] +Searching alignments... [0.024s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.043s] +Building query seed array... [0.02s] +Computing hash join... [0.003s] +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 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [0s] +Building reference seed array... [0.062s] +Building query seed array... [0.023s] +Computing hash join... [0.006s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.007s] +Computing hash join... [0.022s] 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... [0.005s] +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... [0.015s] +Searching alignments... [0.01s] 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] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.017s] +Building query seed array... [0.021s] +Computing hash join... [0.016s] +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 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building reference seed array... [0.014s] +Building query seed array... [0.012s] 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 9/16, 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... [0.012s] +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 9/16, 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] -Searching alignments... [0.001s] +Building query seed array... [0.027s] +Computing hash join... [0.004s] +Masking low complexity seeds... [0.007s] +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... [0.014s] Building query seed array... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Computing hash join... [0.005s] +Masking low complexity seeds... [0.004s] +Searching alignments... [0.01s] 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.012s] +Building query seed array... [0.015s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.016s] +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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.025s] +Building query seed array... [0.02s] +Computing hash join... [0.023s] +Masking low complexity seeds... [0.004s] +Searching alignments... [0.004s] 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... [0.006s] +Building query seed array... [0.029s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [0s] +Building reference seed array... [0.004s] +Building query seed array... [0.004s] +Computing hash join... [0.003s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0.014s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.015s] +Building query seed array... [0.036s] +Computing hash join... [0.023s] +Masking low complexity seeds... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building reference seed array... [0.004s] +Building query seed array... [0.028s] 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 4/4. Building reference seed array... [0.002s] -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] +Masking low complexity seeds... [0.006s] +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... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] +Computing hash join... [0.01s] +Masking low complexity seeds... [0.004s] +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... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.016s] +Building query seed array... [0.004s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.02s] +Building query seed array... [0.007s] +Computing hash join... [0.019s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.02s] +Computing hash join... [0.007s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0.021s] 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] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.016s] +Building query seed array... [0.035s] +Computing hash join... [0.023s] +Masking low complexity seeds... [0.019s] +Searching alignments... [0.029s] 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] -Computing hash join... [0.001s] +Building reference seed array... [0.015s] +Building query seed array... [0.02s] +Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0.018s] 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] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.013s] +Building query seed array... [0.008s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.019s] +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... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.016s] +Building query seed array... [0.031s] +Computing hash join... [0.019s] +Masking low complexity seeds... [0.019s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building reference seed array... [0.005s] +Building query seed array... [0.001s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.012s] +Searching alignments... [0.005s] 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... [0.001s] +Building reference seed array... [0.028s] +Building query seed array... [0.023s] +Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.012s] +Building query seed array... [0.009s] +Computing hash join... [0.006s] +Masking low complexity seeds... [0.015s] +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... [0.017s] +Building query seed array... [0.012s] +Computing hash join... [0.007s] 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 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] -Searching alignments... [0.001s] +Building reference seed array... [0.015s] +Building query seed array... [0.019s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.011s] +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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.008s] +Building query seed array... [0.023s] +Computing hash join... [0.019s] +Masking low complexity seeds... [0.011s] +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... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.008s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.011s] +Searching alignments... [0.006s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building reference seed array... [0.007s] +Building query seed array... [0.016s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Masking low complexity seeds... [0.014s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [0s] +Building reference seed array... [0.012s] +Building query seed array... [0.009s] +Computing hash join... [0.006s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building reference seed array... [0.012s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.006s] +Building query seed array... [0.016s] +Computing hash join... [0.005s] +Masking low complexity seeds... [0.008s] +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 reference seed array... [0.01s] Building query seed array... [0.005s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.005s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0.004s] +Computing alignments... Loading trace points... [0.07s] Sorting trace points... [0s] -Computing alignments... [0.604s] +Computing alignments... [0.671s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.611s] + [0.743s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -6094,17 +6130,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 1.613s +Total time = 3.888s 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.5NVdiqKBrK/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.UghWydqRLz/M.faa.vs.E.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.9.163 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.5NVdiqKBrK +Temporary directory: /tmp/tmp.UghWydqRLz #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/E.faa.diamond (type: Diamond database, sequences: 72, letters: 54509) @@ -6112,471 +6148,471 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.024s] +Masking queries... [0.029s] Algorithm: Double-indexed -Building query histograms... [0.013s] +Building query histograms... [0.019s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.008s] +Masking reference... [0.002s] Initializing temporary storage... [0s] -Building reference histograms... [0.026s] +Building reference histograms... [0.009s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. -Building reference seed array... [0.005s] -Building query seed array... [0.003s] -Computing hash join... [0.001s] +Building reference seed array... [0.018s] +Building query seed array... [0.001s] +Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.006s] +Building query seed array... [0.011s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.006s] +Searching alignments... [0.005s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 4/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.008s] +Building query seed array... [0.015s] +Computing hash join... [0.02s] +Masking low complexity seeds... [0.008s] +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... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.006s] +Building query seed array... [0.019s] +Computing hash join... [0.007s] +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 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] +Building reference seed array... [0.004s] +Building query seed array... [0.007s] 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 2/16, index chunk 3/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.01s] +Building query seed array... [0.008s] +Computing hash join... [0.007s] +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... [0.005s] -Building query seed array... [0.002s] +Building query seed array... [0.006s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Masking low complexity seeds... [0.027s] +Searching alignments... [0.007s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 1/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.043s] +Building query seed array... [0.019s] +Computing hash join... [0.016s] +Masking low complexity seeds... [0.019s] +Searching alignments... [0.004s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.051s] +Building query seed array... [0.023s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.011s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 3/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.015s] +Building query seed array... [0.031s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.005s] +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... [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... [0.006s] +Building query seed array... [0.016s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.012s] +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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.01s] +Building query seed array... [0.004s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.008s] +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... [0.005s] -Building query seed array... [0.002s] +Building reference seed array... [0.008s] +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 4/16, index chunk 3/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] +Building reference seed array... [0.021s] +Building query seed array... [0.013s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 4/4. -Building reference seed array... [0.005s] -Building query seed array... [0.003s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.008s] +Building query seed array... [0.011s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.011s] +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... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.016s] +Building query seed array... [0.011s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.011s] +Searching alignments... [0.008s] 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... [0.002s] +Building reference seed array... [0.024s] +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 5/16, index chunk 3/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] +Building reference seed array... [0.008s] +Building query seed array... [0.021s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 4/4. -Building reference seed array... [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... [0.027s] 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] +Building reference seed array... [0.014s] +Building query seed array... [0.014s] +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 6/16, index chunk 2/4. Building reference seed array... [0.005s] Building query seed array... [0.002s] -Computing hash join... [0s] +Computing hash join... [0.006s] 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... [0.005s] -Building query seed array... [0.003s] -Computing hash join... [0s] +Building reference seed array... [0.007s] +Building query seed array... [0.028s] +Computing hash join... [0.018s] 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 6/16, index chunk 4/4. -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... [0.02s] +Building query seed array... [0.011s] +Computing hash join... [0.022s] +Masking low complexity seeds... [0.019s] +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... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.02s] +Building query seed array... [0.007s] +Computing hash join... [0.013s] 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... [0.005s] +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... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 3/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.012s] +Building query seed array... [0.047s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.015s] 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.011s] +Building query seed array... [0.015s] +Computing hash join... [0.02s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.007s] 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... [0.016s] +Building query seed array... [0.004s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Masking low complexity seeds... [0.022s] +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... [0.005s] -Building query 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... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 3/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] +Building reference seed array... [0.014s] +Building query seed array... [0.001s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Masking low complexity seeds... [0.019s] +Searching alignments... [0.004s] 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... [0.01s] +Building query seed array... [0.02s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0.018s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 1/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] +Building reference seed array... [0.025s] +Building query seed array... [0.011s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.015s] +Computing hash join... [0.019s] +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... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.022s] +Building query seed array... [0.039s] +Computing hash join... [0.004s] +Masking low complexity seeds... [0.011s] +Searching alignments... [0.011s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 4/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.019s] +Building query seed array... [0.008s] +Computing hash join... [0.013s] +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 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] 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] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.011s] +Building query seed array... [0.008s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.014s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 3/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.02s] +Building query seed array... [0.007s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.007s] +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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.013s] +Building query seed array... [0.016s] +Computing hash join... [0.019s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.006s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 1/4. Building reference seed array... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building query seed array... [0.006s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.011s] +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... [0.005s] -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... [0.006s] 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... [0.027s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0.008s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 4/4. -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... [0.011s] +Building query seed array... [0.008s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.017s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 1/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.006s] +Building query seed array... [0.015s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.01s] 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... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.035s] +Building query seed array... [0.015s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.012s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 3/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] +Building reference seed array... [0.02s] +Building query seed array... [0.004s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Masking low complexity seeds... [0.014s] +Searching alignments... [0.009s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 4/4. Building reference seed array... [0.005s] -Building query seed array... [0.002s] +Building 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 13/16, index chunk 1/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] +Building reference seed array... [0.016s] +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... [0.005s] -Building query seed array... [0.002s] +Building reference seed array... [0.004s] +Building query seed array... [0.016s] 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 13/16, index chunk 3/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.009s] +Building query seed array... [0.022s] +Computing hash join... [0.005s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.005s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 4/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.027s] +Building query seed array... [0.015s] +Computing hash join... [0.004s] +Masking low complexity seeds... [0.027s] +Searching alignments... [0.009s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 1/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.019s] +Building query seed array... [0.015s] +Computing hash join... [0.02s] +Masking low complexity seeds... [0.011s] +Searching alignments... [0.005s] 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] +Building reference seed array... [0.028s] +Building query seed array... [0.019s] 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 3/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] +Building reference seed array... [0.016s] +Building query seed array... [0.027s] 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... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.01s] +Building query seed array... [0.007s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.004s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 1/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] +Building reference seed array... [0.01s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, 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... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.017s] +Computing hash join... [0.004s] +Masking low complexity seeds... [0.008s] +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] +Building reference seed array... [0.025s] +Building query seed array... [0.012s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 4/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.007s] +Building query seed array... [0.008s] +Computing hash join... [0.003s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0.016s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 1/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] +Building reference seed array... [0.024s] +Building query seed array... [0.012s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Masking low complexity seeds... [0.011s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.023s] +Building query seed array... [0.027s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.005s] +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... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.012s] +Building query seed array... [0.001s] +Computing hash join... [0.014s] +Masking low complexity seeds... [0.011s] +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... [0.005s] -Building query seed array... [0.003s] +Building reference seed array... [0.019s] +Building query seed array... [0.012s] 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] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0.004s] +Computing alignments... Loading trace points... [0.16s] Sorting trace points... [0s] -Computing alignments... [0.352s] -Deallocating buffers... [0s] +Computing alignments... [0.399s] +Deallocating buffers... [0.004s] Loading trace points... [0s] - [0.358s] + [0.564s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -6586,17 +6622,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 1.386s +Total time = 3.623s 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.5NVdiqKBrK/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.UghWydqRLz/E.faa.vs.M.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.9.163 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.5NVdiqKBrK +Temporary directory: /tmp/tmp.UghWydqRLz #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/M.faa.diamond (type: Diamond database, sequences: 40, letters: 26963) @@ -6604,471 +6640,471 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.015s] +Masking queries... [0.016s] Algorithm: Double-indexed -Building query histograms... [0.025s] +Building query histograms... [0.05s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.004s] +Masking reference... [0.011s] 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... [0.003s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Building reference seed array... [0.019s] +Building query seed array... [0.019s] +Computing hash join... [0.004s] +Masking low complexity seeds... [0.007s] +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... [0s] +Building reference seed array... [0.01s] +Building query seed array... [0.004s] +Computing hash join... [0.002s] 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... [0.005s] +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... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.018s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.009s] +Searching alignments... [0.004s] 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... [0.003s] +Building query seed array... [0.012s] 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] -Computing hash join... [0s] +Building reference seed array... [0.011s] +Building query seed array... [0.014s] +Computing hash join... [0.004s] 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 2/16, index chunk 3/4. -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] +Building reference seed array... [0.027s] +Building query seed array... [0.023s] +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 2/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [0s] +Building reference seed array... [0.024s] +Building query seed array... [0.018s] +Computing hash join... [0.013s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] +Building reference seed array... [0.01s] +Building query seed array... [0.008s] +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 3/16, 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] -Searching alignments... [0.001s] +Building reference seed array... [0.019s] +Building query seed array... [0.011s] +Computing hash join... [0.005s] +Masking low complexity seeds... [0.008s] +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... [0.004s] +Building query seed array... [0.003s] 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 3/16, 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... [0.004s] +Building query seed array... [0.015s] +Computing hash join... [0.015s] 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 4/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building reference seed array... [0.016s] +Building query seed array... [0.016s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Masking low complexity seeds... [0.01s] +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... [0.005s] +Building reference seed array... [0.014s] +Building query seed array... [0.024s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0.022s] 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... [0.004s] +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 4/16, 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] -Searching alignments... [0.001s] +Building query seed array... [0.007s] +Computing hash join... [0s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.022s] +Building query seed array... [0.027s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.007s] 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... [0.013s] +Building query seed array... [0.014s] 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 5/16, 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... [0.008s] 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 5/16, 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... [0.005s] +Building query seed array... [0.009s] +Computing hash join... [0.002s] 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... [0.002s] -Building query seed array... [0.005s] +Building reference seed array... [0.008s] +Building query seed array... [0.015s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.022s] +Building query seed array... [0.007s] +Computing hash join... [0.012s] +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 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 reference seed array... [0.023s] +Building query seed array... [0.008s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.007s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building reference seed array... [0.027s] +Building query seed array... [0.032s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Masking low complexity seeds... [0.006s] +Searching alignments... [0.007s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4. -Building reference seed array... [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... [0.039s] +Building query seed array... [0.004s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.011s] +Searching alignments... [0.019s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.015s] Building query seed array... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Computing hash join... [0.006s] +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 3/4. -Building reference 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... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building reference seed array... [0.004s] +Building query seed array... [0.011s] 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 8/16, 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... [0.011s] +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... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.013s] +Building query seed array... [0.032s] +Computing hash join... [0.015s] +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] +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... [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... [0.005s] -Computing hash join... [0.001s] +Building reference seed array... [0.011s] +Building query seed array... [0.016s] +Computing hash join... [0.007s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0.016s] 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] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.012s] +Building query seed array... [0.019s] +Computing hash join... [0.023s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.011s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building reference seed array... [0.029s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0.014s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building reference seed array... [0.011s] +Building query seed array... [0.008s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Masking low complexity seeds... [0.022s] +Searching alignments... [0.027s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] +Building reference seed array... [0.012s] +Building query seed array... [0.051s] +Computing hash join... [0.008s] 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 10/16, 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... [0.012s] +Building query seed array... [0.008s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.008s] +Searching alignments... [0.03s] 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] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.027s] +Building query seed array... [0.035s] +Computing hash join... [0s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.007s] 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] -Computing hash join... [0s] +Building reference seed array... [0.011s] +Building query seed array... [0.008s] +Computing hash join... [0.007s] 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 10/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building reference seed array... [0.02s] +Building query seed array... [0.02s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0.004s] +Computing hash join... [0.026s] +Masking low complexity seeds... [0.003s] +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... [0.005s] +Building reference seed array... [0.012s] +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 11/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building reference seed array... [0.015s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0.015s] 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... [0.019s] +Building query seed array... [0.02s] 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 12/16, 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... [0.001s] +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 12/16, 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... [0.023s] +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 12/16, 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... [0.001s] +Building reference seed array... [0.008s] +Building query seed array... [0.012s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.01s] +Searching alignments... [0.013s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.009s] +Building query seed array... [0.016s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.011s] +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... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.01s] +Building query seed array... [0.015s] +Computing hash join... [0.008s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.014s] 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.011s] +Building query seed array... [0.02s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.009s] +Searching alignments... [0.004s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.019s] +Building query seed array... [0.047s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.005s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [0s] +Building reference seed array... [0.011s] +Building query seed array... [0.008s] +Computing hash join... [0.011s] 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 14/16, 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... [0.024s] +Building query seed array... [0.032s] +Computing hash join... [0.01s] +Masking low complexity seeds... [0.023s] +Searching alignments... [0.002s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building 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... [0.021s] 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 reference seed array... [0.019s] +Building query seed array... [0.015s] +Computing hash join... [0.019s] +Masking low complexity seeds... [0.012s] +Searching alignments... [0.017s] 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... [0.017s] +Building query seed array... [0.008s] 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 15/16, 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... [0.016s] +Building query seed array... [0.016s] +Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.011s] +Building query seed array... [0.012s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.006s] 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... [0.02s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0.008s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] +Building reference seed array... [0.009s] +Building query seed array... [0.02s] +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 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... [0.003s] +Building query seed array... [0.004s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.009s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] -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... [0.006s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.012s] 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... [0.001s] +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 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.015s] 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... [0.008s] +Searching alignments... [0.009s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0.004s] +Computing alignments... Loading trace points... [0.074s] Sorting trace points... [0s] -Computing alignments... [0.642s] +Computing alignments... [0.713s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.648s] + [0.788s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -7078,17 +7114,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 1.666s +Total time = 3.765s 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.5NVdiqKBrK/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.UghWydqRLz/C2.faa.vs.E.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.9.163 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.5NVdiqKBrK +Temporary directory: /tmp/tmp.UghWydqRLz #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/E.faa.diamond (type: Diamond database, sequences: 72, letters: 54509) @@ -7096,311 +7132,311 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.001s] +Masking queries... [0.005s] Algorithm: Double-indexed -Building query histograms... [0s] +Building query histograms... [0.015s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.008s] +Masking reference... [0.015s] Initializing temporary storage... [0s] -Building reference histograms... [0.03s] +Building reference histograms... [0.02s] 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... [0s] +Building reference seed array... [0.007s] +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... [0.005s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.01s] +Building query seed array... [0.012s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.016s] 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 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 1/16, index chunk 4/4. -Building reference seed array... [0.005s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.008s] +Building query seed array... [0.026s] +Computing hash join... [0.027s] +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 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 2/16, index chunk 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.025s] +Building query seed array... [0.007s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.009s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 3/4. -Building reference seed array... [0.005s] +Building reference seed array... [0.014s] 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.011s] +Building query seed array... [0.015s] +Computing hash join... [0.004s] +Masking low complexity seeds... [0.007s] 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 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... [0.015s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 2/4. -Building reference seed array... [0.005s] -Building query seed array... [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 3/16, index chunk 3/4. -Building reference seed array... [0.005s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.002s] +Building query seed array... [0.011s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.011s] +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... [0.005s] -Building query seed array... [0s] -Computing hash join... [0s] +Building reference seed array... [0.004s] +Building query seed array... [0.031s] +Computing hash join... [0.006s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 1/4. -Building reference seed array... [0.005s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.022s] +Building query seed array... [0.031s] +Computing hash join... [0.016s] +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... [0.005s] -Building query seed array... [0s] -Computing hash join... [0s] +Building reference seed array... [0.023s] +Building query seed array... [0.011s] +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 3/4. -Building reference seed array... [0.006s] +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 4/16, index chunk 4/4. -Building reference seed array... [0.005s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.018s] +Building query seed array... [0.011s] +Computing hash join... [0.016s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.027s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 1/4. -Building reference seed array... [0.005s] -Building query seed array... [0s] +Building reference seed array... [0.004s] +Building query seed array... [0.007s] 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 5/16, index chunk 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0s] +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] 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... [0.01s] +Building query seed array... [0.011s] 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 5/16, index chunk 4/4. -Building reference seed array... [0.005s] -Building query seed array... [0s] -Computing hash join... [0s] +Building reference seed array... [0.012s] +Building query seed array... [0.011s] +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 6/16, index chunk 1/4. -Building reference seed array... [0.005s] -Building query seed array... [0s] -Computing hash join... [0s] +Building reference seed array... [0.003s] +Building query seed array... [0.031s] +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 6/16, 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... [0.006s] 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... [0.031s] +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] Processing query block 1, reference block 1/1, shape 6/16, index chunk 4/4. -Building reference seed array... [0.005s] -Building query seed array... [0s] -Computing hash join... [0s] +Building reference seed array... [0.026s] +Building query seed array... [0.004s] +Computing hash join... [0.007s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.01s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4. -Building reference seed array... [0.005s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.006s] +Building query seed array... [0.013s] +Computing hash join... [0.016s] +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 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.008s] +Building query seed array... [0.019s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.007s] +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 query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.023s] +Building query seed array... [0.008s] +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 7/16, index chunk 4/4. -Building reference seed array... [0.005s] -Building query seed array... [0s] +Building reference seed array... [0.024s] +Building query seed array... [0.006s] 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... [0.005s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.007s] +Building query seed array... [0.019s] +Computing hash join... [0.002s] +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 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... [0.006s] 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... [0.012s] +Building query seed array... [0.024s] 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 4/4. -Building reference seed array... [0.005s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.008s] +Building query seed array... [0.035s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.007s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 1/4. -Building reference seed array... [0.005s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.008s] +Building query seed array... [0.019s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.008s] +Searching alignments... [0.015s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0s] -Computing hash join... [0s] +Building reference seed array... [0.016s] +Building query seed array... [0.007s] +Computing hash join... [0.007s] 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... [0.005s] -Building query seed array... [0s] +Building reference seed array... [0.011s] +Building query seed array... [0.015s] 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... [0s] +Building reference seed array... [0.006s] +Building query seed array... [0.02s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.007s] +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... [0.005s] -Building query seed array... [0s] -Computing hash join... [0s] +Building reference seed array... [0.028s] +Building query seed array... [0.014s] +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 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.012s] +Building query seed array... [0.006s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.011s] 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... [0s] +Building reference seed array... [0.026s] +Building query seed array... [0.02s] 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 10/16, index chunk 4/4. -Building reference seed array... [0.005s] -Building query seed array... [0s] +Building reference seed array... [0.008s] +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... [0.005s] -Building query seed array... [0s] +Building reference seed array... [0.012s] +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 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 11/16, index chunk 3/4. -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] @@ -7408,159 +7444,159 @@ 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 query seed array... [0.005s] 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 12/16, index chunk 1/4. -Building reference seed array... [0.005s] -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] 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... [0.001s] 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 12/16, 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] Masking low complexity seeds... [0s] -Searching alignments... [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... [0.005s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.009s] +Building query seed array... [0.005s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.009s] 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] +Building reference seed array... [0.023s] +Building query seed array... [0.01s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.01s] 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... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.015s] +Building query seed array... [0.023s] +Computing hash join... [0.002s] +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. -Building reference seed array... [0.005s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.016s] +Building query seed array... [0.02s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.011s] +Searching alignments... [0.01s] 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.015s] +Building query seed array... [0.016s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.015s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 1/4. -Building reference seed array... [0.005s] -Building query seed array... [0s] -Computing hash join... [0s] +Building reference seed array... [0.006s] +Building query seed array... [0.019s] +Computing hash join... [0.015s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0s] +Building reference seed array... [0.013s] +Building query seed array... [0.02s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.014s] 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... [0s] +Building reference seed array... [0.022s] +Building query seed array... [0.009s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.008s] +Searching alignments... [0.007s] 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... [0s] +Building reference seed array... [0.012s] +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... [0.005s] -Building query seed array... [0s] -Computing hash join... [0s] +Building reference seed array... [0.009s] +Building query seed array... [0.003s] +Computing hash join... [0.013s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.011s] 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... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.008s] +Building query seed array... [0.008s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.007s] +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... [0.005s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.015s] +Building query seed array... [0.015s] +Computing hash join... [0.008s] +Masking low complexity seeds... [0.011s] +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... [0.005s] +Building reference seed array... [0.01s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 1/4. -Building reference seed array... [0.005s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.018s] +Building query seed array... [0.015s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.004s] +Searching alignments... [0.002s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 2/4. -Building reference seed array... [0.005s] -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] +Searching alignments... [0.012s] 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.023s] +Building query seed array... [0.015s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.007s] +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... [0.005s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.004s] +Building query seed array... [0.011s] +Computing hash join... [0.005s] +Masking low complexity seeds... [0.004s] +Searching alignments... [0.004s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0.004s] +Computing alignments... Loading trace points... [0.012s] Sorting trace points... [0s] -Computing alignments... [0.005s] +Computing alignments... [0.007s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.011s] + [0.019s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -7570,17 +7606,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.741s +Total time = 2.494s 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.5NVdiqKBrK/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.UghWydqRLz/E.faa.vs.C2.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.9.163 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.5NVdiqKBrK +Temporary directory: /tmp/tmp.UghWydqRLz #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C2.faa.diamond (type: Diamond database, sequences: 2, letters: 726) @@ -7588,45 +7624,45 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.015s] +Masking queries... [0.024s] Algorithm: Double-indexed -Building query histograms... [0.026s] +Building query histograms... [0.027s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0s] +Masking reference... [0.011s] Initializing temporary storage... [0s] Building reference histograms... [0s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building query seed array... [0.007s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.007s] 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] +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 1/16, index chunk 3/4. -Building reference seed array... [0s] -Building query seed array... [0.005s] +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 1/16, 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] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4. -Building reference seed array... [0s] +Building reference seed array... [0.01s] Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -7634,28 +7670,28 @@ 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... [0.005s] 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 3/4. Building reference seed array... [0s] -Building query seed array... [0.004s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, 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] 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 query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -7666,52 +7702,52 @@ Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] -Deallocating memory... [0s] +Deallocating memory... [0.003s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 3/4. -Building reference seed array... [0s] -Building query seed array... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.013s] +Building query seed array... [0.027s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.011s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 4/4. -Building reference seed array... [0s] -Building query seed array... [0.005s] -Computing hash join... [0s] +Building reference seed array... [0.019s] +Building query seed array... [0.012s] +Computing hash join... [0.007s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.007s] 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] +Building reference seed array... [0.01s] +Building query seed array... [0.012s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.005s] +Searching alignments... [0.015s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 2/4. -Building reference seed array... [0s] -Building query seed array... [0.005s] -Computing hash join... [0s] +Building reference seed array... [0.016s] +Building query seed array... [0.008s] +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 3/4. -Building reference seed array... [0s] -Building query seed array... [0.005s] +Building reference seed array... [0.007s] +Building query seed array... [0.016s] 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... [0.005s] +Building reference seed array... [0.005s] +Building query seed array... [0.008s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 1/4. -Building reference seed array... [0s] -Building query seed array... [0.005s] +Building reference seed array... [0.002s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -7725,334 +7761,334 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.005s] -Computing hash join... [0s] +Building query seed array... [0.002s] +Computing hash join... [0.006s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +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... [0s] -Building query seed array... [0.005s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building query seed array... [0.013s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.004s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 2/4. -Building reference seed array... [0s] -Building query seed array... [0.005s] +Building reference seed array... [0.011s] +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... [0.005s] +Building reference seed array... [0.002s] +Building query seed array... [0.016s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.005s] -Computing hash join... [0s] +Building query seed array... [0.001s] +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 7/16, index chunk 1/4. -Building reference seed array... [0s] -Building query seed array... [0.005s] -Computing hash join... [0s] +Building reference seed array... [0.014s] +Building query seed array... [0.035s] +Computing hash join... [0.015s] 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... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.01s] +Building query seed array... [0.008s] +Computing hash join... [0.019s] +Masking low complexity seeds... [0.007s] 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] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 4/4. -Building reference seed array... [0s] -Building query seed array... [0.005s] +Building reference seed array... [0.025s] +Building query seed array... [0.015s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.007s] 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... [0.005s] -Computing hash join... [0s] +Building reference seed array... [0.015s] +Building query seed array... [0.009s] +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 2/4. -Building reference seed array... [0s] +Building reference seed array... [0.001s] Building query seed array... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.005s] +Searching alignments... [0.01s] 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 reference seed array... [0.004s] +Building query seed array... [0.019s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 4/4. -Building reference seed array... [0s] -Building query seed array... [0.005s] +Building reference seed array... [0.006s] +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 9/16, index chunk 1/4. -Building reference seed array... [0s] -Building query seed array... [0.005s] +Building reference seed array... [0.006s] +Building query seed array... [0.015s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 2/4. -Building reference seed array... [0s] -Building query seed array... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.007s] +Building query seed array... [0.018s] +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 9/16, index chunk 3/4. -Building reference seed array... [0s] -Building query seed array... [0.005s] -Computing hash join... [0s] +Building reference seed array... [0.028s] +Building query seed array... [0.016s] +Computing hash join... [0.015s] 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 4/4. -Building reference seed array... [0s] -Building query seed array... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.027s] +Building query seed array... [0.032s] +Computing hash join... [0.016s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.019s] 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] -Computing hash join... [0s] +Building reference seed array... [0.015s] +Building query seed array... [0.004s] +Computing hash join... [0.027s] 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 2/4. -Building reference seed array... [0s] -Building query seed array... [0.005s] +Building reference seed array... [0.03s] +Building query seed array... [0.018s] 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 3/4. -Building reference seed array... [0s] -Building query seed array... [0.005s] -Computing hash join... [0s] +Building reference seed array... [0.02s] +Building query seed array... [0.008s] +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 10/16, index chunk 4/4. -Building reference seed array... [0s] -Building query seed array... [0.005s] +Building reference seed array... [0.014s] +Building query seed array... [0.015s] 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 11/16, index chunk 1/4. -Building reference seed array... [0s] -Building query seed array... [0.005s] +Building reference seed array... [0.011s] +Building query seed array... [0.016s] 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 2/4. Building reference seed array... [0s] -Building query seed array... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building query seed array... [0.004s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.004s] +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... [0s] -Building query seed array... [0.005s] +Building reference seed array... [0.007s] +Building query seed array... [0.02s] 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... [0.005s] +Building reference seed array... [0.008s] +Building query seed array... [0.02s] 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 12/16, 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 reference seed array... [0.051s] +Building query seed array... [0.015s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.007s] 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.017s] +Building query seed array... [0.004s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.013s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 3/4. -Building reference seed array... [0s] -Building query seed array... [0.005s] +Building reference seed array... [0.008s] +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 4/4. -Building reference seed array... [0s] -Building query seed array... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.003s] +Building query seed array... [0.008s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.007s] 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 reference seed array... [0.005s] +Building query seed array... [0.024s] 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... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building query seed array... [0.019s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.012s] +Searching alignments... [0.009s] 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] -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... [0.003s] +Masking low complexity seeds... [0.015s] +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... [0s] -Building query seed array... [0.005s] +Building reference seed array... [0.012s] +Building query seed array... [0.012s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.006s] +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... [0s] +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 14/16, index chunk 2/4. -Building reference seed array... [0s] -Building query seed array... [0.005s] +Building reference seed array... [0.01s] +Building query seed array... [0.008s] Computing hash join... [0s] -Masking low complexity seeds... [0s] +Masking low complexity seeds... [0.001s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 3/4. -Building reference seed array... [0s] -Building query seed array... [0.005s] -Computing hash join... [0s] +Building reference seed array... [0.018s] +Building query seed array... [0.014s] +Computing hash join... [0.003s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.009s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 4/4. -Building reference seed array... [0s] -Building query seed array... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.012s] +Building query seed array... [0.003s] +Computing hash join... [0.004s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.005s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 1/4. -Building reference seed array... [0s] -Building query seed array... [0.005s] +Building reference seed array... [0.007s] +Building query seed array... [0.014s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.005s] +Searching alignments... [0.005s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 2/4. -Building reference seed array... [0s] -Building query seed array... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.012s] +Building query seed array... [0.01s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.019s] 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... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.02s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.005s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 4/4. -Building reference seed array... [0s] -Building query seed array... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.027s] +Building query seed array... [0.024s] +Computing hash join... [0.018s] +Masking low complexity seeds... [0.023s] +Searching alignments... [0.005s] 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] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.035s] +Building query seed array... [0.036s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.016s] +Searching alignments... [0.016s] 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... [0.005s] +Building reference seed array... [0.012s] +Building query seed array... [0.009s] 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 16/16, index chunk 3/4. -Building reference seed array... [0s] -Building query seed array... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.003s] +Building query seed array... [0.009s] +Computing hash join... [0.006s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.029s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 4/4. -Building reference seed array... [0s] -Building query seed array... [0.005s] +Building reference seed array... [0.033s] +Building query seed array... [0.011s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0.001s] +Computing alignments... Loading trace points... [0.013s] Sorting trace points... [0s] -Computing alignments... [0.005s] -Deallocating buffers... [0s] +Computing alignments... [0.006s] +Deallocating buffers... [0.024s] Loading trace points... [0s] - [0.007s] + [0.043s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -8062,17 +8098,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.746s +Total time = 2.397s 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.5NVdiqKBrK/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.UghWydqRLz/M.faa.vs.L.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.9.163 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.5NVdiqKBrK +Temporary directory: /tmp/tmp.UghWydqRLz #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/L.faa.diamond (type: Diamond database, sequences: 40, letters: 26652) @@ -8080,471 +8116,471 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.024s] +Masking queries... [0.055s] Algorithm: Double-indexed -Building query histograms... [0.013s] +Building query histograms... [0.022s] 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... [0.034s] 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] -Masking low complexity seeds... [0s] -Searching alignments... [0.012s] +Building reference seed array... [0.035s] +Building query seed array... [0.041s] +Computing hash join... [0.006s] +Masking low complexity seeds... [0.011s] +Searching alignments... [0.011s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Building reference seed array... [0.019s] +Building query seed array... [0.01s] +Computing hash join... [0.02s] +Masking low complexity seeds... [0.004s] +Searching alignments... [0.015s] 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... [0.011s] +Building query seed array... [0.009s] 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... [0.001s] 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 2/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Building reference seed array... [0.011s] +Building query seed array... [0.013s] +Computing hash join... [0.023s] +Masking low complexity seeds... [0.011s] +Searching alignments... [0.011s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.019s] +Building query seed array... [0.007s] +Computing hash join... [0.009s] Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Searching alignments... [0.009s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Building reference seed array... [0.008s] +Building query seed array... [0.015s] +Computing hash join... [0.019s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.01s] 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] +Building reference seed array... [0.02s] +Building query seed array... [0.016s] +Computing hash join... [0.011s] 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 3/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0s] +Building query seed array... [0.015s] 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 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... [0.007s] +Building query seed array... [0.023s] +Computing hash join... [0.008s] Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Searching alignments... [0.015s] 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... [0.007s] +Building query seed array... [0.008s] 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 3/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.01s] +Building query seed array... [0.027s] +Computing hash join... [0.012s] 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] -Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Building reference seed array... [0.015s] +Building query seed array... [0.008s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.006s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +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... [0.003s] 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... [0.019s] +Building query seed array... [0.016s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Searching alignments... [0.005s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.025s] +Building query seed array... [0.015s] 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 5/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.007s] +Building query seed array... [0.023s] +Computing hash join... [0.002s] Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Searching alignments... [0.012s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.012s] +Building query seed array... [0.02s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Searching alignments... [0.014s] 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... [0.015s] +Building query seed array... [0.023s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.022s] +Masking low complexity seeds... [0.011s] +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] -Computing hash join... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.027s] +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 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.015s] +Building query seed array... [0.011s] +Computing hash join... [0.004s] 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... [0.015s] +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 6/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query 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... [0.008s] +Searching alignments... [0.011s] 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 reference seed array... [0.016s] +Building query seed array... [0.015s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.014s] 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Building reference seed array... [0.005s] +Building query seed array... [0.015s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.023s] +Searching alignments... [0.015s] 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Building reference seed array... [0.019s] +Building query seed array... [0.008s] +Computing hash join... [0.008s] +Masking low complexity seeds... [0.022s] +Searching alignments... [0.006s] 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... [0.013s] +Building query seed array... [0.007s] +Computing hash join... [0.004s] +Masking low complexity seeds... [0.004s] +Searching alignments... [0.014s] 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... [0.005s] +Building query seed array... [0.014s] +Computing hash join... [0.012s] 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 8/16, 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... [0.007s] 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Building reference seed array... [0.01s] +Building query seed array... [0.009s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.006s] +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... [0.002s] -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... [0.023s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.011s] +Searching alignments... [0.015s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, 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... [0.019s] +Building query seed array... [0.023s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.015s] 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... [0.019s] +Building query seed array... [0.023s] +Computing hash join... [0.008s] 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 9/16, 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... [0.017s] +Building query seed array... [0.019s] +Computing hash join... [0.006s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.01s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Building reference seed array... [0.013s] +Building query seed array... [0.023s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.011s] +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 query seed array... [0.002s] +Building reference seed array... [0.023s] +Building query seed array... [0.023s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Searching alignments... [0.014s] 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... [0.009s] +Building reference seed array... [0.009s] +Building query seed array... [0.025s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.004s] +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... [0.002s] -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... [0.019s] +Masking low complexity seeds... [0.016s] +Searching alignments... [0.013s] 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... [0.009s] +Building query seed array... [0.016s] +Computing hash join... [0.014s] Masking low complexity seeds... [0s] Searching alignments... [0.009s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.023s] +Building query seed array... [0.027s] +Computing hash join... [0.012s] Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Searching alignments... [0.025s] 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... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Building reference seed array... [0.008s] +Building query seed array... [0.039s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.004s] +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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Building reference seed array... [0.016s] +Building query seed array... [0.01s] +Computing hash join... [0.005s] +Masking low complexity seeds... [0.011s] +Searching alignments... [0.01s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] -Computing hash join... [0.001s] +Building reference seed array... [0.016s] +Building query seed array... [0.011s] +Computing hash join... [0.008s] 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 11/16, 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... [0.009s] +Searching alignments... [0.003s] 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... [0.031s] +Building query seed array... [0.02s] 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 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... [0.021s] +Building query seed array... [0.051s] +Computing hash join... [0.008s] 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 12/16, 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... [0.021s] +Building query seed array... [0.008s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.011s] +Searching alignments... [0.009s] 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] -Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Building reference seed array... [0.004s] +Building query seed array... [0.008s] +Computing hash join... [0.014s] +Masking low complexity seeds... [0.012s] +Searching alignments... [0.02s] 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... [0.032s] +Building query seed array... [0.009s] 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 13/16, 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... [0.005s] +Building query seed array... [0.013s] +Computing hash join... [0.001s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.017s] 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... [0.005s] +Building query seed array... [0.015s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.009s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Searching alignments... [0.011s] 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] +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... [0.003s] 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... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.015s] +Computing hash join... [0.007s] Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Searching alignments... [0.007s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building 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... [0.008s] +Searching alignments... [0.011s] 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... [0.02s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Searching alignments... [0.015s] 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... [0.015s] +Building query seed array... [0.007s] +Computing hash join... [0.008s] Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Searching alignments... [0.008s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 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... [0.009s] 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... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Searching alignments... [0.007s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.009s] +Building query seed array... [0.007s] Computing hash join... [0s] 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 16/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.008s] +Building query seed array... [0.011s] +Computing hash join... [0.003s] 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 16/16, 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... [0.007s] +Building query seed array... [0.016s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.017s] +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] +Building reference seed array... [0.005s] +Building query seed array... [0.007s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.015s] 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... [0.009s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Searching alignments... [0.007s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0.004s] +Computing alignments... Loading trace points... [0.152s] Sorting trace points... [0s] -Computing alignments... [0.249s] +Computing alignments... [0.279s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.255s] + [0.432s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -8554,17 +8590,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 1.618s +Total time = 3.568s 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.5NVdiqKBrK/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.UghWydqRLz/L.faa.vs.M.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.9.163 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.5NVdiqKBrK +Temporary directory: /tmp/tmp.UghWydqRLz #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/M.faa.diamond (type: Diamond database, sequences: 40, letters: 26963) @@ -8572,471 +8608,471 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.023s] +Masking queries... [0.052s] Algorithm: Double-indexed -Building query histograms... [0.013s] +Building query histograms... [0.04s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.004s] +Masking reference... [0.015s] Initializing temporary storage... [0s] -Building reference histograms... [0.013s] +Building reference histograms... [0.023s] 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... [0.008s] +Building query seed array... [0.015s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.012s] +Searching alignments... [0.018s] 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... [0.023s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Searching alignments... [0.013s] 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... [0.013s] +Building query seed array... [0.006s] +Computing hash join... [0.008s] 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] -Computing hash join... [0.001s] +Building reference seed array... [0.011s] +Building query seed array... [0.013s] +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 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0s] +Building query seed array... [0.009s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Masking low complexity seeds... [0.004s] +Searching alignments... [0.007s] 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... [0.007s] +Building query seed array... [0.007s] 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 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... [0.007s] +Building query seed array... [0.036s] +Computing hash join... [0.003s] 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 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... [0.028s] +Building query seed array... [0.031s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.011s] +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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Building reference seed array... [0.016s] +Building query seed array... [0.024s] +Computing hash join... [0.012s] +Masking low complexity seeds... [0.006s] +Searching alignments... [0.011s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.004s] +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 3/16, 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 query seed array... [0.01s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.015s] +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... [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... [0.02s] +Building query seed array... [0.023s] +Computing hash join... [0.023s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.015s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 1/4. -Building reference seed array... [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... [0.023s] +Building query seed array... [0.012s] +Computing hash join... [0.014s] +Masking low complexity seeds... [0.012s] +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 query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Building reference seed array... [0.001s] +Building query seed array... [0.026s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.007s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.023s] +Building query seed array... [0.011s] +Computing hash join... [0.008s] 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 4/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.02s] +Building query seed array... [0.008s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Masking low complexity seeds... [0.004s] +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 query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Building reference seed array... [0.008s] +Building query seed array... [0.01s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.004s] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Building reference seed array... [0.024s] +Building query seed array... [0.035s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.023s] +Searching alignments... [0.019s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Building reference seed array... [0.031s] +Building query seed array... [0.009s] +Computing hash join... [0.018s] +Masking low complexity seeds... [0.007s] +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... [0.002s] -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... [0.007s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.015s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.011s] +Building query seed array... [0.015s] +Computing hash join... [0.004s] 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 6/16, 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... [0.009s] +Building reference seed array... [0.004s] +Building query seed array... [0.019s] +Computing hash join... [0.007s] +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 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.016s] +Building query seed array... [0.013s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.026s] +Masking low complexity seeds... [0.012s] +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... [0.003s] -Building query seed array... [0.002s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Building reference seed array... [0.017s] +Building query seed array... [0.008s] +Computing hash join... [0s] +Masking low complexity seeds... [0.002s] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, 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... [0.015s] +Building query seed array... [0.01s] +Computing hash join... [0.005s] +Masking low complexity seeds... [0.028s] +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... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.006s] +Building query seed array... [0s] 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 7/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.021s] +Building query seed array... [0.008s] +Computing hash join... [0.003s] 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 7/16, 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... [0.006s] +Building query seed array... [0.006s] +Computing hash join... [0.018s] +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 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.015s] +Building query seed array... [0.011s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Searching alignments... [0.006s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.003s] +Building query seed array... [0.024s] 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 8/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.01s] +Building query seed array... [0.012s] 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 8/16, 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... [0.004s] 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 9/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.01s] +Building query seed array... [0.011s] 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 9/16, 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... [0.007s] +Building query seed array... [0.007s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.011s] 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] +Building reference seed array... [0.016s] +Building query seed array... [0.007s] 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 9/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.017s] +Building query seed array... [0.007s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Searching alignments... [0.014s] 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] +Building reference seed array... [0.015s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.009s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, 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... [0.008s] +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... [0.003s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Searching alignments... [0.005s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.008s] +Building query seed array... [0.011s] +Computing hash join... [0.004s] Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Searching alignments... [0.012s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Building reference seed array... [0.004s] +Building query seed array... [0.001s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.006s] +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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Building reference seed array... [0.004s] +Building query seed array... [0.015s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.017s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Building reference seed array... [0.009s] +Building query seed array... [0.008s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.01s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.027s] +Building query seed array... [0.015s] 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 12/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.006s] +Building query seed array... [0.007s] +Computing hash join... [0.004s] 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 12/16, 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... [0.009s] +Searching alignments... [0.011s] 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 reference seed array... [0.015s] +Building query seed array... [0.011s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Masking low complexity seeds... [0.019s] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.026s] +Building query seed array... [0.007s] +Computing hash join... [0.008s] Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Building reference seed array... [0.013s] +Building query seed array... [0.02s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.022s] 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] -Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Building reference seed array... [0.009s] +Building query seed array... [0.014s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.011s] +Searching alignments... [0.017s] 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] -Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Building reference seed array... [0.015s] +Building query seed array... [0.007s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.021s] 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... [0.008s] +Building reference seed array... [0.019s] +Building query seed array... [0.031s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.011s] +Searching alignments... [0.013s] 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] -Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Building reference seed array... [0.016s] +Building query seed array... [0.007s] +Computing hash join... [0.007s] +Masking low complexity seeds... [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... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.024s] +Building query seed array... [0.007s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.005s] 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... [0.016s] +Building query seed array... [0.015s] 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Building query seed array... [0.01s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.007s] +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 reference seed array... [0.017s] +Building query seed array... [0.007s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Searching alignments... [0.012s] 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... [0.015s] +Building query seed array... [0.012s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Searching alignments... [0.016s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Building reference seed array... [0.008s] +Building query seed array... [0.019s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.019s] +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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Building reference seed array... [0.009s] +Building query seed array... [0.012s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.003s] +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... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.014s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Searching alignments... [0.004s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, 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... [0.014s] +Building query seed array... [0.001s] +Computing hash join... [0.002s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.013s] 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... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Searching alignments... [0.006s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 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... [0.012s] +Building query seed array... [0.019s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.004s] +Searching alignments... [0.003s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0.004s] +Computing alignments... Loading trace points... [0.32s] Sorting trace points... [0s] -Computing alignments... [0.255s] +Computing alignments... [0.306s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.261s] + [0.628s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -9046,17 +9082,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 1.617s +Total time = 3.621s 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.5NVdiqKBrK/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.UghWydqRLz/C2.faa.vs.L.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.9.163 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.5NVdiqKBrK +Temporary directory: /tmp/tmp.UghWydqRLz #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/L.faa.diamond (type: Diamond database, sequences: 40, letters: 26652) @@ -9064,471 +9100,471 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.001s] +Masking queries... [0.006s] Algorithm: Double-indexed -Building query histograms... [0.001s] +Building query histograms... [0.011s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.004s] +Masking reference... [0.007s] Initializing temporary storage... [0s] -Building reference histograms... [0.013s] +Building reference histograms... [0.023s] 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... [0s] +Building reference seed array... [0.005s] +Building query seed array... [0.014s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. -Building reference seed array... [0.003s] -Building query seed array... [0s] -Computing hash join... [0s] +Building reference seed array... [0.024s] +Building query seed array... [0.014s] +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 1/16, 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 reference seed array... [0.023s] +Building query seed array... [0.035s] +Computing hash join... [0.004s] +Masking low complexity seeds... [0.011s] +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... [0.002s] -Building query seed array... [0s] +Building reference seed array... [0.008s] +Building query seed array... [0.011s] 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... [0s] +Building reference seed array... [0.031s] +Building query seed array... [0.023s] 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 2/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] +Building reference seed array... [0.031s] +Building query seed array... [0.02s] 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 2/16, 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 reference seed array... [0.011s] +Building query seed array... [0.015s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.019s] +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... [0s] -Computing hash join... [0s] +Building reference seed array... [0.043s] +Building query seed array... [0.019s] +Computing hash join... [0.015s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.012s] 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... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.031s] +Building query seed array... [0.027s] +Computing hash join... [0.019s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.019s] 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... [0.019s] +Building query seed array... [0.027s] +Computing hash join... [0.019s] +Masking low complexity seeds... [0.016s] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.023s] +Building query seed array... [0.035s] +Computing hash join... [0.008s] +Masking low complexity seeds... [0.004s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 4/4. -Building reference seed array... [0.002s] +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 query seed array... [0s] +Building reference seed array... [0.016s] +Building query seed array... [0.031s] 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 4/16, 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... [0.012s] +Building query seed array... [0.031s] +Computing hash join... [0.008s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.007s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] +Building reference seed array... [0.035s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] +Building reference seed array... [0.029s] +Building query seed array... [0.019s] 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 1/4. -Building reference seed array... [0.003s] -Building query seed array... [0s] +Building reference seed array... [0.004s] +Building query seed array... [0.007s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 2/4. -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 5/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] +Building reference seed array... [0.02s] +Building query seed array... [0.023s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.031s] 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] -Computing hash join... [0s] +Building reference seed array... [0.02s] +Building query seed array... [0.023s] +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 6/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.023s] +Building query seed array... [0.015s] +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 6/16, index chunk 2/4. -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 6/16, 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 reference seed array... [0.018s] +Building query seed array... [0.015s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.019s] +Searching alignments... [0.015s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 4/4. -Building reference seed array... [0.002s] -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 7/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.022s] +Building query seed array... [0.007s] +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 7/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] -Computing hash join... [0s] +Building reference seed array... [0.003s] +Building query seed array... [0.007s] +Computing hash join... [0.007s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.01s] 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.016s] +Building query seed array... [0.006s] +Computing hash join... [0.004s] +Masking low complexity seeds... [0.012s] +Searching alignments... [0.01s] 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... [0.008s] 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 8/16, 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... [0.031s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.007s] +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... [0s] -Computing hash join... [0s] +Building reference seed array... [0.013s] +Building query seed array... [0.014s] +Computing hash join... [0.011s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.022s] 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... [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... [0.024s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.006s] 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] +Building reference seed array... [0.015s] +Building query seed array... [0.032s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.018s] 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... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.008s] +Building query seed array... [0.011s] +Computing hash join... [0.019s] +Masking low complexity seeds... [0.007s] 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... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.026s] +Building query seed array... [0.011s] +Computing hash join... [0.019s] +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... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.014s] +Building query seed array... [0.031s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.011s] +Searching alignments... [0.011s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] +Building reference seed array... [0.027s] +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 1/4. -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... [0.007s] +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 10/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] -Computing hash join... [0s] +Building reference seed array... [0.037s] +Building query seed array... [0.008s] +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 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] +Building reference seed array... [0.014s] +Building query seed array... [0.011s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.007s] 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... [0s] +Building reference seed array... [0.014s] +Building query seed array... [0.011s] 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 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... [0.026s] +Building query seed array... [0.031s] +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 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... [0.022s] +Building query seed array... [0.047s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.009s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] +Building reference seed array... [0.02s] +Building query seed array... [0.039s] 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 11/16, 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... [0.011s] +Computing hash join... [0.009s] 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... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.019s] +Building query seed array... [0.008s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] +Building reference seed array... [0.007s] +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 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] +Computing hash join... [0.005s] +Masking low complexity seeds... [0.01s] +Searching alignments... [0.005s] 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... [0s] +Building reference seed array... [0.02s] +Building query seed array... [0.004s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.002s] +Searching alignments... [0.005s] 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] +Building reference seed array... [0.02s] +Building query seed array... [0.015s] 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 13/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] -Computing hash join... [0s] +Building reference seed array... [0.016s] +Building query seed array... [0.008s] +Computing hash join... [0.015s] 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... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.017s] +Building query seed array... [0.003s] +Computing hash join... [0.023s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.008s] +Building query seed array... [0.035s] +Computing hash join... [0.019s] +Masking low complexity seeds... [0.019s] 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... [0s] +Building reference seed array... [0.005s] +Building query seed array... [0.039s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.019s] +Searching alignments... [0.005s] 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] +Building reference seed array... [0.023s] +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... [0.002s] -Building query seed array... [0s] +Building reference seed array... [0.009s] +Building query seed array... [0.023s] 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... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.013s] +Building query seed array... [0.007s] +Computing hash join... [0.001s] +Masking low complexity seeds... [0.006s] 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] -Computing hash join... [0s] +Building reference seed array... [0.007s] +Building query seed array... [0.014s] +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 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... [0.005s] +Building query seed array... [0.007s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.015s] +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... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.039s] +Building query seed array... [0.027s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.011s] +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 query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.016s] +Building query seed array... [0.019s] +Computing hash join... [0.007s] +Masking low complexity seeds... [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... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.006s] +Building query seed array... [0.011s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.007s] +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... [0s] +Building reference seed array... [0.016s] +Building query seed array... [0.022s] 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 16/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] +Building reference seed array... [0.031s] +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 16/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.008s] +Building query seed array... [0.007s] +Computing hash join... [0.019s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.005s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0.001s] +Computing alignments... Loading trace points... [0.023s] Sorting trace points... [0s] -Computing alignments... [0.006s] +Computing alignments... [0.005s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.008s] + [0.03s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -9538,17 +9574,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.537s +Total time = 3.394s 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.5NVdiqKBrK/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.UghWydqRLz/L.faa.vs.C2.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.9.163 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.5NVdiqKBrK +Temporary directory: /tmp/tmp.UghWydqRLz #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C2.faa.diamond (type: Diamond database, sequences: 2, letters: 726) @@ -9556,471 +9592,471 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.025s] +Masking queries... [0.03s] Algorithm: Double-indexed -Building query histograms... [0.013s] +Building query histograms... [0.038s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0s] +Masking reference... [0.006s] Initializing temporary storage... [0s] -Building reference histograms... [0s] +Building reference histograms... [0.027s] 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... [0.023s] +Building query seed array... [0.016s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.004s] +Searching alignments... [0.008s] 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] +Building reference seed array... [0.006s] +Building query seed array... [0.012s] +Computing hash join... [0.013s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. -Building reference seed array... [0s] -Building query seed array... [0.002s] +Building reference seed array... [0.004s] +Building query seed array... [0.021s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, 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... [0.005s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.005s] +Searching alignments... [0.008s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4. -Building reference seed array... [0s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.015s] +Building query seed array... [0.017s] +Computing hash join... [0.01s] +Masking low complexity seeds... [0.019s] +Searching alignments... [0.019s] 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.031s] +Building query seed array... [0.027s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.019s] +Searching alignments... [0.007s] 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... [0.001s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.011s] +Searching alignments... [0.008s] 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... [0.003s] +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... [0s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.027s] +Building query seed array... [0.005s] +Computing hash join... [0.009s] +Masking low complexity seeds... [0.007s] +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... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.003s] +Building query seed array... [0.007s] +Computing hash join... [0.008s] +Masking low complexity seeds... [0.011s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 3/4. -Building reference seed array... [0s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.027s] +Building query seed array... [0.019s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.011s] +Searching alignments... [0.015s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 4/4. -Building reference seed array... [0s] -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... [0.031s] +Computing hash join... [0.007s] +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 1/4. -Building reference seed array... [0s] -Building query seed array... [0.002s] +Building reference seed array... [0.017s] +Building query seed array... [0.012s] 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 4/16, 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 reference seed array... [0.023s] +Building query seed array... [0.023s] +Computing hash join... [0.007s] +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 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 4/16, 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... [0.013s] +Building query seed array... [0.015s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.011s] +Searching alignments... [0.011s] 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.019s] +Building query seed array... [0.011s] +Computing hash join... [0.004s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.007s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 2/4. -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... [0.004s] +Building query seed array... [0.011s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.007s] 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] -Computing hash join... [0s] +Building reference seed array... [0.024s] +Building query seed array... [0.015s] +Computing hash join... [0.007s] 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... [0s] -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... [0.013s] +Computing hash join... [0.002s] +Masking low complexity seeds... [0.007s] +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... [0s] -Building query seed array... [0.002s] +Building reference seed array... [0.011s] +Building query seed array... [0.015s] 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 2/4. -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... [0.022s] +Building query seed array... [0.016s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.011s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 3/4. -Building reference seed array... [0s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.011s] +Building query seed array... [0.016s] +Computing hash join... [0.004s] +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 4/4. -Building reference seed array... [0s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.016s] +Building query seed array... [0.004s] +Computing hash join... [0.011s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.014s] 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] -Computing hash join... [0s] +Building query seed array... [0.016s] +Computing hash join... [0.007s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.011s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 2/4. -Building reference seed array... [0s] -Building query seed array... [0.002s] +Building reference seed array... [0.02s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.009s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 3/4. -Building reference seed array... [0s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.008s] +Building query seed array... [0.005s] +Computing hash join... [0.02s] +Masking low complexity seeds... [0.006s] +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... [0s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.023s] +Building query seed array... [0.019s] +Computing hash join... [0.011s] +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 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 8/16, index chunk 2/4. -Building reference seed array... [0s] -Building query seed array... [0.002s] +Building reference seed array... [0.004s] +Building query seed array... [0.012s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 3/4. -Building reference seed array... [0s] -Building query seed array... [0.002s] +Building reference seed array... [0.006s] +Building query seed array... [0.015s] 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 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... [0.019s] +Building query seed array... [0.031s] +Computing hash join... [0.008s] +Masking low complexity seeds... [0.011s] +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... [0s] -Building query seed array... [0.002s] +Building reference seed array... [0.003s] +Building query seed array... [0.02s] 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 2/4. -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... [0.007s] +Building query seed array... [0.023s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.007s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 3/4. -Building reference seed array... [0s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.032s] +Building query seed array... [0.008s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.011s] 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... [0.002s] +Building reference seed array... [0.03s] +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 10/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building query seed array... [0.008s] +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 10/16, index chunk 2/4. -Building reference seed array... [0s] -Building query seed array... [0.003s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.006s] +Building query seed array... [0.019s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.015s] 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... [0.012s] +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 10/16, index chunk 4/4. -Building reference seed array... [0s] -Building query seed array... [0.002s] +Building reference seed array... [0.031s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.017s] 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] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.003s] +Building query seed array... [0.008s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.015s] +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... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.007s] +Building query seed array... [0.019s] +Computing hash join... [0.004s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.006s] 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] -Computing hash join... [0s] +Building reference seed array... [0.007s] +Building query seed array... [0.012s] +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 11/16, index chunk 4/4. -Building reference seed array... [0s] -Building query seed array... [0.002s] +Building reference seed array... [0.019s] +Building query seed array... [0.024s] 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building query seed array... [0s] +Computing hash join... [0.004s] +Masking low complexity seeds... [0.027s] 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... [0.002s] +Building reference seed array... [0.005s] +Building query seed array... [0.027s] 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... [0s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +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... [0.002s] 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.003s] +Building query seed array... [0.004s] +Computing hash join... [0.005s] +Masking low complexity seeds... [0.002s] +Searching alignments... [0.009s] 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 reference seed array... [0.007s] +Building query seed array... [0.015s] 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 13/16, index chunk 2/4. -Building reference seed array... [0s] -Building query seed array... [0.002s] +Building reference seed array... [0.01s] +Building query seed array... [0.009s] 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 13/16, index chunk 3/4. -Building reference seed array... [0s] -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... [0.017s] 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] -Computing hash join... [0s] +Building reference seed array... [0.015s] +Building query seed array... [0.023s] +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 14/16, 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... [0s] +Building query seed array... [0s] +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 14/16, index chunk 2/4. -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... [0.012s] +Computing hash join... [0.003s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.009s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 3/4. -Building reference seed array... [0s] -Building query seed array... [0.002s] +Building reference seed array... [0.005s] +Building query seed array... [0.017s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 4/4. -Building reference seed array... [0s] -Building query seed array... [0.002s] +Building reference seed array... [0.013s] +Building query seed array... [0.019s] 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 1/4. -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... [0.003s] +Building query seed array... [0.008s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.005s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 2/4. -Building reference seed array... [0s] -Building query seed array... [0.002s] +Building reference seed array... [0.039s] +Building query seed array... [0.035s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.007s] +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... [0s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.007s] +Building query seed array... [0.019s] +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 15/16, index chunk 4/4. -Building reference seed array... [0s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.031s] +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 16/16, index chunk 1/4. -Building reference seed array... [0s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.008s] +Building query seed array... [0.006s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.019s] 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... [0.005s] +Building query seed array... [0.024s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.02s] 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 reference seed array... [0.019s] +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 16/16, 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... [0.007s] +Building query seed array... [0.011s] +Computing hash join... [0.004s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.006s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0.001s] +Computing alignments... Loading trace points... [0.043s] Sorting trace points... [0s] -Computing alignments... [0.006s] +Computing alignments... [0.002s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.008s] + [0.046s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -10030,17 +10066,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.575s +Total time = 2.851s 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.5NVdiqKBrK/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.UghWydqRLz/C2.faa.vs.M.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.9.163 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.5NVdiqKBrK +Temporary directory: /tmp/tmp.UghWydqRLz #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/M.faa.diamond (type: Diamond database, sequences: 40, letters: 26963) @@ -10048,471 +10084,471 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.001s] +Masking queries... [0.004s] Algorithm: Double-indexed -Building query histograms... [0s] +Building query histograms... [0.015s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.004s] +Masking reference... [0.012s] Initializing temporary storage... [0s] -Building reference histograms... [0.013s] +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... [0.002s] -Building query seed array... [0s] +Building reference seed array... [0.028s] +Building query seed array... [0.015s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Masking low complexity seeds... [0.011s] +Searching alignments... [0.011s] 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... [0s] +Building reference seed array... [0.019s] +Building query seed array... [0.009s] 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... [0s] +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... [0.007s] 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] +Building reference seed array... [0.023s] +Building query seed array... [0.021s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] +Building reference seed array... [0.01s] +Building query seed array... [0.02s] 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... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.007s] +Computing hash join... [0.004s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.013s] 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... [0.022s] +Building query seed array... [0.003s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.013s] +Searching alignments... [0.022s] 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] -Computing hash join... [0s] +Building reference seed array... [0.011s] +Building query seed array... [0.027s] +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 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... [0.005s] +Building query seed array... [0.003s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.011s] +Searching alignments... [0.019s] 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] +Building reference seed array... [0.012s] +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 3/16, 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 reference seed array... [0.003s] +Building query seed array... [0.026s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.023s] +Searching alignments... [0.004s] 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] +Building reference seed array... [0.035s] +Building query seed array... [0.01s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 1/4. -Building reference seed array... [0.002s] +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 2/4. -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 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] +Searching alignments... [0.007s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 4/4. -Building reference seed array... [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] 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... [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... [0.008s] +Building query seed array... [0.018s] 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... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.006s] +Building query seed array... [0.015s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.004s] 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... [0.003s] +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... [0.008s] 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] -Computing hash join... [0s] +Building reference seed array... [0.02s] +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 6/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] -Computing hash join... [0s] +Building reference seed array... [0.017s] +Building query seed array... [0.009s] +Computing hash join... [0.008s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, 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 reference seed array... [0.014s] +Building query seed array... [0.035s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.019s] 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... [0s] +Building reference seed array... [0.008s] +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... [0.007s] 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... [0s] +Building reference seed array... [0.028s] +Building query seed array... [0.011s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.023s] +Searching alignments... [0.019s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.02s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +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... [0s] -Computing hash join... [0s] +Building reference seed array... [0.005s] +Building query seed array... [0.01s] +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 7/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.011s] +Building query seed array... [0.003s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.023s] +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 query seed array... [0s] +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 8/16, 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... [0.022s] +Building query seed array... [0.04s] +Computing hash join... [0.004s] +Masking low complexity seeds... [0.012s] 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... [0s] -Computing hash join... [0s] +Building reference seed array... [0.033s] +Building query seed array... [0.02s] +Computing hash join... [0.003s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] +Building reference seed array... [0.003s] +Building query seed array... [0.015s] 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 9/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.025s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] -Computing hash join... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.015s] +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 3/4. -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 9/16, 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 reference seed array... [0.012s] +Building query seed array... [0.015s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.007s] 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... [0.011s] Building query seed array... [0s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.01s] +Searching alignments... [0.006s] 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... [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... [0.007s] +Searching alignments... [0.004s] 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] +Building reference seed array... [0.006s] +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 4/4. -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... [0.018s] +Building query seed array... [0.016s] +Computing hash join... [0.019s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.002s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] +Building reference seed array... [0.015s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] -Computing hash join... [0s] +Building reference seed array... [0.009s] +Building query seed array... [0.027s] +Computing hash join... [0.008s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.013s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.008s] +Building query seed array... [0.023s] +Computing hash join... [0.004s] +Masking low complexity seeds... [0.001s] +Searching alignments... [0.012s] 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... [0s] +Building reference seed array... [0.006s] +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 12/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.02s] +Building query seed array... [0.023s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.011s] 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.005s] +Building query seed array... [0.008s] +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 12/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] -Computing hash join... [0s] +Building reference seed array... [0.012s] +Building query seed array... [0.027s] +Computing hash join... [0.019s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.025s] 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... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.016s] +Building query seed array... [0.011s] +Computing hash join... [0.004s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.025s] 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] +Building reference seed array... [0.019s] +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 13/16, 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... [0.003s] +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 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 reference seed array... [0.001s] +Building query seed array... [0.009s] +Computing hash join... [0.019s] +Masking low complexity seeds... [0.023s] +Searching alignments... [0.013s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.011s] +Building query seed array... [0.015s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.009s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] +Building reference seed array... [0.012s] +Building query seed array... [0.011s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.019s] +Searching alignments... [0.005s] 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] +Building reference seed array... [0.011s] +Building query seed array... [0.015s] +Computing hash join... [0.012s] 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... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.015s] +Computing hash join... [0.028s] +Masking low complexity seeds... [0.015s] +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... [0.002s] -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... [0.019s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.019s] +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... [0s] +Building reference seed array... [0.012s] +Building query seed array... [0.015s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.008s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.005s] 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] +Building reference seed array... [0.022s] +Building query seed array... [0.017s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.011s] +Searching alignments... [0.013s] 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.011s] +Building query seed array... [0.017s] +Computing hash join... [0.022s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.01s] 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... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.009s] +Building query seed array... [0.029s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.013s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.005s] +Building query seed array... [0.013s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.019s] +Searching alignments... [0.005s] 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... [0.014s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 4/4. -Building reference seed array... [0.002s] -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... [0.015s] +Computing hash join... [0.006s] +Masking low complexity seeds... [0.017s] +Searching alignments... [0.017s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0.001s] +Computing alignments... Loading trace points... [0.019s] Sorting trace points... [0s] -Computing alignments... [0.005s] +Computing alignments... [0.015s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.008s] + [0.036s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -10522,17 +10558,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.563s +Total time = 2.733s 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.5NVdiqKBrK/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.UghWydqRLz/M.faa.vs.C2.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.9.163 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.5NVdiqKBrK +Temporary directory: /tmp/tmp.UghWydqRLz #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C2.faa.diamond (type: Diamond database, sequences: 2, letters: 726) @@ -10540,471 +10576,471 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.024s] +Masking queries... [0.029s] Algorithm: Double-indexed -Building query histograms... [0.013s] +Building query histograms... [0.014s] Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0s] Initializing temporary storage... [0s] -Building reference histograms... [0s] +Building reference histograms... [0.005s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. -Building reference seed array... [0s] -Building query seed array... [0.003s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.003s] +Building query seed array... [0.023s] +Computing hash join... [0.013s] +Masking low complexity seeds... [0.014s] +Searching alignments... [0.003s] 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] +Building reference seed array... [0.016s] +Building query seed array... [0.02s] +Computing hash join... [0.006s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. -Building reference seed array... [0s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.01s] +Building query seed array... [0.008s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.008s] +Searching alignments... [0.011s] 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.008s] +Building query seed array... [0.011s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.017s] +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... [0s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.023s] +Building query seed array... [0.017s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.011s] +Searching alignments... [0.007s] 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] -Computing hash join... [0s] +Building reference seed array... [0.019s] +Building query seed array... [0.025s] +Computing hash join... [0.018s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.027s] 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... [0.011s] +Building query seed array... [0.015s] 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... [0.003s] +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 3/16, 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... [0s] +Building reference seed array... [0.007s] +Building query seed array... [0.023s] +Computing hash join... [0.004s] +Masking low complexity seeds... [0.004s] +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... [0.002s] +Building reference seed array... [0.007s] +Building query seed array... [0.02s] 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 3/4. -Building reference seed array... [0s] -Building query seed array... [0.002s] +Building reference seed array... [0.027s] +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 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... [0.006s] +Building query seed array... [0.035s] +Computing hash join... [0.012s] +Masking low complexity seeds... [0.013s] +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... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.01s] +Building query seed array... [0.001s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.007s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 2/4. -Building reference seed array... [0s] -Building query seed array... [0.002s] +Building reference seed array... [0.019s] +Building query seed array... [0.016s] 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 4/16, 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... [0.015s] +Building query seed array... [0.003s] +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... [0s] -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... [0.004s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.011s] +Searching alignments... [0.011s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 1/4. -Building reference seed array... [0s] -Building query seed array... [0.002s] +Building reference seed array... [0.031s] +Building query seed array... [0.011s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.011s] +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... [0s] -Building query seed array... [0.002s] +Building reference seed array... [0.022s] +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 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... [0.03s] +Building query seed array... [0.007s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.019s] +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... [0s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.023s] +Building query seed array... [0.027s] +Computing hash join... [0.012s] +Masking low complexity seeds... [0.007s] +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... [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] +Masking low complexity seeds... [0.006s] +Searching alignments... [0.004s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building query seed array... [0s] +Computing hash join... [0.006s] 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 3/4. -Building reference seed array... [0s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.017s] +Building query seed array... [0.012s] +Computing hash join... [0.001s] +Masking low complexity seeds... [0.006s] 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.01s] +Building query seed array... [0.015s] +Computing hash join... [0.023s] +Masking low complexity seeds... [0.007s] +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... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.006s] +Building query seed array... [0.011s] +Computing hash join... [0.008s] +Masking low complexity seeds... [0.007s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 2/4. -Building reference seed array... [0s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.01s] +Building query seed array... [0.015s] +Computing hash join... [0.004s] +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 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... [0.023s] +Building query seed array... [0.01s] +Computing hash join... [0.005s] +Masking low complexity seeds... [0.005s] +Searching alignments... [0.006s] 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] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.003s] +Building query seed array... [0.015s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.004s] +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... [0s] -Building query seed array... [0.002s] +Building reference seed array... [0.023s] +Building query seed array... [0.018s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 2/4. -Building reference seed array... [0s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.008s] +Building query seed array... [0.012s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.015s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 3/4. -Building reference seed array... [0s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.008s] +Building query seed array... [0.023s] +Computing hash join... [0.017s] +Masking low complexity seeds... [0.008s] 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 reference seed array... [0.008s] +Building query seed array... [0.001s] +Computing hash join... [0.007s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.007s] 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] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.003s] +Building query seed array... [0.015s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.011s] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 2/4. -Building reference seed array... [0s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.019s] +Building query seed array... [0.023s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.011s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 3/4. -Building reference seed array... [0s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.043s] +Building query seed array... [0.027s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 4/4. -Building reference seed array... [0s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.007s] +Building query seed array... [0.001s] +Computing hash join... [0.008s] +Masking low complexity seeds... [0.019s] +Searching alignments... [0.007s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 1/4. Building reference seed array... [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 10/16, index chunk 2/4. 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 10/16, index chunk 3/4. -Building reference seed array... [0s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.025s] +Building query seed array... [0.031s] +Computing hash join... [0.007s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.018s] 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... [0.012s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 1/4. -Building reference seed array... [0s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.004s] +Building query seed array... [0.009s] +Computing hash join... [0.006s] +Masking low complexity seeds... [0.012s] 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] +Building reference seed array... [0.005s] +Building query seed array... [0.02s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 3/4. -Building reference seed array... [0s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.012s] +Building query seed array... [0.004s] +Computing hash join... [0.019s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.018s] 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.011s] +Building query seed array... [0.016s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.011s] +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... [0.002s] +Building reference seed array... [0.015s] +Building query seed array... [0.024s] 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... [0s] -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... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 3/4. -Building reference seed array... [0s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.013s] +Building query seed array... [0.02s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.005s] 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... [0.019s] +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 13/16, index chunk 1/4. -Building reference seed array... [0s] -Building query seed array... [0.002s] +Building reference seed array... [0.023s] +Building query seed array... [0.007s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 2/4. -Building reference seed array... [0s] -Building query seed array... [0.002s] +Building reference seed array... [0.009s] +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 13/16, index chunk 3/4. -Building reference seed array... [0s] -Building query seed array... [0.002s] +Building reference seed array... [0.023s] +Building query seed array... [0.016s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 4/4. -Building reference seed array... [0s] -Building query seed array... [0.002s] +Building reference seed array... [0.006s] +Building query seed array... [0.014s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.006s] 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.012s] +Building query seed array... [0.001s] +Computing hash join... [0.01s] +Masking low complexity seeds... [0.012s] 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.025s] +Building query seed array... [0.021s] +Computing hash join... [0.005s] +Masking low complexity seeds... [0.025s] +Searching alignments... [0.024s] 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.035s] +Building query seed array... [0.031s] +Computing hash join... [0.016s] +Masking low complexity seeds... [0.006s] 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] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.029s] +Building query seed array... [0.039s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 1/4. -Building reference seed array... [0s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.016s] +Building query seed array... [0.004s] +Computing hash join... [0.016s] +Masking low complexity seeds... [0.011s] +Searching alignments... [0.021s] 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] -Computing hash join... [0s] +Building reference seed array... [0.019s] +Building query seed array... [0.015s] +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 3/4. -Building reference seed array... [0s] -Building query seed array... [0.002s] +Building reference seed array... [0.008s] +Building query seed array... [0.014s] 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... [0.002s] +Building reference seed array... [0.008s] +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 16/16, index chunk 1/4. -Building reference seed array... [0s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.02s] +Building query seed array... [0.016s] +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 16/16, index chunk 2/4. -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] 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] -Computing hash join... [0s] +Building reference seed array... [0.007s] +Building query seed array... [0.004s] +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 16/16, index chunk 4/4. -Building reference seed array... [0s] +Building reference seed array... [0.014s] Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Computing hash join... [0.006s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.009s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0.001s] +Computing alignments... Loading trace points... [0.055s] Sorting trace points... [0s] -Computing alignments... [0.005s] -Deallocating buffers... [0s] +Computing alignments... [0.011s] +Deallocating buffers... [0.004s] Loading trace points... [0s] - [0.007s] + [0.072s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -11014,10 +11050,10 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.577s +Total time = 3.078s Reported 1 pairwise alignments, 1 HSPs. 1 queries aligned. -+ rm -rf /tmp/tmp.5NVdiqKBrK ++ rm -rf /tmp/tmp.UghWydqRLz make[1]: Leaving directory '/build/reproducible-path/diamond-aligner-2.1.9' create-stamp debian/debhelper-build-stamp dh_prep @@ -11067,12 +11103,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/1926292/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1926292/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/414869 and its subdirectories -I: Current time: Sun Mar 22 13:15:29 -12 2026 -I: pbuilder-time-stamp: 1774228529 +I: removing directory /srv/workspace/pbuilder/1926292 and its subdirectories +I: Current time: Tue Feb 18 09:01:24 +14 2025 +I: pbuilder-time-stamp: 1739818884