Diff of the two buildlogs: -- --- b1/build.log 2025-07-16 01:30:07.847782035 +0000 +++ b2/build.log 2025-07-16 01:34:16.748107195 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Jul 15 13:26:30 -12 2025 -I: pbuilder-time-stamp: 1752629190 +I: Current time: Tue Aug 18 21:53:12 +14 2026 +I: pbuilder-time-stamp: 1787039593 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -25,52 +25,84 @@ dpkg-source: info: applying fix_missing_cstring_riscv64.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/197098/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2294378/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Aug 18 07:53 /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/2294378/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2294378/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='c77a393fcf1445dd90239842ea55a0a5' - 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='197098' - PS1='# ' - PS2='> ' + INVOCATION_ID=ba792ccc419246c89717053cb9daf16e + 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=2294378 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.xviAxsQt/pbuilderrc_l6XX --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.xviAxsQt/b1 --logfile b1/build.log diamond-aligner_2.1.11-2.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.xviAxsQt/pbuilderrc_XuUq --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.xviAxsQt/b2 --logfile b2/build.log diamond-aligner_2.1.11-2.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 codethink04-arm64 6.1.0-37-cloud-arm64 #1 SMP Debian 6.1.140-1 (2025-05-22) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-37-cloud-arm64 #1 SMP Debian 6.1.140-1 (2025-05-22) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 12 19:25 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/197098/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 12 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2294378/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -172,7 +204,7 @@ Get: 58 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.24.2 [919 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] -Fetched 29.7 MB in 0s (134 MB/s) +Fetched 29.7 MB in 0s (141 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 ... 19964 files and directories currently installed.) @@ -427,7 +459,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/diamond-aligner-2.1.11/ && 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_2.1.11-2_source.changes +I: user script /srv/workspace/pbuilder/2294378/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/2294378/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/diamond-aligner-2.1.11/ && 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_2.1.11-2_source.changes dpkg-buildpackage: info: source package diamond-aligner dpkg-buildpackage: info: source version 2.1.11-2 dpkg-buildpackage: info: source distribution unstable @@ -486,7 +522,7 @@ -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE --- Configuring done (3.3s) +-- 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CMakeFiles/arch_generic.dir/src/dp/swipe/banded_3frame_swipe.cpp.o -[ 2%] Building CXX object CMakeFiles/arch_neon.dir/src/tools/benchmark.cpp.o -[ 3%] Building CXX object CMakeFiles/arch_generic.dir/src/search/stage1_2.cpp.o -[ 3%] Building CXX object CMakeFiles/arch_generic.dir/src/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-2.1.11/src -I/build/reproducible-path/diamond-aligner-2.1.11/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.11=. -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 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-ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.11=. -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-2.1.11/src/masking/tantan.cpp [ 8%] 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-2.1.11/src -I/build/reproducible-path/diamond-aligner-2.1.11/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.11=. -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/scan_diags.cpp.o -MF CMakeFiles/arch_neon.dir/src/dp/scan_diags.cpp.o.d -o CMakeFiles/arch_neon.dir/src/dp/scan_diags.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.11/src/dp/scan_diags.cpp [ 9%] Building CXX object CMakeFiles/arch_neon.dir/src/dp/ungapped_simd.cpp.o @@ -596,32 +632,32 @@ In function ‘typename __gnu_cxx::__enable_if::__value, void>::__type std::__fill_a1(_ForwardIterator, _ForwardIterator, const _Tp&) [with _ForwardIterator = int*; _Tp = int]’, inlined from ‘void std::__fill_a(_FIte, _FIte, const _Tp&) [with _FIte = int*; _Tp = int]’ at /usr/include/c++/14/bits/stl_algobase.h:998:21, inlined from ‘void std::fill(_ForwardIterator, _ForwardIterator, const _Tp&) [with _ForwardIterator = int*; _Tp = int]’ at /usr/include/c++/14/bits/stl_algobase.h:1029:20, - inlined from ‘DP::Swipe::ARCH_NEON::Matrix::Matrix(int, int) [with Sv = int]’ at /build/reproducible-path/diamond-aligner-2.1.11/src/dp/swipe/full_matrix.h:66:12, - inlined from ‘std::__cxx11::list DP::Swipe::ARCH_NEON::swipe(It, It, std::atomic*, Cbs, DP::TargetVec&, DP::Params&) [with Sv = int; Cbs = DP::NoCBS; It = StringSetBase::ConstIterator; Cfg = SwipeConfig, int, DummyIdMask >]’ at /build/reproducible-path/diamond-aligner-2.1.11/src/dp/swipe/full_swipe.h:160:9: + inlined from ‘DP::Swipe::ARCH_GENERIC::Matrix::Matrix(int, int) [with Sv = int]’ at /build/reproducible-path/diamond-aligner-2.1.11/src/dp/swipe/full_matrix.h:66:12, + inlined from ‘std::__cxx11::list DP::Swipe::ARCH_GENERIC::swipe(It, It, std::atomic*, Cbs, DP::TargetVec&, DP::Params&) [with Sv = int; Cbs = DP::NoCBS; It = StringSetBase::ConstIterator; Cfg = SwipeConfig, int, DummyIdMask >]’ at /build/reproducible-path/diamond-aligner-2.1.11/src/dp/swipe/full_swipe.h:160:9: /usr/include/c++/14/bits/stl_algobase.h:952:18: warning: ‘void* __builtin_memset(void*, int, long unsigned int)’ specified bound 18446744073709551612 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 952 | *__first = __tmp; | ~~~~~~~~~^~~~~~~ In function ‘typename __gnu_cxx::__enable_if::__value, void>::__type std::__fill_a1(_ForwardIterator, _ForwardIterator, const _Tp&) [with _ForwardIterator = int*; _Tp = int]’, inlined from ‘void std::__fill_a(_FIte, _FIte, const _Tp&) [with _FIte = int*; _Tp = int]’ at /usr/include/c++/14/bits/stl_algobase.h:998:21, inlined from ‘void std::fill(_ForwardIterator, _ForwardIterator, const _Tp&) [with _ForwardIterator = int*; _Tp = int]’ at /usr/include/c++/14/bits/stl_algobase.h:1029:20, - inlined from ‘DP::Swipe::ARCH_NEON::Matrix::Matrix(int, int) [with Sv = int]’ at /build/reproducible-path/diamond-aligner-2.1.11/src/dp/swipe/full_matrix.h:66:12, - inlined from ‘std::__cxx11::list DP::Swipe::ARCH_NEON::swipe(It, It, std::atomic*, Cbs, DP::TargetVec&, DP::Params&) [with Sv = int; Cbs = DP::NoCBS; It = StringSetBase::ConstIterator; Cfg = SwipeConfig, int, DummyIdMask >]’ at /build/reproducible-path/diamond-aligner-2.1.11/src/dp/swipe/full_swipe.h:160:9: + inlined from ‘DP::Swipe::ARCH_GENERIC::Matrix::Matrix(int, int) [with Sv = int]’ at /build/reproducible-path/diamond-aligner-2.1.11/src/dp/swipe/full_matrix.h:66:12, + inlined from ‘std::__cxx11::list DP::Swipe::ARCH_GENERIC::swipe(It, It, std::atomic*, Cbs, DP::TargetVec&, DP::Params&) [with Sv = int; Cbs = DP::NoCBS; It = StringSetBase::ConstIterator; Cfg = SwipeConfig, int, DummyIdMask >]’ at /build/reproducible-path/diamond-aligner-2.1.11/src/dp/swipe/full_swipe.h:160:9: /usr/include/c++/14/bits/stl_algobase.h:952:18: warning: ‘void* __builtin_memset(void*, int, long unsigned int)’ specified bound 18446744073709551612 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 952 | *__first = __tmp; | ~~~~~~~~~^~~~~~~ In function ‘typename __gnu_cxx::__enable_if::__value, void>::__type std::__fill_a1(_ForwardIterator, _ForwardIterator, const _Tp&) [with _ForwardIterator = int*; _Tp = int]’, inlined from ‘void std::__fill_a(_FIte, _FIte, const _Tp&) [with _FIte = int*; _Tp = int]’ at /usr/include/c++/14/bits/stl_algobase.h:998:21, inlined from ‘void std::fill(_ForwardIterator, _ForwardIterator, const _Tp&) [with _ForwardIterator = int*; _Tp = int]’ at /usr/include/c++/14/bits/stl_algobase.h:1029:20, - inlined from ‘DP::Swipe::ARCH_GENERIC::Matrix::Matrix(int, int) [with Sv = int]’ at /build/reproducible-path/diamond-aligner-2.1.11/src/dp/swipe/full_matrix.h:66:12, - inlined from ‘std::__cxx11::list DP::Swipe::ARCH_GENERIC::swipe(It, It, std::atomic*, Cbs, DP::TargetVec&, DP::Params&) [with Sv = int; Cbs = DP::NoCBS; It = StringSetBase::ConstIterator; Cfg = SwipeConfig, int, DummyIdMask >]’ at /build/reproducible-path/diamond-aligner-2.1.11/src/dp/swipe/full_swipe.h:160:9: + inlined from ‘DP::Swipe::ARCH_NEON::Matrix::Matrix(int, int) [with Sv = int]’ at /build/reproducible-path/diamond-aligner-2.1.11/src/dp/swipe/full_matrix.h:66:12, + inlined from ‘std::__cxx11::list DP::Swipe::ARCH_NEON::swipe(It, It, std::atomic*, Cbs, DP::TargetVec&, DP::Params&) [with Sv = int; Cbs = DP::NoCBS; It = StringSetBase::ConstIterator; Cfg = SwipeConfig, int, DummyIdMask >]’ at /build/reproducible-path/diamond-aligner-2.1.11/src/dp/swipe/full_swipe.h:160:9: /usr/include/c++/14/bits/stl_algobase.h:952:18: warning: ‘void* __builtin_memset(void*, int, long unsigned int)’ specified bound 18446744073709551612 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 952 | *__first = __tmp; | ~~~~~~~~~^~~~~~~ In function ‘typename __gnu_cxx::__enable_if::__value, void>::__type std::__fill_a1(_ForwardIterator, _ForwardIterator, const _Tp&) [with _ForwardIterator = int*; _Tp = int]’, inlined from ‘void std::__fill_a(_FIte, _FIte, const _Tp&) [with _FIte = int*; _Tp = int]’ at /usr/include/c++/14/bits/stl_algobase.h:998:21, inlined from ‘void std::fill(_ForwardIterator, _ForwardIterator, const _Tp&) [with _ForwardIterator = int*; _Tp = int]’ at /usr/include/c++/14/bits/stl_algobase.h:1029:20, - inlined from ‘DP::Swipe::ARCH_GENERIC::Matrix::Matrix(int, int) [with Sv = int]’ at /build/reproducible-path/diamond-aligner-2.1.11/src/dp/swipe/full_matrix.h:66:12, - inlined from ‘std::__cxx11::list DP::Swipe::ARCH_GENERIC::swipe(It, It, std::atomic*, Cbs, DP::TargetVec&, DP::Params&) [with Sv = int; Cbs = DP::NoCBS; It = StringSetBase::ConstIterator; Cfg = SwipeConfig, int, DummyIdMask >]’ at /build/reproducible-path/diamond-aligner-2.1.11/src/dp/swipe/full_swipe.h:160:9: + inlined from ‘DP::Swipe::ARCH_NEON::Matrix::Matrix(int, int) [with Sv = int]’ at /build/reproducible-path/diamond-aligner-2.1.11/src/dp/swipe/full_matrix.h:66:12, + inlined from ‘std::__cxx11::list DP::Swipe::ARCH_NEON::swipe(It, It, std::atomic*, Cbs, DP::TargetVec&, DP::Params&) [with Sv = int; Cbs = DP::NoCBS; It = StringSetBase::ConstIterator; Cfg = SwipeConfig, int, DummyIdMask >]’ at /build/reproducible-path/diamond-aligner-2.1.11/src/dp/swipe/full_swipe.h:160:9: /usr/include/c++/14/bits/stl_algobase.h:952:18: warning: ‘void* __builtin_memset(void*, int, long unsigned int)’ specified bound 18446744073709551612 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 952 | *__first = __tmp; | ~~~~~~~~~^~~~~~~ @@ -639,26 +675,26 @@ make[3]: Leaving directory '/build/reproducible-path/diamond-aligner-2.1.11/obj-aarch64-linux-gnu' make -f 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CMakeFiles/diamond.dir/src/dp/ungapped_align.cpp.o -MF CMakeFiles/diamond.dir/src/dp/ungapped_align.cpp.o.d -o CMakeFiles/diamond.dir/src/dp/ungapped_align.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.11/src/dp/ungapped_align.cpp [ 17%] Building CXX object CMakeFiles/diamond.dir/src/run/tools.cpp.o @@ -671,8 +707,6 @@ cc1plus: note: unrecognized command-line option ‘-Wno-unknown-warning-option’ may have been intended to silence earlier diagnostics [ 18%] Building CXX object CMakeFiles/diamond.dir/src/chaining/greedy_align.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-2.1.11/src -I/build/reproducible-path/diamond-aligner-2.1.11/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall 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/build/reproducible-path/diamond-aligner-2.1.11/src/lib/alp/njn_dynprogprob.hpp:110:37: warning: ‘virtual Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] @@ -871,9 +902,13 @@ /build/reproducible-path/diamond-aligner-2.1.11/src/lib/alp/njn_dynprogproblim.hpp:101:29: note: by ‘Njn::DynProgProbLim::copy’ 101 | virtual inline void copy ( | ^~~~ -[ 61%] Building CXX object CMakeFiles/diamond.dir/src/lib/alp/sls_alp_data.cpp.o -/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_NEON -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.11/src -I/build/reproducible-path/diamond-aligner-2.1.11/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.11=. -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 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-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-2.1.11/src/lib/blast/blast_message.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-2.1.11/src -I/build/reproducible-path/diamond-aligner-2.1.11/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.11=. -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-2.1.11/src/lib/blast/blast_stat.cpp [ 91%] 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-2.1.11/src -I/build/reproducible-path/diamond-aligner-2.1.11/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.11=. -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-2.1.11/src/lib/blast/blastn_score.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-2.1.11/src -I/build/reproducible-path/diamond-aligner-2.1.11/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.11=. -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-2.1.11/src/lib/blast/blast_stat.cpp [ 91%] Building CXX object CMakeFiles/diamond.dir/src/lib/blast/ncbi_std.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-2.1.11/src -I/build/reproducible-path/diamond-aligner-2.1.11/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.11=. -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/ncbi_std.cpp.o -MF CMakeFiles/diamond.dir/src/lib/blast/ncbi_std.cpp.o.d -o CMakeFiles/diamond.dir/src/lib/blast/ncbi_std.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.11/src/lib/blast/ncbi_std.cpp [ 92%] Building CXX object CMakeFiles/diamond.dir/src/util/tsv/table.cpp.o @@ -1038,17 +1074,17 @@ make[1]: Leaving directory '/build/reproducible-path/diamond-aligner-2.1.11/obj-aarch64-linux-gnu' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/diamond-aligner-2.1.11' -cd debian/tests && PATH=/build/reproducible-path/diamond-aligner-2.1.11/obj-aarch64-linux-gnu:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games sh diamond-calls -+ mktemp -d -+ TESTDIR=/tmp/tmp.oPe4Dj9h06 -+ diamond blastp --threads 1 --db test/C.faa.diamond --query test/E.faa --out /tmp/tmp.oPe4Dj9h06/E.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive +cd debian/tests && PATH=/build/reproducible-path/diamond-aligner-2.1.11/obj-aarch64-linux-gnu:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path sh diamond-calls +++ mktemp -d ++ TESTDIR=/tmp/tmp.IS8I8V3gp0 ++ diamond blastp --threads 1 --db test/C.faa.diamond --query test/E.faa --out /tmp/tmp.IS8I8V3gp0/E.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.11.165 (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.oPe4Dj9h06 +Temporary directory: /tmp/tmp.IS8I8V3gp0 #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C.faa.diamond (type: Diamond database, sequences: 109, letters: 51213) @@ -1056,31 +1092,31 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0.001s] -Masking queries... [0.004s] +Masking queries... [0.008s] Algorithm: Double-indexed -Building query histograms... [0.017s] +Building query histograms... [0.027s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.005s] +Masking reference... [0.007s] Initializing temporary storage... [0s] -Building reference histograms... [0.024s] +Building reference histograms... [0.025s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. -Building reference seed array... [0.007s] +Building reference seed array... [0.005s] Building query seed array... [0.005s] -Computing hash join... [0s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. -Building reference seed array... [0.003s] -Building query seed array... [0.004s] -Computing hash join... [0s] +Building reference seed array... [0.004s] +Building query seed array... [0.005s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. -Building reference seed array... [0.004s] +Building reference seed array... [0.005s] Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -1088,15 +1124,15 @@ 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... [0.003s] -Computing hash join... [0s] +Building query seed array... [0.005s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4. Building reference seed array... [0.004s] -Building query seed array... [0.003s] -Computing hash join... [0s] +Building query seed array... [0.005s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] @@ -1109,8 +1145,8 @@ 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... [0.004s] -Computing hash join... [0s] +Building query seed array... [0.005s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] @@ -1136,30 +1172,30 @@ 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 reference seed array... [0.004s] Building query seed array... [0.005s] -Computing hash join... [0s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 4/4. Building reference seed array... [0.004s] Building query seed array... [0.005s] -Computing hash join... [0s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 1/4. Building reference seed array... [0.004s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building query seed array... [0.005s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 2/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.004s] Building query seed array... [0.005s] -Computing hash join... [0.001s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] @@ -1171,8 +1207,8 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 4/4. -Building reference seed array... [0.003s] -Building query seed array... [0.003s] +Building reference seed array... [0.004s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -1180,7 +1216,7 @@ 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... [0.005s] -Computing hash join... [0s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] @@ -1194,55 +1230,55 @@ 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... [0s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 4/4. -Building reference seed array... [0.003s] -Building query seed array... [0.003s] -Computing hash join... [0s] +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] 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] +Building reference seed array... [0.004s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 2/4. -Building reference seed array... [0.005s] +Building reference seed array... [0.004s] Building query seed array... [0.005s] -Computing hash join... [0s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 3/4. Building reference seed array... [0.004s] Building query seed array... [0.005s] -Computing hash join... [0.001s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 4/4. Building reference seed array... [0.004s] -Building query seed array... [0.003s] -Computing hash join... [0s] +Building query seed array... [0.005s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.004s] Building query seed array... [0.005s] -Computing hash join... [0s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 2/4. Building reference seed array... [0.004s] -Building query seed array... [0.004s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -1255,267 +1291,267 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 4/4. -Building reference seed array... [0.003s] -Building query seed array... [0.003s] -Computing hash join... [0s] +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] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 1/4. Building reference seed array... [0.004s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building query seed array... [0.005s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 2/4. Building reference seed array... [0.004s] -Building query seed array... [0.003s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 3/4. -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... [0.005s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 4/4. Building reference seed array... [0.004s] -Building query seed array... [0.003s] -Computing hash join... [0.001s] +Building query seed array... [0.005s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.003s] +Building reference seed array... [0.005s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.003s] +Building reference seed array... [0.005s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [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... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.004s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 2/4. -Building reference seed array... [0.003s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.008s] -Computing hash join... [0.003s] +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] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.004s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.004s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 2/4. -Building reference seed array... [0.003s] -Building query seed array... [0.003s] +Building reference seed array... [0.004s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] -Computing hash join... [0s] +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] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 1/4. -Building reference seed array... [0.003s] -Building query seed array... [0.001s] -Computing hash join... [0s] +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] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.004s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] -Computing hash join... [0s] +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] 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... [0.004s] +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 13/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.004s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] -Computing hash join... [0s] +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] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.004s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] -Computing hash join... [0s] +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] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] -Computing hash join... [0s] +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] 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] +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] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.004s] +Building query seed array... [0.005s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.005s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.004s] +Building query seed array... [0.005s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] -Computing hash join... [0s] +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] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.004s] +Building query seed array... [0.005s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.004s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.004s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.189s] +Computing alignments... [0.254s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -1525,17 +1561,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.92s +Total time = 1.317s 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.oPe4Dj9h06/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.IS8I8V3gp0/C.faa.vs.E.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.11.165 (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.oPe4Dj9h06 +Temporary directory: /tmp/tmp.IS8I8V3gp0 #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/E.faa.diamond (type: Diamond database, sequences: 72, letters: 54509) @@ -1543,466 +1579,466 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.002s] +Masking queries... [0.007s] Algorithm: Double-indexed -Building query histograms... [0.011s] +Building query histograms... [0.025s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.002s] +Masking reference... [0.007s] Initializing temporary storage... [0s] -Building reference histograms... [0.009s] +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... [0.001s] -Building query seed array... [0.001s] -Computing hash join... [0s] +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] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] -Computing hash join... [0s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] -Computing hash join... [0s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 4/4. -Building reference seed array... [0.003s] -Building query seed array... [0.002s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] 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 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.005s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [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... [0.002s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] 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... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] -Computing hash join... [0s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0s] 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... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] 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... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] 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... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 4/4. -Building reference seed array... [0.003s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, 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... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.007s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] 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... [0.005s] +Building query seed array... [0.005s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] 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... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 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... [0.004s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.037s] +Computing alignments... [0.083s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -2012,17 +2048,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.504s +Total time = 1.123s 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.oPe4Dj9h06/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.IS8I8V3gp0/L.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.11.165 (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.oPe4Dj9h06 +Temporary directory: /tmp/tmp.IS8I8V3gp0 #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C.faa.diamond (type: Diamond database, sequences: 109, letters: 51213) @@ -2030,466 +2066,466 @@ 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... [0.004s] +Building query histograms... [0.013s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.002s] +Masking reference... [0.007s] Initializing temporary storage... [0s] -Building reference histograms... [0.009s] +Building reference histograms... [0.025s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] 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... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 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... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] 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... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] 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... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.081s] +Computing alignments... [0.132s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -2499,484 +2535,484 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.457s +Total time = 1.01s 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.oPe4Dj9h06/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.IS8I8V3gp0/C.faa.vs.L.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.11.165 (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.oPe4Dj9h06 +Temporary directory: /tmp/tmp.IS8I8V3gp0 #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/L.faa.diamond (type: Diamond database, sequences: 40, letters: 26652) Block size = 2000000000 Opening the input file... [0s] Opening the output file... [0s] -Loading query sequences... [0s] -Masking queries... [0.003s] +Loading query sequences... [0.001s] +Masking queries... [0.007s] Algorithm: Double-indexed -Building query histograms... [0.008s] +Building query histograms... [0.025s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.001s] +Masking reference... [0.004s] Initializing temporary storage... [0s] -Building reference histograms... [0.004s] +Building reference histograms... [0.013s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.003s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. -Building reference seed array... [0s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 4/4. -Building reference seed array... [0s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] -Computing hash join... [0s] +Building reference seed array... [0.003s] +Building query seed array... [0.005s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 3/4. -Building reference seed array... [0s] -Building query seed array... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 4/4. -Building reference seed array... [0s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 1/4. -Building reference seed array... [0s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.005s] 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... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.003s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [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 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 3/4. -Building reference seed array... [0s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] -Computing hash join... [0s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 2/4. -Building reference seed array... [0s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] 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 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] 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... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 1/4. -Building reference seed array... [0s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] 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 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 1/4. -Building reference seed array... [0s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] 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... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.003s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 3/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.002s] Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.147s] +Computing alignments... [0.205s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -2986,17 +3022,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.522s +Total time = 1.12s 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.oPe4Dj9h06/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.IS8I8V3gp0/M.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.11.165 (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.oPe4Dj9h06 +Temporary directory: /tmp/tmp.IS8I8V3gp0 #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C.faa.diamond (type: Diamond database, sequences: 109, letters: 51213) @@ -3004,437 +3040,437 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.001s] +Masking queries... [0.003s] Algorithm: Double-indexed -Building query histograms... [0.012s] +Building query histograms... [0.013s] Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0.007s] Initializing temporary storage... [0s] -Building reference histograms... [0.023s] +Building reference histograms... [0.025s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +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 7/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 2/4. -Building reference seed array... [0.003s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 4/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.005s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 2/4. -Building reference seed array... [0.003s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +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 9/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0s] +Building reference seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 4/4. -Building reference seed array... [0.003s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +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 11/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.004s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 1/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.004s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -3448,14 +3484,14 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 3/4. -Building reference seed array... [0.003s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 4/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.004s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -3463,7 +3499,7 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.081s] +Computing alignments... [0.141s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -3473,133 +3509,133 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.499s +Total time = 1.028s 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.oPe4Dj9h06/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.IS8I8V3gp0/C.faa.vs.M.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.11.165 (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.oPe4Dj9h06 +Temporary directory: /tmp/tmp.IS8I8V3gp0 #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/M.faa.diamond (type: Diamond database, sequences: 40, letters: 26963) Block size = 2000000000 Opening the input file... [0s] Opening the output file... [0s] -Loading query sequences... [0s] -Masking queries... [0.002s] +Loading query sequences... [0.001s] +Masking queries... [0.007s] Algorithm: Double-indexed -Building query histograms... [0.008s] +Building query histograms... [0.025s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.001s] +Masking reference... [0.004s] Initializing temporary storage... [0s] -Building reference histograms... [0.004s] +Building reference histograms... [0.013s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.003s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [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... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 4/4. -Building reference seed array... [0s] -Building query seed array... [0.003s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 3/4. -Building reference seed array... [0s] +Building reference seed array... [0.002s] Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.003s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] -Computing hash join... [0s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 3/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.003s] Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -3607,350 +3643,350 @@ 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 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 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] 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... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 3/4. -Building reference seed array... [0s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [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 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] 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... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 4/4. -Building reference seed array... [0s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] 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 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 1/4. -Building reference seed array... [0s] -Building query seed array... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] 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 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.006s] -Computing hash join... [0.003s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.003s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.165s] +Computing alignments... [0.208s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -3960,17 +3996,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.599s +Total time = 1.083s 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.oPe4Dj9h06/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.IS8I8V3gp0/C2.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.11.165 (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.oPe4Dj9h06 +Temporary directory: /tmp/tmp.IS8I8V3gp0 #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C.faa.diamond (type: Diamond database, sequences: 109, letters: 51213) @@ -3983,194 +4019,194 @@ Building query histograms... [0s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.003s] +Masking reference... [0.007s] Initializing temporary storage... [0s] -Building reference histograms... [0.012s] +Building reference histograms... [0.025s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.005s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 3/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 1/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 2/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 4/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.003s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [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... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 4/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] 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... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 3/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 3/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 4/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 2/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 3/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -4184,252 +4220,252 @@ 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 reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 2/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] 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... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 4/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 1/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 2/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 3/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.004s] Building query seed array... [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... [0.001s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 3/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] 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... [0.001s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 1/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 3/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 1/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] 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 reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 1/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] 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... [0.001s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 3/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] 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... [0.001s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 2/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] 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 reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 4/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] 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 reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 2/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 3/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 4/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 1/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -4437,7 +4473,7 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.002s] +Computing alignments... [0.006s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -4447,27 +4483,27 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.333s +Total time = 0.694s 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.oPe4Dj9h06/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.IS8I8V3gp0/C.faa.vs.C2.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.11.165 (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.oPe4Dj9h06 +Temporary directory: /tmp/tmp.IS8I8V3gp0 #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C2.faa.diamond (type: Diamond database, sequences: 2, letters: 726) Block size = 2000000000 Opening the input file... [0s] Opening the output file... [0s] -Loading query sequences... [0s] -Masking queries... [0.004s] +Loading query sequences... [0.001s] +Masking queries... [0.008s] Algorithm: Double-indexed -Building query histograms... [0.011s] +Building query histograms... [0.025s] Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0s] @@ -4476,441 +4512,441 @@ Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building 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 3/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] 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... [0.001s] +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 3/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 4/4. Building reference seed array... [0s] -Building query 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 4/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +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 5/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +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 1/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] 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... [0.001s] +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... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.003s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.003s] +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 10/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] 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] +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... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0.004s] 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... [0s] -Building query 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 13/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] 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... [0.003s] +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 15/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.003s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -4924,7 +4960,7 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.002s] +Computing alignments... [0.006s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -4934,17 +4970,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.327s +Total time = 0.71s 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.oPe4Dj9h06/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.IS8I8V3gp0/L.faa.vs.E.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.11.165 (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.oPe4Dj9h06 +Temporary directory: /tmp/tmp.IS8I8V3gp0 #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/E.faa.diamond (type: Diamond database, sequences: 72, letters: 54509) @@ -4952,276 +4988,276 @@ 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... [0.004s] +Building query histograms... [0.013s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.003s] +Masking reference... [0.008s] Initializing temporary storage... [0s] -Building reference histograms... [0.018s] +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... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0.002s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.002s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 4/4. -Building reference seed array... [0.003s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] 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... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 2/4. -Building reference seed array... [0.003s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] 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... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 1/4. -Building reference seed array... [0.003s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] 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... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] -Computing hash join... [0s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] 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... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +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... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 4/4. -Building reference seed array... [0.003s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 1/4. Building reference seed array... [0.005s] -Building query seed array... [0.003s] -Computing hash join... [0.001s] +Building query seed array... [0.002s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 2/4. -Building reference seed array... [0.004s] +Building reference seed array... [0.005s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -5229,111 +5265,111 @@ 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... [0.001s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 4/4. -Building reference seed array... [0.003s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 1/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.005s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +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... [0.001s] +Building reference seed array... [0.005s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 2/4. -Building reference seed array... [0.003s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 3/4. -Building reference seed array... [0.004s] +Building reference seed array... [0.005s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +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... [0.003s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.005s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 2/4. Building reference seed array... [0.005s] -Building query seed array... [0.001s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 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... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 4/4. -Building reference seed array... [0.004s] +Building reference seed array... [0.005s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 1/4. -Building reference seed array... [0.003s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 2/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.005s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -5347,14 +5383,14 @@ Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 4/4. -Building reference seed array... [0.004s] +Building reference seed array... [0.005s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 1/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.005s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -5368,7 +5404,7 @@ 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... [0.004s] +Building reference seed array... [0.005s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -5379,21 +5415,21 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 1/4. -Building reference seed array... [0.004s] -Building query seed array... [0.001s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 2/4. -Building reference seed array... [0.004s] +Building reference seed array... [0.005s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 3/4. Building reference seed array... [0.005s] @@ -5411,7 +5447,7 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.333s] +Computing alignments... [0.349s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -5421,17 +5457,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.94s +Total time = 1.285s 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.oPe4Dj9h06/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.IS8I8V3gp0/E.faa.vs.L.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.11.165 (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.oPe4Dj9h06 +Temporary directory: /tmp/tmp.IS8I8V3gp0 #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/L.faa.diamond (type: Diamond database, sequences: 40, letters: 26652) @@ -5439,95 +5475,95 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0.001s] -Masking queries... [0.003s] +Masking queries... [0.008s] Algorithm: Double-indexed -Building query histograms... [0.014s] +Building query histograms... [0.027s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.001s] +Masking reference... [0.004s] Initializing temporary storage... [0s] -Building reference histograms... [0.012s] +Building reference histograms... [0.013s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.003s] +Building reference seed array... [0.002s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0.002s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.002s] Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0.002s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 4/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.002s] Building query seed array... [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 2/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.003s] +Building reference seed array... [0.002s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.004s] +Building reference seed array... [0.002s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 1/4. Building reference seed array... [0.002s] -Building query seed array... [0.003s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.003s] +Building reference seed array... [0.002s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 4/4. Building reference seed array... [0.002s] -Building query seed array... [0.003s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] @@ -5537,53 +5573,53 @@ Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 2/4. Building reference seed array... [0.002s] -Building query seed array... [0.012s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.002s] +Building query seed array... [0.005s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 4/4. Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 1/4. Building reference seed array... [0.002s] -Building query seed array... [0.003s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.004s] +Building reference seed array... [0.002s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 3/4. Building reference seed array... [0.002s] -Building query seed array... [0.003s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 4/4. Building reference seed array... [0.002s] -Building query seed array... [0.003s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] @@ -5604,24 +5640,24 @@ 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... [0.004s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 4/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.002s] Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 2/4. Building reference seed array... [0.002s] @@ -5632,29 +5668,29 @@ 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... [0.003s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 4/4. Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 1/4. Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 2/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.002s] Building query seed array... [0.005s] -Computing hash join... [0.001s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] @@ -5666,7 +5702,7 @@ Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 4/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -5674,7 +5710,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 1/4. Building reference seed array... [0.002s] -Building query seed array... [0.003s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] @@ -5682,7 +5718,7 @@ Processing query block 1, reference block 1/1, shape 9/16, index chunk 2/4. Building reference seed array... [0.002s] Building query seed array... [0.005s] -Computing hash join... [0.001s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] @@ -5730,7 +5766,7 @@ 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 query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] @@ -5738,30 +5774,30 @@ Processing query block 1, reference block 1/1, shape 11/16, index chunk 2/4. Building reference seed array... [0.002s] Building query seed array... [0.005s] -Computing hash join... [0.001s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 3/4. Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 4/4. Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building reference seed array... [0.001s] +Building query seed array... [0.003s] 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 12/16, index chunk 2/4. Building reference seed array... [0.002s] @@ -5772,7 +5808,7 @@ 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] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] @@ -5824,18 +5860,18 @@ Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 3/4. Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 4/4. Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] @@ -5849,7 +5885,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 2/4. Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] @@ -5877,7 +5913,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 2/4. Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] @@ -5891,14 +5927,14 @@ 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... [0.003s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.591s] +Computing alignments... [0.606s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -5908,17 +5944,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 1.447s +Total time = 1.544s 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.oPe4Dj9h06/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.IS8I8V3gp0/M.faa.vs.E.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.11.165 (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.oPe4Dj9h06 +Temporary directory: /tmp/tmp.IS8I8V3gp0 #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/E.faa.diamond (type: Diamond database, sequences: 72, letters: 54509) @@ -5938,7 +5974,7 @@ 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] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0.002s] Deallocating memory... [0s] @@ -5958,7 +5994,7 @@ 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... [0.001s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] @@ -5975,7 +6011,7 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 3/4. Building reference seed array... [0.005s] @@ -6000,7 +6036,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 2/4. Building reference seed array... [0.005s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] @@ -6048,8 +6084,8 @@ Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 1/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] +Building reference seed array... [0.022s] +Building query seed array... [0.01s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] @@ -6080,7 +6116,7 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 2/4. Building reference seed array... [0.005s] @@ -6091,7 +6127,7 @@ 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 query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] @@ -6143,7 +6179,7 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 3/4. Building reference seed array... [0.005s] @@ -6171,7 +6207,7 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 3/4. Building reference seed array... [0.005s] @@ -6188,7 +6224,7 @@ Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 1/4. -Building reference seed array... [0.005s] +Building reference seed array... [0.003s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -6237,18 +6273,18 @@ Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 4/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.005s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +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... [0.005s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 2/4. Building reference seed array... [0.005s] @@ -6297,21 +6333,21 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 1/4. Building reference seed array... [0.005s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 2/4. Building reference seed array... [0.005s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 3/4. Building reference seed array... [0.005s] @@ -6360,17 +6396,17 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 2/4. Building reference seed array... [0.005s] -Building query seed array... [0.001s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 3/4. -Building reference seed array... [0.005s] +Building reference seed array... [0.004s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -6381,11 +6417,11 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.353s] +Computing alignments... [0.357s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -6395,17 +6431,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 1.297s +Total time = 1.307s 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.oPe4Dj9h06/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.IS8I8V3gp0/E.faa.vs.M.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.11.165 (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.oPe4Dj9h06 +Temporary directory: /tmp/tmp.IS8I8V3gp0 #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/M.faa.diamond (type: Diamond database, sequences: 40, letters: 26963) @@ -6415,12 +6451,12 @@ Loading query sequences... [0.001s] Masking queries... [0.008s] Algorithm: Double-indexed -Building query histograms... [0.025s] +Building query histograms... [0.015s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.003s] +Masking reference... [0.004s] Initializing temporary storage... [0s] -Building reference histograms... [0.014s] +Building reference histograms... [0.013s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. Building reference seed array... [0.002s] @@ -6431,10 +6467,10 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0.002s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. Building reference seed array... [0.002s] @@ -6445,7 +6481,7 @@ 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 query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] @@ -6453,21 +6489,21 @@ 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... [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 2/16, index chunk 2/4. Building reference seed array... [0.002s] Building query seed array... [0.005s] -Computing hash join... [0.001s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 3/4. -Building reference seed array... [0.003s] -Building query seed array... [0.006s] -Computing hash join... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.005s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] @@ -6518,7 +6554,7 @@ Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 3/4. Building reference seed array... [0.002s] @@ -6529,7 +6565,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 4/4. Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] @@ -6543,21 +6579,21 @@ 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 query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 3/4. Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 4/4. Building reference seed array... [0.002s] -Building query seed array... [0.003s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] @@ -6570,7 +6606,7 @@ Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 2/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -6578,7 +6614,7 @@ 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... [0.004s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] @@ -6593,7 +6629,7 @@ Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4. Building reference seed array... [0.002s] Building query seed array... [0.005s] -Computing hash join... [0s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] @@ -6663,7 +6699,7 @@ 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] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] @@ -6697,7 +6733,7 @@ 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] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] @@ -6719,7 +6755,7 @@ Processing query block 1, reference block 1/1, shape 11/16, index chunk 3/4. Building reference seed array... [0.002s] Building query seed array... [0.005s] -Computing hash join... [0.001s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] @@ -6735,7 +6771,7 @@ Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 2/4. Building reference seed array... [0.002s] @@ -6756,7 +6792,7 @@ 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 13/16, index chunk 1/4. Building reference seed array... [0.002s] @@ -6782,7 +6818,7 @@ Processing query block 1, reference block 1/1, shape 13/16, index chunk 4/4. Building reference seed array... [0.002s] Building query seed array... [0.005s] -Computing hash join... [0s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] @@ -6808,7 +6844,7 @@ Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 4/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -6865,14 +6901,14 @@ 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... [0.003s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.643s] +Computing alignments... [0.642s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -6882,17 +6918,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 1.605s +Total time = 1.584s 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.oPe4Dj9h06/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.IS8I8V3gp0/C2.faa.vs.E.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.11.165 (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.oPe4Dj9h06 +Temporary directory: /tmp/tmp.IS8I8V3gp0 #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/E.faa.diamond (type: Diamond database, sequences: 72, letters: 54509) @@ -6907,7 +6943,7 @@ Loading reference sequences... [0s] Masking reference... [0.007s] Initializing temporary storage... [0s] -Building reference histograms... [0.014s] +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... [0.005s] @@ -6921,7 +6957,7 @@ Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. Building reference seed array... [0.005s] @@ -6931,14 +6967,14 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 4/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.005s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4. -Building reference seed array... [0.004s] +Building reference seed array... [0.005s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -6959,7 +6995,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 4/4. -Building reference seed array... [0.004s] +Building reference seed array... [0.005s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -7082,7 +7118,7 @@ Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 2/4. Building reference seed array... [0.005s] @@ -7110,7 +7146,7 @@ Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 2/4. Building reference seed array... [0.005s] @@ -7369,17 +7405,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.686s +Total time = 0.709s 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.oPe4Dj9h06/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.IS8I8V3gp0/E.faa.vs.C2.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.11.165 (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.oPe4Dj9h06 +Temporary directory: /tmp/tmp.IS8I8V3gp0 #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C2.faa.diamond (type: Diamond database, sequences: 2, letters: 726) @@ -7461,7 +7497,7 @@ 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... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -7685,7 +7721,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.004s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -7790,7 +7826,7 @@ 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 query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -7856,17 +7892,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.718s +Total time = 0.714s 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.oPe4Dj9h06/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.IS8I8V3gp0/M.faa.vs.L.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.11.165 (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.oPe4Dj9h06 +Temporary directory: /tmp/tmp.IS8I8V3gp0 #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/L.faa.diamond (type: Diamond database, sequences: 40, letters: 26652) @@ -7881,7 +7917,7 @@ Loading reference sequences... [0s] Masking reference... [0.004s] Initializing temporary storage... [0s] -Building reference histograms... [0.009s] +Building reference histograms... [0.013s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. Building reference seed array... [0.002s] @@ -7920,10 +7956,10 @@ 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... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Searching alignments... [0.008s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 3/4. Building reference seed array... [0.002s] @@ -7986,7 +8022,7 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Searching alignments... [0.008s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 4/4. Building reference seed array... [0.002s] @@ -8000,7 +8036,7 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Searching alignments... [0.009s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 2/4. Building reference seed array... [0.002s] @@ -8014,7 +8050,7 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Searching alignments... [0.008s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 4/4. Building reference seed array... [0.002s] @@ -8042,7 +8078,7 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Searching alignments... [0.008s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 4/4. Building reference seed array... [0.002s] @@ -8074,7 +8110,7 @@ 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] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.008s] @@ -8112,7 +8148,7 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Searching alignments... [0.008s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 2/4. Building reference seed array... [0.002s] @@ -8126,7 +8162,7 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Searching alignments... [0.009s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 4/4. Building reference seed array... [0.002s] @@ -8147,14 +8183,14 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Searching alignments... [0.008s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 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... [0.011s] +Searching alignments... [0.008s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 4/4. Building reference seed array... [0.002s] @@ -8206,7 +8242,7 @@ 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... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -8217,11 +8253,11 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.007s] +Searching alignments... [0.008s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 1/4. Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.008s] @@ -8235,7 +8271,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 3/4. Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.008s] @@ -8249,10 +8285,10 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 1/4. Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Searching alignments... [0.008s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 2/4. Building reference seed array... [0.002s] @@ -8266,7 +8302,7 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Searching alignments... [0.008s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 4/4. Building reference seed array... [0.002s] @@ -8290,11 +8326,11 @@ 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... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +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] @@ -8333,7 +8369,7 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.24s] +Computing alignments... [0.251s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -8343,17 +8379,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 1.53s +Total time = 1.514s 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.oPe4Dj9h06/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.IS8I8V3gp0/L.faa.vs.M.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.11.165 (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.oPe4Dj9h06 +Temporary directory: /tmp/tmp.IS8I8V3gp0 #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/M.faa.diamond (type: Diamond database, sequences: 40, letters: 26963) @@ -8361,7 +8397,7 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.004s] +Masking queries... [0.001s] Algorithm: Double-indexed Building query histograms... [0.013s] Seeking in database... [0s] @@ -8410,14 +8446,14 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Searching alignments... [0.008s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 3/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.003s] +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... [0.002s] @@ -8487,7 +8523,7 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Searching alignments... [0.008s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 2/4. Building reference seed array... [0.002s] @@ -8529,46 +8565,46 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.003s] +Searching alignments... [0.008s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 4/4. Building reference seed array... [0.002s] Building query seed array... [0.002s] -Computing hash join... [0.001s] +Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Searching alignments... [0.008s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4. -Building reference seed array... [0.003s] -Building query seed array... [0.003s] -Computing hash join... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.002s] +Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.004s] +Searching alignments... [0.008s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 2/4. Building reference seed array... [0.002s] -Building query seed array... [0.003s] -Computing hash join... [0.001s] +Building query seed array... [0.002s] +Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.007s] +Searching alignments... [0.009s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 3/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.006s] +Searching alignments... [0.008s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 4/4. Building reference seed array... [0.002s] -Building query seed array... [0.003s] -Computing hash join... [0.001s] +Building query seed array... [0.002s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.008s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 1/4. -Building reference seed array... [0.003s] -Building query seed array... [0.003s] +Building reference seed array... [0.002s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.008s] @@ -8613,14 +8649,14 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.004s] +Searching alignments... [0.008s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 4/4. Building reference seed array... [0.002s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Searching alignments... [0.008s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 1/4. Building reference seed array... [0.002s] @@ -8634,7 +8670,7 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Searching alignments... [0.008s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 3/4. Building reference seed array... [0.002s] @@ -8673,24 +8709,24 @@ 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... [0.001s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.003s] +Searching alignments... [0.008s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 1/4. Building reference seed array... [0.002s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.005s] +Searching alignments... [0.009s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, 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... [0.007s] +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... [0.002s] @@ -8732,7 +8768,7 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Searching alignments... [0.008s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 1/4. Building reference seed array... [0.002s] @@ -8767,7 +8803,7 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.004s] +Searching alignments... [0.009s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 2/4. Building reference seed array... [0.002s] @@ -8781,11 +8817,11 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.004s] +Searching alignments... [0.008s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 4/4. Building reference seed array... [0.002s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.008s] @@ -8820,7 +8856,7 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.239s] +Computing alignments... [0.258s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -8830,17 +8866,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 1.47s +Total time = 1.514s 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.oPe4Dj9h06/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.IS8I8V3gp0/C2.faa.vs.L.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.11.165 (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.oPe4Dj9h06 +Temporary directory: /tmp/tmp.IS8I8V3gp0 #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/L.faa.diamond (type: Diamond database, sequences: 40, letters: 26652) @@ -8853,9 +8889,9 @@ Building query histograms... [0s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.004s] +Masking reference... [0.001s] Initializing temporary storage... [0s] -Building reference histograms... [0.011s] +Building reference histograms... [0.013s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. Building reference seed array... [0.002s] @@ -8900,14 +8936,14 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 3/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.002s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 4/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.002s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -8928,7 +8964,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 3/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.002s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -8967,7 +9003,7 @@ Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 1/4. Building reference seed array... [0.002s] @@ -8984,21 +9020,21 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 3/4. -Building reference seed array... [0s] +Building reference seed array... [0.002s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 4/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.002s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 1/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.002s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -9012,7 +9048,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 3/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -9096,7 +9132,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 3/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.002s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -9166,7 +9202,7 @@ 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 reference seed array... [0.005s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -9195,7 +9231,7 @@ 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 query seed array... [0.006s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -9216,7 +9252,7 @@ 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] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -9307,7 +9343,7 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.008s] +Computing alignments... [0.009s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -9317,17 +9353,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.48s +Total time = 0.526s 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.oPe4Dj9h06/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.IS8I8V3gp0/L.faa.vs.C2.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.11.165 (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.oPe4Dj9h06 +Temporary directory: /tmp/tmp.IS8I8V3gp0 #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C2.faa.diamond (type: Diamond database, sequences: 2, letters: 726) @@ -9335,7 +9371,7 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.002s] +Masking queries... [0.004s] Algorithm: Double-indexed Building query histograms... [0.013s] Seeking in database... [0s] @@ -9381,7 +9417,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -9394,7 +9430,7 @@ 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 reference seed array... [0.004s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -9410,7 +9446,7 @@ 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] +Computing hash join... [0.004s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] @@ -9423,21 +9459,21 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -9500,27 +9536,27 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.006s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4. -Building reference seed array... [0s] +Building reference seed array... [0.003s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 2/4. -Building reference seed array... [0s] +Building reference seed array... [0.002s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -9529,15 +9565,15 @@ 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] +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 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] +Masking low complexity seeds... [0.002s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 1/4. @@ -9555,7 +9591,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 3/4. -Building reference seed array... [0s] +Building reference seed array... [0.001s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -9618,7 +9654,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 4/4. -Building reference seed array... [0s] +Building reference seed array... [0.001s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -9804,17 +9840,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.518s +Total time = 0.555s 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.oPe4Dj9h06/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.IS8I8V3gp0/C2.faa.vs.M.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.11.165 (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.oPe4Dj9h06 +Temporary directory: /tmp/tmp.IS8I8V3gp0 #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/M.faa.diamond (type: Diamond database, sequences: 40, letters: 26963) @@ -9832,7 +9868,7 @@ Building reference histograms... [0.013s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -10037,7 +10073,7 @@ Processing query block 1, reference block 1/1, shape 8/16, index chunk 2/4. Building reference seed array... [0.002s] Building query seed array... [0s] -Computing hash join... [0.003s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] @@ -10077,7 +10113,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 4/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -10119,7 +10155,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 2/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -10133,7 +10169,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 4/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -10291,17 +10327,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.528s +Total time = 0.515s 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.oPe4Dj9h06/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.IS8I8V3gp0/M.faa.vs.C2.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.11.165 (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.oPe4Dj9h06 +Temporary directory: /tmp/tmp.IS8I8V3gp0 #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C2.faa.diamond (type: Diamond database, sequences: 2, letters: 726) @@ -10311,7 +10347,7 @@ Loading query sequences... [0s] Masking queries... [0.004s] Algorithm: Double-indexed -Building query histograms... [0.014s] +Building query histograms... [0.013s] Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0s] @@ -10330,7 +10366,7 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. Building reference seed array... [0s] @@ -10474,7 +10510,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -10495,7 +10531,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -10572,7 +10608,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -10656,7 +10692,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -10778,10 +10814,10 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.531s +Total time = 0.51s Reported 1 pairwise alignments, 1 HSPs. 1 queries aligned. -+ rm -rf /tmp/tmp.oPe4Dj9h06 ++ rm -rf /tmp/tmp.IS8I8V3gp0 make[1]: Leaving directory '/build/reproducible-path/diamond-aligner-2.1.11' create-stamp debian/debhelper-build-stamp dh_prep @@ -10831,12 +10867,14 @@ 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/2294378/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2294378/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/197098 and its subdirectories -I: Current time: Tue Jul 15 13:30:06 -12 2025 -I: pbuilder-time-stamp: 1752629406 +I: removing directory /srv/workspace/pbuilder/2294378 and its subdirectories +I: Current time: Tue Aug 18 21:57:15 +14 2026 +I: pbuilder-time-stamp: 1787039835