Diff of the two buildlogs: -- --- b1/build.log 2025-10-19 05:13:06.412740748 +0000 +++ b2/build.log 2025-10-19 05:17:26.221083175 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Nov 20 23:32:14 -12 2026 -I: pbuilder-time-stamp: 1795260734 +I: Current time: Sun Oct 19 19:13:08 +14 2025 +I: pbuilder-time-stamp: 1760850788 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -22,52 +22,84 @@ dpkg-source: info: unpacking diamond-aligner_2.1.14-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/640735/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2149993/tmp/hooks/D01_modify_environment starting +debug: Running on infom01-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Oct 19 05:13 /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/2149993/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2149993/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 ' - DISTRIBUTION='forky' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='3cf44638a6ef4c32b62e01dcea8fcadb' - 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='640735' - PS1='# ' - PS2='> ' + INVOCATION_ID=f398f7a42ab543728a786e0d81b38923 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=2149993 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.XkXxysy7/pbuilderrc_On6M --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.XkXxysy7/b1 --logfile b1/build.log diamond-aligner_2.1.14-1.dsc' - SUDO_GID='109' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + 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.XkXxysy7/pbuilderrc_4bDW --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.XkXxysy7/b2 --logfile b2/build.log diamond-aligner_2.1.14-1.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom02-amd64 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.48+deb13-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/640735/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2149993/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -169,7 +201,7 @@ Get: 60 http://deb.debian.org/debian forky/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 61 http://deb.debian.org/debian forky/main amd64 debhelper all 13.28 [941 kB] Get: 62 http://deb.debian.org/debian forky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] -Fetched 32.8 MB in 0s (84.0 MB/s) +Fetched 32.8 MB in 0s (79.7 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19898 files and directories currently installed.) @@ -432,7 +464,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/diamond-aligner-2.1.14/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../diamond-aligner_2.1.14-1_source.changes +I: user script /srv/workspace/pbuilder/2149993/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/2149993/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/diamond-aligner-2.1.14/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../diamond-aligner_2.1.14-1_source.changes dpkg-buildpackage: info: source package diamond-aligner dpkg-buildpackage: info: source version 2.1.14-1 dpkg-buildpackage: info: source distribution unstable @@ -493,7 +529,7 @@ -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE --- Configuring done (1.9s) +-- Configuring done (1.7s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -511,7 +547,7 @@ -- Build files have been written to: /build/reproducible-path/diamond-aligner-2.1.14/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/diamond-aligner-2.1.14' dh_auto_build - cd obj-x86_64-linux-gnu && make -j16 INSTALL="install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j12 INSTALL="install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/diamond-aligner-2.1.14/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/diamond-aligner-2.1.14 -B/build/reproducible-path/diamond-aligner-2.1.14/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/diamond-aligner-2.1.14/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/diamond-aligner-2.1.14/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -528,45 +564,37 @@ cd /build/reproducible-path/diamond-aligner-2.1.14/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/diamond-aligner-2.1.14 /build/reproducible-path/diamond-aligner-2.1.14 /build/reproducible-path/diamond-aligner-2.1.14/obj-x86_64-linux-gnu /build/reproducible-path/diamond-aligner-2.1.14/obj-x86_64-linux-gnu /build/reproducible-path/diamond-aligner-2.1.14/obj-x86_64-linux-gnu/CMakeFiles/arch_avx2.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/diamond-aligner-2.1.14/obj-x86_64-linux-gnu' make -f CMakeFiles/arch_generic.dir/build.make CMakeFiles/arch_generic.dir/build -make[3]: Entering directory '/build/reproducible-path/diamond-aligner-2.1.14/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/diamond-aligner-2.1.14/obj-x86_64-linux-gnu' -make -f CMakeFiles/arch_sse4_1.dir/build.make CMakeFiles/arch_sse4_1.dir/build make[3]: Leaving directory '/build/reproducible-path/diamond-aligner-2.1.14/obj-x86_64-linux-gnu' make -f CMakeFiles/arch_avx2.dir/build.make CMakeFiles/arch_avx2.dir/build +make[3]: Leaving directory '/build/reproducible-path/diamond-aligner-2.1.14/obj-x86_64-linux-gnu' +make[3]: Entering directory '/build/reproducible-path/diamond-aligner-2.1.14/obj-x86_64-linux-gnu' +make -f CMakeFiles/arch_sse4_1.dir/build.make CMakeFiles/arch_sse4_1.dir/build make[3]: Entering directory '/build/reproducible-path/diamond-aligner-2.1.14/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/diamond-aligner-2.1.14/obj-x86_64-linux-gnu' -[ 0%] Building CXX object CMakeFiles/arch_generic.dir/src/dp/swipe/banded_3frame_swipe.cpp.o -[ 1%] Building CXX object CMakeFiles/arch_generic.dir/src/search/stage1_2.cpp.o +[ 1%] Building CXX object CMakeFiles/arch_avx2.dir/src/search/stage1_2.cpp.o [ 1%] Building CXX object CMakeFiles/arch_generic.dir/src/tools/benchmark.cpp.o +[ 1%] Building CXX object CMakeFiles/arch_generic.dir/src/dp/swipe/banded_3frame_swipe.cpp.o +/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.14/src -I/build/reproducible-path/diamond-aligner-2.1.14/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++20 -DDISPATCH_ARCH=ARCH_GENERIC -DARCH_ID=0 -DEigen=Eigen_GENERIC -MD -MT CMakeFiles/arch_generic.dir/src/tools/benchmark.cpp.o -MF CMakeFiles/arch_generic.dir/src/tools/benchmark.cpp.o.d -o CMakeFiles/arch_generic.dir/src/tools/benchmark.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.14/src/tools/benchmark.cpp [ 2%] Building CXX object CMakeFiles/arch_generic.dir/src/dp/swipe/swipe_wrapper.cpp.o -[ 2%] Building CXX object CMakeFiles/arch_generic.dir/src/masking/tantan.cpp.o -[ 2%] Building CXX object CMakeFiles/arch_generic.dir/src/dp/swipe/anchored_wrapper.cpp.o -/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.14/src -I/build/reproducible-path/diamond-aligner-2.1.14/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++20 -DDISPATCH_ARCH=ARCH_GENERIC -DARCH_ID=0 -DEigen=Eigen_GENERIC -MD -MT CMakeFiles/arch_generic.dir/src/dp/swipe/banded_3frame_swipe.cpp.o -MF CMakeFiles/arch_generic.dir/src/dp/swipe/banded_3frame_swipe.cpp.o.d -o CMakeFiles/arch_generic.dir/src/dp/swipe/banded_3frame_swipe.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.14/src/dp/swipe/banded_3frame_swipe.cpp -[ 3%] Building CXX object CMakeFiles/arch_avx2.dir/src/search/stage1_2.cpp.o -[ 4%] Building CXX object CMakeFiles/arch_generic.dir/src/dp/scan_diags.cpp.o -[ 5%] Building CXX object CMakeFiles/arch_generic.dir/src/dp/ungapped_simd.cpp.o -[ 5%] Building CXX object CMakeFiles/arch_sse4_1.dir/src/dp/swipe/banded_3frame_swipe.cpp.o -[ 6%] Building CXX object CMakeFiles/arch_sse4_1.dir/src/search/stage1_2.cpp.o -/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.14/src -I/build/reproducible-path/diamond-aligner-2.1.14/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++20 -DDISPATCH_ARCH=ARCH_GENERIC -DARCH_ID=0 -DEigen=Eigen_GENERIC -MD -MT CMakeFiles/arch_generic.dir/src/search/stage1_2.cpp.o -MF CMakeFiles/arch_generic.dir/src/search/stage1_2.cpp.o.d -o CMakeFiles/arch_generic.dir/src/search/stage1_2.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.14/src/search/stage1_2.cpp -[ 7%] Building CXX object CMakeFiles/arch_sse4_1.dir/src/dp/swipe/swipe_wrapper.cpp.o -[ 8%] Building CXX object CMakeFiles/arch_sse4_1.dir/src/tools/benchmark.cpp.o -[ 8%] Building CXX object CMakeFiles/arch_generic.dir/src/dp/score_profile.cpp.o /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.14/src -I/build/reproducible-path/diamond-aligner-2.1.14/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++20 -DDISPATCH_ARCH=ARCH_AVX2 -DARCH_ID=2 -mssse3 -mpopcnt -msse4.1 -msse4.2 -mavx -mavx2 -DEigen=Eigen_AVX2 -MD -MT CMakeFiles/arch_avx2.dir/src/search/stage1_2.cpp.o -MF CMakeFiles/arch_avx2.dir/src/search/stage1_2.cpp.o.d -o CMakeFiles/arch_avx2.dir/src/search/stage1_2.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.14/src/search/stage1_2.cpp -/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.14/src -I/build/reproducible-path/diamond-aligner-2.1.14/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++20 -DDISPATCH_ARCH=ARCH_GENERIC -DARCH_ID=0 -DEigen=Eigen_GENERIC -MD -MT CMakeFiles/arch_generic.dir/src/tools/benchmark.cpp.o -MF 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-DDISPATCH_ARCH=ARCH_AVX2 -DARCH_ID=2 -mssse3 -mpopcnt -msse4.1 -msse4.2 -mavx -mavx2 -DEigen=Eigen_AVX2 -MD -MT CMakeFiles/arch_avx2.dir/src/tools/benchmark.cpp.o -MF CMakeFiles/arch_avx2.dir/src/tools/benchmark.cpp.o.d -o CMakeFiles/arch_avx2.dir/src/tools/benchmark.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.14/src/tools/benchmark.cpp In file included from /build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/Core:369, from /build/reproducible-path/diamond-aligner-2.1.14/src/masking/tantan.cpp:27: /build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/PlainObjectBase.h: In instantiation of ‘static void Eigen_GENERIC::PlainObjectBase::_check_template_params() [with Derived = Eigen_GENERIC::Array]’: @@ -806,16 +834,25 @@ /build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:432:31: warning: arithmetic between different enumeration types ‘Eigen_GENERIC::Array::’ and ‘Eigen_GENERIC::internal::unpacket_traits<__vector(4) float>::’ is deprecated [-Wdeprecated-enum-enum-conversion] 432 | alignedSize = (size/packetSize)*packetSize }; | ~~~~~^~~~~~~~~~~~ +cc1plus: note: unrecognized command-line option ‘-Wno-unknown-warning-option’ may have been intended to silence earlier diagnostics +[ 6%] Building CXX object CMakeFiles/arch_avx2.dir/src/dp/swipe/swipe_wrapper.cpp.o +/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.14/src -I/build/reproducible-path/diamond-aligner-2.1.14/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++20 -DDISPATCH_ARCH=ARCH_AVX2 -DARCH_ID=2 -mssse3 -mpopcnt -msse4.1 -msse4.2 -mavx -mavx2 -DEigen=Eigen_AVX2 -MD -MT CMakeFiles/arch_avx2.dir/src/dp/swipe/swipe_wrapper.cpp.o -MF CMakeFiles/arch_avx2.dir/src/dp/swipe/swipe_wrapper.cpp.o.d -o CMakeFiles/arch_avx2.dir/src/dp/swipe/swipe_wrapper.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.14/src/dp/swipe/swipe_wrapper.cpp +[ 7%] Building CXX object CMakeFiles/arch_generic.dir/src/dp/ungapped_simd.cpp.o +/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.14/src -I/build/reproducible-path/diamond-aligner-2.1.14/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++20 -DDISPATCH_ARCH=ARCH_GENERIC -DARCH_ID=0 -DEigen=Eigen_GENERIC -MD -MT CMakeFiles/arch_generic.dir/src/dp/ungapped_simd.cpp.o -MF CMakeFiles/arch_generic.dir/src/dp/ungapped_simd.cpp.o.d -o CMakeFiles/arch_generic.dir/src/dp/ungapped_simd.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.14/src/dp/ungapped_simd.cpp +[ 7%] Building CXX object CMakeFiles/arch_avx2.dir/src/masking/tantan.cpp.o +/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.14/src -I/build/reproducible-path/diamond-aligner-2.1.14/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++20 -DDISPATCH_ARCH=ARCH_AVX2 -DARCH_ID=2 -mssse3 -mpopcnt -msse4.1 -msse4.2 -mavx -mavx2 -DEigen=Eigen_AVX2 -MD -MT CMakeFiles/arch_avx2.dir/src/masking/tantan.cpp.o -MF CMakeFiles/arch_avx2.dir/src/masking/tantan.cpp.o.d -o CMakeFiles/arch_avx2.dir/src/masking/tantan.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.14/src/masking/tantan.cpp +[ 7%] Building CXX object CMakeFiles/arch_generic.dir/src/dp/swipe/anchored_wrapper.cpp.o +/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.14/src -I/build/reproducible-path/diamond-aligner-2.1.14/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++20 -DDISPATCH_ARCH=ARCH_GENERIC -DARCH_ID=0 -DEigen=Eigen_GENERIC -MD -MT CMakeFiles/arch_generic.dir/src/dp/swipe/anchored_wrapper.cpp.o -MF CMakeFiles/arch_generic.dir/src/dp/swipe/anchored_wrapper.cpp.o.d -o CMakeFiles/arch_generic.dir/src/dp/swipe/anchored_wrapper.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.14/src/dp/swipe/anchored_wrapper.cpp In file included from /build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/Core:369, from /build/reproducible-path/diamond-aligner-2.1.14/src/masking/tantan.cpp:27: -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/PlainObjectBase.h: In instantiation of ‘static void Eigen_SSE4_1::PlainObjectBase::_check_template_params() [with Derived = Eigen_SSE4_1::Array]’: -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/Array.h:134:35: required from ‘Eigen_SSE4_1::Array<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::Array() [with _Scalar = float; int _Rows = -1; int _Cols = 1; int _Options = 0; int _MaxRows = -1; int _MaxCols = 1]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/PlainObjectBase.h: In instantiation of ‘static void Eigen_AVX2::PlainObjectBase::_check_template_params() [with Derived = Eigen_AVX2::Array]’: +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/Array.h:134:35: required from ‘Eigen_AVX2::Array<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::Array() [with _Scalar = float; int _Rows = -1; int _Cols = 1; int _Options = 0; int _MaxRows = -1; int _MaxCols = 1]’ 134 | Base::_check_template_params(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /usr/include/c++/15/array:102:12: required from here 102 | struct array | ^~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/PlainObjectBase.h:905:102: warning: bitwise operation between different enumeration types ‘Eigen_SSE4_1::PlainObjectBase >::’ and ‘Eigen_SSE4_1::StorageOptions’ is deprecated [-Wdeprecated-enum-enum-conversion] +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/PlainObjectBase.h:905:102: warning: bitwise operation between different enumeration types ‘Eigen_AVX2::PlainObjectBase >::’ and ‘Eigen_AVX2::StorageOptions’ is deprecated [-Wdeprecated-enum-enum-conversion] 905 | EIGEN_STATIC_ASSERT((EIGEN_IMPLIES(MaxRowsAtCompileTime==1 && MaxColsAtCompileTime!=1, (Options&RowMajor)==RowMajor) | ~~~~~~~~^~~~~~~~~~ /build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/util/StaticAssert.h:33:54: note: in definition of macro ‘EIGEN_STATIC_ASSERT’ @@ -824,7 +861,7 @@ /build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/PlainObjectBase.h:905:28: note: in expansion of macro ‘EIGEN_IMPLIES’ 905 | EIGEN_STATIC_ASSERT((EIGEN_IMPLIES(MaxRowsAtCompileTime==1 && MaxColsAtCompileTime!=1, (Options&RowMajor)==RowMajor) | ^~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/PlainObjectBase.h:906:102: warning: bitwise operation between different enumeration types ‘Eigen_SSE4_1::PlainObjectBase >::’ and ‘Eigen_SSE4_1::StorageOptions’ is deprecated [-Wdeprecated-enum-enum-conversion] +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/PlainObjectBase.h:906:102: warning: bitwise operation between different enumeration types ‘Eigen_AVX2::PlainObjectBase >::’ and ‘Eigen_AVX2::StorageOptions’ is deprecated [-Wdeprecated-enum-enum-conversion] 906 | && EIGEN_IMPLIES(MaxColsAtCompileTime==1 && MaxRowsAtCompileTime!=1, (Options&RowMajor)==0) | ~~~~~~~~^~~~~~~~~~ /build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/util/StaticAssert.h:33:54: note: in definition of macro ‘EIGEN_STATIC_ASSERT’ @@ -833,14 +870,14 @@ /build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/PlainObjectBase.h:906:28: note: in expansion of macro ‘EIGEN_IMPLIES’ 906 | && EIGEN_IMPLIES(MaxColsAtCompileTime==1 && MaxRowsAtCompileTime!=1, (Options&RowMajor)==0) | ^~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/PlainObjectBase.h: In instantiation of ‘static void Eigen_SSE4_1::PlainObjectBase::_check_template_params() [with Derived = Eigen_SSE4_1::Array]’: -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/Array.h:170:35: required from ‘Eigen_SSE4_1::Array<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::Array(const T&) [with T = double; _Scalar = float; int _Rows = 50; int _Cols = 1; int _Options = 0; int _MaxRows = 50; int _MaxCols = 1]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/PlainObjectBase.h: In instantiation of ‘static void Eigen_AVX2::PlainObjectBase::_check_template_params() [with Derived = Eigen_AVX2::Array]’: +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/Array.h:170:35: required from ‘Eigen_AVX2::Array<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::Array(const T&) [with T = double; _Scalar = float; int _Rows = 50; int _Cols = 1; int _Options = 0; int _MaxRows = 50; int _MaxCols = 1]’ 170 | Base::_check_template_params(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/diamond-aligner-2.1.14/src/masking/tantan.cpp:61:31: required from here 61 | Array f(0.0), d, t; | ^ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/PlainObjectBase.h:905:102: warning: bitwise operation between different enumeration types ‘Eigen_SSE4_1::PlainObjectBase >::’ and ‘Eigen_SSE4_1::StorageOptions’ is deprecated [-Wdeprecated-enum-enum-conversion] +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/PlainObjectBase.h:905:102: warning: bitwise operation between different enumeration types ‘Eigen_AVX2::PlainObjectBase >::’ and ‘Eigen_AVX2::StorageOptions’ is deprecated [-Wdeprecated-enum-enum-conversion] 905 | EIGEN_STATIC_ASSERT((EIGEN_IMPLIES(MaxRowsAtCompileTime==1 && MaxColsAtCompileTime!=1, (Options&RowMajor)==RowMajor) | ~~~~~~~~^~~~~~~~~~ /build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/util/StaticAssert.h:33:54: note: in definition of macro ‘EIGEN_STATIC_ASSERT’ @@ -849,7 +886,7 @@ /build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/PlainObjectBase.h:905:28: note: in expansion of macro ‘EIGEN_IMPLIES’ 905 | EIGEN_STATIC_ASSERT((EIGEN_IMPLIES(MaxRowsAtCompileTime==1 && MaxColsAtCompileTime!=1, (Options&RowMajor)==RowMajor) | ^~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/PlainObjectBase.h:906:102: warning: bitwise operation between different enumeration types ‘Eigen_SSE4_1::PlainObjectBase >::’ and ‘Eigen_SSE4_1::StorageOptions’ is deprecated [-Wdeprecated-enum-enum-conversion] +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/PlainObjectBase.h:906:102: warning: bitwise operation between different enumeration types ‘Eigen_AVX2::PlainObjectBase >::’ and ‘Eigen_AVX2::StorageOptions’ is deprecated [-Wdeprecated-enum-enum-conversion] 906 | && EIGEN_IMPLIES(MaxColsAtCompileTime==1 && MaxRowsAtCompileTime!=1, (Options&RowMajor)==0) | ~~~~~~~~^~~~~~~~~~ /build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/util/StaticAssert.h:33:54: note: in definition of macro ‘EIGEN_STATIC_ASSERT’ @@ -859,218 +896,217 @@ 906 | && EIGEN_IMPLIES(MaxColsAtCompileTime==1 && MaxRowsAtCompileTime!=1, (Options&RowMajor)==0) | ^~~~~~~~~~~~~ In file included from /build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/Core:483: -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/Redux.h: In instantiation of ‘struct Eigen_SSE4_1::internal::redux_impl, Eigen_SSE4_1::internal::redux_evaluator >, 3, 2>’: -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/Redux.h:418:56: required from ‘typename Eigen_SSE4_1::internal::traits::Scalar Eigen_SSE4_1::DenseBase::redux(const Func&) const [with BinaryOp = Eigen_SSE4_1::internal::scalar_sum_op; Derived = Eigen_SSE4_1::Array; typename Eigen_SSE4_1::internal::traits::Scalar = float]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/Redux.h: In instantiation of ‘struct Eigen_AVX2::internal::redux_impl, Eigen_AVX2::internal::redux_evaluator >, 3, 2>’: +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/Redux.h:418:56: required from ‘typename Eigen_AVX2::internal::traits::Scalar Eigen_AVX2::DenseBase::redux(const Func&) const [with BinaryOp = Eigen_AVX2::internal::scalar_sum_op; Derived = Eigen_AVX2::Array; typename Eigen_AVX2::internal::traits::Scalar = float]’ 418 | return internal::redux_impl::run(thisEval, func); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/Redux.h:453:25: required from ‘typename Eigen_SSE4_1::internal::traits::Scalar Eigen_SSE4_1::DenseBase::sum() const [with Derived = Eigen_SSE4_1::Array; typename Eigen_SSE4_1::internal::traits::Scalar = float]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/Redux.h:453:25: required from ‘typename Eigen_AVX2::internal::traits::Scalar Eigen_AVX2::DenseBase::sum() const [with Derived = Eigen_AVX2::Array; typename Eigen_AVX2::internal::traits::Scalar = float]’ 453 | return derived().redux(Eigen::internal::scalar_sum_op()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/diamond-aligner-2.1.14/src/masking/tantan.cpp:82:24: required from here 82 | const float s = f.sum(); | ~~~~~^~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/Redux.h:315:28: warning: arithmetic between different enumeration types ‘Eigen_SSE4_1::internal::redux_evaluator >::’ and ‘Eigen_SSE4_1::internal::redux_traits, Eigen_SSE4_1::internal::redux_evaluator > >::’ is deprecated [-Wdeprecated-enum-enum-conversion] +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/Redux.h:315:28: warning: arithmetic between different enumeration types ‘Eigen_AVX2::internal::redux_evaluator >::’ and ‘Eigen_AVX2::internal::redux_traits, Eigen_AVX2::internal::redux_evaluator > >::’ is deprecated [-Wdeprecated-enum-enum-conversion] 315 | VectorizedSize = (Size / PacketSize) * PacketSize | ~~~~~~^~~~~~~~~~~~~ +[ 8%] Building CXX object CMakeFiles/arch_generic.dir/src/dp/score_profile.cpp.o +/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.14/src -I/build/reproducible-path/diamond-aligner-2.1.14/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++20 -DDISPATCH_ARCH=ARCH_GENERIC -DARCH_ID=0 -DEigen=Eigen_GENERIC -MD -MT CMakeFiles/arch_generic.dir/src/dp/score_profile.cpp.o -MF CMakeFiles/arch_generic.dir/src/dp/score_profile.cpp.o.d -o CMakeFiles/arch_generic.dir/src/dp/score_profile.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.14/src/dp/score_profile.cpp In file included from /build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/Core:446: -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h: In instantiation of ‘static void Eigen_SSE4_1::internal::dense_assignment_loop::run(Kernel&) [with Kernel = Eigen_SSE4_1::internal::generic_dense_assignment_kernel >, Eigen_SSE4_1::internal::evaluator >, Eigen_SSE4_1::internal::mul_assign_op, 0>]’: -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:741:37: required from ‘void Eigen_SSE4_1::internal::call_dense_assignment_loop(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_SSE4_1::Array; SrcXprType = Eigen_SSE4_1::Array; Functor = mul_assign_op]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h: In instantiation of ‘static void Eigen_AVX2::internal::dense_assignment_loop::run(Kernel&) [with Kernel = Eigen_AVX2::internal::generic_dense_assignment_kernel >, Eigen_AVX2::internal::evaluator >, Eigen_AVX2::internal::mul_assign_op, 0>]’: +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:741:37: required from ‘void Eigen_AVX2::internal::call_dense_assignment_loop(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_AVX2::Array; SrcXprType = Eigen_AVX2::Array; Functor = mul_assign_op]’ 741 | dense_assignment_loop::run(kernel); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:879:31: required from ‘static void Eigen_SSE4_1::internal::Assignment::run(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_SSE4_1::Array; SrcXprType = Eigen_SSE4_1::Array; Functor = Eigen_SSE4_1::internal::mul_assign_op; Weak = void]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:879:31: required from ‘static void Eigen_AVX2::internal::Assignment::run(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_AVX2::Array; SrcXprType = Eigen_AVX2::Array; Functor = Eigen_AVX2::internal::mul_assign_op; Weak = void]’ 879 | call_dense_assignment_loop(dst, src, func); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:836:49: required from ‘void Eigen_SSE4_1::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen_SSE4_1::Array; Src = Eigen_SSE4_1::Array; Func = mul_assign_op]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:836:49: required from ‘void Eigen_AVX2::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen_AVX2::Array; Src = Eigen_AVX2::Array; Func = mul_assign_op]’ 836 | Assignment::run(actualDst, src, func); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:804:27: required from ‘void Eigen_SSE4_1::internal::call_assignment(Dst&, const Src&, const Func&, typename enable_if<(! evaluator_assume_aliasing::value), void*>::type) [with Dst = Eigen_SSE4_1::Array; Src = Eigen_SSE4_1::Array; Func = mul_assign_op; typename enable_if<(! evaluator_assume_aliasing::value), void*>::type = void*; typename evaluator_traits::Shape = Eigen_SSE4_1::DenseShape]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:804:27: required from ‘void Eigen_AVX2::internal::call_assignment(Dst&, const Src&, const Func&, typename enable_if<(! evaluator_assume_aliasing::value), void*>::type) [with Dst = Eigen_AVX2::Array; Src = Eigen_AVX2::Array; Func = mul_assign_op; typename enable_if<(! evaluator_assume_aliasing::value), void*>::type = void*; typename evaluator_traits::Shape = Eigen_AVX2::DenseShape]’ 804 | call_assignment_no_alias(dst, src, func); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/ArrayBase.h:207:18: required from ‘Derived& Eigen_SSE4_1::ArrayBase::operator*=(const Eigen_SSE4_1::ArrayBase&) [with OtherDerived = Eigen_SSE4_1::Array; Derived = Eigen_SSE4_1::Array]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/ArrayBase.h:207:18: required from ‘Derived& Eigen_AVX2::ArrayBase::operator*=(const Eigen_AVX2::ArrayBase&) [with OtherDerived = Eigen_AVX2::Array; Derived = Eigen_AVX2::Array]’ 207 | call_assignment(derived(), other.derived(), internal::mul_assign_op()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/diamond-aligner-2.1.14/src/masking/tantan.cpp:84:8: required from here 84 | t *= d; | ^ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:432:31: warning: arithmetic between different enumeration types ‘Eigen_SSE4_1::Array::’ and ‘Eigen_SSE4_1::internal::unpacket_traits<__vector(4) float>::’ is deprecated [-Wdeprecated-enum-enum-conversion] +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:432:31: warning: arithmetic between different enumeration types ‘Eigen_AVX2::Array::’ and ‘Eigen_AVX2::internal::unpacket_traits<__vector(4) float>::’ is deprecated [-Wdeprecated-enum-enum-conversion] 432 | alignedSize = (size/packetSize)*packetSize }; | ~~~~~^~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h: In instantiation of ‘static void Eigen_SSE4_1::internal::dense_assignment_loop::run(Kernel&) [with Kernel = Eigen_SSE4_1::internal::generic_dense_assignment_kernel >, Eigen_SSE4_1::internal::evaluator, Eigen_SSE4_1::Array > >, Eigen_SSE4_1::internal::mul_assign_op, 0>]’: -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:741:37: required from ‘void Eigen_SSE4_1::internal::call_dense_assignment_loop(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_SSE4_1::Array; SrcXprType = Eigen_SSE4_1::CwiseNullaryOp, Eigen_SSE4_1::Array >; Functor = mul_assign_op]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h: In instantiation of ‘static void Eigen_AVX2::internal::dense_assignment_loop::run(Kernel&) [with Kernel = Eigen_AVX2::internal::generic_dense_assignment_kernel >, Eigen_AVX2::internal::evaluator, Eigen_AVX2::Array > >, Eigen_AVX2::internal::mul_assign_op, 0>]’: +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:741:37: required from ‘void Eigen_AVX2::internal::call_dense_assignment_loop(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_AVX2::Array; SrcXprType = Eigen_AVX2::CwiseNullaryOp, Eigen_AVX2::Array >; Functor = mul_assign_op]’ 741 | dense_assignment_loop::run(kernel); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:879:31: required from ‘static void Eigen_SSE4_1::internal::Assignment::run(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_SSE4_1::Array; SrcXprType = Eigen_SSE4_1::CwiseNullaryOp, Eigen_SSE4_1::Array >; Functor = Eigen_SSE4_1::internal::mul_assign_op; Weak = void]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:879:31: required from ‘static void Eigen_AVX2::internal::Assignment::run(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_AVX2::Array; SrcXprType = Eigen_AVX2::CwiseNullaryOp, Eigen_AVX2::Array >; Functor = Eigen_AVX2::internal::mul_assign_op; Weak = void]’ 879 | call_dense_assignment_loop(dst, src, func); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:836:49: required from ‘void Eigen_SSE4_1::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen_SSE4_1::Array; Src = Eigen_SSE4_1::CwiseNullaryOp, Eigen_SSE4_1::Array >; Func = mul_assign_op]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:836:49: required from ‘void Eigen_AVX2::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen_AVX2::Array; Src = Eigen_AVX2::CwiseNullaryOp, Eigen_AVX2::Array >; Func = mul_assign_op]’ 836 | Assignment::run(actualDst, src, func); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:804:27: required from ‘void Eigen_SSE4_1::internal::call_assignment(Dst&, const Src&, const Func&, typename enable_if<(! evaluator_assume_aliasing::value), void*>::type) [with Dst = Eigen_SSE4_1::Array; Src = Eigen_SSE4_1::CwiseNullaryOp, Eigen_SSE4_1::Array >; Func = mul_assign_op; typename enable_if<(! evaluator_assume_aliasing::value), void*>::type = void*; typename evaluator_traits::Shape = Eigen_SSE4_1::DenseShape]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:804:27: required from ‘void Eigen_AVX2::internal::call_assignment(Dst&, const Src&, const Func&, typename enable_if<(! evaluator_assume_aliasing::value), void*>::type) [with Dst = Eigen_AVX2::Array; Src = Eigen_AVX2::CwiseNullaryOp, Eigen_AVX2::Array >; Func = mul_assign_op; typename enable_if<(! evaluator_assume_aliasing::value), void*>::type = void*; typename evaluator_traits::Shape = Eigen_AVX2::DenseShape]’ 804 | call_assignment_no_alias(dst, src, func); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/SelfCwiseBinaryOp.h:20:28: required from ‘Derived& Eigen_SSE4_1::DenseBase::operator*=(const Scalar&) [with Derived = Eigen_SSE4_1::Array; Scalar = float]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/SelfCwiseBinaryOp.h:20:28: required from ‘Derived& Eigen_AVX2::DenseBase::operator*=(const Scalar&) [with Derived = Eigen_AVX2::Array; Scalar = float]’ 20 | internal::call_assignment(this->derived(), PlainObject::Constant(rows(),cols(),other), internal::mul_assign_op()); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/diamond-aligner-2.1.14/src/masking/tantan.cpp:85:8: required from here 85 | f *= f2f; | ^~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:432:31: warning: arithmetic between different enumeration types ‘Eigen_SSE4_1::Array::’ and ‘Eigen_SSE4_1::internal::unpacket_traits<__vector(4) float>::’ is deprecated [-Wdeprecated-enum-enum-conversion] +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:432:31: warning: arithmetic between different enumeration types ‘Eigen_AVX2::Array::’ and ‘Eigen_AVX2::internal::unpacket_traits<__vector(4) float>::’ is deprecated [-Wdeprecated-enum-enum-conversion] 432 | alignedSize = (size/packetSize)*packetSize }; | ~~~~~^~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h: In instantiation of ‘static void Eigen_SSE4_1::internal::dense_assignment_loop::run(Kernel&) [with Kernel = Eigen_SSE4_1::internal::generic_dense_assignment_kernel >, Eigen_SSE4_1::internal::evaluator >, Eigen_SSE4_1::internal::add_assign_op, 0>]’: -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:741:37: required from ‘void Eigen_SSE4_1::internal::call_dense_assignment_loop(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_SSE4_1::Array; SrcXprType = Eigen_SSE4_1::Array; Functor = add_assign_op]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h: In instantiation of ‘static void Eigen_AVX2::internal::dense_assignment_loop::run(Kernel&) [with Kernel = Eigen_AVX2::internal::generic_dense_assignment_kernel >, Eigen_AVX2::internal::evaluator >, Eigen_AVX2::internal::add_assign_op, 0>]’: +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:741:37: required from ‘void Eigen_AVX2::internal::call_dense_assignment_loop(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_AVX2::Array; SrcXprType = Eigen_AVX2::Array; Functor = add_assign_op]’ 741 | dense_assignment_loop::run(kernel); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:879:31: required from ‘static void Eigen_SSE4_1::internal::Assignment::run(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_SSE4_1::Array; SrcXprType = Eigen_SSE4_1::Array; Functor = Eigen_SSE4_1::internal::add_assign_op; Weak = void]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:879:31: required from ‘static void Eigen_AVX2::internal::Assignment::run(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_AVX2::Array; SrcXprType = Eigen_AVX2::Array; Functor = Eigen_AVX2::internal::add_assign_op; Weak = void]’ 879 | call_dense_assignment_loop(dst, src, func); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:836:49: required from ‘void Eigen_SSE4_1::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen_SSE4_1::Array; Src = Eigen_SSE4_1::Array; Func = add_assign_op]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:836:49: required from ‘void Eigen_AVX2::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen_AVX2::Array; Src = Eigen_AVX2::Array; Func = add_assign_op]’ 836 | Assignment::run(actualDst, src, func); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:804:27: required from ‘void Eigen_SSE4_1::internal::call_assignment(Dst&, const Src&, const Func&, typename enable_if<(! evaluator_assume_aliasing::value), void*>::type) [with Dst = Eigen_SSE4_1::Array; Src = Eigen_SSE4_1::Array; Func = add_assign_op; typename enable_if<(! evaluator_assume_aliasing::value), void*>::type = void*; typename evaluator_traits::Shape = Eigen_SSE4_1::DenseShape]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:804:27: required from ‘void Eigen_AVX2::internal::call_assignment(Dst&, const Src&, const Func&, typename enable_if<(! evaluator_assume_aliasing::value), void*>::type) [with Dst = Eigen_AVX2::Array; Src = Eigen_AVX2::Array; Func = add_assign_op; typename enable_if<(! evaluator_assume_aliasing::value), void*>::type = void*; typename evaluator_traits::Shape = Eigen_AVX2::DenseShape]’ 804 | call_assignment_no_alias(dst, src, func); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/ArrayBase.h:194:18: required from ‘Derived& Eigen_SSE4_1::ArrayBase::operator+=(const Eigen_SSE4_1::ArrayBase&) [with OtherDerived = Eigen_SSE4_1::Array; Derived = Eigen_SSE4_1::Array]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/ArrayBase.h:194:18: required from ‘Derived& Eigen_AVX2::ArrayBase::operator+=(const Eigen_AVX2::ArrayBase&) [with OtherDerived = Eigen_AVX2::Array; Derived = Eigen_AVX2::Array]’ 194 | call_assignment(derived(), other.derived(), internal::add_assign_op()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/diamond-aligner-2.1.14/src/masking/tantan.cpp:86:8: required from here 86 | f += t; | ^ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:432:31: warning: arithmetic between different enumeration types ‘Eigen_SSE4_1::Array::’ and ‘Eigen_SSE4_1::internal::unpacket_traits<__vector(4) float>::’ is deprecated [-Wdeprecated-enum-enum-conversion] +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:432:31: warning: arithmetic between different enumeration types ‘Eigen_AVX2::Array::’ and ‘Eigen_AVX2::internal::unpacket_traits<__vector(4) float>::’ is deprecated [-Wdeprecated-enum-enum-conversion] 432 | alignedSize = (size/packetSize)*packetSize }; | ~~~~~^~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h: In instantiation of ‘static void Eigen_SSE4_1::internal::dense_assignment_loop::run(Kernel&) [with Kernel = Eigen_SSE4_1::internal::generic_dense_assignment_kernel >, Eigen_SSE4_1::internal::evaluator, 50, 1, false> >, Eigen_SSE4_1::internal::mul_assign_op, 0>]’: -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:741:37: required from ‘void Eigen_SSE4_1::internal::call_dense_assignment_loop(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_SSE4_1::Array; SrcXprType = Eigen_SSE4_1::Block, 50, 1, false>; Functor = mul_assign_op]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h: In instantiation of ‘static void Eigen_AVX2::internal::dense_assignment_loop::run(Kernel&) [with Kernel = Eigen_AVX2::internal::generic_dense_assignment_kernel >, Eigen_AVX2::internal::evaluator, 50, 1, false> >, Eigen_AVX2::internal::mul_assign_op, 0>]’: +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:741:37: required from ‘void Eigen_AVX2::internal::call_dense_assignment_loop(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_AVX2::Array; SrcXprType = Eigen_AVX2::Block, 50, 1, false>; Functor = mul_assign_op]’ 741 | dense_assignment_loop::run(kernel); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:879:31: required from ‘static void Eigen_SSE4_1::internal::Assignment::run(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_SSE4_1::Array; SrcXprType = Eigen_SSE4_1::Block, 50, 1, false>; Functor = Eigen_SSE4_1::internal::mul_assign_op; Weak = void]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:879:31: required from ‘static void Eigen_AVX2::internal::Assignment::run(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_AVX2::Array; SrcXprType = Eigen_AVX2::Block, 50, 1, false>; Functor = Eigen_AVX2::internal::mul_assign_op; Weak = void]’ 879 | call_dense_assignment_loop(dst, src, func); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:836:49: required from ‘void Eigen_SSE4_1::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen_SSE4_1::Array; Src = Eigen_SSE4_1::Block, 50, 1, false>; Func = mul_assign_op]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:836:49: required from ‘void Eigen_AVX2::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen_AVX2::Array; Src = Eigen_AVX2::Block, 50, 1, false>; Func = mul_assign_op]’ 836 | Assignment::run(actualDst, src, func); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:804:27: required from ‘void Eigen_SSE4_1::internal::call_assignment(Dst&, const Src&, const Func&, typename enable_if<(! evaluator_assume_aliasing::value), void*>::type) [with Dst = Eigen_SSE4_1::Array; Src = Eigen_SSE4_1::Block, 50, 1, false>; Func = mul_assign_op; typename enable_if<(! evaluator_assume_aliasing::value), void*>::type = void*; typename evaluator_traits::Shape = Eigen_SSE4_1::DenseShape]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:804:27: required from ‘void Eigen_AVX2::internal::call_assignment(Dst&, const Src&, const Func&, typename enable_if<(! evaluator_assume_aliasing::value), void*>::type) [with Dst = Eigen_AVX2::Array; Src = Eigen_AVX2::Block, 50, 1, false>; Func = mul_assign_op; typename enable_if<(! evaluator_assume_aliasing::value), void*>::type = void*; typename evaluator_traits::Shape = Eigen_AVX2::DenseShape]’ 804 | call_assignment_no_alias(dst, src, func); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/ArrayBase.h:207:18: required from ‘Derived& Eigen_SSE4_1::ArrayBase::operator*=(const Eigen_SSE4_1::ArrayBase&) [with OtherDerived = Eigen_SSE4_1::Block, 50, 1, false>; Derived = Eigen_SSE4_1::Array]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/ArrayBase.h:207:18: required from ‘Derived& Eigen_AVX2::ArrayBase::operator*=(const Eigen_AVX2::ArrayBase&) [with OtherDerived = Eigen_AVX2::Block, 50, 1, false>; Derived = Eigen_AVX2::Array]’ 207 | call_assignment(derived(), other.derived(), internal::mul_assign_op()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/diamond-aligner-2.1.14/src/masking/tantan.cpp:88:79: required from here 88 | f *= e[(size_t)letter_mask(seq[i])].template segment(len - i, WINDOW); | ^ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:432:31: warning: arithmetic between different enumeration types ‘Eigen_SSE4_1::Array::’ and ‘Eigen_SSE4_1::internal::unpacket_traits<__vector(4) float>::’ is deprecated [-Wdeprecated-enum-enum-conversion] +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:432:31: warning: arithmetic between different enumeration types ‘Eigen_AVX2::Array::’ and ‘Eigen_AVX2::internal::unpacket_traits<__vector(4) float>::’ is deprecated [-Wdeprecated-enum-enum-conversion] 432 | alignedSize = (size/packetSize)*packetSize }; | ~~~~~^~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h: In instantiation of ‘static void Eigen_SSE4_1::internal::dense_assignment_loop::run(Kernel&) [with Kernel = Eigen_SSE4_1::internal::generic_dense_assignment_kernel >, Eigen_SSE4_1::internal::evaluator, Eigen_SSE4_1::Array > >, Eigen_SSE4_1::internal::add_assign_op, 0>]’: -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:741:37: required from ‘void Eigen_SSE4_1::internal::call_dense_assignment_loop(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_SSE4_1::Array; SrcXprType = Eigen_SSE4_1::CwiseNullaryOp, Eigen_SSE4_1::Array >; Functor = add_assign_op]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h: In instantiation of ‘static void Eigen_AVX2::internal::dense_assignment_loop::run(Kernel&) [with Kernel = Eigen_AVX2::internal::generic_dense_assignment_kernel >, Eigen_AVX2::internal::evaluator, Eigen_AVX2::Array > >, Eigen_AVX2::internal::add_assign_op, 0>]’: +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:741:37: required from ‘void Eigen_AVX2::internal::call_dense_assignment_loop(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_AVX2::Array; SrcXprType = Eigen_AVX2::CwiseNullaryOp, Eigen_AVX2::Array >; Functor = add_assign_op]’ 741 | dense_assignment_loop::run(kernel); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:879:31: required from ‘static void Eigen_SSE4_1::internal::Assignment::run(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_SSE4_1::Array; SrcXprType = Eigen_SSE4_1::CwiseNullaryOp, Eigen_SSE4_1::Array >; Functor = Eigen_SSE4_1::internal::add_assign_op; Weak = void]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:879:31: required from ‘static void Eigen_AVX2::internal::Assignment::run(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_AVX2::Array; SrcXprType = Eigen_AVX2::CwiseNullaryOp, Eigen_AVX2::Array >; Functor = Eigen_AVX2::internal::add_assign_op; Weak = void]’ 879 | call_dense_assignment_loop(dst, src, func); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:836:49: required from ‘void Eigen_SSE4_1::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen_SSE4_1::Array; Src = Eigen_SSE4_1::CwiseNullaryOp, Eigen_SSE4_1::Array >; Func = add_assign_op]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:836:49: required from ‘void Eigen_AVX2::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen_AVX2::Array; Src = Eigen_AVX2::CwiseNullaryOp, Eigen_AVX2::Array >; Func = add_assign_op]’ 836 | Assignment::run(actualDst, src, func); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:804:27: required from ‘void Eigen_SSE4_1::internal::call_assignment(Dst&, const Src&, const Func&, typename enable_if<(! evaluator_assume_aliasing::value), void*>::type) [with Dst = Eigen_SSE4_1::Array; Src = Eigen_SSE4_1::CwiseNullaryOp, Eigen_SSE4_1::Array >; Func = add_assign_op; typename enable_if<(! evaluator_assume_aliasing::value), void*>::type = void*; typename evaluator_traits::Shape = Eigen_SSE4_1::DenseShape]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:804:27: required from ‘void Eigen_AVX2::internal::call_assignment(Dst&, const Src&, const Func&, typename enable_if<(! evaluator_assume_aliasing::value), void*>::type) [with Dst = Eigen_AVX2::Array; Src = Eigen_AVX2::CwiseNullaryOp, Eigen_AVX2::Array >; Func = add_assign_op; typename enable_if<(! evaluator_assume_aliasing::value), void*>::type = void*; typename evaluator_traits::Shape = Eigen_AVX2::DenseShape]’ 804 | call_assignment_no_alias(dst, src, func); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/SelfCwiseBinaryOp.h:27:28: required from ‘Derived& Eigen_SSE4_1::ArrayBase::operator+=(const Scalar&) [with Derived = Eigen_SSE4_1::Array; Scalar = float]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/SelfCwiseBinaryOp.h:27:28: required from ‘Derived& Eigen_AVX2::ArrayBase::operator+=(const Scalar&) [with Derived = Eigen_AVX2::Array; Scalar = float]’ 27 | internal::call_assignment(this->derived(), PlainObject::Constant(rows(),cols(),other), internal::add_assign_op()); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/diamond-aligner-2.1.14/src/masking/tantan.cpp:127:23: required from here 127 | f += p_repeat_end * b; | ^ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:432:31: warning: arithmetic between different enumeration types ‘Eigen_SSE4_1::Array::’ and ‘Eigen_SSE4_1::internal::unpacket_traits<__vector(4) float>::’ is deprecated [-Wdeprecated-enum-enum-conversion] +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:432:31: warning: arithmetic between different enumeration types ‘Eigen_AVX2::Array::’ and ‘Eigen_AVX2::internal::unpacket_traits<__vector(4) float>::’ is deprecated [-Wdeprecated-enum-enum-conversion] 432 | alignedSize = (size/packetSize)*packetSize }; | ~~~~~^~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h: In instantiation of ‘static void Eigen_SSE4_1::internal::dense_assignment_loop::run(Kernel&) [with Kernel = Eigen_SSE4_1::internal::generic_dense_assignment_kernel >, Eigen_SSE4_1::internal::evaluator >, Eigen_SSE4_1::internal::assign_op, 0>]’: -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:741:37: required from ‘void Eigen_SSE4_1::internal::call_dense_assignment_loop(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_SSE4_1::Array; SrcXprType = Eigen_SSE4_1::Array; Functor = assign_op]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h: In instantiation of ‘static void Eigen_AVX2::internal::dense_assignment_loop::run(Kernel&) [with Kernel = Eigen_AVX2::internal::generic_dense_assignment_kernel >, Eigen_AVX2::internal::evaluator >, Eigen_AVX2::internal::assign_op, 0>]’: +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:741:37: required from ‘void Eigen_AVX2::internal::call_dense_assignment_loop(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_AVX2::Array; SrcXprType = Eigen_AVX2::Array; Functor = assign_op]’ 741 | dense_assignment_loop::run(kernel); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:879:31: required from ‘static void Eigen_SSE4_1::internal::Assignment::run(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_SSE4_1::Array; SrcXprType = Eigen_SSE4_1::Array; Functor = Eigen_SSE4_1::internal::assign_op; Weak = void]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:879:31: required from ‘static void Eigen_AVX2::internal::Assignment::run(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_AVX2::Array; SrcXprType = Eigen_AVX2::Array; Functor = Eigen_AVX2::internal::assign_op; Weak = void]’ 879 | call_dense_assignment_loop(dst, src, func); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:836:49: required from ‘void Eigen_SSE4_1::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen_SSE4_1::Array; Src = Eigen_SSE4_1::Array; Func = assign_op]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:836:49: required from ‘void Eigen_AVX2::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen_AVX2::Array; Src = Eigen_AVX2::Array; Func = assign_op]’ 836 | Assignment::run(actualDst, src, func); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:804:27: required from ‘void Eigen_SSE4_1::internal::call_assignment(Dst&, const Src&, const Func&, typename enable_if<(! evaluator_assume_aliasing::value), void*>::type) [with Dst = Eigen_SSE4_1::Array; Src = Eigen_SSE4_1::Array; Func = assign_op; typename enable_if<(! evaluator_assume_aliasing::value), void*>::type = void*; typename evaluator_traits::Shape = Eigen_SSE4_1::DenseShape]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:804:27: required from ‘void Eigen_AVX2::internal::call_assignment(Dst&, const Src&, const Func&, typename enable_if<(! evaluator_assume_aliasing::value), void*>::type) [with Dst = Eigen_AVX2::Array; Src = Eigen_AVX2::Array; Func = assign_op; typename enable_if<(! evaluator_assume_aliasing::value), void*>::type = void*; typename evaluator_traits::Shape = Eigen_AVX2::DenseShape]’ 804 | call_assignment_no_alias(dst, src, func); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:782:18: required from ‘void Eigen_SSE4_1::internal::call_assignment(Dst&, const Src&) [with Dst = Eigen_SSE4_1::Array; Src = Eigen_SSE4_1::Array]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:782:18: required from ‘void Eigen_AVX2::internal::call_assignment(Dst&, const Src&) [with Dst = Eigen_AVX2::Array; Src = Eigen_AVX2::Array]’ 782 | call_assignment(dst, src, internal::assign_op()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/PlainObjectBase.h:714:32: required from ‘Derived& Eigen_SSE4_1::PlainObjectBase::_set(const Eigen_SSE4_1::DenseBase&) [with OtherDerived = Eigen_SSE4_1::Array; Derived = Eigen_SSE4_1::Array]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/PlainObjectBase.h:714:32: required from ‘Derived& Eigen_AVX2::PlainObjectBase::_set(const Eigen_AVX2::DenseBase&) [with OtherDerived = Eigen_AVX2::Array; Derived = Eigen_AVX2::Array]’ 714 | internal::call_assignment(this->derived(), other.derived()); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/Array.h:118:24: required from ‘Eigen_SSE4_1::Array<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>& Eigen_SSE4_1::Array<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::operator=(const Eigen_SSE4_1::Array<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>&) [with _Scalar = float; int _Rows = 50; int _Cols = 1; int _Options = 0; int _MaxRows = 50; int _MaxCols = 1]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/Array.h:118:24: required from ‘Eigen_AVX2::Array<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>& Eigen_AVX2::Array<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::operator=(const Eigen_AVX2::Array<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>&) [with _Scalar = float; int _Rows = 50; int _Cols = 1; int _Options = 0; int _MaxRows = 50; int _MaxCols = 1]’ 118 | return Base::_set(other); | ~~~~~~~~~~^~~~~~~ /build/reproducible-path/diamond-aligner-2.1.14/src/masking/tantan.cpp:124:7: required from here 124 | t = f; | ^ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:432:31: warning: arithmetic between different enumeration types ‘Eigen_SSE4_1::Array::’ and ‘Eigen_SSE4_1::internal::unpacket_traits<__vector(4) float>::’ is deprecated [-Wdeprecated-enum-enum-conversion] +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:432:31: warning: arithmetic between different enumeration types ‘Eigen_AVX2::Array::’ and ‘Eigen_AVX2::internal::unpacket_traits<__vector(4) float>::’ is deprecated [-Wdeprecated-enum-enum-conversion] 432 | alignedSize = (size/packetSize)*packetSize }; | ~~~~~^~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h: In instantiation of ‘static void Eigen_SSE4_1::internal::dense_assignment_loop::run(Kernel&) [with Kernel = Eigen_SSE4_1::internal::generic_dense_assignment_kernel >, Eigen_SSE4_1::internal::evaluator, Eigen_SSE4_1::Array > >, Eigen_SSE4_1::internal::assign_op, 0>]’: -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:741:37: required from ‘void Eigen_SSE4_1::internal::call_dense_assignment_loop(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_SSE4_1::Array; SrcXprType = Eigen_SSE4_1::CwiseNullaryOp, Eigen_SSE4_1::Array >; Functor = assign_op]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h: In instantiation of ‘static void Eigen_AVX2::internal::dense_assignment_loop::run(Kernel&) [with Kernel = Eigen_AVX2::internal::generic_dense_assignment_kernel >, Eigen_AVX2::internal::evaluator, Eigen_AVX2::Array > >, Eigen_AVX2::internal::assign_op, 0>]’: +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:741:37: required from ‘void Eigen_AVX2::internal::call_dense_assignment_loop(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_AVX2::Array; SrcXprType = Eigen_AVX2::CwiseNullaryOp, Eigen_AVX2::Array >; Functor = assign_op]’ 741 | dense_assignment_loop::run(kernel); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:879:31: required from ‘static void Eigen_SSE4_1::internal::Assignment::run(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_SSE4_1::Array; SrcXprType = Eigen_SSE4_1::CwiseNullaryOp, Eigen_SSE4_1::Array >; Functor = Eigen_SSE4_1::internal::assign_op; Weak = void]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:879:31: required from ‘static void Eigen_AVX2::internal::Assignment::run(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_AVX2::Array; SrcXprType = Eigen_AVX2::CwiseNullaryOp, Eigen_AVX2::Array >; Functor = Eigen_AVX2::internal::assign_op; Weak = void]’ 879 | call_dense_assignment_loop(dst, src, func); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:836:49: required from ‘void Eigen_SSE4_1::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen_SSE4_1::Array; Src = Eigen_SSE4_1::CwiseNullaryOp, Eigen_SSE4_1::Array >; Func = assign_op]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:836:49: required from ‘void Eigen_AVX2::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen_AVX2::Array; Src = Eigen_AVX2::CwiseNullaryOp, Eigen_AVX2::Array >; Func = assign_op]’ 836 | Assignment::run(actualDst, src, func); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:804:27: required from ‘void Eigen_SSE4_1::internal::call_assignment(Dst&, const Src&, const Func&, typename enable_if<(! evaluator_assume_aliasing::value), void*>::type) [with Dst = Eigen_SSE4_1::Array; Src = Eigen_SSE4_1::CwiseNullaryOp, Eigen_SSE4_1::Array >; Func = assign_op; typename enable_if<(! evaluator_assume_aliasing::value), void*>::type = void*; typename evaluator_traits::Shape = Eigen_SSE4_1::DenseShape]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:804:27: required from ‘void Eigen_AVX2::internal::call_assignment(Dst&, const Src&, const Func&, typename enable_if<(! evaluator_assume_aliasing::value), void*>::type) [with Dst = Eigen_AVX2::Array; Src = Eigen_AVX2::CwiseNullaryOp, Eigen_AVX2::Array >; Func = assign_op; typename enable_if<(! evaluator_assume_aliasing::value), void*>::type = void*; typename evaluator_traits::Shape = Eigen_AVX2::DenseShape]’ 804 | call_assignment_no_alias(dst, src, func); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:782:18: required from ‘void Eigen_SSE4_1::internal::call_assignment(Dst&, const Src&) [with Dst = Eigen_SSE4_1::Array; Src = Eigen_SSE4_1::CwiseNullaryOp, Eigen_SSE4_1::Array >]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:782:18: required from ‘void Eigen_AVX2::internal::call_assignment(Dst&, const Src&) [with Dst = Eigen_AVX2::Array; Src = Eigen_AVX2::CwiseNullaryOp, Eigen_AVX2::Array >]’ 782 | call_assignment(dst, src, internal::assign_op()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/PlainObjectBase.h:714:32: required from ‘Derived& Eigen_SSE4_1::PlainObjectBase::_set(const Eigen_SSE4_1::DenseBase&) [with OtherDerived = Eigen_SSE4_1::CwiseNullaryOp, Eigen_SSE4_1::Array >; Derived = Eigen_SSE4_1::Array]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/PlainObjectBase.h:714:32: required from ‘Derived& Eigen_AVX2::PlainObjectBase::_set(const Eigen_AVX2::DenseBase&) [with OtherDerived = Eigen_AVX2::CwiseNullaryOp, Eigen_AVX2::Array >; Derived = Eigen_AVX2::Array]’ 714 | internal::call_assignment(this->derived(), other.derived()); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/Array.h:109:24: required from ‘Eigen_SSE4_1::Array<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>& Eigen_SSE4_1::Array<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::operator=(const Eigen_SSE4_1::DenseBase&) [with OtherDerived = Eigen_SSE4_1::CwiseNullaryOp, Eigen_SSE4_1::Array >; _Scalar = float; int _Rows = 50; int _Cols = 1; int _Options = 0; int _MaxRows = 50; int _MaxCols = 1]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/Array.h:109:24: required from ‘Eigen_AVX2::Array<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>& Eigen_AVX2::Array<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::operator=(const Eigen_AVX2::DenseBase&) [with OtherDerived = Eigen_AVX2::CwiseNullaryOp, Eigen_AVX2::Array >; _Scalar = float; int _Rows = 50; int _Cols = 1; int _Options = 0; int _MaxRows = 50; int _MaxCols = 1]’ 109 | return Base::_set(other); | ~~~~~~~~~~^~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/CwiseNullaryOp.h:327:20: required from ‘Derived& Eigen_SSE4_1::DenseBase::setConstant(const Scalar&) [with Derived = Eigen_SSE4_1::Array; Scalar = float]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/CwiseNullaryOp.h:327:20: required from ‘Derived& Eigen_AVX2::DenseBase::setConstant(const Scalar&) [with Derived = Eigen_AVX2::Array; Scalar = float]’ 327 | return derived() = Constant(rows(), cols(), val); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/Array.h:92:24: required from ‘Eigen_SSE4_1::Array<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>& Eigen_SSE4_1::Array<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::operator=(const Scalar&) [with _Scalar = float; int _Rows = 50; int _Cols = 1; int _Options = 0; int _MaxRows = 50; int _MaxCols = 1; Scalar = float]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/Array.h:92:24: required from ‘Eigen_AVX2::Array<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>& Eigen_AVX2::Array<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::operator=(const Scalar&) [with _Scalar = float; int _Rows = 50; int _Cols = 1; int _Options = 0; int _MaxRows = 50; int _MaxCols = 1; Scalar = float]’ 92 | Base::setConstant(value); | ~~~~~~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/diamond-aligner-2.1.14/src/masking/tantan.cpp:83:7: required from here 83 | t = b; | ^ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:432:31: warning: arithmetic between different enumeration types ‘Eigen_SSE4_1::Array::’ and ‘Eigen_SSE4_1::internal::unpacket_traits<__vector(4) float>::’ is deprecated [-Wdeprecated-enum-enum-conversion] +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:432:31: warning: arithmetic between different enumeration types ‘Eigen_AVX2::Array::’ and ‘Eigen_AVX2::internal::unpacket_traits<__vector(4) float>::’ is deprecated [-Wdeprecated-enum-enum-conversion] 432 | alignedSize = (size/packetSize)*packetSize }; | ~~~~~^~~~~~~~~~~~ -cc1plus: note: unrecognized command-line option ‘-Wno-unknown-warning-option’ may have been intended to silence earlier diagnostics -[ 9%] Building CXX object CMakeFiles/arch_sse4_1.dir/src/dp/scan_diags.cpp.o -/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.14/src -I/build/reproducible-path/diamond-aligner-2.1.14/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable 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/build/reproducible-path/diamond-aligner-2.1.14/src/masking/tantan.cpp:27: -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/PlainObjectBase.h: In instantiation of ‘static void Eigen_AVX2::PlainObjectBase::_check_template_params() [with Derived = Eigen_AVX2::Array]’: -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/Array.h:134:35: required from ‘Eigen_AVX2::Array<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::Array() [with _Scalar = float; int _Rows = -1; int _Cols = 1; int _Options = 0; int _MaxRows = -1; int _MaxCols = 1]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/PlainObjectBase.h: In instantiation of ‘static void Eigen_SSE4_1::PlainObjectBase::_check_template_params() [with Derived = Eigen_SSE4_1::Array]’: +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/Array.h:134:35: required from ‘Eigen_SSE4_1::Array<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::Array() [with _Scalar = float; int _Rows = -1; int _Cols = 1; int _Options = 0; int _MaxRows = -1; int _MaxCols = 1]’ 134 | Base::_check_template_params(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /usr/include/c++/15/array:102:12: required from here 102 | struct array | ^~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/PlainObjectBase.h:905:102: warning: bitwise operation between different enumeration types ‘Eigen_AVX2::PlainObjectBase >::’ and ‘Eigen_AVX2::StorageOptions’ is deprecated [-Wdeprecated-enum-enum-conversion] +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/PlainObjectBase.h:905:102: warning: bitwise operation between different enumeration types ‘Eigen_SSE4_1::PlainObjectBase >::’ and ‘Eigen_SSE4_1::StorageOptions’ is deprecated [-Wdeprecated-enum-enum-conversion] 905 | EIGEN_STATIC_ASSERT((EIGEN_IMPLIES(MaxRowsAtCompileTime==1 && MaxColsAtCompileTime!=1, (Options&RowMajor)==RowMajor) | ~~~~~~~~^~~~~~~~~~ /build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/util/StaticAssert.h:33:54: note: in definition of macro ‘EIGEN_STATIC_ASSERT’ @@ -1079,7 +1115,7 @@ /build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/PlainObjectBase.h:905:28: note: in expansion of macro ‘EIGEN_IMPLIES’ 905 | EIGEN_STATIC_ASSERT((EIGEN_IMPLIES(MaxRowsAtCompileTime==1 && MaxColsAtCompileTime!=1, (Options&RowMajor)==RowMajor) | ^~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/PlainObjectBase.h:906:102: warning: bitwise operation between different enumeration types ‘Eigen_AVX2::PlainObjectBase >::’ and ‘Eigen_AVX2::StorageOptions’ is deprecated [-Wdeprecated-enum-enum-conversion] +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/PlainObjectBase.h:906:102: warning: bitwise operation between different enumeration types ‘Eigen_SSE4_1::PlainObjectBase >::’ and ‘Eigen_SSE4_1::StorageOptions’ is deprecated [-Wdeprecated-enum-enum-conversion] 906 | && EIGEN_IMPLIES(MaxColsAtCompileTime==1 && MaxRowsAtCompileTime!=1, (Options&RowMajor)==0) | ~~~~~~~~^~~~~~~~~~ /build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/util/StaticAssert.h:33:54: note: in definition of macro ‘EIGEN_STATIC_ASSERT’ @@ -1088,14 +1124,14 @@ /build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/PlainObjectBase.h:906:28: note: in expansion of macro ‘EIGEN_IMPLIES’ 906 | && EIGEN_IMPLIES(MaxColsAtCompileTime==1 && MaxRowsAtCompileTime!=1, (Options&RowMajor)==0) | ^~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/PlainObjectBase.h: In instantiation of ‘static void Eigen_AVX2::PlainObjectBase::_check_template_params() [with Derived = Eigen_AVX2::Array]’: -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/Array.h:170:35: required from ‘Eigen_AVX2::Array<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::Array(const T&) [with T = double; _Scalar = float; int _Rows = 50; int _Cols = 1; int _Options = 0; int _MaxRows = 50; int _MaxCols = 1]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/PlainObjectBase.h: In instantiation of ‘static void Eigen_SSE4_1::PlainObjectBase::_check_template_params() [with Derived = Eigen_SSE4_1::Array]’: +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/Array.h:170:35: required from ‘Eigen_SSE4_1::Array<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::Array(const T&) [with T = double; _Scalar = float; int _Rows = 50; int _Cols = 1; int _Options = 0; int _MaxRows = 50; int _MaxCols = 1]’ 170 | Base::_check_template_params(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/diamond-aligner-2.1.14/src/masking/tantan.cpp:61:31: required from here 61 | Array f(0.0), d, t; | ^ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/PlainObjectBase.h:905:102: warning: bitwise operation between different enumeration types ‘Eigen_AVX2::PlainObjectBase >::’ and ‘Eigen_AVX2::StorageOptions’ is deprecated [-Wdeprecated-enum-enum-conversion] +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/PlainObjectBase.h:905:102: warning: bitwise operation between different enumeration types ‘Eigen_SSE4_1::PlainObjectBase >::’ and ‘Eigen_SSE4_1::StorageOptions’ is deprecated [-Wdeprecated-enum-enum-conversion] 905 | EIGEN_STATIC_ASSERT((EIGEN_IMPLIES(MaxRowsAtCompileTime==1 && MaxColsAtCompileTime!=1, (Options&RowMajor)==RowMajor) | ~~~~~~~~^~~~~~~~~~ /build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/util/StaticAssert.h:33:54: note: in definition of macro ‘EIGEN_STATIC_ASSERT’ @@ -1104,7 +1140,7 @@ /build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/PlainObjectBase.h:905:28: note: in expansion of macro ‘EIGEN_IMPLIES’ 905 | EIGEN_STATIC_ASSERT((EIGEN_IMPLIES(MaxRowsAtCompileTime==1 && MaxColsAtCompileTime!=1, (Options&RowMajor)==RowMajor) | ^~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/PlainObjectBase.h:906:102: warning: bitwise operation between different enumeration types ‘Eigen_AVX2::PlainObjectBase >::’ and ‘Eigen_AVX2::StorageOptions’ is deprecated [-Wdeprecated-enum-enum-conversion] +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/PlainObjectBase.h:906:102: warning: bitwise operation between different enumeration types ‘Eigen_SSE4_1::PlainObjectBase >::’ and ‘Eigen_SSE4_1::StorageOptions’ is deprecated [-Wdeprecated-enum-enum-conversion] 906 | && EIGEN_IMPLIES(MaxColsAtCompileTime==1 && MaxRowsAtCompileTime!=1, (Options&RowMajor)==0) | ~~~~~~~~^~~~~~~~~~ /build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/util/StaticAssert.h:33:54: note: in definition of macro ‘EIGEN_STATIC_ASSERT’ @@ -1114,199 +1150,199 @@ 906 | && EIGEN_IMPLIES(MaxColsAtCompileTime==1 && MaxRowsAtCompileTime!=1, (Options&RowMajor)==0) | ^~~~~~~~~~~~~ In file included from /build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/Core:483: -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/Redux.h: In instantiation of ‘struct Eigen_AVX2::internal::redux_impl, Eigen_AVX2::internal::redux_evaluator >, 3, 2>’: -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/Redux.h:418:56: required from ‘typename Eigen_AVX2::internal::traits::Scalar Eigen_AVX2::DenseBase::redux(const Func&) const [with BinaryOp = Eigen_AVX2::internal::scalar_sum_op; Derived = Eigen_AVX2::Array; typename Eigen_AVX2::internal::traits::Scalar = float]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/Redux.h: In instantiation of ‘struct Eigen_SSE4_1::internal::redux_impl, Eigen_SSE4_1::internal::redux_evaluator >, 3, 2>’: +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/Redux.h:418:56: required from ‘typename Eigen_SSE4_1::internal::traits::Scalar Eigen_SSE4_1::DenseBase::redux(const Func&) const [with BinaryOp = Eigen_SSE4_1::internal::scalar_sum_op; Derived = Eigen_SSE4_1::Array; typename Eigen_SSE4_1::internal::traits::Scalar = float]’ 418 | return internal::redux_impl::run(thisEval, func); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/Redux.h:453:25: required from ‘typename Eigen_AVX2::internal::traits::Scalar Eigen_AVX2::DenseBase::sum() const [with Derived = Eigen_AVX2::Array; typename Eigen_AVX2::internal::traits::Scalar = float]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/Redux.h:453:25: required from ‘typename Eigen_SSE4_1::internal::traits::Scalar Eigen_SSE4_1::DenseBase::sum() const [with Derived = Eigen_SSE4_1::Array; typename Eigen_SSE4_1::internal::traits::Scalar = float]’ 453 | return derived().redux(Eigen::internal::scalar_sum_op()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/diamond-aligner-2.1.14/src/masking/tantan.cpp:82:24: required from here 82 | const float s = f.sum(); | ~~~~~^~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/Redux.h:315:28: warning: arithmetic between different enumeration types ‘Eigen_AVX2::internal::redux_evaluator >::’ and ‘Eigen_AVX2::internal::redux_traits, Eigen_AVX2::internal::redux_evaluator > >::’ is deprecated [-Wdeprecated-enum-enum-conversion] +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/Redux.h:315:28: warning: arithmetic between different enumeration types ‘Eigen_SSE4_1::internal::redux_evaluator >::’ and ‘Eigen_SSE4_1::internal::redux_traits, Eigen_SSE4_1::internal::redux_evaluator > >::’ is deprecated [-Wdeprecated-enum-enum-conversion] 315 | VectorizedSize = (Size / PacketSize) * PacketSize | ~~~~~~^~~~~~~~~~~~~ In file included from /build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/Core:446: -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h: In instantiation of ‘static void Eigen_AVX2::internal::dense_assignment_loop::run(Kernel&) [with Kernel = Eigen_AVX2::internal::generic_dense_assignment_kernel >, Eigen_AVX2::internal::evaluator >, Eigen_AVX2::internal::mul_assign_op, 0>]’: -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:741:37: required from ‘void Eigen_AVX2::internal::call_dense_assignment_loop(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_AVX2::Array; SrcXprType = Eigen_AVX2::Array; Functor = mul_assign_op]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h: In instantiation of ‘static void Eigen_SSE4_1::internal::dense_assignment_loop::run(Kernel&) [with Kernel = Eigen_SSE4_1::internal::generic_dense_assignment_kernel >, Eigen_SSE4_1::internal::evaluator >, Eigen_SSE4_1::internal::mul_assign_op, 0>]’: +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:741:37: required from ‘void Eigen_SSE4_1::internal::call_dense_assignment_loop(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_SSE4_1::Array; SrcXprType = Eigen_SSE4_1::Array; Functor = mul_assign_op]’ 741 | dense_assignment_loop::run(kernel); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:879:31: required from ‘static void Eigen_AVX2::internal::Assignment::run(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_AVX2::Array; SrcXprType = Eigen_AVX2::Array; Functor = Eigen_AVX2::internal::mul_assign_op; Weak = void]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:879:31: required from ‘static void Eigen_SSE4_1::internal::Assignment::run(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_SSE4_1::Array; SrcXprType = Eigen_SSE4_1::Array; Functor = Eigen_SSE4_1::internal::mul_assign_op; Weak = void]’ 879 | call_dense_assignment_loop(dst, src, func); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:836:49: required from ‘void Eigen_AVX2::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen_AVX2::Array; Src = Eigen_AVX2::Array; Func = mul_assign_op]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:836:49: required from ‘void Eigen_SSE4_1::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen_SSE4_1::Array; Src = Eigen_SSE4_1::Array; Func = mul_assign_op]’ 836 | Assignment::run(actualDst, src, func); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:804:27: required from ‘void Eigen_AVX2::internal::call_assignment(Dst&, const Src&, const Func&, typename enable_if<(! evaluator_assume_aliasing::value), void*>::type) [with Dst = Eigen_AVX2::Array; Src = Eigen_AVX2::Array; Func = mul_assign_op; typename enable_if<(! evaluator_assume_aliasing::value), void*>::type = void*; typename evaluator_traits::Shape = Eigen_AVX2::DenseShape]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:804:27: required from ‘void Eigen_SSE4_1::internal::call_assignment(Dst&, const Src&, const Func&, typename enable_if<(! evaluator_assume_aliasing::value), void*>::type) [with Dst = Eigen_SSE4_1::Array; Src = Eigen_SSE4_1::Array; Func = mul_assign_op; typename enable_if<(! evaluator_assume_aliasing::value), void*>::type = void*; typename evaluator_traits::Shape = Eigen_SSE4_1::DenseShape]’ 804 | call_assignment_no_alias(dst, src, func); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/ArrayBase.h:207:18: required from ‘Derived& Eigen_AVX2::ArrayBase::operator*=(const Eigen_AVX2::ArrayBase&) [with OtherDerived = Eigen_AVX2::Array; Derived = Eigen_AVX2::Array]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/ArrayBase.h:207:18: required from ‘Derived& Eigen_SSE4_1::ArrayBase::operator*=(const Eigen_SSE4_1::ArrayBase&) [with OtherDerived = Eigen_SSE4_1::Array; Derived = Eigen_SSE4_1::Array]’ 207 | call_assignment(derived(), other.derived(), internal::mul_assign_op()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/diamond-aligner-2.1.14/src/masking/tantan.cpp:84:8: required from here 84 | t *= d; | ^ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:432:31: warning: arithmetic between different enumeration types ‘Eigen_AVX2::Array::’ and ‘Eigen_AVX2::internal::unpacket_traits<__vector(4) float>::’ is deprecated [-Wdeprecated-enum-enum-conversion] +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:432:31: warning: arithmetic between different enumeration types ‘Eigen_SSE4_1::Array::’ and ‘Eigen_SSE4_1::internal::unpacket_traits<__vector(4) float>::’ is deprecated [-Wdeprecated-enum-enum-conversion] 432 | alignedSize = (size/packetSize)*packetSize }; | ~~~~~^~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h: In instantiation of ‘static void Eigen_AVX2::internal::dense_assignment_loop::run(Kernel&) [with Kernel = Eigen_AVX2::internal::generic_dense_assignment_kernel >, Eigen_AVX2::internal::evaluator, Eigen_AVX2::Array > >, Eigen_AVX2::internal::mul_assign_op, 0>]’: -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:741:37: required from ‘void Eigen_AVX2::internal::call_dense_assignment_loop(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_AVX2::Array; SrcXprType = Eigen_AVX2::CwiseNullaryOp, Eigen_AVX2::Array >; Functor = mul_assign_op]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h: In instantiation of ‘static void Eigen_SSE4_1::internal::dense_assignment_loop::run(Kernel&) [with Kernel = Eigen_SSE4_1::internal::generic_dense_assignment_kernel >, Eigen_SSE4_1::internal::evaluator, Eigen_SSE4_1::Array > >, Eigen_SSE4_1::internal::mul_assign_op, 0>]’: +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:741:37: required from ‘void Eigen_SSE4_1::internal::call_dense_assignment_loop(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_SSE4_1::Array; SrcXprType = Eigen_SSE4_1::CwiseNullaryOp, Eigen_SSE4_1::Array >; Functor = mul_assign_op]’ 741 | dense_assignment_loop::run(kernel); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:879:31: required from ‘static void Eigen_AVX2::internal::Assignment::run(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_AVX2::Array; SrcXprType = Eigen_AVX2::CwiseNullaryOp, Eigen_AVX2::Array >; Functor = Eigen_AVX2::internal::mul_assign_op; Weak = void]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:879:31: required from ‘static void Eigen_SSE4_1::internal::Assignment::run(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_SSE4_1::Array; SrcXprType = Eigen_SSE4_1::CwiseNullaryOp, Eigen_SSE4_1::Array >; Functor = Eigen_SSE4_1::internal::mul_assign_op; Weak = void]’ 879 | call_dense_assignment_loop(dst, src, func); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:836:49: required from ‘void Eigen_AVX2::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen_AVX2::Array; Src = Eigen_AVX2::CwiseNullaryOp, Eigen_AVX2::Array >; Func = mul_assign_op]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:836:49: required from ‘void Eigen_SSE4_1::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen_SSE4_1::Array; Src = Eigen_SSE4_1::CwiseNullaryOp, Eigen_SSE4_1::Array >; Func = mul_assign_op]’ 836 | Assignment::run(actualDst, src, func); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:804:27: required from ‘void Eigen_AVX2::internal::call_assignment(Dst&, const Src&, const Func&, typename enable_if<(! evaluator_assume_aliasing::value), void*>::type) [with Dst = Eigen_AVX2::Array; Src = Eigen_AVX2::CwiseNullaryOp, Eigen_AVX2::Array >; Func = mul_assign_op; typename enable_if<(! evaluator_assume_aliasing::value), void*>::type = void*; typename evaluator_traits::Shape = Eigen_AVX2::DenseShape]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:804:27: required from ‘void Eigen_SSE4_1::internal::call_assignment(Dst&, const Src&, const Func&, typename enable_if<(! evaluator_assume_aliasing::value), void*>::type) [with Dst = Eigen_SSE4_1::Array; Src = Eigen_SSE4_1::CwiseNullaryOp, Eigen_SSE4_1::Array >; Func = mul_assign_op; typename enable_if<(! evaluator_assume_aliasing::value), void*>::type = void*; typename evaluator_traits::Shape = Eigen_SSE4_1::DenseShape]’ 804 | call_assignment_no_alias(dst, src, func); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/SelfCwiseBinaryOp.h:20:28: required from ‘Derived& Eigen_AVX2::DenseBase::operator*=(const Scalar&) [with Derived = Eigen_AVX2::Array; Scalar = float]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/SelfCwiseBinaryOp.h:20:28: required from ‘Derived& Eigen_SSE4_1::DenseBase::operator*=(const Scalar&) [with Derived = Eigen_SSE4_1::Array; Scalar = float]’ 20 | internal::call_assignment(this->derived(), PlainObject::Constant(rows(),cols(),other), internal::mul_assign_op()); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/diamond-aligner-2.1.14/src/masking/tantan.cpp:85:8: required from here 85 | f *= f2f; | ^~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:432:31: warning: arithmetic between different enumeration types ‘Eigen_AVX2::Array::’ and ‘Eigen_AVX2::internal::unpacket_traits<__vector(4) float>::’ is deprecated [-Wdeprecated-enum-enum-conversion] +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:432:31: warning: arithmetic between different enumeration types ‘Eigen_SSE4_1::Array::’ and ‘Eigen_SSE4_1::internal::unpacket_traits<__vector(4) float>::’ is deprecated [-Wdeprecated-enum-enum-conversion] 432 | alignedSize = (size/packetSize)*packetSize }; | ~~~~~^~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h: In instantiation of ‘static void Eigen_AVX2::internal::dense_assignment_loop::run(Kernel&) [with Kernel = Eigen_AVX2::internal::generic_dense_assignment_kernel >, Eigen_AVX2::internal::evaluator >, Eigen_AVX2::internal::add_assign_op, 0>]’: -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:741:37: required from ‘void Eigen_AVX2::internal::call_dense_assignment_loop(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_AVX2::Array; SrcXprType = Eigen_AVX2::Array; Functor = add_assign_op]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h: In instantiation of ‘static void Eigen_SSE4_1::internal::dense_assignment_loop::run(Kernel&) [with Kernel = Eigen_SSE4_1::internal::generic_dense_assignment_kernel >, Eigen_SSE4_1::internal::evaluator >, Eigen_SSE4_1::internal::add_assign_op, 0>]’: +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:741:37: required from ‘void Eigen_SSE4_1::internal::call_dense_assignment_loop(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_SSE4_1::Array; SrcXprType = Eigen_SSE4_1::Array; Functor = add_assign_op]’ 741 | dense_assignment_loop::run(kernel); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:879:31: required from ‘static void Eigen_AVX2::internal::Assignment::run(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_AVX2::Array; SrcXprType = Eigen_AVX2::Array; Functor = Eigen_AVX2::internal::add_assign_op; Weak = void]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:879:31: required from ‘static void Eigen_SSE4_1::internal::Assignment::run(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_SSE4_1::Array; SrcXprType = Eigen_SSE4_1::Array; Functor = Eigen_SSE4_1::internal::add_assign_op; Weak = void]’ 879 | call_dense_assignment_loop(dst, src, func); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:836:49: required from ‘void Eigen_AVX2::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen_AVX2::Array; Src = Eigen_AVX2::Array; Func = add_assign_op]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:836:49: required from ‘void Eigen_SSE4_1::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen_SSE4_1::Array; Src = Eigen_SSE4_1::Array; Func = add_assign_op]’ 836 | Assignment::run(actualDst, src, func); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:804:27: required from ‘void Eigen_AVX2::internal::call_assignment(Dst&, const Src&, const Func&, typename enable_if<(! evaluator_assume_aliasing::value), void*>::type) [with Dst = Eigen_AVX2::Array; Src = Eigen_AVX2::Array; Func = add_assign_op; typename enable_if<(! evaluator_assume_aliasing::value), void*>::type = void*; typename evaluator_traits::Shape = Eigen_AVX2::DenseShape]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:804:27: required from ‘void Eigen_SSE4_1::internal::call_assignment(Dst&, const Src&, const Func&, typename enable_if<(! evaluator_assume_aliasing::value), void*>::type) [with Dst = Eigen_SSE4_1::Array; Src = Eigen_SSE4_1::Array; Func = add_assign_op; typename enable_if<(! evaluator_assume_aliasing::value), void*>::type = void*; typename evaluator_traits::Shape = Eigen_SSE4_1::DenseShape]’ 804 | call_assignment_no_alias(dst, src, func); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/ArrayBase.h:194:18: required from ‘Derived& Eigen_AVX2::ArrayBase::operator+=(const Eigen_AVX2::ArrayBase&) [with OtherDerived = Eigen_AVX2::Array; Derived = Eigen_AVX2::Array]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/ArrayBase.h:194:18: required from ‘Derived& Eigen_SSE4_1::ArrayBase::operator+=(const Eigen_SSE4_1::ArrayBase&) [with OtherDerived = Eigen_SSE4_1::Array; Derived = Eigen_SSE4_1::Array]’ 194 | call_assignment(derived(), other.derived(), internal::add_assign_op()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/diamond-aligner-2.1.14/src/masking/tantan.cpp:86:8: required from here 86 | f += t; | ^ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:432:31: warning: arithmetic between different enumeration types ‘Eigen_AVX2::Array::’ and ‘Eigen_AVX2::internal::unpacket_traits<__vector(4) float>::’ is deprecated [-Wdeprecated-enum-enum-conversion] +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:432:31: warning: arithmetic between different enumeration types ‘Eigen_SSE4_1::Array::’ and ‘Eigen_SSE4_1::internal::unpacket_traits<__vector(4) float>::’ is deprecated [-Wdeprecated-enum-enum-conversion] 432 | alignedSize = (size/packetSize)*packetSize }; | ~~~~~^~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h: In instantiation of ‘static void Eigen_AVX2::internal::dense_assignment_loop::run(Kernel&) [with Kernel = Eigen_AVX2::internal::generic_dense_assignment_kernel >, Eigen_AVX2::internal::evaluator, 50, 1, false> >, Eigen_AVX2::internal::mul_assign_op, 0>]’: -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:741:37: required from ‘void Eigen_AVX2::internal::call_dense_assignment_loop(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_AVX2::Array; SrcXprType = Eigen_AVX2::Block, 50, 1, false>; Functor = mul_assign_op]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h: In instantiation of ‘static void Eigen_SSE4_1::internal::dense_assignment_loop::run(Kernel&) [with Kernel = Eigen_SSE4_1::internal::generic_dense_assignment_kernel >, Eigen_SSE4_1::internal::evaluator, 50, 1, false> >, Eigen_SSE4_1::internal::mul_assign_op, 0>]’: +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:741:37: required from ‘void Eigen_SSE4_1::internal::call_dense_assignment_loop(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_SSE4_1::Array; SrcXprType = Eigen_SSE4_1::Block, 50, 1, false>; Functor = mul_assign_op]’ 741 | dense_assignment_loop::run(kernel); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:879:31: required from ‘static void Eigen_AVX2::internal::Assignment::run(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_AVX2::Array; SrcXprType = Eigen_AVX2::Block, 50, 1, false>; Functor = Eigen_AVX2::internal::mul_assign_op; Weak = void]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:879:31: required from ‘static void Eigen_SSE4_1::internal::Assignment::run(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_SSE4_1::Array; SrcXprType = Eigen_SSE4_1::Block, 50, 1, false>; Functor = Eigen_SSE4_1::internal::mul_assign_op; Weak = void]’ 879 | call_dense_assignment_loop(dst, src, func); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:836:49: required from ‘void Eigen_AVX2::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen_AVX2::Array; Src = Eigen_AVX2::Block, 50, 1, false>; Func = mul_assign_op]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:836:49: required from ‘void Eigen_SSE4_1::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen_SSE4_1::Array; Src = Eigen_SSE4_1::Block, 50, 1, false>; Func = mul_assign_op]’ 836 | Assignment::run(actualDst, src, func); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:804:27: required from ‘void Eigen_AVX2::internal::call_assignment(Dst&, const Src&, const Func&, typename enable_if<(! evaluator_assume_aliasing::value), void*>::type) [with Dst = Eigen_AVX2::Array; Src = Eigen_AVX2::Block, 50, 1, false>; Func = mul_assign_op; typename enable_if<(! evaluator_assume_aliasing::value), void*>::type = void*; typename evaluator_traits::Shape = Eigen_AVX2::DenseShape]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:804:27: required from ‘void Eigen_SSE4_1::internal::call_assignment(Dst&, const Src&, const Func&, typename enable_if<(! evaluator_assume_aliasing::value), void*>::type) [with Dst = Eigen_SSE4_1::Array; Src = Eigen_SSE4_1::Block, 50, 1, false>; Func = mul_assign_op; typename enable_if<(! evaluator_assume_aliasing::value), void*>::type = void*; typename evaluator_traits::Shape = Eigen_SSE4_1::DenseShape]’ 804 | call_assignment_no_alias(dst, src, func); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/ArrayBase.h:207:18: required from ‘Derived& Eigen_AVX2::ArrayBase::operator*=(const Eigen_AVX2::ArrayBase&) [with OtherDerived = Eigen_AVX2::Block, 50, 1, false>; Derived = Eigen_AVX2::Array]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/ArrayBase.h:207:18: required from ‘Derived& Eigen_SSE4_1::ArrayBase::operator*=(const Eigen_SSE4_1::ArrayBase&) [with OtherDerived = Eigen_SSE4_1::Block, 50, 1, false>; Derived = Eigen_SSE4_1::Array]’ 207 | call_assignment(derived(), other.derived(), internal::mul_assign_op()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/diamond-aligner-2.1.14/src/masking/tantan.cpp:88:79: required from here 88 | f *= e[(size_t)letter_mask(seq[i])].template segment(len - i, WINDOW); | ^ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:432:31: warning: arithmetic between different enumeration types ‘Eigen_AVX2::Array::’ and ‘Eigen_AVX2::internal::unpacket_traits<__vector(4) float>::’ is deprecated [-Wdeprecated-enum-enum-conversion] +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:432:31: warning: arithmetic between different enumeration types ‘Eigen_SSE4_1::Array::’ and ‘Eigen_SSE4_1::internal::unpacket_traits<__vector(4) float>::’ is deprecated [-Wdeprecated-enum-enum-conversion] 432 | alignedSize = (size/packetSize)*packetSize }; | ~~~~~^~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h: In instantiation of ‘static void Eigen_AVX2::internal::dense_assignment_loop::run(Kernel&) [with Kernel = Eigen_AVX2::internal::generic_dense_assignment_kernel >, Eigen_AVX2::internal::evaluator, Eigen_AVX2::Array > >, Eigen_AVX2::internal::add_assign_op, 0>]’: -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:741:37: required from ‘void Eigen_AVX2::internal::call_dense_assignment_loop(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_AVX2::Array; SrcXprType = Eigen_AVX2::CwiseNullaryOp, Eigen_AVX2::Array >; Functor = add_assign_op]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h: In instantiation of ‘static void Eigen_SSE4_1::internal::dense_assignment_loop::run(Kernel&) [with Kernel = Eigen_SSE4_1::internal::generic_dense_assignment_kernel >, Eigen_SSE4_1::internal::evaluator, Eigen_SSE4_1::Array > >, Eigen_SSE4_1::internal::add_assign_op, 0>]’: +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:741:37: required from ‘void Eigen_SSE4_1::internal::call_dense_assignment_loop(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_SSE4_1::Array; SrcXprType = Eigen_SSE4_1::CwiseNullaryOp, Eigen_SSE4_1::Array >; Functor = add_assign_op]’ 741 | dense_assignment_loop::run(kernel); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:879:31: required from ‘static void Eigen_AVX2::internal::Assignment::run(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_AVX2::Array; SrcXprType = Eigen_AVX2::CwiseNullaryOp, Eigen_AVX2::Array >; Functor = Eigen_AVX2::internal::add_assign_op; Weak = void]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:879:31: required from ‘static void Eigen_SSE4_1::internal::Assignment::run(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_SSE4_1::Array; SrcXprType = Eigen_SSE4_1::CwiseNullaryOp, Eigen_SSE4_1::Array >; Functor = Eigen_SSE4_1::internal::add_assign_op; Weak = void]’ 879 | call_dense_assignment_loop(dst, src, func); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:836:49: required from ‘void Eigen_AVX2::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen_AVX2::Array; Src = Eigen_AVX2::CwiseNullaryOp, Eigen_AVX2::Array >; Func = add_assign_op]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:836:49: required from ‘void Eigen_SSE4_1::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen_SSE4_1::Array; Src = Eigen_SSE4_1::CwiseNullaryOp, Eigen_SSE4_1::Array >; Func = add_assign_op]’ 836 | Assignment::run(actualDst, src, func); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:804:27: required from ‘void Eigen_AVX2::internal::call_assignment(Dst&, const Src&, const Func&, typename enable_if<(! evaluator_assume_aliasing::value), void*>::type) [with Dst = Eigen_AVX2::Array; Src = Eigen_AVX2::CwiseNullaryOp, Eigen_AVX2::Array >; Func = add_assign_op; typename enable_if<(! evaluator_assume_aliasing::value), void*>::type = void*; typename evaluator_traits::Shape = Eigen_AVX2::DenseShape]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:804:27: required from ‘void Eigen_SSE4_1::internal::call_assignment(Dst&, const Src&, const Func&, typename enable_if<(! evaluator_assume_aliasing::value), void*>::type) [with Dst = Eigen_SSE4_1::Array; Src = Eigen_SSE4_1::CwiseNullaryOp, Eigen_SSE4_1::Array >; Func = add_assign_op; typename enable_if<(! evaluator_assume_aliasing::value), void*>::type = void*; typename evaluator_traits::Shape = Eigen_SSE4_1::DenseShape]’ 804 | call_assignment_no_alias(dst, src, func); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/SelfCwiseBinaryOp.h:27:28: required from ‘Derived& Eigen_AVX2::ArrayBase::operator+=(const Scalar&) [with Derived = Eigen_AVX2::Array; Scalar = float]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/SelfCwiseBinaryOp.h:27:28: required from ‘Derived& Eigen_SSE4_1::ArrayBase::operator+=(const Scalar&) [with Derived = Eigen_SSE4_1::Array; Scalar = float]’ 27 | internal::call_assignment(this->derived(), PlainObject::Constant(rows(),cols(),other), internal::add_assign_op()); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/diamond-aligner-2.1.14/src/masking/tantan.cpp:127:23: required from here 127 | f += p_repeat_end * b; | ^ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:432:31: warning: arithmetic between different enumeration types ‘Eigen_AVX2::Array::’ and ‘Eigen_AVX2::internal::unpacket_traits<__vector(4) float>::’ is deprecated [-Wdeprecated-enum-enum-conversion] +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:432:31: warning: arithmetic between different enumeration types ‘Eigen_SSE4_1::Array::’ and ‘Eigen_SSE4_1::internal::unpacket_traits<__vector(4) float>::’ is deprecated [-Wdeprecated-enum-enum-conversion] 432 | alignedSize = (size/packetSize)*packetSize }; | ~~~~~^~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h: In instantiation of ‘static void Eigen_AVX2::internal::dense_assignment_loop::run(Kernel&) [with Kernel = Eigen_AVX2::internal::generic_dense_assignment_kernel >, Eigen_AVX2::internal::evaluator >, Eigen_AVX2::internal::assign_op, 0>]’: -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:741:37: required from ‘void Eigen_AVX2::internal::call_dense_assignment_loop(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_AVX2::Array; SrcXprType = Eigen_AVX2::Array; Functor = assign_op]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h: In instantiation of ‘static void Eigen_SSE4_1::internal::dense_assignment_loop::run(Kernel&) [with Kernel = Eigen_SSE4_1::internal::generic_dense_assignment_kernel >, Eigen_SSE4_1::internal::evaluator >, Eigen_SSE4_1::internal::assign_op, 0>]’: +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:741:37: required from ‘void Eigen_SSE4_1::internal::call_dense_assignment_loop(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_SSE4_1::Array; SrcXprType = Eigen_SSE4_1::Array; Functor = assign_op]’ 741 | dense_assignment_loop::run(kernel); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:879:31: required from ‘static void Eigen_AVX2::internal::Assignment::run(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_AVX2::Array; SrcXprType = Eigen_AVX2::Array; Functor = Eigen_AVX2::internal::assign_op; Weak = void]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:879:31: required from ‘static void Eigen_SSE4_1::internal::Assignment::run(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_SSE4_1::Array; SrcXprType = Eigen_SSE4_1::Array; Functor = Eigen_SSE4_1::internal::assign_op; Weak = void]’ 879 | call_dense_assignment_loop(dst, src, func); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:836:49: required from ‘void Eigen_AVX2::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen_AVX2::Array; Src = Eigen_AVX2::Array; Func = assign_op]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:836:49: required from ‘void Eigen_SSE4_1::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen_SSE4_1::Array; Src = Eigen_SSE4_1::Array; Func = assign_op]’ 836 | Assignment::run(actualDst, src, func); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:804:27: required from ‘void Eigen_AVX2::internal::call_assignment(Dst&, const Src&, const Func&, typename enable_if<(! evaluator_assume_aliasing::value), void*>::type) [with Dst = Eigen_AVX2::Array; Src = Eigen_AVX2::Array; Func = assign_op; typename enable_if<(! evaluator_assume_aliasing::value), void*>::type = void*; typename evaluator_traits::Shape = Eigen_AVX2::DenseShape]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:804:27: required from ‘void Eigen_SSE4_1::internal::call_assignment(Dst&, const Src&, const Func&, typename enable_if<(! evaluator_assume_aliasing::value), void*>::type) [with Dst = Eigen_SSE4_1::Array; Src = Eigen_SSE4_1::Array; Func = assign_op; typename enable_if<(! evaluator_assume_aliasing::value), void*>::type = void*; typename evaluator_traits::Shape = Eigen_SSE4_1::DenseShape]’ 804 | call_assignment_no_alias(dst, src, func); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:782:18: required from ‘void Eigen_AVX2::internal::call_assignment(Dst&, const Src&) [with Dst = Eigen_AVX2::Array; Src = Eigen_AVX2::Array]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:782:18: required from ‘void Eigen_SSE4_1::internal::call_assignment(Dst&, const Src&) [with Dst = Eigen_SSE4_1::Array; Src = Eigen_SSE4_1::Array]’ 782 | call_assignment(dst, src, internal::assign_op()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/PlainObjectBase.h:714:32: required from ‘Derived& Eigen_AVX2::PlainObjectBase::_set(const Eigen_AVX2::DenseBase&) [with OtherDerived = Eigen_AVX2::Array; Derived = Eigen_AVX2::Array]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/PlainObjectBase.h:714:32: required from ‘Derived& Eigen_SSE4_1::PlainObjectBase::_set(const Eigen_SSE4_1::DenseBase&) [with OtherDerived = Eigen_SSE4_1::Array; Derived = Eigen_SSE4_1::Array]’ 714 | internal::call_assignment(this->derived(), other.derived()); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/Array.h:118:24: required from ‘Eigen_AVX2::Array<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>& Eigen_AVX2::Array<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::operator=(const Eigen_AVX2::Array<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>&) [with _Scalar = float; int _Rows = 50; int _Cols = 1; int _Options = 0; int _MaxRows = 50; int _MaxCols = 1]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/Array.h:118:24: required from ‘Eigen_SSE4_1::Array<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>& Eigen_SSE4_1::Array<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::operator=(const Eigen_SSE4_1::Array<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>&) [with _Scalar = float; int _Rows = 50; int _Cols = 1; int _Options = 0; int _MaxRows = 50; int _MaxCols = 1]’ 118 | return Base::_set(other); | ~~~~~~~~~~^~~~~~~ /build/reproducible-path/diamond-aligner-2.1.14/src/masking/tantan.cpp:124:7: required from here 124 | t = f; | ^ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:432:31: warning: arithmetic between different enumeration types ‘Eigen_AVX2::Array::’ and ‘Eigen_AVX2::internal::unpacket_traits<__vector(4) float>::’ is deprecated [-Wdeprecated-enum-enum-conversion] +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:432:31: warning: arithmetic between different enumeration types ‘Eigen_SSE4_1::Array::’ and ‘Eigen_SSE4_1::internal::unpacket_traits<__vector(4) float>::’ is deprecated [-Wdeprecated-enum-enum-conversion] 432 | alignedSize = (size/packetSize)*packetSize }; | ~~~~~^~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h: In instantiation of ‘static void Eigen_AVX2::internal::dense_assignment_loop::run(Kernel&) [with Kernel = Eigen_AVX2::internal::generic_dense_assignment_kernel >, Eigen_AVX2::internal::evaluator, Eigen_AVX2::Array > >, Eigen_AVX2::internal::assign_op, 0>]’: -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:741:37: required from ‘void Eigen_AVX2::internal::call_dense_assignment_loop(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_AVX2::Array; SrcXprType = Eigen_AVX2::CwiseNullaryOp, Eigen_AVX2::Array >; Functor = assign_op]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h: In instantiation of ‘static void Eigen_SSE4_1::internal::dense_assignment_loop::run(Kernel&) [with Kernel = Eigen_SSE4_1::internal::generic_dense_assignment_kernel >, Eigen_SSE4_1::internal::evaluator, Eigen_SSE4_1::Array > >, Eigen_SSE4_1::internal::assign_op, 0>]’: +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:741:37: required from ‘void Eigen_SSE4_1::internal::call_dense_assignment_loop(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_SSE4_1::Array; SrcXprType = Eigen_SSE4_1::CwiseNullaryOp, Eigen_SSE4_1::Array >; Functor = assign_op]’ 741 | dense_assignment_loop::run(kernel); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:879:31: required from ‘static void Eigen_AVX2::internal::Assignment::run(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_AVX2::Array; SrcXprType = Eigen_AVX2::CwiseNullaryOp, Eigen_AVX2::Array >; Functor = Eigen_AVX2::internal::assign_op; Weak = void]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:879:31: required from ‘static void Eigen_SSE4_1::internal::Assignment::run(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_SSE4_1::Array; SrcXprType = Eigen_SSE4_1::CwiseNullaryOp, Eigen_SSE4_1::Array >; Functor = Eigen_SSE4_1::internal::assign_op; Weak = void]’ 879 | call_dense_assignment_loop(dst, src, func); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:836:49: required from ‘void Eigen_AVX2::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen_AVX2::Array; Src = Eigen_AVX2::CwiseNullaryOp, Eigen_AVX2::Array >; Func = assign_op]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:836:49: required from ‘void Eigen_SSE4_1::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen_SSE4_1::Array; Src = Eigen_SSE4_1::CwiseNullaryOp, Eigen_SSE4_1::Array >; Func = assign_op]’ 836 | Assignment::run(actualDst, src, func); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:804:27: required from ‘void Eigen_AVX2::internal::call_assignment(Dst&, const Src&, const Func&, typename enable_if<(! evaluator_assume_aliasing::value), void*>::type) [with Dst = Eigen_AVX2::Array; Src = Eigen_AVX2::CwiseNullaryOp, Eigen_AVX2::Array >; Func = assign_op; typename enable_if<(! evaluator_assume_aliasing::value), void*>::type = void*; typename evaluator_traits::Shape = Eigen_AVX2::DenseShape]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:804:27: required from ‘void Eigen_SSE4_1::internal::call_assignment(Dst&, const Src&, const Func&, typename enable_if<(! evaluator_assume_aliasing::value), void*>::type) [with Dst = Eigen_SSE4_1::Array; Src = Eigen_SSE4_1::CwiseNullaryOp, Eigen_SSE4_1::Array >; Func = assign_op; typename enable_if<(! evaluator_assume_aliasing::value), void*>::type = void*; typename evaluator_traits::Shape = Eigen_SSE4_1::DenseShape]’ 804 | call_assignment_no_alias(dst, src, func); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:782:18: required from ‘void Eigen_AVX2::internal::call_assignment(Dst&, const Src&) [with Dst = Eigen_AVX2::Array; Src = Eigen_AVX2::CwiseNullaryOp, Eigen_AVX2::Array >]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:782:18: required from ‘void Eigen_SSE4_1::internal::call_assignment(Dst&, const Src&) [with Dst = Eigen_SSE4_1::Array; Src = Eigen_SSE4_1::CwiseNullaryOp, Eigen_SSE4_1::Array >]’ 782 | call_assignment(dst, src, internal::assign_op()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/PlainObjectBase.h:714:32: required from ‘Derived& Eigen_AVX2::PlainObjectBase::_set(const Eigen_AVX2::DenseBase&) [with OtherDerived = Eigen_AVX2::CwiseNullaryOp, Eigen_AVX2::Array >; Derived = Eigen_AVX2::Array]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/PlainObjectBase.h:714:32: required from ‘Derived& Eigen_SSE4_1::PlainObjectBase::_set(const Eigen_SSE4_1::DenseBase&) [with OtherDerived = Eigen_SSE4_1::CwiseNullaryOp, Eigen_SSE4_1::Array >; Derived = Eigen_SSE4_1::Array]’ 714 | internal::call_assignment(this->derived(), other.derived()); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/Array.h:109:24: required from ‘Eigen_AVX2::Array<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>& Eigen_AVX2::Array<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::operator=(const Eigen_AVX2::DenseBase&) [with OtherDerived = Eigen_AVX2::CwiseNullaryOp, Eigen_AVX2::Array >; _Scalar = float; int _Rows = 50; int _Cols = 1; int _Options = 0; int _MaxRows = 50; int _MaxCols = 1]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/Array.h:109:24: required from ‘Eigen_SSE4_1::Array<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>& Eigen_SSE4_1::Array<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::operator=(const Eigen_SSE4_1::DenseBase&) [with OtherDerived = Eigen_SSE4_1::CwiseNullaryOp, Eigen_SSE4_1::Array >; _Scalar = float; int _Rows = 50; int _Cols = 1; int _Options = 0; int _MaxRows = 50; int _MaxCols = 1]’ 109 | return Base::_set(other); | ~~~~~~~~~~^~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/CwiseNullaryOp.h:327:20: required from ‘Derived& Eigen_AVX2::DenseBase::setConstant(const Scalar&) [with Derived = Eigen_AVX2::Array; Scalar = float]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/CwiseNullaryOp.h:327:20: required from ‘Derived& Eigen_SSE4_1::DenseBase::setConstant(const Scalar&) [with Derived = Eigen_SSE4_1::Array; Scalar = float]’ 327 | return derived() = Constant(rows(), cols(), val); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/Array.h:92:24: required from ‘Eigen_AVX2::Array<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>& Eigen_AVX2::Array<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::operator=(const Scalar&) [with _Scalar = float; int _Rows = 50; int _Cols = 1; int _Options = 0; int _MaxRows = 50; int _MaxCols = 1; Scalar = float]’ +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/Array.h:92:24: required from ‘Eigen_SSE4_1::Array<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>& Eigen_SSE4_1::Array<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::operator=(const Scalar&) [with _Scalar = float; int _Rows = 50; int _Cols = 1; int _Options = 0; int _MaxRows = 50; int _MaxCols = 1; Scalar = float]’ 92 | Base::setConstant(value); | ~~~~~~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/diamond-aligner-2.1.14/src/masking/tantan.cpp:83:7: required from here 83 | t = b; | ^ -/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:432:31: warning: arithmetic between different enumeration types ‘Eigen_AVX2::Array::’ and ‘Eigen_AVX2::internal::unpacket_traits<__vector(4) float>::’ is deprecated [-Wdeprecated-enum-enum-conversion] +/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:432:31: warning: arithmetic between different enumeration types ‘Eigen_SSE4_1::Array::’ and ‘Eigen_SSE4_1::internal::unpacket_traits<__vector(4) float>::’ is deprecated [-Wdeprecated-enum-enum-conversion] 432 | alignedSize = (size/packetSize)*packetSize }; | ~~~~~^~~~~~~~~~~~ -[ 13%] Building CXX object CMakeFiles/arch_avx2.dir/src/dp/swipe/anchored_wrapper.cpp.o -/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.14/src -I/build/reproducible-path/diamond-aligner-2.1.14/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++20 -DDISPATCH_ARCH=ARCH_AVX2 -DARCH_ID=2 -mssse3 -mpopcnt -msse4.1 -msse4.2 -mavx -mavx2 -DEigen=Eigen_AVX2 -MD -MT CMakeFiles/arch_avx2.dir/src/dp/swipe/anchored_wrapper.cpp.o -MF CMakeFiles/arch_avx2.dir/src/dp/swipe/anchored_wrapper.cpp.o.d -o CMakeFiles/arch_avx2.dir/src/dp/swipe/anchored_wrapper.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.14/src/dp/swipe/anchored_wrapper.cpp +[ 13%] Building CXX object CMakeFiles/arch_sse4_1.dir/src/dp/ungapped_simd.cpp.o +/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.14/src -I/build/reproducible-path/diamond-aligner-2.1.14/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++20 -DDISPATCH_ARCH=ARCH_SSE4_1 -DARCH_ID=1 -mssse3 -mpopcnt -msse4.1 -DEigen=Eigen_SSE4_1 -MD -MT CMakeFiles/arch_sse4_1.dir/src/dp/ungapped_simd.cpp.o -MF CMakeFiles/arch_sse4_1.dir/src/dp/ungapped_simd.cpp.o.d -o CMakeFiles/arch_sse4_1.dir/src/dp/ungapped_simd.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.14/src/dp/ungapped_simd.cpp +[ 13%] Building CXX object CMakeFiles/arch_sse4_1.dir/src/dp/swipe/anchored_wrapper.cpp.o +/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.14/src -I/build/reproducible-path/diamond-aligner-2.1.14/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++20 -DDISPATCH_ARCH=ARCH_SSE4_1 -DARCH_ID=1 -mssse3 -mpopcnt -msse4.1 -DEigen=Eigen_SSE4_1 -MD -MT CMakeFiles/arch_sse4_1.dir/src/dp/swipe/anchored_wrapper.cpp.o -MF CMakeFiles/arch_sse4_1.dir/src/dp/swipe/anchored_wrapper.cpp.o.d -o CMakeFiles/arch_sse4_1.dir/src/dp/swipe/anchored_wrapper.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.14/src/dp/swipe/anchored_wrapper.cpp +cc1plus: note: unrecognized command-line option ‘-Wno-unknown-warning-option’ may have been intended to silence earlier diagnostics [ 14%] Building CXX object CMakeFiles/arch_avx2.dir/src/dp/score_profile.cpp.o /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.14/src -I/build/reproducible-path/diamond-aligner-2.1.14/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++20 -DDISPATCH_ARCH=ARCH_AVX2 -DARCH_ID=2 -mssse3 -mpopcnt -msse4.1 -msse4.2 -mavx -mavx2 -DEigen=Eigen_AVX2 -MD -MT CMakeFiles/arch_avx2.dir/src/dp/score_profile.cpp.o -MF CMakeFiles/arch_avx2.dir/src/dp/score_profile.cpp.o.d -o CMakeFiles/arch_avx2.dir/src/dp/score_profile.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.14/src/dp/score_profile.cpp -cc1plus: note: unrecognized command-line option ‘-Wno-unknown-warning-option’ may have been intended to silence earlier diagnostics -[ 14%] Building CXX object CMakeFiles/arch_sse4_1.dir/src/dp/swipe/anchored_wrapper.cpp.o -/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.14/src -I/build/reproducible-path/diamond-aligner-2.1.14/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++20 -DDISPATCH_ARCH=ARCH_SSE4_1 -DARCH_ID=1 -mssse3 -mpopcnt -msse4.1 -DEigen=Eigen_SSE4_1 -MD -MT CMakeFiles/arch_sse4_1.dir/src/dp/swipe/anchored_wrapper.cpp.o -MF CMakeFiles/arch_sse4_1.dir/src/dp/swipe/anchored_wrapper.cpp.o.d -o CMakeFiles/arch_sse4_1.dir/src/dp/swipe/anchored_wrapper.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.14/src/dp/swipe/anchored_wrapper.cpp [ 15%] Building CXX object CMakeFiles/arch_sse4_1.dir/src/dp/score_profile.cpp.o /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.14/src -I/build/reproducible-path/diamond-aligner-2.1.14/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++20 -DDISPATCH_ARCH=ARCH_SSE4_1 -DARCH_ID=1 -mssse3 -mpopcnt -msse4.1 -DEigen=Eigen_SSE4_1 -MD -MT CMakeFiles/arch_sse4_1.dir/src/dp/score_profile.cpp.o -MF CMakeFiles/arch_sse4_1.dir/src/dp/score_profile.cpp.o.d -o CMakeFiles/arch_sse4_1.dir/src/dp/score_profile.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.14/src/dp/score_profile.cpp In file included from /usr/include/c++/15/bits/stl_pair.h:65, @@ -2096,227 +2132,6 @@ inlined from ‘constexpr void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = pair*; _Size = long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1890:38, inlined from ‘constexpr void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1906:25, inlined from ‘constexpr void std::sort(_RAIter, _RAIter) [with _RAIter = pair*]’ at /usr/include/c++/15/bits/stl_algo.h:4841:18, - inlined from ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’ at /build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:17:12: -/usr/include/c++/15/compare:1244:28: warning: array subscript 16 is outside array bounds of ‘std::array, 8> [1]’ [-Warray-bounds=] - 1244 | return __t <=> __u; - | ^~~ -In file included from /build/reproducible-path/diamond-aligner-2.1.14/src/dp/swipe/banded_swipe.h:29, - from /build/reproducible-path/diamond-aligner-2.1.14/src/dp/swipe/swipe_wrapper.cpp:38: -/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h: In constructor ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’: -/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:14:52: note: at offset 64 into object ‘b’ of size 64 - 14 | std::array, N> b; - | ^ -In member function ‘constexpr auto std::__detail::_Synth3way::operator()(const _Tp&, const _Up&) const requires requires{{std::__detail::_Synth3way::operator()::__t < std::__detail::_Synth3way::operator()::__u} -> decltype(auto) [requires std::__detail::__boolean_testable<, >];{std::__detail::_Synth3way::operator()::__u < std::__detail::_Synth3way::operator()::__t} -> decltype(auto) [requires std::__detail::__boolean_testable<, >];} [with _Tp = int; _Up = int]’, - inlined from ‘constexpr std::common_comparison_category_t(), declval<_U1&>())), decltype (std::__detail::__synth3way(declval<_T2&>(), declval<_U2&>()))> std::operator<=>(const pair<_T1, _T2>&, const pair<_U1, _U2>&) [with _T1 = int; _T2 = int; _U1 = int; _U2 = int]’ at /usr/include/c++/15/bits/stl_pair.h:1053:35, - inlined from ‘constexpr bool __gnu_cxx::__ops::_Iter_less_iter::operator()(_Iterator1, _Iterator2) const [with _Iterator1 = std::pair*; _Iterator2 = std::pair*]’ at /usr/include/c++/15/bits/predefined_ops.h:45:23, - inlined from ‘constexpr void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:91:17, - inlined from ‘constexpr _RandomAccessIterator std::__unguarded_partition_pivot(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1856:34, - inlined from ‘constexpr void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = pair*; _Size = long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1890:38, - inlined from ‘constexpr void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1906:25, - inlined from ‘constexpr void std::sort(_RAIter, _RAIter) [with _RAIter = pair*]’ at /usr/include/c++/15/bits/stl_algo.h:4841:18, - inlined from ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’ at /build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:17:12: -/usr/include/c++/15/compare:1244:28: warning: array subscript 17 is outside array bounds of ‘std::array, 8> [1]’ [-Warray-bounds=] - 1244 | return __t <=> __u; - | ^~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h: In constructor ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’: -/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:14:52: note: at offset 68 into object ‘b’ of size 64 - 14 | std::array, N> b; - | ^ -In member function ‘constexpr auto std::__detail::_Synth3way::operator()(const _Tp&, const _Up&) const requires requires{{std::__detail::_Synth3way::operator()::__t < std::__detail::_Synth3way::operator()::__u} -> decltype(auto) [requires std::__detail::__boolean_testable<, >];{std::__detail::_Synth3way::operator()::__u < std::__detail::_Synth3way::operator()::__t} -> decltype(auto) [requires std::__detail::__boolean_testable<, >];} [with _Tp = int; _Up = int]’, - inlined from ‘constexpr std::common_comparison_category_t(), declval<_U1&>())), decltype (std::__detail::__synth3way(declval<_T2&>(), declval<_U2&>()))> std::operator<=>(const pair<_T1, _T2>&, const pair<_U1, _U2>&) [with _T1 = int; _T2 = int; _U1 = int; _U2 = int]’ at /usr/include/c++/15/bits/stl_pair.h:1053:35, - inlined from ‘constexpr bool __gnu_cxx::__ops::_Iter_less_iter::operator()(_Iterator1, _Iterator2) const [with _Iterator1 = std::pair*; _Iterator2 = std::pair*]’ at /usr/include/c++/15/bits/predefined_ops.h:45:23, - inlined from ‘constexpr void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:93:14, - inlined from ‘constexpr _RandomAccessIterator std::__unguarded_partition_pivot(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1856:34, - inlined from ‘constexpr void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = pair*; _Size = long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1890:38, - inlined from ‘constexpr void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1906:25, - inlined from ‘constexpr void std::sort(_RAIter, _RAIter) [with _RAIter = pair*]’ at /usr/include/c++/15/bits/stl_algo.h:4841:18, - inlined from ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’ at /build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:17:12: -/usr/include/c++/15/compare:1244:28: warning: array subscript 17 is outside array bounds of ‘std::array, 8> [1]’ [-Warray-bounds=] - 1244 | return __t <=> __u; - | ^~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h: In constructor ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’: -/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:14:52: note: at offset 68 into object ‘b’ of size 64 - 14 | std::array, N> b; - | ^ -In member function ‘constexpr auto std::__detail::_Synth3way::operator()(const _Tp&, const _Up&) const requires requires{{std::__detail::_Synth3way::operator()::__t < std::__detail::_Synth3way::operator()::__u} -> decltype(auto) [requires std::__detail::__boolean_testable<, >];{std::__detail::_Synth3way::operator()::__u < std::__detail::_Synth3way::operator()::__t} -> decltype(auto) [requires std::__detail::__boolean_testable<, >];} [with _Tp = int; _Up = int]’, - inlined from ‘constexpr std::common_comparison_category_t(), declval<_U1&>())), decltype (std::__detail::__synth3way(declval<_T2&>(), declval<_U2&>()))> std::operator<=>(const pair<_T1, _T2>&, const pair<_U1, _U2>&) [with _T1 = int; _T2 = int; _U1 = int; _U2 = int]’ at /usr/include/c++/15/bits/stl_pair.h:1053:35, - inlined from ‘constexpr bool __gnu_cxx::__ops::_Iter_less_iter::operator()(_Iterator1, _Iterator2) const [with _Iterator1 = std::pair*; _Iterator2 = std::pair*]’ at /usr/include/c++/15/bits/predefined_ops.h:45:23, - inlined from ‘constexpr void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:93:14, - inlined from ‘constexpr _RandomAccessIterator std::__unguarded_partition_pivot(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1856:34, - inlined from ‘constexpr void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = pair*; _Size = long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1890:38, - inlined from ‘constexpr void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1906:25, - inlined from ‘constexpr void std::sort(_RAIter, _RAIter) [with _RAIter = pair*]’ at /usr/include/c++/15/bits/stl_algo.h:4841:18, - inlined from ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’ at /build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:17:12: -/usr/include/c++/15/compare:1244:28: warning: array subscript 17 is outside array bounds of ‘std::array, 8> [1]’ [-Warray-bounds=] - 1244 | return __t <=> __u; - | ^~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h: In constructor ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’: -/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:14:52: note: at offset 68 into object ‘b’ of size 64 - 14 | std::array, N> b; - | ^ -In member function ‘constexpr auto std::__detail::_Synth3way::operator()(const _Tp&, const _Up&) const requires requires{{std::__detail::_Synth3way::operator()::__t < std::__detail::_Synth3way::operator()::__u} -> decltype(auto) [requires std::__detail::__boolean_testable<, >];{std::__detail::_Synth3way::operator()::__u < std::__detail::_Synth3way::operator()::__t} -> decltype(auto) [requires std::__detail::__boolean_testable<, >];} [with _Tp = int; _Up = int]’, - inlined from ‘constexpr std::common_comparison_category_t(), declval<_U1&>())), decltype (std::__detail::__synth3way(declval<_T2&>(), declval<_U2&>()))> std::operator<=>(const pair<_T1, _T2>&, const pair<_U1, _U2>&) [with _T1 = int; _T2 = int; _U1 = int; _U2 = int]’ at /usr/include/c++/15/bits/stl_pair.h:1053:35, - inlined from ‘constexpr bool __gnu_cxx::__ops::_Iter_less_iter::operator()(_Iterator1, _Iterator2) const [with _Iterator1 = std::pair*; _Iterator2 = std::pair*]’ at /usr/include/c++/15/bits/predefined_ops.h:45:23, - inlined from ‘constexpr void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:102:22, - inlined from ‘constexpr _RandomAccessIterator std::__unguarded_partition_pivot(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1856:34, - inlined from ‘constexpr void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = pair*; _Size = long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1890:38, - inlined from ‘constexpr void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1906:25, - inlined from ‘constexpr void std::sort(_RAIter, _RAIter) [with _RAIter = pair*]’ at /usr/include/c++/15/bits/stl_algo.h:4841:18, - inlined from ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’ at /build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:17:12: -/usr/include/c++/15/compare:1244:28: warning: array subscript 17 is outside array bounds of ‘std::array, 8> [1]’ [-Warray-bounds=] - 1244 | return __t <=> __u; - | ^~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h: In constructor ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’: -/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:14:52: note: at offset 68 into object ‘b’ of size 64 - 14 | std::array, N> b; - | ^ -In file included from /usr/include/c++/15/bits/stl_pair.h:61: -In function ‘constexpr std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = int]’, - inlined from ‘constexpr void std::pair<_T1, _T2>::swap(std::pair<_T1, _T2>&) [with _T1 = int; _T2 = int]’ at /usr/include/c++/15/bits/stl_pair.h:326:6, - inlined from ‘constexpr typename std::enable_if, std::__is_swappable<_T2> >::value>::type std::swap(pair<_T1, _T2>&, pair<_T1, _T2>&) [with _T1 = int; _T2 = int]’ at /usr/include/c++/15/bits/stl_pair.h:1123:15, - inlined from ‘constexpr void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = pair*; _ForwardIterator2 = pair*]’ at /usr/include/c++/15/bits/stl_algobase.h:186:11, - inlined from ‘constexpr void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:105:16, - inlined from ‘constexpr _RandomAccessIterator std::__unguarded_partition_pivot(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1856:34, - inlined from ‘constexpr void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = pair*; _Size = long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1890:38, - inlined from ‘constexpr void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1906:25, - inlined from ‘constexpr void std::sort(_RAIter, _RAIter) [with _RAIter = pair*]’ at /usr/include/c++/15/bits/stl_algo.h:4841:18, - inlined from ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’ at /build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:17:12: -/usr/include/c++/15/bits/move.h:237:11: warning: array subscript 16 is outside array bounds of ‘std::array, 8> [1]’ [-Warray-bounds=] - 237 | __b = _GLIBCXX_MOVE(__tmp); - | ^ -/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h: In constructor ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’: -/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:14:52: note: at offset 64 into object ‘b’ of size 64 - 14 | std::array, N> b; - | ^ -In function ‘constexpr std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = int]’, - inlined from ‘constexpr void std::pair<_T1, _T2>::swap(std::pair<_T1, _T2>&) [with _T1 = int; _T2 = int]’ at /usr/include/c++/15/bits/stl_pair.h:327:6, - inlined from ‘constexpr typename std::enable_if, std::__is_swappable<_T2> >::value>::type std::swap(pair<_T1, _T2>&, pair<_T1, _T2>&) [with _T1 = int; _T2 = int]’ at /usr/include/c++/15/bits/stl_pair.h:1123:15, - inlined from ‘constexpr void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = pair*; _ForwardIterator2 = pair*]’ at /usr/include/c++/15/bits/stl_algobase.h:186:11, - inlined from ‘constexpr void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:105:16, - inlined from ‘constexpr _RandomAccessIterator std::__unguarded_partition_pivot(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1856:34, - inlined from ‘constexpr void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = pair*; _Size = long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1890:38, - inlined from ‘constexpr void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1906:25, - inlined from ‘constexpr void std::sort(_RAIter, _RAIter) [with _RAIter = pair*]’ at /usr/include/c++/15/bits/stl_algo.h:4841:18, - inlined from ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’ at /build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:17:12: -/usr/include/c++/15/bits/move.h:236:11: warning: array subscript 17 is outside array bounds of ‘std::array, 8> [1]’ [-Warray-bounds=] - 236 | __a = _GLIBCXX_MOVE(__b); - | ^ -/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h: In constructor ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’: -/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:14:52: note: at offset 68 into object ‘b’ of size 64 - 14 | std::array, N> b; - | ^ -In function ‘constexpr std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = int]’, - inlined from ‘constexpr void std::pair<_T1, _T2>::swap(std::pair<_T1, _T2>&) [with _T1 = int; _T2 = int]’ at /usr/include/c++/15/bits/stl_pair.h:327:6, - inlined from ‘constexpr typename std::enable_if, std::__is_swappable<_T2> >::value>::type std::swap(pair<_T1, _T2>&, pair<_T1, _T2>&) [with _T1 = int; _T2 = int]’ at /usr/include/c++/15/bits/stl_pair.h:1123:15, - inlined from ‘constexpr void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = pair*; _ForwardIterator2 = pair*]’ at /usr/include/c++/15/bits/stl_algobase.h:186:11, - inlined from ‘constexpr void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:105:16, - inlined from ‘constexpr _RandomAccessIterator std::__unguarded_partition_pivot(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1856:34, - inlined from ‘constexpr void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = pair*; _Size = long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1890:38, - inlined from ‘constexpr void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1906:25, - inlined from ‘constexpr void std::sort(_RAIter, _RAIter) [with _RAIter = pair*]’ at /usr/include/c++/15/bits/stl_algo.h:4841:18, - inlined from ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’ at /build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:17:12: -/usr/include/c++/15/bits/move.h:237:11: warning: array subscript 17 is outside array bounds of ‘std::array, 8> [1]’ [-Warray-bounds=] - 237 | __b = _GLIBCXX_MOVE(__tmp); - | ^ -/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h: In constructor ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’: -/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:14:52: note: at offset 68 into object ‘b’ of size 64 - 14 | std::array, N> b; - | ^ -In function ‘constexpr std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = int]’, - inlined from ‘constexpr void std::pair<_T1, _T2>::swap(std::pair<_T1, _T2>&) [with _T1 = int; _T2 = int]’ at /usr/include/c++/15/bits/stl_pair.h:326:6, - inlined from ‘constexpr typename std::enable_if, std::__is_swappable<_T2> >::value>::type std::swap(pair<_T1, _T2>&, pair<_T1, _T2>&) [with _T1 = int; _T2 = int]’ at /usr/include/c++/15/bits/stl_pair.h:1123:15, - inlined from ‘constexpr void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = pair*; _ForwardIterator2 = pair*]’ at /usr/include/c++/15/bits/stl_algobase.h:186:11, - inlined from ‘constexpr void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:94:20, - inlined from ‘constexpr _RandomAccessIterator std::__unguarded_partition_pivot(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1856:34, - inlined from ‘constexpr void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = pair*; _Size = long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1890:38, - inlined from ‘constexpr void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1906:25, - inlined from ‘constexpr void std::sort(_RAIter, _RAIter) [with _RAIter = pair*]’ at /usr/include/c++/15/bits/stl_algo.h:4841:18, - inlined from ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’ at /build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:17:12: -/usr/include/c++/15/bits/move.h:237:11: warning: array subscript 16 is outside array bounds of ‘std::array, 8> [1]’ [-Warray-bounds=] - 237 | __b = _GLIBCXX_MOVE(__tmp); - | ^ -/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h: In constructor ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’: -/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:14:52: note: at offset 64 into object ‘b’ of size 64 - 14 | std::array, N> b; - | ^ -In function ‘constexpr std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = int]’, - inlined from ‘constexpr void std::pair<_T1, _T2>::swap(std::pair<_T1, _T2>&) [with _T1 = int; _T2 = int]’ at /usr/include/c++/15/bits/stl_pair.h:327:6, - inlined from ‘constexpr typename std::enable_if, std::__is_swappable<_T2> >::value>::type std::swap(pair<_T1, _T2>&, pair<_T1, _T2>&) [with _T1 = int; _T2 = int]’ at /usr/include/c++/15/bits/stl_pair.h:1123:15, - inlined from ‘constexpr void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = pair*; _ForwardIterator2 = pair*]’ at /usr/include/c++/15/bits/stl_algobase.h:186:11, - inlined from ‘constexpr void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:94:20, - inlined from ‘constexpr _RandomAccessIterator std::__unguarded_partition_pivot(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1856:34, - inlined from ‘constexpr void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = pair*; _Size = long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1890:38, - inlined from ‘constexpr void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1906:25, - inlined from ‘constexpr void std::sort(_RAIter, _RAIter) [with _RAIter = pair*]’ at /usr/include/c++/15/bits/stl_algo.h:4841:18, - inlined from ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’ at /build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:17:12: -/usr/include/c++/15/bits/move.h:236:11: warning: array subscript 17 is outside array bounds of ‘std::array, 8> [1]’ [-Warray-bounds=] - 236 | __a = _GLIBCXX_MOVE(__b); - | ^ -/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h: In constructor ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’: -/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:14:52: note: at offset 68 into object ‘b’ of size 64 - 14 | std::array, N> b; - | ^ -In function ‘constexpr std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = int]’, - inlined from ‘constexpr void std::pair<_T1, _T2>::swap(std::pair<_T1, _T2>&) [with _T1 = int; _T2 = int]’ at /usr/include/c++/15/bits/stl_pair.h:327:6, - inlined from ‘constexpr typename std::enable_if, std::__is_swappable<_T2> >::value>::type std::swap(pair<_T1, _T2>&, pair<_T1, _T2>&) [with _T1 = int; _T2 = int]’ at /usr/include/c++/15/bits/stl_pair.h:1123:15, - inlined from ‘constexpr void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = pair*; _ForwardIterator2 = pair*]’ at /usr/include/c++/15/bits/stl_algobase.h:186:11, - inlined from ‘constexpr void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:94:20, - inlined from ‘constexpr _RandomAccessIterator std::__unguarded_partition_pivot(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1856:34, - inlined from ‘constexpr void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = pair*; _Size = long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1890:38, - inlined from ‘constexpr void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1906:25, - inlined from ‘constexpr void std::sort(_RAIter, _RAIter) [with _RAIter = pair*]’ at /usr/include/c++/15/bits/stl_algo.h:4841:18, - inlined from ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’ at /build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:17:12: -/usr/include/c++/15/bits/move.h:237:11: warning: array subscript 17 is outside array bounds of ‘std::array, 8> [1]’ [-Warray-bounds=] - 237 | __b = _GLIBCXX_MOVE(__tmp); - | ^ -/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h: In constructor ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’: -/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:14:52: note: at offset 68 into object ‘b’ of size 64 - 14 | std::array, N> b; - | ^ -In member function ‘constexpr std::pair<_T1, _T2>& std::pair<_T1, _T2>::operator=(std::pair<_T1, _T2>&&) requires _S_assignable<_T1, _T2>() [with _T1 = int; _T2 = int]’, - inlined from ‘constexpr void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = pair*; _Distance = long int; _Tp = pair; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_heap.h:241:29, - inlined from ‘constexpr void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_heap.h:356:22, - inlined from ‘constexpr void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1594:23, - inlined from ‘constexpr void std::__partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1869:25, - inlined from ‘constexpr void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = pair*; _Size = long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1885:27, - inlined from ‘constexpr void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1906:25, - inlined from ‘constexpr void std::sort(_RAIter, _RAIter) [with _RAIter = pair*]’ at /usr/include/c++/15/bits/stl_algo.h:4841:18, - inlined from ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’ at /build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:17:12: -/usr/include/c++/15/bits/stl_pair.h:626:46: warning: array subscript [15, 1152921504606846973] is outside array bounds of ‘std::array, 8> [1]’ [-Warray-bounds=] - 626 | first = std::forward(__p.first); - | ~~~~^~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h: In constructor ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’: -/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:14:52: note: at offset [120, 9223372036854775784] into object ‘b’ of size 64 - 14 | std::array, N> b; - | ^ -In member function ‘constexpr std::pair<_T1, _T2>& std::pair<_T1, _T2>::operator=(std::pair<_T1, _T2>&&) requires _S_assignable<_T1, _T2>() [with _T1 = int; _T2 = int]’, - inlined from ‘constexpr void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = pair*; _Distance = long int; _Tp = pair; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_heap.h:241:29, - inlined from ‘constexpr void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_heap.h:356:22, - inlined from ‘constexpr void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1594:23, - inlined from ‘constexpr void std::__partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1869:25, - inlined from ‘constexpr void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = pair*; _Size = long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1885:27, - inlined from ‘constexpr void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1906:25, - inlined from ‘constexpr void std::sort(_RAIter, _RAIter) [with _RAIter = pair*]’ at /usr/include/c++/15/bits/stl_algo.h:4841:18, - inlined from ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’ at /build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:17:12: -/usr/include/c++/15/bits/stl_pair.h:627:48: warning: array subscript [15, 1152921504606846973] is outside array bounds of ‘std::array, 8> [1]’ [-Warray-bounds=] - 627 | second = std::forward(__p.second); - | ~~~~^~~~~~ -/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h: In constructor ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’: -/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:14:52: note: at offset [120, 9223372036854775784] into object ‘b’ of size 64 - 14 | std::array, N> b; - | ^ -In file included from /usr/include/c++/15/bits/stl_pair.h:65, - from /usr/include/c++/15/bits/stl_algobase.h:64, - from /usr/include/c++/15/list:64, - from /build/reproducible-path/diamond-aligner-2.1.14/src/dp/swipe/swipe_wrapper.cpp:22: -In member function ‘constexpr auto std::__detail::_Synth3way::operator()(const _Tp&, const _Up&) const requires requires{{std::__detail::_Synth3way::operator()::__t < std::__detail::_Synth3way::operator()::__u} -> decltype(auto) [requires std::__detail::__boolean_testable<, >];{std::__detail::_Synth3way::operator()::__u < std::__detail::_Synth3way::operator()::__t} -> decltype(auto) [requires std::__detail::__boolean_testable<, >];} [with _Tp = int; _Up = int]’, - inlined from ‘constexpr std::common_comparison_category_t(), declval<_U1&>())), decltype (std::__detail::__synth3way(declval<_T2&>(), declval<_U2&>()))> std::operator<=>(const pair<_T1, _T2>&, const pair<_U1, _U2>&) [with _T1 = int; _T2 = int; _U1 = int; _U2 = int]’ at /usr/include/c++/15/bits/stl_pair.h:1051:43, - inlined from ‘constexpr bool __gnu_cxx::__ops::_Iter_less_iter::operator()(_Iterator1, _Iterator2) const [with _Iterator1 = std::pair*; _Iterator2 = std::pair*]’ at /usr/include/c++/15/bits/predefined_ops.h:45:23, - inlined from ‘constexpr void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:91:17, - inlined from ‘constexpr _RandomAccessIterator std::__unguarded_partition_pivot(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1856:34, - inlined from ‘constexpr void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = pair*; _Size = long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1890:38, - inlined from ‘constexpr void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1906:25, - inlined from ‘constexpr void std::sort(_RAIter, _RAIter) [with _RAIter = pair*]’ at /usr/include/c++/15/bits/stl_algo.h:4841:18, inlined from ‘RangePartition::RangePartition(const int*, int, int) [with int N = 1; T = int]’ at /build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:17:12: /usr/include/c++/15/compare:1244:28: warning: array subscript 2 is outside array bounds of ‘std::array, 1> [1]’ [-Warray-bounds=] 1244 | return __t <=> __u; @@ -2862,6 +2677,227 @@ /build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:14:52: note: at offset 12 into object ‘b’ of size 8 14 | std::array, N> b; | ^ +In file included from /usr/include/c++/15/bits/stl_pair.h:65, + from /usr/include/c++/15/bits/stl_algobase.h:64, + from /usr/include/c++/15/list:64, + from /build/reproducible-path/diamond-aligner-2.1.14/src/dp/swipe/swipe_wrapper.cpp:22: +In member function ‘constexpr auto std::__detail::_Synth3way::operator()(const _Tp&, const _Up&) const requires requires{{std::__detail::_Synth3way::operator()::__t < std::__detail::_Synth3way::operator()::__u} -> decltype(auto) [requires std::__detail::__boolean_testable<, >];{std::__detail::_Synth3way::operator()::__u < std::__detail::_Synth3way::operator()::__t} -> decltype(auto) [requires std::__detail::__boolean_testable<, >];} [with _Tp = int; _Up = int]’, + inlined from ‘constexpr std::common_comparison_category_t(), declval<_U1&>())), decltype (std::__detail::__synth3way(declval<_T2&>(), declval<_U2&>()))> std::operator<=>(const pair<_T1, _T2>&, const pair<_U1, _U2>&) [with _T1 = int; _T2 = int; _U1 = int; _U2 = int]’ at /usr/include/c++/15/bits/stl_pair.h:1051:43, + inlined from ‘constexpr bool __gnu_cxx::__ops::_Iter_less_iter::operator()(_Iterator1, _Iterator2) const [with _Iterator1 = std::pair*; _Iterator2 = std::pair*]’ at /usr/include/c++/15/bits/predefined_ops.h:45:23, + inlined from ‘constexpr void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:91:17, + inlined from ‘constexpr _RandomAccessIterator std::__unguarded_partition_pivot(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1856:34, + inlined from ‘constexpr void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = pair*; _Size = long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1890:38, + inlined from ‘constexpr void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1906:25, + inlined from ‘constexpr void std::sort(_RAIter, _RAIter) [with _RAIter = pair*]’ at /usr/include/c++/15/bits/stl_algo.h:4841:18, + inlined from ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’ at /build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:17:12: +/usr/include/c++/15/compare:1244:28: warning: array subscript 16 is outside array bounds of ‘std::array, 8> [1]’ [-Warray-bounds=] + 1244 | return __t <=> __u; + | ^~~ +In file included from /build/reproducible-path/diamond-aligner-2.1.14/src/dp/swipe/banded_swipe.h:29, + from /build/reproducible-path/diamond-aligner-2.1.14/src/dp/swipe/swipe_wrapper.cpp:38: +/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h: In constructor ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’: +/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:14:52: note: at offset 64 into object ‘b’ of size 64 + 14 | std::array, N> b; + | ^ +In member function ‘constexpr auto std::__detail::_Synth3way::operator()(const _Tp&, const _Up&) const requires requires{{std::__detail::_Synth3way::operator()::__t < std::__detail::_Synth3way::operator()::__u} -> decltype(auto) [requires std::__detail::__boolean_testable<, >];{std::__detail::_Synth3way::operator()::__u < std::__detail::_Synth3way::operator()::__t} -> decltype(auto) [requires std::__detail::__boolean_testable<, >];} [with _Tp = int; _Up = int]’, + inlined from ‘constexpr std::common_comparison_category_t(), declval<_U1&>())), decltype (std::__detail::__synth3way(declval<_T2&>(), declval<_U2&>()))> std::operator<=>(const pair<_T1, _T2>&, const pair<_U1, _U2>&) [with _T1 = int; _T2 = int; _U1 = int; _U2 = int]’ at /usr/include/c++/15/bits/stl_pair.h:1053:35, + inlined from ‘constexpr bool __gnu_cxx::__ops::_Iter_less_iter::operator()(_Iterator1, _Iterator2) const [with _Iterator1 = std::pair*; _Iterator2 = std::pair*]’ at /usr/include/c++/15/bits/predefined_ops.h:45:23, + inlined from ‘constexpr void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:91:17, + inlined from ‘constexpr _RandomAccessIterator std::__unguarded_partition_pivot(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1856:34, + inlined from ‘constexpr void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = pair*; _Size = long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1890:38, + inlined from ‘constexpr void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1906:25, + inlined from ‘constexpr void std::sort(_RAIter, _RAIter) [with _RAIter = pair*]’ at /usr/include/c++/15/bits/stl_algo.h:4841:18, + inlined from ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’ at /build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:17:12: +/usr/include/c++/15/compare:1244:28: warning: array subscript 17 is outside array bounds of ‘std::array, 8> [1]’ [-Warray-bounds=] + 1244 | return __t <=> __u; + | ^~~ +/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h: In constructor ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’: +/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:14:52: note: at offset 68 into object ‘b’ of size 64 + 14 | std::array, N> b; + | ^ +In member function ‘constexpr auto std::__detail::_Synth3way::operator()(const _Tp&, const _Up&) const requires requires{{std::__detail::_Synth3way::operator()::__t < std::__detail::_Synth3way::operator()::__u} -> decltype(auto) [requires std::__detail::__boolean_testable<, >];{std::__detail::_Synth3way::operator()::__u < std::__detail::_Synth3way::operator()::__t} -> decltype(auto) [requires std::__detail::__boolean_testable<, >];} [with _Tp = int; _Up = int]’, + inlined from ‘constexpr std::common_comparison_category_t(), declval<_U1&>())), decltype (std::__detail::__synth3way(declval<_T2&>(), declval<_U2&>()))> std::operator<=>(const pair<_T1, _T2>&, const pair<_U1, _U2>&) [with _T1 = int; _T2 = int; _U1 = int; _U2 = int]’ at /usr/include/c++/15/bits/stl_pair.h:1053:35, + inlined from ‘constexpr bool __gnu_cxx::__ops::_Iter_less_iter::operator()(_Iterator1, _Iterator2) const [with _Iterator1 = std::pair*; _Iterator2 = std::pair*]’ at /usr/include/c++/15/bits/predefined_ops.h:45:23, + inlined from ‘constexpr void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:93:14, + inlined from ‘constexpr _RandomAccessIterator std::__unguarded_partition_pivot(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1856:34, + inlined from ‘constexpr void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = pair*; _Size = long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1890:38, + inlined from ‘constexpr void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1906:25, + inlined from ‘constexpr void std::sort(_RAIter, _RAIter) [with _RAIter = pair*]’ at /usr/include/c++/15/bits/stl_algo.h:4841:18, + inlined from ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’ at /build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:17:12: +/usr/include/c++/15/compare:1244:28: warning: array subscript 17 is outside array bounds of ‘std::array, 8> [1]’ [-Warray-bounds=] + 1244 | return __t <=> __u; + | ^~~ +/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h: In constructor ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’: +/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:14:52: note: at offset 68 into object ‘b’ of size 64 + 14 | std::array, N> b; + | ^ +In member function ‘constexpr auto std::__detail::_Synth3way::operator()(const _Tp&, const _Up&) const requires requires{{std::__detail::_Synth3way::operator()::__t < std::__detail::_Synth3way::operator()::__u} -> decltype(auto) [requires std::__detail::__boolean_testable<, >];{std::__detail::_Synth3way::operator()::__u < std::__detail::_Synth3way::operator()::__t} -> decltype(auto) [requires std::__detail::__boolean_testable<, >];} [with _Tp = int; _Up = int]’, + inlined from ‘constexpr std::common_comparison_category_t(), declval<_U1&>())), decltype (std::__detail::__synth3way(declval<_T2&>(), declval<_U2&>()))> std::operator<=>(const pair<_T1, _T2>&, const pair<_U1, _U2>&) [with _T1 = int; _T2 = int; _U1 = int; _U2 = int]’ at /usr/include/c++/15/bits/stl_pair.h:1053:35, + inlined from ‘constexpr bool __gnu_cxx::__ops::_Iter_less_iter::operator()(_Iterator1, _Iterator2) const [with _Iterator1 = std::pair*; _Iterator2 = std::pair*]’ at /usr/include/c++/15/bits/predefined_ops.h:45:23, + inlined from ‘constexpr void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:93:14, + inlined from ‘constexpr _RandomAccessIterator std::__unguarded_partition_pivot(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1856:34, + inlined from ‘constexpr void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = pair*; _Size = long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1890:38, + inlined from ‘constexpr void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1906:25, + inlined from ‘constexpr void std::sort(_RAIter, _RAIter) [with _RAIter = pair*]’ at /usr/include/c++/15/bits/stl_algo.h:4841:18, + inlined from ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’ at /build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:17:12: +/usr/include/c++/15/compare:1244:28: warning: array subscript 17 is outside array bounds of ‘std::array, 8> [1]’ [-Warray-bounds=] + 1244 | return __t <=> __u; + | ^~~ +/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h: In constructor ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’: +/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:14:52: note: at offset 68 into object ‘b’ of size 64 + 14 | std::array, N> b; + | ^ +In member function ‘constexpr auto std::__detail::_Synth3way::operator()(const _Tp&, const _Up&) const requires requires{{std::__detail::_Synth3way::operator()::__t < std::__detail::_Synth3way::operator()::__u} -> decltype(auto) [requires std::__detail::__boolean_testable<, >];{std::__detail::_Synth3way::operator()::__u < std::__detail::_Synth3way::operator()::__t} -> decltype(auto) [requires std::__detail::__boolean_testable<, >];} [with _Tp = int; _Up = int]’, + inlined from ‘constexpr std::common_comparison_category_t(), declval<_U1&>())), decltype (std::__detail::__synth3way(declval<_T2&>(), declval<_U2&>()))> std::operator<=>(const pair<_T1, _T2>&, const pair<_U1, _U2>&) [with _T1 = int; _T2 = int; _U1 = int; _U2 = int]’ at /usr/include/c++/15/bits/stl_pair.h:1053:35, + inlined from ‘constexpr bool __gnu_cxx::__ops::_Iter_less_iter::operator()(_Iterator1, _Iterator2) const [with _Iterator1 = std::pair*; _Iterator2 = std::pair*]’ at /usr/include/c++/15/bits/predefined_ops.h:45:23, + inlined from ‘constexpr void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:102:22, + inlined from ‘constexpr _RandomAccessIterator std::__unguarded_partition_pivot(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1856:34, + inlined from ‘constexpr void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = pair*; _Size = long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1890:38, + inlined from ‘constexpr void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1906:25, + inlined from ‘constexpr void std::sort(_RAIter, _RAIter) [with _RAIter = pair*]’ at /usr/include/c++/15/bits/stl_algo.h:4841:18, + inlined from ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’ at /build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:17:12: +/usr/include/c++/15/compare:1244:28: warning: array subscript 17 is outside array bounds of ‘std::array, 8> [1]’ [-Warray-bounds=] + 1244 | return __t <=> __u; + | ^~~ +/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h: In constructor ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’: +/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:14:52: note: at offset 68 into object ‘b’ of size 64 + 14 | std::array, N> b; + | ^ +In file included from /usr/include/c++/15/bits/stl_pair.h:61: +In function ‘constexpr std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = int]’, + inlined from ‘constexpr void std::pair<_T1, _T2>::swap(std::pair<_T1, _T2>&) [with _T1 = int; _T2 = int]’ at /usr/include/c++/15/bits/stl_pair.h:326:6, + inlined from ‘constexpr typename std::enable_if, std::__is_swappable<_T2> >::value>::type std::swap(pair<_T1, _T2>&, pair<_T1, _T2>&) [with _T1 = int; _T2 = int]’ at /usr/include/c++/15/bits/stl_pair.h:1123:15, + inlined from ‘constexpr void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = pair*; _ForwardIterator2 = pair*]’ at /usr/include/c++/15/bits/stl_algobase.h:186:11, + inlined from ‘constexpr void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:105:16, + inlined from ‘constexpr _RandomAccessIterator std::__unguarded_partition_pivot(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1856:34, + inlined from ‘constexpr void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = pair*; _Size = long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1890:38, + inlined from ‘constexpr void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1906:25, + inlined from ‘constexpr void std::sort(_RAIter, _RAIter) [with _RAIter = pair*]’ at /usr/include/c++/15/bits/stl_algo.h:4841:18, + inlined from ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’ at /build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:17:12: +/usr/include/c++/15/bits/move.h:237:11: warning: array subscript 16 is outside array bounds of ‘std::array, 8> [1]’ [-Warray-bounds=] + 237 | __b = _GLIBCXX_MOVE(__tmp); + | ^ +/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h: In constructor ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’: +/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:14:52: note: at offset 64 into object ‘b’ of size 64 + 14 | std::array, N> b; + | ^ +In function ‘constexpr std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = int]’, + inlined from ‘constexpr void std::pair<_T1, _T2>::swap(std::pair<_T1, _T2>&) [with _T1 = int; _T2 = int]’ at /usr/include/c++/15/bits/stl_pair.h:327:6, + inlined from ‘constexpr typename std::enable_if, std::__is_swappable<_T2> >::value>::type std::swap(pair<_T1, _T2>&, pair<_T1, _T2>&) [with _T1 = int; _T2 = int]’ at /usr/include/c++/15/bits/stl_pair.h:1123:15, + inlined from ‘constexpr void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = pair*; _ForwardIterator2 = pair*]’ at /usr/include/c++/15/bits/stl_algobase.h:186:11, + inlined from ‘constexpr void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:105:16, + inlined from ‘constexpr _RandomAccessIterator std::__unguarded_partition_pivot(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1856:34, + inlined from ‘constexpr void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = pair*; _Size = long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1890:38, + inlined from ‘constexpr void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1906:25, + inlined from ‘constexpr void std::sort(_RAIter, _RAIter) [with _RAIter = pair*]’ at /usr/include/c++/15/bits/stl_algo.h:4841:18, + inlined from ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’ at /build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:17:12: +/usr/include/c++/15/bits/move.h:236:11: warning: array subscript 17 is outside array bounds of ‘std::array, 8> [1]’ [-Warray-bounds=] + 236 | __a = _GLIBCXX_MOVE(__b); + | ^ +/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h: In constructor ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’: +/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:14:52: note: at offset 68 into object ‘b’ of size 64 + 14 | std::array, N> b; + | ^ +In function ‘constexpr std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = int]’, + inlined from ‘constexpr void std::pair<_T1, _T2>::swap(std::pair<_T1, _T2>&) [with _T1 = int; _T2 = int]’ at /usr/include/c++/15/bits/stl_pair.h:327:6, + inlined from ‘constexpr typename std::enable_if, std::__is_swappable<_T2> >::value>::type std::swap(pair<_T1, _T2>&, pair<_T1, _T2>&) [with _T1 = int; _T2 = int]’ at /usr/include/c++/15/bits/stl_pair.h:1123:15, + inlined from ‘constexpr void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = pair*; _ForwardIterator2 = pair*]’ at /usr/include/c++/15/bits/stl_algobase.h:186:11, + inlined from ‘constexpr void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:105:16, + inlined from ‘constexpr _RandomAccessIterator std::__unguarded_partition_pivot(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1856:34, + inlined from ‘constexpr void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = pair*; _Size = long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1890:38, + inlined from ‘constexpr void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1906:25, + inlined from ‘constexpr void std::sort(_RAIter, _RAIter) [with _RAIter = pair*]’ at /usr/include/c++/15/bits/stl_algo.h:4841:18, + inlined from ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’ at /build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:17:12: +/usr/include/c++/15/bits/move.h:237:11: warning: array subscript 17 is outside array bounds of ‘std::array, 8> [1]’ [-Warray-bounds=] + 237 | __b = _GLIBCXX_MOVE(__tmp); + | ^ +/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h: In constructor ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’: +/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:14:52: note: at offset 68 into object ‘b’ of size 64 + 14 | std::array, N> b; + | ^ +In function ‘constexpr std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = int]’, + inlined from ‘constexpr void std::pair<_T1, _T2>::swap(std::pair<_T1, _T2>&) [with _T1 = int; _T2 = int]’ at /usr/include/c++/15/bits/stl_pair.h:326:6, + inlined from ‘constexpr typename std::enable_if, std::__is_swappable<_T2> >::value>::type std::swap(pair<_T1, _T2>&, pair<_T1, _T2>&) [with _T1 = int; _T2 = int]’ at /usr/include/c++/15/bits/stl_pair.h:1123:15, + inlined from ‘constexpr void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = pair*; _ForwardIterator2 = pair*]’ at /usr/include/c++/15/bits/stl_algobase.h:186:11, + inlined from ‘constexpr void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:94:20, + inlined from ‘constexpr _RandomAccessIterator std::__unguarded_partition_pivot(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1856:34, + inlined from ‘constexpr void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = pair*; _Size = long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1890:38, + inlined from ‘constexpr void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1906:25, + inlined from ‘constexpr void std::sort(_RAIter, _RAIter) [with _RAIter = pair*]’ at /usr/include/c++/15/bits/stl_algo.h:4841:18, + inlined from ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’ at /build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:17:12: +/usr/include/c++/15/bits/move.h:237:11: warning: array subscript 16 is outside array bounds of ‘std::array, 8> [1]’ [-Warray-bounds=] + 237 | __b = _GLIBCXX_MOVE(__tmp); + | ^ +/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h: In constructor ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’: +/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:14:52: note: at offset 64 into object ‘b’ of size 64 + 14 | std::array, N> b; + | ^ +In function ‘constexpr std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = int]’, + inlined from ‘constexpr void std::pair<_T1, _T2>::swap(std::pair<_T1, _T2>&) [with _T1 = int; _T2 = int]’ at /usr/include/c++/15/bits/stl_pair.h:327:6, + inlined from ‘constexpr typename std::enable_if, std::__is_swappable<_T2> >::value>::type std::swap(pair<_T1, _T2>&, pair<_T1, _T2>&) [with _T1 = int; _T2 = int]’ at /usr/include/c++/15/bits/stl_pair.h:1123:15, + inlined from ‘constexpr void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = pair*; _ForwardIterator2 = pair*]’ at /usr/include/c++/15/bits/stl_algobase.h:186:11, + inlined from ‘constexpr void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:94:20, + inlined from ‘constexpr _RandomAccessIterator std::__unguarded_partition_pivot(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1856:34, + inlined from ‘constexpr void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = pair*; _Size = long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1890:38, + inlined from ‘constexpr void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1906:25, + inlined from ‘constexpr void std::sort(_RAIter, _RAIter) [with _RAIter = pair*]’ at /usr/include/c++/15/bits/stl_algo.h:4841:18, + inlined from ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’ at /build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:17:12: +/usr/include/c++/15/bits/move.h:236:11: warning: array subscript 17 is outside array bounds of ‘std::array, 8> [1]’ [-Warray-bounds=] + 236 | __a = _GLIBCXX_MOVE(__b); + | ^ +/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h: In constructor ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’: +/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:14:52: note: at offset 68 into object ‘b’ of size 64 + 14 | std::array, N> b; + | ^ +In function ‘constexpr std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = int]’, + inlined from ‘constexpr void std::pair<_T1, _T2>::swap(std::pair<_T1, _T2>&) [with _T1 = int; _T2 = int]’ at /usr/include/c++/15/bits/stl_pair.h:327:6, + inlined from ‘constexpr typename std::enable_if, std::__is_swappable<_T2> >::value>::type std::swap(pair<_T1, _T2>&, pair<_T1, _T2>&) [with _T1 = int; _T2 = int]’ at /usr/include/c++/15/bits/stl_pair.h:1123:15, + inlined from ‘constexpr void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = pair*; _ForwardIterator2 = pair*]’ at /usr/include/c++/15/bits/stl_algobase.h:186:11, + inlined from ‘constexpr void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:94:20, + inlined from ‘constexpr _RandomAccessIterator std::__unguarded_partition_pivot(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1856:34, + inlined from ‘constexpr void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = pair*; _Size = long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1890:38, + inlined from ‘constexpr void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1906:25, + inlined from ‘constexpr void std::sort(_RAIter, _RAIter) [with _RAIter = pair*]’ at /usr/include/c++/15/bits/stl_algo.h:4841:18, + inlined from ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’ at /build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:17:12: +/usr/include/c++/15/bits/move.h:237:11: warning: array subscript 17 is outside array bounds of ‘std::array, 8> [1]’ [-Warray-bounds=] + 237 | __b = _GLIBCXX_MOVE(__tmp); + | ^ +/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h: In constructor ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’: +/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:14:52: note: at offset 68 into object ‘b’ of size 64 + 14 | std::array, N> b; + | ^ +In member function ‘constexpr std::pair<_T1, _T2>& std::pair<_T1, _T2>::operator=(std::pair<_T1, _T2>&&) requires _S_assignable<_T1, _T2>() [with _T1 = int; _T2 = int]’, + inlined from ‘constexpr void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = pair*; _Distance = long int; _Tp = pair; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_heap.h:241:29, + inlined from ‘constexpr void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_heap.h:356:22, + inlined from ‘constexpr void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1594:23, + inlined from ‘constexpr void std::__partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1869:25, + inlined from ‘constexpr void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = pair*; _Size = long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1885:27, + inlined from ‘constexpr void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1906:25, + inlined from ‘constexpr void std::sort(_RAIter, _RAIter) [with _RAIter = pair*]’ at /usr/include/c++/15/bits/stl_algo.h:4841:18, + inlined from ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’ at /build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:17:12: +/usr/include/c++/15/bits/stl_pair.h:626:46: warning: array subscript [15, 1152921504606846973] is outside array bounds of ‘std::array, 8> [1]’ [-Warray-bounds=] + 626 | first = std::forward(__p.first); + | ~~~~^~~~~ +/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h: In constructor ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’: +/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:14:52: note: at offset [120, 9223372036854775784] into object ‘b’ of size 64 + 14 | std::array, N> b; + | ^ +In member function ‘constexpr std::pair<_T1, _T2>& std::pair<_T1, _T2>::operator=(std::pair<_T1, _T2>&&) requires _S_assignable<_T1, _T2>() [with _T1 = int; _T2 = int]’, + inlined from ‘constexpr void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = pair*; _Distance = long int; _Tp = pair; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_heap.h:241:29, + inlined from ‘constexpr void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_heap.h:356:22, + inlined from ‘constexpr void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1594:23, + inlined from ‘constexpr void std::__partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1869:25, + inlined from ‘constexpr void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = pair*; _Size = long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1885:27, + inlined from ‘constexpr void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = pair*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/15/bits/stl_algo.h:1906:25, + inlined from ‘constexpr void std::sort(_RAIter, _RAIter) [with _RAIter = pair*]’ at /usr/include/c++/15/bits/stl_algo.h:4841:18, + inlined from ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’ at /build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:17:12: +/usr/include/c++/15/bits/stl_pair.h:627:48: warning: array subscript [15, 1152921504606846973] is outside array bounds of ‘std::array, 8> [1]’ [-Warray-bounds=] + 627 | second = std::forward(__p.second); + | ~~~~^~~~~~ +/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h: In constructor ‘RangePartition::RangePartition(const int*, int, int) [with int N = 8; T = short int]’: +/build/reproducible-path/diamond-aligner-2.1.14/src/util/data_structures/range_partition.h:14:52: note: at offset [120, 9223372036854775784] into object ‘b’ of size 64 + 14 | std::array, N> b; + | ^ At global scope: cc1plus: note: unrecognized command-line option ‘-Wno-unknown-warning-option’ may have been intended to silence earlier diagnostics In member function ‘constexpr auto std::__detail::_Synth3way::operator()(const _Tp&, const _Up&) const requires requires{{std::__detail::_Synth3way::operator()::__t < std::__detail::_Synth3way::operator()::__u} -> decltype(auto) [requires std::__detail::__boolean_testable<, >];{std::__detail::_Synth3way::operator()::__u < std::__detail::_Synth3way::operator()::__t} -> decltype(auto) [requires std::__detail::__boolean_testable<, >];} [with _Tp = int; _Up = int]’, @@ -3427,37 +3463,37 @@ make -f CMakeFiles/diamond.dir/build.make CMakeFiles/diamond.dir/build make[3]: Entering directory '/build/reproducible-path/diamond-aligner-2.1.14/obj-x86_64-linux-gnu' [ 15%] Building CXX object CMakeFiles/diamond.dir/src/run/main.cpp.o -[ 16%] Building CXX object CMakeFiles/diamond.dir/src/util/util.cpp.o -[ 16%] Building CXX object CMakeFiles/diamond.dir/src/util/command_line_parser.cpp.o +[ 17%] Building CXX object CMakeFiles/diamond.dir/src/data/queries.cpp.o +[ 17%] Building CXX object 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-D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.14/src -I/build/reproducible-path/diamond-aligner-2.1.14/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++20 -MD -MT CMakeFiles/diamond.dir/src/util/system/getRSS.cpp.o -MF CMakeFiles/diamond.dir/src/util/system/getRSS.cpp.o.d -o CMakeFiles/diamond.dir/src/util/system/getRSS.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.14/src/util/system/getRSS.cpp [ 46%] Building CXX object CMakeFiles/diamond.dir/src/util/string/string.cpp.o /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 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-I/build/reproducible-path/diamond-aligner-2.1.14/src -I/build/reproducible-path/diamond-aligner-2.1.14/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++20 -MD -MT CMakeFiles/diamond.dir/src/align/gapped_final.cpp.o -MF CMakeFiles/diamond.dir/src/align/gapped_final.cpp.o.d -o CMakeFiles/diamond.dir/src/align/gapped_final.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.14/src/align/gapped_final.cpp -[ 50%] Building CXX object CMakeFiles/diamond.dir/src/align/full_db.cpp.o -/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 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-I/build/reproducible-path/diamond-aligner-2.1.14/src -I/build/reproducible-path/diamond-aligner-2.1.14/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++20 -MD -MT CMakeFiles/diamond.dir/src/util/algo/mcl.cpp.o -MF CMakeFiles/diamond.dir/src/util/algo/mcl.cpp.o.d -o CMakeFiles/diamond.dir/src/util/algo/mcl.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.14/src/util/algo/mcl.cpp [ 98%] Building CXX object CMakeFiles/diamond.dir/src/stats/blast/matrix_adjust.cpp.o /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.14/src -I/build/reproducible-path/diamond-aligner-2.1.14/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++20 -MD -MT CMakeFiles/diamond.dir/src/stats/blast/matrix_adjust.cpp.o -MF CMakeFiles/diamond.dir/src/stats/blast/matrix_adjust.cpp.o.d -o CMakeFiles/diamond.dir/src/stats/blast/matrix_adjust.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.14/src/stats/blast/matrix_adjust.cpp +[ 98%] Building CXX object CMakeFiles/diamond.dir/src/stats/blast/ncbi.cpp.o +/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.14/src -I/build/reproducible-path/diamond-aligner-2.1.14/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++20 -MD -MT CMakeFiles/diamond.dir/src/stats/blast/ncbi.cpp.o -MF CMakeFiles/diamond.dir/src/stats/blast/ncbi.cpp.o.d -o CMakeFiles/diamond.dir/src/stats/blast/ncbi.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.14/src/stats/blast/ncbi.cpp +[ 99%] Building CXX object CMakeFiles/diamond.dir/src/search/hit_buffer.cpp.o +/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.14/src -I/build/reproducible-path/diamond-aligner-2.1.14/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++20 -MD -MT CMakeFiles/diamond.dir/src/search/hit_buffer.cpp.o -MF CMakeFiles/diamond.dir/src/search/hit_buffer.cpp.o.d -o CMakeFiles/diamond.dir/src/search/hit_buffer.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.14/src/search/hit_buffer.cpp In file included from /build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/Core:369, from /build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/Dense:1, from /build/reproducible-path/diamond-aligner-2.1.14/src/util/algo/mcl.cpp:1: @@ -3835,8 +3875,6 @@ /build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/CoreEvaluators.h:681:51: warning: arithmetic between different enumeration types ‘Eigen::internal::evaluator_wrapper_base > >::’ and ‘Eigen::internal::evaluator, const Eigen::Array > >::’ is deprecated [-Wdeprecated-enum-enum-conversion] 681 | CoeffReadCost = evaluator::CoeffReadCost + evaluator::CoeffReadCost + functor_traits::Cost, | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 98%] Building CXX object CMakeFiles/diamond.dir/src/stats/blast/ncbi.cpp.o -/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.14/src -I/build/reproducible-path/diamond-aligner-2.1.14/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++20 -MD -MT CMakeFiles/diamond.dir/src/stats/blast/ncbi.cpp.o -MF CMakeFiles/diamond.dir/src/stats/blast/ncbi.cpp.o.d -o CMakeFiles/diamond.dir/src/stats/blast/ncbi.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.14/src/stats/blast/ncbi.cpp In file included from /build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/Core:498: /build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/ProductEvaluators.h: In instantiation of ‘struct Eigen::internal::product_evaluator, Eigen::Matrix, 1>, 8, Eigen::DenseShape, Eigen::DenseShape, double, double>’: /build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/ProductEvaluators.h:29:8: required from ‘struct Eigen::internal::evaluator, Eigen::Matrix, 1> >’ @@ -3972,8 +4010,6 @@ /build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/CoreEvaluators.h:681:51: warning: arithmetic between different enumeration types ‘Eigen::internal::unary_evaluator, 1, -1, false> >, Eigen::internal::IndexBased, double>::’ and ‘Eigen::internal::evaluator, -1, 1, true> >::’ is deprecated [-Wdeprecated-enum-enum-conversion] 681 | CoeffReadCost = evaluator::CoeffReadCost + evaluator::CoeffReadCost + functor_traits::Cost, | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 99%] Building CXX object CMakeFiles/diamond.dir/src/search/hit_buffer.cpp.o -/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.14/src -I/build/reproducible-path/diamond-aligner-2.1.14/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++20 -MD -MT CMakeFiles/diamond.dir/src/search/hit_buffer.cpp.o -MF CMakeFiles/diamond.dir/src/search/hit_buffer.cpp.o.d -o CMakeFiles/diamond.dir/src/search/hit_buffer.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.14/src/search/hit_buffer.cpp cc1plus: note: unrecognized command-line option ‘-Wno-unknown-warning-option’ may have been intended to silence earlier diagnostics [100%] Linking CXX executable diamond /usr/bin/cmake -E cmake_link_script CMakeFiles/diamond.dir/link.txt --verbose=1 @@ -3985,39 +4021,39 @@ make[1]: Leaving directory '/build/reproducible-path/diamond-aligner-2.1.14/obj-x86_64-linux-gnu' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/diamond-aligner-2.1.14' -cd debian/tests && PATH=/build/reproducible-path/diamond-aligner-2.1.14/obj-x86_64-linux-gnu:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games sh diamond-calls -+ mktemp -d -+ TESTDIR=/tmp/tmp.ilJqE2Lw8D -+ diamond blastp --threads 1 --db test/C.faa.diamond --query test/E.faa --out /tmp/tmp.ilJqE2Lw8D/E.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive +cd debian/tests && PATH=/build/reproducible-path/diamond-aligner-2.1.14/obj-x86_64-linux-gnu:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path sh diamond-calls +++ mktemp -d ++ TESTDIR=/tmp/tmp.ojIE77lpUe ++ diamond blastp --threads 1 --db test/C.faa.diamond --query test/E.faa --out /tmp/tmp.ojIE77lpUe/E.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.14.168 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.ilJqE2Lw8D +Temporary directory: /tmp/tmp.ojIE77lpUe #Target sequences to report alignments for: 25 -Opening the database... [0s] +Opening the database... [0.001s] Database: test/C.faa.diamond (type: Diamond database, sequences: 109, letters: 51213) Block size = 2000000000 -Opening the input file... [0s] +Opening the input file... [0.001s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.003s] +Masking queries... [0.002s] Algorithm: Double-indexed -Building query histograms... [0.01s] +Building query histograms... [0.008s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.003s] +Masking reference... [0.002s] Initializing temporary storage... [0s] -Building reference histograms... [0.009s] +Building reference histograms... [0.007s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. Building reference seed array... [0.002s] @@ -4027,22 +4063,22 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -4062,14 +4098,14 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -4083,22 +4119,22 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.002s] 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... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -4111,22 +4147,22 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -4147,20 +4183,20 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 4/4. Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -4175,14 +4211,14 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 4/4. Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -4202,14 +4238,14 @@ 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... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -4223,22 +4259,22 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -4251,22 +4287,22 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] 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... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -4286,15 +4322,15 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -4307,21 +4343,21 @@ 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... [0.003s] +Building reference seed array... [0.001s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -4342,71 +4378,71 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 2/4. -Building reference seed array... [0.003s] -Building query seed array... [0.003s] +Building reference seed array... [0.002s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [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... [0.001s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -4426,14 +4462,14 @@ 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... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -4454,15 +4490,15 @@ 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] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.083s] +Computing alignments... [0.074s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -4472,39 +4508,39 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.579s +Total time = 0.518s 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.ilJqE2Lw8D/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.ojIE77lpUe/C.faa.vs.E.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.14.168 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.ilJqE2Lw8D +Temporary directory: /tmp/tmp.ojIE77lpUe #Target sequences to report alignments for: 25 -Opening the database... [0s] +Opening the database... [0.001s] Database: test/E.faa.diamond (type: Diamond database, sequences: 72, letters: 54509) Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] +Opening the input file... [0.001s] +Opening the output file... [0.002s] Loading query sequences... [0s] -Masking queries... [0.003s] +Masking queries... [0.002s] Algorithm: Double-indexed -Building query histograms... [0.009s] +Building query histograms... [0.008s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.003s] +Masking reference... [0.002s] Initializing temporary storage... [0s] -Building reference histograms... [0.01s] +Building reference histograms... [0.008s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. Building reference seed array... [0.002s] @@ -4515,41 +4551,41 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] 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... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4. Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 2/4. Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -4557,13 +4593,13 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 1/4. Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 2/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -4571,27 +4607,27 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 3/4. Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [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... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 2/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -4599,21 +4635,21 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 3/4. Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] 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... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 1/4. Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -4627,21 +4663,21 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 3/4. Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] 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... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -4655,27 +4691,27 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 3/4. Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 2/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -4683,21 +4719,21 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 3/4. Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -4711,21 +4747,21 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 3/4. Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -4739,21 +4775,21 @@ 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 query seed array... [0.001s] 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 query seed array... [0.001s] 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 query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -4767,7 +4803,7 @@ 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 query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -4781,7 +4817,7 @@ 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... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -4802,14 +4838,14 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 4/4. Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] 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... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -4823,21 +4859,21 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 3/4. Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -4851,21 +4887,21 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 3/4. Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -4879,21 +4915,21 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 3/4. Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] 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... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -4914,14 +4950,14 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 4/4. Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -4935,21 +4971,21 @@ 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 query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 4/4. Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.018s] +Computing alignments... [0.013s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -4959,35 +4995,35 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.52s +Total time = 0.446s 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.ilJqE2Lw8D/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.ojIE77lpUe/L.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.14.168 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.ilJqE2Lw8D +Temporary directory: /tmp/tmp.ojIE77lpUe #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C.faa.diamond (type: Diamond database, sequences: 109, letters: 51213) Block size = 2000000000 -Opening the input file... [0s] +Opening the input file... [0.001s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.002s] +Masking queries... [0.001s] Algorithm: Double-indexed -Building query histograms... [0.005s] +Building query histograms... [0.004s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.003s] +Masking reference... [0.002s] Initializing temporary storage... [0s] -Building reference histograms... [0.01s] +Building reference histograms... [0.011s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -5008,15 +5044,15 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -5029,22 +5065,22 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] 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... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -5057,21 +5093,21 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -5092,71 +5128,71 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] 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... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] 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... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [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... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -5169,22 +5205,22 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -5204,14 +5240,14 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -5225,28 +5261,28 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] 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... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -5260,14 +5296,14 @@ 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... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -5281,22 +5317,22 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] 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... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -5310,14 +5346,14 @@ 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 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 query seed array... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -5337,56 +5373,56 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] 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... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [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... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -5394,21 +5430,21 @@ 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 query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -5421,14 +5457,14 @@ 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... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -5436,7 +5472,7 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.041s] +Computing alignments... [0.028s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -5446,17 +5482,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.447s +Total time = 0.371s 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.ilJqE2Lw8D/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.ojIE77lpUe/C.faa.vs.L.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.14.168 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.ilJqE2Lw8D +Temporary directory: /tmp/tmp.ojIE77lpUe #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/L.faa.diamond (type: Diamond database, sequences: 40, letters: 26652) @@ -5464,21 +5500,21 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.003s] +Masking queries... [0.002s] Algorithm: Double-indexed -Building query histograms... [0.01s] +Building query histograms... [0.007s] Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0.001s] Initializing temporary storage... [0s] -Building reference histograms... [0.005s] +Building reference histograms... [0.004s] 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... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. Building reference seed array... [0.001s] @@ -5489,28 +5525,28 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] 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... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 2/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -5524,70 +5560,70 @@ 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 query seed array... [0.001s] 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... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 2/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [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 query seed array... [0.001s] 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... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 1/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 2/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [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... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -5601,21 +5637,21 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 1/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -5629,21 +5665,21 @@ 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... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 4/4. -Building reference seed array... [0.001s] +Building reference seed array... [0s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -5657,21 +5693,21 @@ 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 query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 4/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 1/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -5685,49 +5721,49 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] 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... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 1/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 2/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [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... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 4/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 1/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -5748,14 +5784,14 @@ 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 query seed array... [0.001s] 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 query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -5769,21 +5805,21 @@ 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 query seed array... [0.001s] 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 query seed array... [0.001s] 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 query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -5797,7 +5833,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -5811,63 +5847,63 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 1/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] 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 query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] 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 query seed array... [0.001s] 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 query seed array... [0.001s] 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 query seed array... [0.001s] 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... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 4/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] 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... [0.002s] +Building reference seed array... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -5881,14 +5917,14 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] 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 query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -5909,21 +5945,21 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [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 query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.062s] +Computing alignments... [0.052s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -5933,36 +5969,36 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.452s +Total time = 0.393s 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.ilJqE2Lw8D/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.ojIE77lpUe/M.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.14.168 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.ilJqE2Lw8D +Temporary directory: /tmp/tmp.ojIE77lpUe #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C.faa.diamond (type: Diamond database, sequences: 109, letters: 51213) Block size = 2000000000 -Opening the input file... [0s] +Opening the input file... [0.001s] Opening the output file... [0s] Loading query sequences... [0s] Masking queries... [0.001s] Algorithm: Double-indexed -Building query histograms... [0.005s] +Building query histograms... [0.004s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.003s] +Masking reference... [0.002s] Initializing temporary storage... [0s] -Building reference histograms... [0.01s] +Building reference histograms... [0.007s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] @@ -5975,22 +6011,22 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [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 query seed array... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -6003,21 +6039,21 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] 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... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -6031,21 +6067,21 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] 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... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -6059,21 +6095,21 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -6087,22 +6123,22 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] 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... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -6122,14 +6158,14 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -6143,21 +6179,21 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -6171,21 +6207,21 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -6199,49 +6235,49 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] 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... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [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... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -6255,50 +6291,50 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] 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... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -6318,15 +6354,15 @@ 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... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -6353,7 +6389,7 @@ 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... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -6367,35 +6403,35 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] 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... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [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... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -6410,7 +6446,7 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.036s] +Computing alignments... [0.033s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -6420,39 +6456,39 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.431s +Total time = 0.362s 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.ilJqE2Lw8D/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.ojIE77lpUe/C.faa.vs.M.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.14.168 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.ilJqE2Lw8D +Temporary directory: /tmp/tmp.ojIE77lpUe #Target sequences to report alignments for: 25 -Opening the database... [0s] +Opening the database... [0.001s] 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... [0.003s] +Masking queries... [0.002s] Algorithm: Double-indexed -Building query histograms... [0.011s] +Building query histograms... [0.007s] Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0.001s] Initializing temporary storage... [0s] -Building reference histograms... [0.005s] +Building reference histograms... [0.004s] 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... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. Building reference seed array... [0.001s] @@ -6463,21 +6499,21 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] 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... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -6490,189 +6526,189 @@ 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... [0.002s] +Building reference seed array... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [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... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 2/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [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 query seed array... [0.001s] 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... [0.002s] +Building reference seed array... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 2/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [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... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 2/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [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... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 2/4. Building reference seed array... [0.001s] -Building query seed array... [0.003s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] 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 query seed array... [0.001s] 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... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 2/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [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... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 4/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 1/4. -Building reference seed array... [0.001s] +Building reference seed array... [0s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -6680,196 +6716,196 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 2/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] 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... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 2/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [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 query seed array... [0.001s] 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... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 1/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 2/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [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 query seed array... [0.001s] 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... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 2/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [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 query seed array... [0.001s] 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 query seed array... [0.001s] 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... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 2/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [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 query seed array... [0.001s] 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 query seed array... [0.001s] 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 query seed array... [0.001s] 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... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 2/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [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... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 1/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -6883,21 +6919,21 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [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... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.067s] +Computing alignments... [0.052s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -6907,17 +6943,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.482s +Total time = 0.369s 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.ilJqE2Lw8D/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.ojIE77lpUe/C2.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.14.168 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.ilJqE2Lw8D +Temporary directory: /tmp/tmp.ojIE77lpUe #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C.faa.diamond (type: Diamond database, sequences: 109, letters: 51213) @@ -6930,124 +6966,124 @@ Building query histograms... [0s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.003s] +Masking reference... [0.002s] Initializing temporary storage... [0s] -Building reference histograms... [0.012s] +Building reference histograms... [0.008s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -7061,49 +7097,49 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [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... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -7117,28 +7153,28 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -7152,21 +7188,21 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -7180,14 +7216,14 @@ 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... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -7201,49 +7237,49 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [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... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -7257,49 +7293,49 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [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... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -7313,21 +7349,21 @@ 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... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -7348,35 +7384,35 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [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... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -7384,7 +7420,7 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.002s] +Computing alignments... [0.001s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -7394,17 +7430,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.336s +Total time = 0.262s 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.ilJqE2Lw8D/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.ojIE77lpUe/C.faa.vs.C2.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.14.168 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.ilJqE2Lw8D +Temporary directory: /tmp/tmp.ojIE77lpUe #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C2.faa.diamond (type: Diamond database, sequences: 2, letters: 726) @@ -7412,9 +7448,9 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.003s] +Masking queries... [0.002s] Algorithm: Double-indexed -Building query histograms... [0.009s] +Building query histograms... [0.007s] Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0s] @@ -7423,182 +7459,182 @@ 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... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] 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... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] 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... [0.001s] 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... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -7612,126 +7648,126 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] 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... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] 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... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] 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... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] 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... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -7745,105 +7781,105 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -7857,21 +7893,21 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.002s] +Computing alignments... [0.001s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -7881,17 +7917,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.319s +Total time = 0.257s 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.ilJqE2Lw8D/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.ojIE77lpUe/L.faa.vs.E.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.14.168 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.ilJqE2Lw8D +Temporary directory: /tmp/tmp.ojIE77lpUe #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/E.faa.diamond (type: Diamond database, sequences: 72, letters: 54509) @@ -7899,17 +7935,17 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.002s] +Masking queries... [0.001s] Algorithm: Double-indexed -Building query histograms... [0.005s] +Building query histograms... [0.004s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.003s] +Masking reference... [0.002s] Initializing temporary storage... [0s] -Building reference histograms... [0.01s] +Building reference histograms... [0.008s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -7930,14 +7966,14 @@ 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... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -7965,8 +8001,8 @@ 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... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -7986,15 +8022,15 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] 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... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -8014,14 +8050,14 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -8042,14 +8078,14 @@ 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... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -8070,14 +8106,14 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -8099,14 +8135,14 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 4/4. Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 1/4. Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -8126,15 +8162,15 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] 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... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -8148,21 +8184,21 @@ 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 query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -8182,21 +8218,21 @@ 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... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [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... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -8211,20 +8247,20 @@ 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... [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... [0.002s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 2/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -8245,8 +8281,8 @@ 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... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -8266,15 +8302,15 @@ 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... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -8294,14 +8330,14 @@ 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... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -8323,13 +8359,13 @@ 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 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... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -8358,7 +8394,7 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.099s] +Computing alignments... [0.092s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -8368,35 +8404,35 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.525s +Total time = 0.46s 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.ilJqE2Lw8D/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.ojIE77lpUe/E.faa.vs.L.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.14.168 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.ilJqE2Lw8D +Temporary directory: /tmp/tmp.ojIE77lpUe #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/L.faa.diamond (type: Diamond database, sequences: 40, letters: 26652) Block size = 2000000000 Opening the input file... [0s] -Opening the output file... [0s] +Opening the output file... [0.002s] Loading query sequences... [0s] Masking queries... [0.003s] Algorithm: Double-indexed -Building query histograms... [0.01s] +Building query histograms... [0.008s] Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0.001s] Initializing temporary storage... [0s] -Building reference histograms... [0.005s] +Building reference histograms... [0.004s] 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... [0s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -8407,25 +8443,25 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] 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... [0.002s] +Building reference seed array... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -8446,14 +8482,14 @@ 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 query seed array... [0.001s] 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 query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -8481,7 +8517,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 1/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -8502,7 +8538,7 @@ 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... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -8529,7 +8565,7 @@ 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... [0s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -8558,14 +8594,14 @@ 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... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -8593,7 +8629,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 1/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -8621,7 +8657,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 1/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -8635,21 +8671,21 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] 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... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -8677,7 +8713,7 @@ 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 query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -8698,14 +8734,14 @@ 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 query seed array... [0.001s] 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... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -8725,15 +8761,15 @@ 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... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 1/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -8754,14 +8790,14 @@ 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 query seed array... [0.001s] 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 query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -8782,21 +8818,21 @@ 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 query seed array... [0.001s] 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... [0.002s] +Building reference seed array... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 2/4. Building reference seed array... [0.001s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -8810,42 +8846,42 @@ 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 query seed array... [0.001s] 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 query seed array... [0.001s] 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... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.205s] +Computing alignments... [0.16s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -8855,17 +8891,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.644s +Total time = 0.536s 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.ilJqE2Lw8D/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.ojIE77lpUe/M.faa.vs.E.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.14.168 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.ilJqE2Lw8D +Temporary directory: /tmp/tmp.ojIE77lpUe #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/E.faa.diamond (type: Diamond database, sequences: 72, letters: 54509) @@ -8875,12 +8911,12 @@ Loading query sequences... [0s] Masking queries... [0.001s] Algorithm: Double-indexed -Building query histograms... [0.005s] +Building query histograms... [0.004s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.003s] +Masking reference... [0.002s] Initializing temporary storage... [0s] -Building reference histograms... [0.01s] +Building reference histograms... [0.008s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. Building reference seed array... [0.002s] @@ -8904,14 +8940,14 @@ 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... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -8932,21 +8968,21 @@ 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... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 2/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -8960,15 +8996,15 @@ 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... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -8988,15 +9024,15 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] 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... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -9016,15 +9052,15 @@ 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... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -9044,15 +9080,15 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -9072,21 +9108,21 @@ 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... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 2/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -9100,15 +9136,15 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -9128,21 +9164,21 @@ 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... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 2/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -9156,21 +9192,21 @@ 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... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 2/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -9184,14 +9220,14 @@ 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... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -9205,22 +9241,22 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 3/4. -Building reference seed array... [0.003s] -Building query seed array... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [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... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -9240,14 +9276,14 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -9269,14 +9305,14 @@ 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 query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -9296,21 +9332,21 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 2/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -9318,21 +9354,21 @@ 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 query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.105s] +Computing alignments... [0.086s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -9342,17 +9378,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.553s +Total time = 0.435s 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.ilJqE2Lw8D/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.ojIE77lpUe/E.faa.vs.M.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.14.168 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.ilJqE2Lw8D +Temporary directory: /tmp/tmp.ojIE77lpUe #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/M.faa.diamond (type: Diamond database, sequences: 40, letters: 26963) @@ -9360,18 +9396,18 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.004s] +Masking queries... [0.002s] Algorithm: Double-indexed -Building query histograms... [0.01s] +Building query histograms... [0.008s] Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0.001s] Initializing temporary storage... [0s] -Building reference histograms... [0.006s] +Building reference histograms... [0.004s] 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... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] @@ -9381,25 +9417,25 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] 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... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -9419,15 +9455,15 @@ 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... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -9441,21 +9477,21 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] 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... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 1/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -9469,21 +9505,21 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] 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... [0.002s] +Building reference seed array... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 1/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -9496,22 +9532,22 @@ 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... [0.003s] +Building reference seed array... [0s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -9525,21 +9561,21 @@ 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... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -9553,21 +9589,21 @@ 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 query seed array... [0.001s] 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... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -9587,7 +9623,7 @@ 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... [0s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -9595,7 +9631,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 1/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -9609,49 +9645,49 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [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... [0.002s] +Building reference seed array... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 2/4. Building reference seed array... [0.001s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.003s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] 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 query seed array... [0.001s] 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... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -9671,15 +9707,15 @@ 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... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -9693,21 +9729,21 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] 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 query seed array... [0.001s] 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... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -9721,14 +9757,14 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] 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 query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -9755,15 +9791,15 @@ 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... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -9798,28 +9834,28 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 2/4. Building reference seed array... [0.001s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] 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 query seed array... [0.001s] 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 query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.236s] +Computing alignments... [0.173s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -9829,17 +9865,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.702s +Total time = 0.516s 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.ilJqE2Lw8D/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.ojIE77lpUe/C2.faa.vs.E.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.14.168 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.ilJqE2Lw8D +Temporary directory: /tmp/tmp.ojIE77lpUe #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/E.faa.diamond (type: Diamond database, sequences: 72, letters: 54509) @@ -9852,9 +9888,9 @@ Building query histograms... [0s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.003s] +Masking reference... [0.002s] Initializing temporary storage... [0s] -Building reference histograms... [0.01s] +Building reference histograms... [0.008s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. Building reference seed array... [0.002s] @@ -9868,7 +9904,7 @@ Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. Building reference seed array... [0.002s] @@ -9878,14 +9914,14 @@ 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... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -9927,21 +9963,21 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -9962,21 +9998,21 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 2/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -9990,14 +10026,14 @@ 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... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -10018,14 +10054,14 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -10046,14 +10082,14 @@ 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 reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -10074,14 +10110,14 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -10102,7 +10138,7 @@ 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... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -10130,7 +10166,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -10158,14 +10194,14 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [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... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -10186,7 +10222,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -10214,14 +10250,14 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -10249,7 +10285,7 @@ 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... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -10277,7 +10313,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -10298,7 +10334,7 @@ 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... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -10316,17 +10352,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.341s +Total time = 0.276s 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.ilJqE2Lw8D/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.ojIE77lpUe/E.faa.vs.C2.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.14.168 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.ilJqE2Lw8D +Temporary directory: /tmp/tmp.ojIE77lpUe #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C2.faa.diamond (type: Diamond database, sequences: 2, letters: 726) @@ -10334,9 +10370,9 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.003s] +Masking queries... [0.002s] Algorithm: Double-indexed -Building query histograms... [0.01s] +Building query histograms... [0.008s] Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0s] @@ -10345,7 +10381,7 @@ 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... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -10366,14 +10402,14 @@ 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... [0.003s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -10422,21 +10458,21 @@ 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... [0.003s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.003s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -10450,14 +10486,14 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -10471,21 +10507,21 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -10506,14 +10542,14 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -10527,56 +10563,56 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] 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... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] 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... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -10590,42 +10626,42 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] 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... [0.001s] 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... [0.002s] 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... [0.003s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -10646,14 +10682,14 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -10667,49 +10703,49 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -10723,21 +10759,21 @@ 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... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -10751,21 +10787,21 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.003s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] 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... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -10779,21 +10815,21 @@ 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... [0.003s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.003s] +Computing alignments... [0.001s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -10803,17 +10839,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.352s +Total time = 0.266s 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.ilJqE2Lw8D/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.ojIE77lpUe/M.faa.vs.L.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.14.168 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.ilJqE2Lw8D +Temporary directory: /tmp/tmp.ojIE77lpUe #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/L.faa.diamond (type: Diamond database, sequences: 40, letters: 26652) @@ -10821,77 +10857,77 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.002s] +Masking queries... [0.001s] Algorithm: Double-indexed -Building query histograms... [0.005s] +Building query histograms... [0.004s] Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0.001s] Initializing temporary storage... [0s] -Building reference histograms... [0.005s] +Building reference histograms... [0.004s] 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... [0s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.005s] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.003s] +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... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 2/4. Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] 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... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 1/4. Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +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] @@ -10905,46 +10941,46 @@ Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 2/4. Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] 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] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 1/4. Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.002s] @@ -10954,109 +10990,109 @@ Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 3/4. Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] 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 query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 2/4. Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 3/4. Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 4/4. Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +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... [0s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 2/4. Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] 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] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 2/4. Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] 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] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 1/4. Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.002s] @@ -11066,63 +11102,63 @@ Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 3/4. Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 4/4. Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 1/4. Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 2/4. Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 3/4. Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] 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... [0s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 1/4. Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.003s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 2/4. Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.003s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 3/4. Building reference seed array... [0.001s] @@ -11132,99 +11168,99 @@ Searching alignments... [0.002s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 1/4. Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +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... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 3/4. Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +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... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 1/4. Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +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... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 3/4. Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] 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 query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 2/4. Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] 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] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.003s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 4/4. Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 1/4. Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.002s] @@ -11234,7 +11270,7 @@ Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 3/4. Building reference seed array... [0.001s] @@ -11248,11 +11284,11 @@ Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 1/4. Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.002s] @@ -11269,7 +11305,7 @@ Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 4/4. Building reference seed array... [0.001s] @@ -11280,7 +11316,7 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.073s] +Computing alignments... [0.06s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -11290,17 +11326,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.566s +Total time = 0.453s 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.ilJqE2Lw8D/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.ojIE77lpUe/L.faa.vs.M.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.14.168 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.ilJqE2Lw8D +Temporary directory: /tmp/tmp.ojIE77lpUe #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/M.faa.diamond (type: Diamond database, sequences: 40, letters: 26963) @@ -11310,12 +11346,12 @@ Loading query sequences... [0s] Masking queries... [0.001s] Algorithm: Double-indexed -Building query histograms... [0.005s] +Building query histograms... [0.004s] Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0.001s] Initializing temporary storage... [0s] -Building reference histograms... [0.007s] +Building reference histograms... [0.008s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. Building reference seed array... [0.001s] @@ -11336,77 +11372,77 @@ Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 4/4. Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] 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] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 2/4. Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] 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... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.003s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 1/4. Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.003s] +Searching alignments... [0.002s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 2/4. Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 3/4. Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] 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... [0s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 1/4. Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +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... [0.001s] @@ -11420,214 +11456,214 @@ Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 1/4. Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 2/4. Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 3/4. Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] 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... [0s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 2/4. Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 3/4. Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4. Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 2/4. Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 3/4. Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] 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... [0s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 2/4. Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] 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] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 4/4. -Building reference seed array... [0.001s] +Building reference seed array... [0s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 1/4. Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 2/4. Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] 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... [0s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 2/4. Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 2/4. Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] 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... [0s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.002s] @@ -11665,109 +11701,109 @@ Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 2/4. Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] 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] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 4/4. Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.002s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 2/4. Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 2/4. Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 3/4. Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.075s] +Computing alignments... [0.057s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -11777,17 +11813,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.575s +Total time = 0.457s 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.ilJqE2Lw8D/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.ojIE77lpUe/C2.faa.vs.L.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.14.168 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.ilJqE2Lw8D +Temporary directory: /tmp/tmp.ojIE77lpUe #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/L.faa.diamond (type: Diamond database, sequences: 40, letters: 26652) @@ -11802,14 +11838,14 @@ Loading reference sequences... [0s] Masking reference... [0.001s] Initializing temporary storage... [0s] -Building reference histograms... [0.006s] +Building reference histograms... [0.004s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. Building reference seed array... [0.001s] @@ -11819,21 +11855,21 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. -Building reference seed array... [0.001s] +Building reference seed array... [0s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 4/4. -Building reference seed array... [0.001s] +Building reference seed array... [0s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4. -Building reference seed array... [0.001s] +Building reference seed array... [0s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -11861,7 +11897,7 @@ 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 reference seed array... [0s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -11889,7 +11925,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 1/4. -Building reference seed array... [0.001s] +Building reference seed array... [0s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -11910,14 +11946,14 @@ 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... [0s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 1/4. -Building reference seed array... [0.001s] +Building reference seed array... [0s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -11945,7 +11981,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 1/4. -Building reference seed array... [0.001s] +Building reference seed array... [0s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -11959,21 +11995,21 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 3/4. -Building reference seed array... [0.001s] +Building reference seed array... [0s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 4/4. -Building reference seed array... [0.001s] +Building reference seed array... [0s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4. -Building reference seed array... [0.001s] +Building reference seed array... [0s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -11987,21 +12023,21 @@ 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... [0s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 4/4. -Building reference seed array... [0.001s] +Building reference seed array... [0s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 1/4. -Building reference seed array... [0.001s] +Building reference seed array... [0s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -12022,14 +12058,14 @@ 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... [0s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 1/4. -Building reference seed array... [0.001s] +Building reference seed array... [0s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -12043,14 +12079,14 @@ 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... [0s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 4/4. -Building reference seed array... [0.001s] +Building reference seed array... [0s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -12071,21 +12107,21 @@ 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... [0s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 4/4. -Building reference seed array... [0.001s] +Building reference seed array... [0s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 1/4. -Building reference seed array... [0.001s] +Building reference seed array... [0s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -12106,14 +12142,14 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 4/4. -Building reference seed array... [0.001s] +Building reference seed array... [0s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 1/4. -Building reference seed array... [0.001s] +Building reference seed array... [0s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -12134,7 +12170,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 4/4. -Building reference seed array... [0.001s] +Building reference seed array... [0s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -12162,14 +12198,14 @@ 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... [0s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 1/4. -Building reference seed array... [0.001s] +Building reference seed array... [0s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -12197,14 +12233,14 @@ 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 reference seed array... [0s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -12225,7 +12261,7 @@ 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... [0s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -12246,7 +12282,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 4/4. -Building reference seed array... [0.001s] +Building reference seed array... [0s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -12254,7 +12290,7 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.003s] +Computing alignments... [0.002s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -12264,17 +12300,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.254s +Total time = 0.183s 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.ilJqE2Lw8D/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.ojIE77lpUe/L.faa.vs.C2.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.14.168 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.ilJqE2Lw8D +Temporary directory: /tmp/tmp.ojIE77lpUe #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C2.faa.diamond (type: Diamond database, sequences: 2, letters: 726) @@ -12282,9 +12318,9 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.002s] +Masking queries... [0.001s] Algorithm: Double-indexed -Building query histograms... [0.005s] +Building query histograms... [0.004s] Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0s] @@ -12314,14 +12350,14 @@ 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... [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... [0s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -12342,7 +12378,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -12377,35 +12413,35 @@ 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... [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... [0s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -12432,8 +12468,8 @@ 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... [0s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -12454,14 +12490,14 @@ 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... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -12475,21 +12511,21 @@ 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... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -12510,14 +12546,14 @@ 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... [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... [0s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -12531,21 +12567,21 @@ 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... [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... [0s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -12559,21 +12595,21 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [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... [0s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -12582,7 +12618,7 @@ Building reference seed array... [0s] Building query seed array... [0.001s] Computing hash join... [0s] -Masking low complexity seeds... [0.001s] +Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 3/4. @@ -12594,7 +12630,7 @@ 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... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -12615,21 +12651,21 @@ 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... [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... [0s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -12650,35 +12686,35 @@ 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... [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... [0s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -12706,14 +12742,14 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [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... [0s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -12734,7 +12770,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -12751,17 +12787,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.259s +Total time = 0.184s 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.ilJqE2Lw8D/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.ojIE77lpUe/C2.faa.vs.M.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.14.168 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.ilJqE2Lw8D +Temporary directory: /tmp/tmp.ojIE77lpUe #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/M.faa.diamond (type: Diamond database, sequences: 40, letters: 26963) @@ -12776,14 +12812,14 @@ Loading reference sequences... [0s] Masking reference... [0.001s] Initializing temporary storage... [0s] -Building reference histograms... [0.005s] +Building reference histograms... [0.004s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. Building reference seed array... [0.001s] @@ -12800,14 +12836,14 @@ 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... [0.001s] +Building reference seed array... [0s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4. -Building reference seed array... [0.001s] +Building reference seed array... [0s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -12835,7 +12871,7 @@ 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 reference seed array... [0s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -12856,7 +12892,7 @@ 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... [0s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -12891,7 +12927,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 1/4. -Building reference seed array... [0.001s] +Building reference seed array... [0s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -12940,7 +12976,7 @@ 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... [0s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -12975,7 +13011,7 @@ 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 reference seed array... [0s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -12996,14 +13032,14 @@ 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... [0s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 1/4. -Building reference seed array... [0.001s] +Building reference seed array... [0s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -13024,14 +13060,14 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 4/4. -Building reference seed array... [0.001s] +Building reference seed array... [0s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 1/4. -Building reference seed array... [0.001s] +Building reference seed array... [0s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -13052,42 +13088,42 @@ 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... [0s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 1/4. -Building reference seed array... [0.001s] +Building reference seed array... [0s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 2/4. -Building reference seed array... [0.001s] +Building reference seed array... [0s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 3/4. -Building reference seed array... [0.001s] +Building reference seed array... [0s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 4/4. -Building reference seed array... [0.001s] +Building reference seed array... [0s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 1/4. -Building reference seed array... [0.001s] +Building reference seed array... [0s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -13108,7 +13144,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 4/4. -Building reference seed array... [0.001s] +Building reference seed array... [0s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -13164,7 +13200,7 @@ 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... [0s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -13228,7 +13264,7 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.003s] +Computing alignments... [0.002s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -13238,17 +13274,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.267s +Total time = 0.201s 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.ilJqE2Lw8D/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.ojIE77lpUe/M.faa.vs.C2.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.14.168 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.ilJqE2Lw8D +Temporary directory: /tmp/tmp.ojIE77lpUe #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C2.faa.diamond (type: Diamond database, sequences: 2, letters: 726) @@ -13256,9 +13292,9 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.002s] +Masking queries... [0.001s] Algorithm: Double-indexed -Building query histograms... [0.005s] +Building query histograms... [0.004s] Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0s] @@ -13270,7 +13306,7 @@ Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. Building reference seed array... [0s] @@ -13288,7 +13324,7 @@ 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... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -13323,7 +13359,7 @@ 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... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -13337,21 +13373,21 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -13386,7 +13422,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.003s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -13421,21 +13457,21 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +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... [0s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -13484,7 +13520,7 @@ 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... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -13512,14 +13548,14 @@ 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... [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... [0s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -13533,14 +13569,14 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [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... [0s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -13596,7 +13632,7 @@ 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... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -13659,7 +13695,7 @@ 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... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -13680,7 +13716,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -13715,7 +13751,7 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.002s] +Computing alignments... [0.001s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -13725,15 +13761,15 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.254s +Total time = 0.206s Reported 1 pairwise alignments, 1 HSPs. 1 queries aligned. -+ rm -rf /tmp/tmp.ilJqE2Lw8D ++ rm -rf /tmp/tmp.ojIE77lpUe make[1]: Leaving directory '/build/reproducible-path/diamond-aligner-2.1.14' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/diamond-aligner/ - cd obj-x86_64-linux-gnu && make -j16 install DESTDIR=/build/reproducible-path/diamond-aligner-2.1.14/debian/diamond-aligner AM_UPDATE_INFO_DIR=no INSTALL="install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j12 install DESTDIR=/build/reproducible-path/diamond-aligner-2.1.14/debian/diamond-aligner AM_UPDATE_INFO_DIR=no INSTALL="install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/diamond-aligner-2.1.14/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/diamond-aligner-2.1.14 -B/build/reproducible-path/diamond-aligner-2.1.14/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -13765,8 +13801,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'diamond-aligner' in '../diamond-aligner_2.1.14-1_amd64.deb'. dpkg-deb: building package 'diamond-aligner-dbgsym' in '../diamond-aligner-dbgsym_2.1.14-1_amd64.deb'. +dpkg-deb: building package 'diamond-aligner' in '../diamond-aligner_2.1.14-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../diamond-aligner_2.1.14-1_amd64.buildinfo dpkg-genchanges --build=binary -O../diamond-aligner_2.1.14-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -13774,12 +13810,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/2149993/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2149993/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/640735 and its subdirectories -I: Current time: Fri Nov 20 23:36:06 -12 2026 -I: pbuilder-time-stamp: 1795260966 +I: removing directory /srv/workspace/pbuilder/2149993 and its subdirectories +I: Current time: Sun Oct 19 19:17:25 +14 2025 +I: pbuilder-time-stamp: 1760851045