Diff of the two buildlogs: -- --- b1/build.log 2024-03-25 16:43:48.653392837 +0000 +++ b2/build.log 2024-03-25 16:58:37.087402812 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Mar 25 04:28:12 -12 2024 -I: pbuilder-time-stamp: 1711384092 +I: Current time: Tue Mar 26 06:44:06 +14 2024 +I: pbuilder-time-stamp: 1711385046 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -30,52 +30,84 @@ dpkg-source: info: applying flaky_test.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/12854/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1635/tmp/hooks/D01_modify_environment starting +debug: Running on virt32c. +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 Mar 25 16:44 /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/1635/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1635/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='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='7b6f1b089d87407fbc976876bbdc280c' - 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='12854' - PS1='# ' - PS2='> ' + INVOCATION_ID=29c08962425c403ea22c9f67c9abae7c + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + 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=1635 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.Xe9poXtK/pbuilderrc_j9vu --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Xe9poXtK/b1 --logfile b1/build.log milib_2.2.0+dfsg-1.dsc' - SUDO_GID='113' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + 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.Xe9poXtK/pbuilderrc_KsvI --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Xe9poXtK/b2 --logfile b2/build.log milib_2.2.0+dfsg-1.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux virt64c 6.1.0-18-arm64 #1 SMP Debian 6.1.76-1 (2024-02-01) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-18-armmp-lpae #1 SMP Debian 6.1.76-1 (2024-02-01) armv7l GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Mar 25 11:26 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/12854/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Mar 24 11:24 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1635/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -486,7 +518,7 @@ Get: 339 http://deb.debian.org/debian trixie/main armhf libmockito-java all 2.23.0-2 [479 kB] Get: 340 http://deb.debian.org/debian trixie/main armhf libredberry-pipe-java all 1.0.0~alpha0-3 [62.7 kB] Get: 341 http://deb.debian.org/debian trixie/main armhf libtrove3-java all 3.0.3-5 [2146 kB] -Fetched 291 MB in 7s (42.5 MB/s) +Fetched 291 MB in 10s (29.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpipeline1:armhf. (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 ... 19577 files and directories currently installed.) @@ -1594,8 +1626,8 @@ Setting up tzdata (2024a-1) ... Current default time zone: 'Etc/UTC' -Local time is now: Mon Mar 25 16:32:05 UTC 2024. -Universal Time is now: Mon Mar 25 16:32:05 UTC 2024. +Local time is now: Mon Mar 25 16:46:15 UTC 2024. +Universal Time is now: Mon Mar 25 16:46:15 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libgeronimo-annotation-1.3-spec-java (1.3-1) ... @@ -2075,7 +2107,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/milib-2.2.0+dfsg/ && 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 > ../milib_2.2.0+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/1635/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/1635/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/milib-2.2.0+dfsg/ && 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 > ../milib_2.2.0+dfsg-1_source.changes dpkg-buildpackage: info: source package milib dpkg-buildpackage: info: source version 2.2.0+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -2109,7 +2145,7 @@ dh_auto_build mkdir -p .gradle/init.d cp /usr/share/gradle-debian-helper/init.gradle .gradle/init.d/ - gradle --info --console plain --offline --stacktrace --no-daemon --refresh-dependencies --gradle-user-home .gradle -Duser.home=. -Duser.name=debian -Ddebian.package=milib -Dfile.encoding=UTF-8 --parallel --max-workers=3 jar + gradle --info --console plain --offline --stacktrace --no-daemon --refresh-dependencies --gradle-user-home .gradle -Duser.home=. -Duser.name=debian -Ddebian.package=milib -Dfile.encoding=UTF-8 --parallel --max-workers=4 jar openjdk version "17.0.10" 2024-01-16 OpenJDK Runtime Environment (build 17.0.10+7-Debian-1) OpenJDK Server VM (build 17.0.10+7-Debian-1, mixed mode, sharing) @@ -2117,12 +2153,12 @@ To honour the JVM settings for this build a new JVM will be forked. Please consider using the daemon: https://docs.gradle.org/4.4.1/userguide/gradle_daemon.html. Starting process 'Gradle build daemon'. Working directory: /build/reproducible-path/milib-2.2.0+dfsg/.gradle/daemon/4.4.1 Command: /usr/lib/jvm/java-17-openjdk-armhf/bin/java --add-opens java.base/java.lang=ALL-UNNAMED -Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar -Dfile.encoding=UTF-8 -Duser.country=US -Duser.language=en -Duser.variant -cp /usr/share/gradle/lib/gradle-launcher-4.4.1.jar org.gradle.launcher.daemon.bootstrap.GradleDaemon 4.4.1 Successfully started process 'Gradle build daemon' -An attempt to start the daemon took 3.397 secs. -The client will now receive all logging from the daemon (pid: 31539). The daemon log file: /build/reproducible-path/milib-2.2.0+dfsg/.gradle/daemon/4.4.1/daemon-31539.out.log +An attempt to start the daemon took 2.966 secs. +The client will now receive all logging from the daemon (pid: 15249). The daemon log file: /build/reproducible-path/milib-2.2.0+dfsg/.gradle/daemon/4.4.1/daemon-15249.out.log Daemon will be stopped at the end of the build stopping after processing Closing daemon's stdin at end of input. The daemon will no longer process any standard input. -Using 3 worker leases. +Using 4 worker leases. Creating new cache for fileHashes, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@1d4b4e6 Creating new cache for resourceHashesCache, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@1d4b4e6 Creating new cache for fileHashes, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@5ffc5b @@ -2152,8 +2188,8 @@ Creating new cache for outputFiles, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@11ec6d0 :compileJava (Thread[Task worker for ':',5,main]) started. :compileJava -Putting task artifact state for task ':compileJava' into context took 0.028 secs. -Creating new cache for metadata-2.36/module-metadata, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@18d65a5 +Putting task artifact state for task ':compileJava' into context took 0.012 secs. +Creating new cache for metadata-2.36/module-metadata, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@17e0ba9 Loading the Maven rules... Replacing org.apache.commons:commons-math3:jar:3.6.1 -> org.apache.commons:commons-math3:jar:debian Replacing cc.redberry:pipe:jar:1.3.0 -> cc.redberry:pipe:jar:1.0.0-alpha0 @@ -2225,7 +2261,7 @@ at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at java.base/java.lang.Thread.run(Thread.java:840) -Up-to-date check for task ':compileJava' took 14.333 secs. It is not up-to-date because: +Up-to-date check for task ':compileJava' took 9.01 secs. It is not up-to-date because: No history is available. All input files are considered out-of-date for incremental task ':compileJava'. Compiling with JDK Java compiler API. @@ -2233,13 +2269,13 @@ Note: Recompile with -Xlint:deprecation for details. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. -:compileJava (Thread[Task worker for ':',5,main]) completed. Took 39.846 secs. +:compileJava (Thread[Task worker for ':',5,main]) completed. Took 30.406 secs. :processResources (Thread[Task worker for ':',5,main]) started. :processResources Putting task artifact state for task ':processResources' into context took 0.0 secs. -Up-to-date check for task ':processResources' took 0.03 secs. It is not up-to-date because: +Up-to-date check for task ':processResources' took 0.033 secs. It is not up-to-date because: No history is available. -:processResources (Thread[Task worker for ':',5,main]) completed. Took 0.125 secs. +:processResources (Thread[Task worker for ':',5,main]) completed. Took 0.135 secs. :classes (Thread[Task worker for ':',5,main]) started. :classes Skipping task ':classes' as it has no actions. @@ -2247,23 +2283,23 @@ :debianMavenPom (Thread[Task worker for ':',5,main]) started. :debianMavenPom Putting task artifact state for task ':debianMavenPom' into context took 0.0 secs. -Up-to-date check for task ':debianMavenPom' took 0.009 secs. It is not up-to-date because: +Up-to-date check for task ':debianMavenPom' took 0.002 secs. It is not up-to-date because: No history is available. Generating pom file /build/reproducible-path/milib-2.2.0+dfsg/build/debian/milib.pom -:debianMavenPom (Thread[Task worker for ':',5,main]) completed. Took 0.452 secs. +:debianMavenPom (Thread[Task worker for ':',5,main]) completed. Took 0.236 secs. :jar (Thread[Task worker for ':',5,main]) started. :jar Putting task artifact state for task ':jar' into context took 0.0 secs. -Up-to-date check for task ':jar' took 0.156 secs. It is not up-to-date because: +Up-to-date check for task ':jar' took 0.174 secs. It is not up-to-date because: No history is available. -:jar (Thread[Task worker for ':',5,main]) completed. Took 0.887 secs. +:jar (Thread[Task worker for ':',5,main]) completed. Took 0.863 secs. -BUILD SUCCESSFUL in 1m 0s +BUILD SUCCESSFUL in 48s 4 actionable tasks: 4 executed dh_auto_test mkdir -p .gradle/init.d cp /usr/share/gradle-debian-helper/init.gradle .gradle/init.d/ - gradle --info --console plain --offline --stacktrace --no-daemon --refresh-dependencies --gradle-user-home .gradle -Duser.home=. -Duser.name=debian -Ddebian.package=milib -Dfile.encoding=UTF-8 --parallel --max-workers=3 test + gradle --info --console plain --offline --stacktrace --no-daemon --refresh-dependencies --gradle-user-home .gradle -Duser.home=. -Duser.name=debian -Ddebian.package=milib -Dfile.encoding=UTF-8 --parallel --max-workers=4 test openjdk version "17.0.10" 2024-01-16 OpenJDK Runtime Environment (build 17.0.10+7-Debian-1) OpenJDK Server VM (build 17.0.10+7-Debian-1, mixed mode, sharing) @@ -2271,17 +2307,17 @@ To honour the JVM settings for this build a new JVM will be forked. Please consider using the daemon: https://docs.gradle.org/4.4.1/userguide/gradle_daemon.html. Starting process 'Gradle build daemon'. Working directory: /build/reproducible-path/milib-2.2.0+dfsg/.gradle/daemon/4.4.1 Command: /usr/lib/jvm/java-17-openjdk-armhf/bin/java --add-opens java.base/java.lang=ALL-UNNAMED -Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar -Dfile.encoding=UTF-8 -Duser.country=US -Duser.language=en -Duser.variant -cp /usr/share/gradle/lib/gradle-launcher-4.4.1.jar org.gradle.launcher.daemon.bootstrap.GradleDaemon 4.4.1 Successfully started process 'Gradle build daemon' -An attempt to start the daemon took 2.923 secs. -The client will now receive all logging from the daemon (pid: 32187). The daemon log file: /build/reproducible-path/milib-2.2.0+dfsg/.gradle/daemon/4.4.1/daemon-32187.out.log +An attempt to start the daemon took 2.752 secs. +The client will now receive all logging from the daemon (pid: 16067). The daemon log file: /build/reproducible-path/milib-2.2.0+dfsg/.gradle/daemon/4.4.1/daemon-16067.out.log Daemon will be stopped at the end of the build stopping after processing Closing daemon's stdin at end of input. The daemon will no longer process any standard input. -Using 3 worker leases. -Creating new cache for fileHashes, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@a6efaa -Creating new cache for resourceHashesCache, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@a6efaa -Creating new cache for fileHashes, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@fb60f3 +Using 4 worker leases. +Creating new cache for fileHashes, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@3c69f7 +Creating new cache for resourceHashesCache, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@3c69f7 +Creating new cache for fileHashes, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@1ca60b5 Starting Build -Creating new cache for metadata-1.1/results, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@fe7bd5 +Creating new cache for metadata-1.1/results, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@84fd57 Settings evaluated using settings file '/build/reproducible-path/milib-2.2.0+dfsg/settings.gradle'. Settings file not found (/build/reproducible-path/milib-2.2.0+dfsg/settings.gradle) Root project name not defined in settings.gradle, defaulting to 'milib' instead of the name of the root directory 'milib-2.2.0+dfsg' @@ -2295,15 +2331,15 @@ Linking the generated javadoc to the system JDK API documentation All projects evaluated. Selected primary task 'test' from project : -Creating new cache for annotation-processors, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@245dc9 +Creating new cache for annotation-processors, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@ef9ea0 Tasks to be executed: [task ':compileJava', task ':processResources', task ':classes', task ':compileTestJava', task ':processTestResources', task ':testClasses', task ':test'] -Creating new cache for resourceHashesCache, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@fb60f3 -Creating new cache for taskHistory, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@579644 -Creating new cache for outputFiles, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@1aa9b0a -:compileJava (Thread[Task worker for ':',5,main]) started. +Creating new cache for resourceHashesCache, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@1ca60b5 +Creating new cache for taskHistory, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@c1d111 +Creating new cache for outputFiles, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@e01ae9 +:compileJava (Thread[Task worker for ':' Thread 2,5,main]) started. :compileJava -Putting task artifact state for task ':compileJava' into context took 0.015 secs. -Creating new cache for metadata-2.36/module-metadata, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@5451a9 +Putting task artifact state for task ':compileJava' into context took 0.013 secs. +Creating new cache for metadata-2.36/module-metadata, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@1470af0 Loading the Maven rules... Replacing org.apache.commons:commons-math3:jar:3.6.1 -> org.apache.commons:commons-math3:jar:debian Replacing cc.redberry:pipe:jar:1.3.0 -> cc.redberry:pipe:jar:1.0.0-alpha0 @@ -2327,21 +2363,21 @@ Passing through org.jsr-305:jsr305:jar:0.x Passing through com.google.errorprone:error_prone_annotations:jar:debian Passing through com.google.errorprone:error_prone_parent:jar:debian -Skipping task ':compileJava' as it is up-to-date (took 2.823 secs). +Skipping task ':compileJava' as it is up-to-date (took 2.417 secs). :compileJava UP-TO-DATE -:compileJava (Thread[Task worker for ':',5,main]) completed. Took 2.918 secs. -:processResources (Thread[Task worker for ':',5,main]) started. +:compileJava (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 2.503 secs. +:processResources (Thread[Task worker for ':' Thread 2,5,main]) started. :processResources Putting task artifact state for task ':processResources' into context took 0.0 secs. -Skipping task ':processResources' as it is up-to-date (took 0.03 secs). +Skipping task ':processResources' as it is up-to-date (took 0.029 secs). :processResources UP-TO-DATE -:processResources (Thread[Task worker for ':',5,main]) completed. Took 0.042 secs. -:classes (Thread[Task worker for ':',5,main]) started. +:processResources (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.038 secs. +:classes (Thread[Task worker for ':' Thread 3,5,main]) started. :classes Skipping task ':classes' as it has no actions. :classes UP-TO-DATE -:classes (Thread[Task worker for ':',5,main]) completed. Took 0.005 secs. -:compileTestJava (Thread[Task worker for ':',5,main]) started. +:classes (Thread[Task worker for ':' Thread 3,5,main]) completed. Took 0.002 secs. +:compileTestJava (Thread[Task worker for ':' Thread 3,5,main]) started. :compileTestJava Putting task artifact state for task ':compileTestJava' into context took 0.0 secs. Replacing junit:junit:jar:4.13.2 -> junit:junit:jar:4.x @@ -2357,7 +2393,7 @@ Passing through net.bytebuddy:byte-buddy-dep:jar:debian Passing through org.ow2.asm:asm:jar:debian Passing through org.ow2.asm:asm-commons:jar:debian -Up-to-date check for task ':compileTestJava' took 7.264 secs. It is not up-to-date because: +Up-to-date check for task ':compileTestJava' took 6.496 secs. It is not up-to-date because: No history is available. All input files are considered out-of-date for incremental task ':compileTestJava'. Compiling with JDK Java compiler API. @@ -2365,602 +2401,26 @@ Note: Recompile with -Xlint:deprecation for details. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. -:compileTestJava (Thread[Task worker for ':',5,main]) completed. Took 27.285 secs. -:processTestResources (Thread[Task worker for ':',5,main]) started. +:compileTestJava (Thread[Task worker for ':' Thread 3,5,main]) completed. Took 24.125 secs. +:processTestResources (Thread[Task worker for ':' Thread 3,5,main]) started. :processTestResources Putting task artifact state for task ':processTestResources' into context took 0.0 secs. -Up-to-date check for task ':processTestResources' took 0.081 secs. It is not up-to-date because: +Up-to-date check for task ':processTestResources' took 0.051 secs. It is not up-to-date because: No history is available. -:processTestResources (Thread[Task worker for ':',5,main]) completed. Took 0.159 secs. -:testClasses (Thread[Task worker for ':',5,main]) started. +:processTestResources (Thread[Task worker for ':' Thread 3,5,main]) completed. Took 0.137 secs. +:testClasses (Thread[Task worker for ':' Thread 3,5,main]) started. :testClasses Skipping task ':testClasses' as it has no actions. -:testClasses (Thread[Task worker for ':',5,main]) completed. Took 0.001 secs. -:test (Thread[Task worker for ':',5,main]) started. +:testClasses (Thread[Task worker for ':' Thread 3,5,main]) completed. Took 0.002 secs. +:test (Thread[Task worker for ':' Thread 3,5,main]) started. :test Putting task artifact state for task ':test' into context took 0.0 secs. -Up-to-date check for task ':test' took 2.385 secs. It is not up-to-date because: +Up-to-date check for task ':test' took 2.117 secs. It is not up-to-date because: No history is available. -Starting process 'Gradle Test Executor 1'. Working directory: /build/reproducible-path/milib-2.2.0+dfsg Command: /usr/lib/jvm/java-17-openjdk-armhf/bin/java -Dorg.gradle.native=false @/tmp/gradle-worker-classpath5375013282113761975txt -Xms1024m -Xmx2048m -Dfile.encoding=UTF-8 -Duser.country=US -Duser.language=en -Duser.variant -ea worker.org.gradle.process.internal.worker.GradleWorkerMain 'Gradle Test Executor 1' +Starting process 'Gradle Test Executor 1'. Working directory: /build/reproducible-path/milib-2.2.0+dfsg Command: /usr/lib/jvm/java-17-openjdk-armhf/bin/java -Dorg.gradle.native=false @/tmp/gradle-worker-classpath478129266545092559txt -Xms1024m -Xmx2048m -Dfile.encoding=UTF-8 -Duser.country=US -Duser.language=en -Duser.variant -ea worker.org.gradle.process.internal.worker.GradleWorkerMain 'Gradle Test Executor 1' Successfully started process 'Gradle Test Executor 1' Gradle Test Executor 1 started executing tests. -com.milaboratory.primitivio.blocks.PrimitivOBlocksTest > benchmark1 SKIPPED - -com.milaboratory.primitivio.blocks.PrimitivOBlocksTest > test1 STANDARD_OUT - - ================== - High compression: false - Concurrency: 4 - File size: 6799510 - Write time: 786.63ms - - O. Stats: - Wall clock time: 807.74ms - Total CPU time: 1.5s - User wait time: 595.63ms - Serialization time: 1.04s (68.95%) - Checksum calculation time: 316.18ms (21.05%) - Compression time: 85.73ms (5.71%) - Total IO delay: 141.68ms - Concurrency overhead: 137.65ms - Uncompressed size: 18.44MiB (~2.08KiB per object) - Output size: 6.48MiB (~748B per object; compression = 35.17%) - IO speed: 45.99MiB/s - Concurrency adjusted uncompressed speed: 33.64MiB/s - Actual uncompressed speed: 22.85MiB/s - Actual speed: 8.04MiB/s - Objects: 9079 - Average object size uncompressed: 2.08KiB - Average object size compressed: 748B - Blocks: 62 (~107.1KiB each) - Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 - - I. Stats 1: - Wall clock time: 536.76ms - Total CPU time: 625.88ms - Serialization time: 508.16ms (81.19%) - Checksum calculation time: 48.06ms (7.68%) - Compression time: 62.24ms (9.95%) - Total IO delay: 149.98ms - Input size: 6.48MiB - Decompressed size: 18.44MiB (compression = 35.17%) - IO speed: 43.52MiB/s - Concurrency adjusted uncompressed speed: 95.53MiB/s - Actual uncompressed speed: 34.4MiB/s - Actual speed: 12.1MiB/s - Objects: 9079 - Average object size uncompressed: 2.08KiB - Average object size compressed: 748B - Blocks: 62 (~107.1KiB each) - Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 - Pending / IO / Serde: 0 / 0 / 0 - - I. Stats 2: - Wall clock time: 1.04s - Total CPU time: 881.18ms - Serialization time: 640.14ms (72.65%) - Checksum calculation time: 94.73ms (10.75%) - Compression time: 129.94ms (14.75%) - Total IO delay: 327.23ms - Input size: 12.97MiB - Decompressed size: 36.87MiB (compression = 35.17%) - IO speed: 39.66MiB/s - Concurrency adjusted uncompressed speed: 122.1MiB/s - Actual uncompressed speed: 35.35MiB/s - Actual speed: 12.43MiB/s - Objects: 18158 - Average object size uncompressed: 2.08KiB - Average object size compressed: 748B - Blocks: 124 (~107.1KiB each) - Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 - - ================== - High compression: false - Concurrency: 4 - File size: 6791878 - Write time: 230.51ms - - O. Stats: - Wall clock time: 233.12ms - Total CPU time: 283.24ms - User wait time: 181.91ms - Serialization time: 135.56ms (47.86%) - Checksum calculation time: 49.28ms (17.4%) - Compression time: 86.64ms (30.59%) - Total IO delay: 58.14ms - Concurrency overhead: 13.97ms - Uncompressed size: 18.44MiB (~2.08KiB per object) - Output size: 6.48MiB (~748B per object; compression = 35.13%) - IO speed: 111.68MiB/s - Concurrency adjusted uncompressed speed: 186.23MiB/s - Actual uncompressed speed: 79.13MiB/s - Actual speed: 27.8MiB/s - Objects: 9079 - Average object size uncompressed: 2.08KiB - Average object size compressed: 748B - Blocks: 20 (~331.63KiB each) - Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 - - I. Stats 1: - Wall clock time: 296.85ms - Total CPU time: 282.9ms - Serialization time: 134.26ms (47.46%) - Checksum calculation time: 64.19ms (22.69%) - Compression time: 83.42ms (29.49%) - Total IO delay: 59.89ms - Input size: 6.48MiB - Decompressed size: 18.44MiB (compression = 35.13%) - IO speed: 109.78MiB/s - Concurrency adjusted uncompressed speed: 216.9MiB/s - Actual uncompressed speed: 62.29MiB/s - Actual speed: 21.88MiB/s - Objects: 9079 - Average object size uncompressed: 2.08KiB - Average object size compressed: 748B - Blocks: 20 (~331.63KiB each) - Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 - - I. Stats 2: - Wall clock time: 595.98ms - Total CPU time: 531.24ms - Serialization time: 237.3ms (44.67%) - Checksum calculation time: 125.47ms (23.62%) - Compression time: 166.65ms (31.37%) - Total IO delay: 103.21ms - Input size: 12.95MiB - Decompressed size: 36.87MiB (compression = 35.13%) - IO speed: 125.77MiB/s - Concurrency adjusted uncompressed speed: 233.38MiB/s - Actual uncompressed speed: 61.97MiB/s - Actual speed: 21.77MiB/s - Objects: 18158 - Average object size uncompressed: 2.08KiB - Average object size compressed: 748B - Blocks: 40 (~331.63KiB each) - Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 - - ================== - High compression: false - Concurrency: 1 - File size: 6799510 - Write time: 371.7ms - - O. Stats: - Wall clock time: 373.28ms - Total CPU time: 258.42ms - User wait time: 328.57ms - Serialization time: 122ms (47.21%) - Checksum calculation time: 46.89ms (18.15%) - Compression time: 72.16ms (27.92%) - Total IO delay: 45.45ms - Concurrency overhead: 9.45ms - Uncompressed size: 18.44MiB (~2.08KiB per object) - Output size: 6.48MiB (~748B per object; compression = 35.17%) - IO speed: 144.1MiB/s - Concurrency adjusted uncompressed speed: 58.9MiB/s - Actual uncompressed speed: 49.43MiB/s - Actual speed: 17.38MiB/s - Objects: 9079 - Average object size uncompressed: 2.08KiB - Average object size compressed: 748B - Blocks: 62 (~107.1KiB each) - Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 - Checksum ok! - - I. Stats 1: - Wall clock time: 218.69ms - Total CPU time: 232.75ms - Serialization time: 109.45ms (47.03%) - Checksum calculation time: 46.89ms (20.15%) - Compression time: 73.03ms (31.38%) - Total IO delay: 67.32ms - Input size: 6.48MiB - Decompressed size: 18.44MiB (compression = 35.17%) - IO speed: 96.78MiB/s - Concurrency adjusted uncompressed speed: 61.46MiB/s - Actual uncompressed speed: 84.57MiB/s - Actual speed: 29.75MiB/s - Objects: 9079 - Average object size uncompressed: 2.08KiB - Average object size compressed: 748B - Blocks: 62 (~107.1KiB each) - Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 - - I. Stats 2: - Wall clock time: 510.86ms - Total CPU time: 513.89ms - Serialization time: 264.25ms (51.42%) - Checksum calculation time: 93.43ms (18.18%) - Compression time: 146.07ms (28.42%) - Total IO delay: 205.47ms - Input size: 12.97MiB - Decompressed size: 36.87MiB (compression = 35.17%) - IO speed: 63.26MiB/s - Concurrency adjusted uncompressed speed: 51.28MiB/s - Actual uncompressed speed: 72.3MiB/s - Actual speed: 25.43MiB/s - Objects: 18158 - Average object size uncompressed: 2.08KiB - Average object size compressed: 748B - Blocks: 124 (~107.1KiB each) - Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 - - ================== - High compression: false - Concurrency: 1 - File size: 6791878 - Write time: 327.55ms - - O. Stats: - Wall clock time: 329.83ms - Total CPU time: 253.93ms - User wait time: 292.75ms - Serialization time: 123.46ms (48.62%) - Checksum calculation time: 47.03ms (18.52%) - Compression time: 72ms (28.35%) - Total IO delay: 38.03ms - Concurrency overhead: 2.24ms - Uncompressed size: 18.44MiB (~2.08KiB per object) - Output size: 6.48MiB (~748B per object; compression = 35.13%) - IO speed: 170.45MiB/s - Concurrency adjusted uncompressed speed: 62.71MiB/s - Actual uncompressed speed: 56.04MiB/s - Actual speed: 19.69MiB/s - Objects: 9079 - Average object size uncompressed: 2.08KiB - Average object size compressed: 748B - Blocks: 20 (~331.63KiB each) - Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 - Checksum ok! - - I. Stats 1: - Wall clock time: 241.87ms - Total CPU time: 250.03ms - Serialization time: 100.46ms (40.18%) - Checksum calculation time: 56.14ms (22.45%) - Compression time: 92.59ms (37.03%) - Total IO delay: 33.07ms - Input size: 6.48MiB - Decompressed size: 18.44MiB (compression = 35.13%) - IO speed: 196.28MiB/s - Concurrency adjusted uncompressed speed: 65.15MiB/s - Actual uncompressed speed: 76.5MiB/s - Actual speed: 26.88MiB/s - Objects: 9079 - Average object size uncompressed: 2.08KiB - Average object size compressed: 748B - Blocks: 20 (~331.63KiB each) - Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 - - I. Stats 2: - Wall clock time: 544.4ms - Total CPU time: 495.51ms - Serialization time: 202.57ms (40.88%) - Checksum calculation time: 112.34ms (22.67%) - Compression time: 178.91ms (36.11%) - Total IO delay: 76.51ms - Input size: 12.95MiB - Decompressed size: 36.87MiB (compression = 35.13%) - IO speed: 170.45MiB/s - Concurrency adjusted uncompressed speed: 64.46MiB/s - Actual uncompressed speed: 67.78MiB/s - Actual speed: 23.81MiB/s - Objects: 18158 - Average object size uncompressed: 2.08KiB - Average object size compressed: 748B - Blocks: 40 (~331.63KiB each) - Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 - Pending / IO / Serde: 0 / 0 / 4 - Pending / IO / Serde: 2 / 0 / 1 - - ================== - High compression: true - Concurrency: 4 - File size: 4156299 - Write time: 3.96s - - O. Stats: - Wall clock time: 3.97s - Total CPU time: 10.55s - User wait time: 3.77s - Serialization time: 133.19ms (1.26%) - Checksum calculation time: 58.88ms (0.56%) - Compression time: 10.34s (98.01%) - Total IO delay: 88.74ms - Concurrency overhead: 61.64ms - Uncompressed size: 18.44MiB (~2.08KiB per object) - Output size: 3.96MiB (~457B per object; compression = 21.5%) - IO speed: 45.04MiB/s - Concurrency adjusted uncompressed speed: 6.78MiB/s - Actual uncompressed speed: 4.65MiB/s - Actual speed: 1023.68KiB/s - Objects: 9079 - Average object size uncompressed: 2.08KiB - Average object size compressed: 457B - Blocks: 62 (~65.47KiB each) - Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 - - I. Stats 1: - Wall clock time: 202ms - Total CPU time: 186.11ms - Serialization time: 80.95ms (43.5%) - Checksum calculation time: 48.27ms (25.94%) - Compression time: 52.81ms (28.38%) - Total IO delay: 88.48ms - Input size: 3.96MiB - Decompressed size: 18.44MiB (compression = 21.5%) - IO speed: 45.04MiB/s - Concurrency adjusted uncompressed speed: 271.13MiB/s - Actual uncompressed speed: 91.27MiB/s - Actual speed: 19.62MiB/s - Objects: 9079 - Average object size uncompressed: 2.08KiB - Average object size compressed: 457B - Blocks: 62 (~65.47KiB each) - Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 - - I. Stats 2: - Wall clock time: 455.3ms - Total CPU time: 360.86ms - Serialization time: 148.71ms (41.21%) - Checksum calculation time: 97.45ms (27%) - Compression time: 105.41ms (29.21%) - Total IO delay: 211.17ms - Input size: 7.93MiB - Decompressed size: 36.87MiB (compression = 21.5%) - IO speed: 37.57MiB/s - Concurrency adjusted uncompressed speed: 257.86MiB/s - Actual uncompressed speed: 81.04MiB/s - Actual speed: 17.42MiB/s - Objects: 18158 - Average object size uncompressed: 2.08KiB - Average object size compressed: 457B - Blocks: 124 (~65.47KiB each) - Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 - Pending / IO / Serde: 2 / 0 / 2 - Pending / IO / Serde: 3 / 0 / 1 - - ================== - High compression: true - Concurrency: 4 - File size: 4098671 - Write time: 5.72s - - O. Stats: - Wall clock time: 5.72s - Total CPU time: 9.55s - User wait time: 5.23s - Serialization time: 92.31ms (0.97%) - Checksum calculation time: 47.24ms (0.49%) - Compression time: 9.4s (98.47%) - Total IO delay: 44.6ms - Concurrency overhead: 6ms - Uncompressed size: 18.44MiB (~2.08KiB per object) - Output size: 3.91MiB (~451B per object; compression = 21.2%) - IO speed: 88.84MiB/s - Concurrency adjusted uncompressed speed: 7.67MiB/s - Actual uncompressed speed: 3.22MiB/s - Actual speed: 699.27KiB/s - Objects: 9079 - Average object size uncompressed: 2.08KiB - Average object size compressed: 451B - Blocks: 20 (~200.13KiB each) - Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 - Pending / IO / Serde: 0 / 0 / 0 - - I. Stats 1: - Wall clock time: 284.9ms - Total CPU time: 245.53ms - Serialization time: 93.76ms (38.19%) - Checksum calculation time: 81.18ms (33.06%) - Compression time: 69.61ms (28.35%) - Total IO delay: 61.77ms - Input size: 3.91MiB - Decompressed size: 18.44MiB (compression = 21.2%) - IO speed: 64.08MiB/s - Concurrency adjusted uncompressed speed: 242.59MiB/s - Actual uncompressed speed: 64.92MiB/s - Actual speed: 13.76MiB/s - Objects: 9079 - Average object size uncompressed: 2.08KiB - Average object size compressed: 451B - Blocks: 20 (~200.13KiB each) - Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 - - I. Stats 2: - Wall clock time: 583.65ms - Total CPU time: 463.47ms - Serialization time: 154.32ms (33.3%) - Checksum calculation time: 162.27ms (35.01%) - Compression time: 145.2ms (31.33%) - Total IO delay: 104.98ms - Input size: 7.82MiB - Decompressed size: 36.87MiB (compression = 21.2%) - IO speed: 75.17MiB/s - Concurrency adjusted uncompressed speed: 259.67MiB/s - Actual uncompressed speed: 63.25MiB/s - Actual speed: 13.41MiB/s - Objects: 18158 - Average object size uncompressed: 2.08KiB - Average object size compressed: 451B - Blocks: 40 (~200.13KiB each) - Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 - Pending / IO / Serde: 0 / 0 / 1 - Pending / IO / Serde: 0 / 0 / 1 - Pending / IO / Serde: 0 / 0 / 1 - Pending / IO / Serde: 0 / 0 / 1 - - ================== - High compression: true - Concurrency: 1 - File size: 4156299 - Write time: 8.56s - - O. Stats: - Wall clock time: 8.56s - Total CPU time: 8.46s - User wait time: 8.53s - Serialization time: 105.18ms (1.24%) - Checksum calculation time: 47.1ms (0.56%) - Compression time: 8.3s (98.1%) - Total IO delay: 44.46ms - Concurrency overhead: 14.4ms - Uncompressed size: 18.44MiB (~2.08KiB per object) - Output size: 3.96MiB (~457B per object; compression = 21.5%) - IO speed: 90.09MiB/s - Concurrency adjusted uncompressed speed: 2.16MiB/s - Actual uncompressed speed: 2.15MiB/s - Actual speed: 473.95KiB/s - Objects: 9079 - Average object size uncompressed: 2.08KiB - Average object size compressed: 457B - Blocks: 62 (~65.47KiB each) - Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 - Checksum ok! - - I. Stats 1: - Wall clock time: 235ms - Total CPU time: 200.76ms - Serialization time: 72.6ms (36.16%) - Checksum calculation time: 60.96ms (30.37%) - Compression time: 62.91ms (31.33%) - Total IO delay: 113.87ms - Input size: 3.96MiB - Decompressed size: 18.44MiB (compression = 21.5%) - IO speed: 35.08MiB/s - Concurrency adjusted uncompressed speed: 58.72MiB/s - Actual uncompressed speed: 78.79MiB/s - Actual speed: 16.94MiB/s - Objects: 9079 - Average object size uncompressed: 2.08KiB - Average object size compressed: 457B - Blocks: 62 (~65.47KiB each) - Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 - - I. Stats 2: - Wall clock time: 472.24ms - Total CPU time: 372.15ms - Serialization time: 136.52ms (36.68%) - Checksum calculation time: 108.63ms (29.19%) - Compression time: 118.18ms (31.76%) - Total IO delay: 200.84ms - Input size: 7.93MiB - Decompressed size: 36.87MiB (compression = 21.5%) - IO speed: 39.64MiB/s - Concurrency adjusted uncompressed speed: 64.46MiB/s - Actual uncompressed speed: 78.12MiB/s - Actual speed: 16.8MiB/s - Objects: 18158 - Average object size uncompressed: 2.08KiB - Average object size compressed: 457B - Blocks: 124 (~65.47KiB each) - Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 - Pending / IO / Serde: 0 / 0 / 1 - Pending / IO / Serde: 0 / 0 / 1 - Pending / IO / Serde: 0 / 0 / 1 - Pending / IO / Serde: 0 / 0 / 1 - Pending / IO / Serde: 0 / 0 / 1 - - ================== - High compression: true - Concurrency: 1 - File size: 4098671 - Write time: 9.98s - - O. Stats: - Wall clock time: 9.98s - Total CPU time: 9.92s - User wait time: 9.95s - Serialization time: 100.99ms (1.02%) - Checksum calculation time: 47.75ms (0.48%) - Compression time: 9.76s (98.44%) - Total IO delay: 30.78ms - Concurrency overhead: 2.27ms - Uncompressed size: 18.44MiB (~2.08KiB per object) - Output size: 3.91MiB (~451B per object; compression = 21.2%) - IO speed: 130.29MiB/s - Concurrency adjusted uncompressed speed: 1.85MiB/s - Actual uncompressed speed: 1.85MiB/s - Actual speed: 401.22KiB/s - Objects: 9079 - Average object size uncompressed: 2.08KiB - Average object size compressed: 451B - Blocks: 20 (~200.13KiB each) - Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 - Checksum ok! - - I. Stats 1: - Wall clock time: 238.84ms - Total CPU time: 221.58ms - Serialization time: 73.44ms (33.14%) - Checksum calculation time: 74.62ms (33.68%) - Compression time: 72.9ms (32.9%) - Total IO delay: 45.56ms - Input size: 3.91MiB - Decompressed size: 18.44MiB (compression = 21.2%) - IO speed: 86.86MiB/s - Concurrency adjusted uncompressed speed: 69.05MiB/s - Actual uncompressed speed: 77.47MiB/s - Actual speed: 16.42MiB/s - Objects: 9079 - Average object size uncompressed: 2.08KiB - Average object size compressed: 451B - Blocks: 20 (~200.13KiB each) - Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 - - I. Stats 2: - Wall clock time: 520.96ms - Total CPU time: 428.37ms - Serialization time: 154.1ms (35.97%) - Checksum calculation time: 130.73ms (30.52%) - Compression time: 142.31ms (33.22%) - Total IO delay: 87.64ms - Input size: 7.82MiB - Decompressed size: 36.87MiB (compression = 21.2%) - IO speed: 89.86MiB/s - Concurrency adjusted uncompressed speed: 71.46MiB/s - Actual uncompressed speed: 70.91MiB/s - Actual speed: 15.03MiB/s - Objects: 18158 - Average object size uncompressed: 2.08KiB - Average object size compressed: 451B - Blocks: 40 (~200.13KiB each) - Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 - -com.milaboratory.primitivio.blocks.PrimitivOBlocksTest > bigBlocks STANDARD_OUT - Pending / IO / Serde / Objs: 0 / 1 / 1 / 1000 - Pending / IO / Serde / Objs: 0 / 1 / 0 / 4000 - Pending / IO / Serde / Objs: 0 / 1 / 1 / 7000 - Pending / IO / Serde / Objs: 0 / 1 / 1 / 10000 - Pending / IO / Serde / Objs: 1 / 1 / 0 / 14000 - Pending / IO / Serde / Objs: 0 / 1 / 1 / 17000 - Pending / IO / Serde / Objs: 1 / 1 / 0 / 20000 - O. Stats: - Wall clock time: 14.46s - Total CPU time: 11.6s - User wait time: 484.25us - Serialization time: 2.65s (22.81%) - Checksum calculation time: 5.64s (48.59%) - Compression time: 1.79s (15.45%) - Total IO delay: 10.45s - Concurrency overhead: 17.98ms - Uncompressed size: 1.86GiB (~97.66KiB per object) - Output size: 1.86GiB (~97.66KiB per object; compression = 100%) - IO speed: 182.6MiB/s - Concurrency adjusted uncompressed speed: 687.86MiB/s - Actual uncompressed speed: 131.92MiB/s - Actual speed: 131.92MiB/s - Objects: 20000 - Average object size uncompressed: 97.66KiB - Average object size compressed: 97.66KiB - Blocks: 20 (~95.37MiB each) - Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 - -com.milaboratory.test.TestUtil > testLT STANDARD_OUT - Short tests. - No system env properties. - com.milaboratory.core.motif.BitapPatternTest > ttt STANDARD_OUT 0 ATTWCCGACA 9 ||| |||| @@ -2969,6 +2429,46 @@ 24 -26 +com.milaboratory.core.mutations.MutationsUtilTest > test1111 STANDARD_OUT + S([\QAGCTNRYSWKMBDHV\E])(\d+)([\QAGCTNRYSWKMBDHV\E])|D([\QAGCTNRYSWKMBDHV\E])(\d+)|I(\d+)([\QAGCTNRYSWKMBDHV\E]) + S([\Q*ACDEFGHIKLMNPQRSTVWY_XBJZ\E])(\d+)([\Q*ACDEFGHIKLMNPQRSTVWY_XBJZ\E])|D([\Q*ACDEFGHIKLMNPQRSTVWY_XBJZ\E])(\d+)|I(\d+)([\Q*ACDEFGHIKLMNPQRSTVWY_XBJZ\E]) + +com.milaboratory.core.mutations.MutationsUtilTest > nt2AAWithMappingManual1 STANDARD_OUT + [I2C::SM0I, I2G::I1A, I2C::I1A, SG2C:SM0I:I1A] + +com.milaboratory.core.mutations.MutationsUtilTest > nt2AAWithMappingManual2 STANDARD_OUT + [S0:T->N,D13:V,S14:S->Y,S15:P->R,S16:W->P,S17:Y->G,S18:D->T,S19:P->I,S20:G->P,S21:D->A,S22:K->T,S23:A->K,S24:F->R,S25:G->S,S26:P->D,I27:S] + [-1, -1, 9, 15] + +com.milaboratory.core.mutations.MutationsUtilTest > nt2AAWithMappingManual3 STANDARD_OUT + 0 CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTACGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA 295 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||| ||||| ||||||||||||||||||||||||||||| ||||||||| ||||||||| ||||||||||||||||||| || ||||| ||| || |||||||||||||| + 0 CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTACGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACATTCTATGCAGAGAAGTTCCAGGGCAGAGTCACCATGACCACAGACGCATCCACGACCACAGCCTATATGGAGCTGAGGAGCCTGACATTTGACG-----GCCACATACTACTGTGCGAGAGA 290 + [S58:N->F,S61:Q->E,S63:L->F,S73:T->A,S76:S->T,S86:R->T,S87:S->F,S89:D->G,D90:T,D91:A,S92:V->H,S93:Y->I,S94:Y->L,S95:C->L,S96:A->C,S97:R->E,S98:_->R] + QVQLVQSGAEVKKPGASVKVSCKASGYTFTSYGISWVRQAPGQGLEWMGWISAYNGNTFYAEKFQGRVTMTTDASTTTAYMELRSLTFDGHILLCER + QVQLVQSGAEVKKPGASVKVSCKASGYTFTSYGISWVRQAPGQGLEWMGWISAYNGNTFYAEKFQGRVTMTTDASTTTAYMELRSLTFDGHILLCER + [S58:N->F,S61:Q->E,S63:L->F,S73:T->A,S76:S->T,S86:R->T,S87:S->F,S89:D->G,D90:T,D91:A,S92:V->H,S93:Y->I,S94:Y->L,S95:C->L,S96:A->C,S97:R->E,S98:_->R] + [0, 0, 1, 2, 3, 4, -1, 5, 6, 7, 7, 8, 8, 8, 10, 10, 11, 12] + +com.milaboratory.core.mutations.MutationsUtilTest > nt2AAWithMappingManual4 STANDARD_OUT + [S3:S->M,D4:D,S5:_->I] + +com.milaboratory.core.mutations.MutationTest > exportRegexps STANDARD_OUT + S([\QAGCTNRYSWKMBDHV\E])(\d+)([\QAGCTNRYSWKMBDHV\E])|D([\QAGCTNRYSWKMBDHV\E])(\d+)|I(\d+)([\QAGCTNRYSWKMBDHV\E]) + S([\Q*ACDEFGHIKLMNPQRSTVWY_XBJZ\E])(\d+)([\Q*ACDEFGHIKLMNPQRSTVWY_XBJZ\E])|D([\Q*ACDEFGHIKLMNPQRSTVWY_XBJZ\E])(\d+)|I(\d+)([\Q*ACDEFGHIKLMNPQRSTVWY_XBJZ\E]) + +com.milaboratory.core.mutations.MutationsTest > testCanonical1 STANDARD_OUT + TCCGCCATCACAGCAAAGACGTGAGGAAAAACAACCCAGTACATGGTACGAAGATGATCTCGTCTATCAACCCGGGGCGGCTGCTAGCCACGAGATTACGCCGCCCCTAGGTTTTTCCAGATACATTACCCAAGGCCTTGGCATTGAGCACTAATCGATAGTTACTCGTGCCAAGATGTAACGCAAAGAATTTACTCGTTCTCTCGACGCTAACGATGGTCAGGGATAGTGTTGACGTCCCTATGTGGTTACTCTTCCCTACGCCTGGATGCGTTGCGCTATACAGGACAGTTTTTTATTTTGGTGCCCCCGTATCGTTACACATTGAGTTGGCAGCTGAAGATTGCACGCCACCCCCCCGCGGGCTGACGGTTGTAAGCCTACCCCTAGTCTGGCGGACTAATTATTCTCGAGTAAATAAAAGCGTCAAGTGAGACTCGATTCTAATGCACATTGCGGGGTTCTCCATTGTAATATTCCCATAACACTCCTGCAGTAATAGCCGTATCTAATAACGTACCTTCTTCCCCACTGAGACTTACAGTCATTGGGTCGACTGTTTGATGACCAACCGCGGGGCTATAGGGGCAAGCTCACTGGGGGGGAACATGCGGGTGATGGGCGCTAACCGCCCGCAGTGACATGCACATGTCAGTCGGCGACTACAGTCCGGGCGTAATCTATTTTTCATCAGCTCGGCTCGCTTATCTTACCGTTATAAGTGCTTTCAG + TCCTCCATCACAGCAAAGACGTGAGGAAAAGACAACCCAGTACATGGTACGAAGATGATCTCGTCTTCAACCCGGGGCGGCTACTAGCCCACGAGATTACGCCGCCCCTGGGTTTTTCCAGATACATTACCCAAGGCCTTGGCATTGAGCACTAACTCGAAGTTTCTCGTGCGAATGTAACGCAAAAGAAATTTCACTCGTTCTCTGACGTAACGAATGGTCAGGGATAGTGTTGACGTCCCCATGTGGTTACTCTCCTACGTCTGGATGACGTTGCGCCTATACAGGCAGTTTTTTATTTTGGTGTCCCCGTATCGTTACACATGAGTTGGCAGCTAAGATTGCACGCCACCCTCCCCGCGGGCTCGGTTGTAAGCTACCCCTAGTCTGGCGGACTAATTATTTCGAGTAAAAATAAGCGCAAGATGAGACTCGATTCTAATGCACATTTCGGGTTCTCCTTGTAATAATCCCATATACACTCCTGCAGTAGTAGCCGTACAATAACGTACCTTCTTCCCCACTAGACTTACAAAGCATTGGGTCGACTATTTGATGACCAACCGCGGGGCTATAGTGCAAGCTCCACTGGGGGGGAACATGGGGTTATGGCGCTACGCCCGCAGTGACATGCTCAGTCAGTCGGCGACTGACAGTCCGGGCGTAATCTATTTTCCATCAGCTCGGCTCGCTTATCTTACCGTTTAAGTGCTTTAG + TCCTCCATCACAGCAAGGATGTGAGGAAAGACAACCCAGTACATGGTACGAAGATGATCTCGTCTTCAACCCGGGGTCGGCACTGCGCCCACAATTACGCCGCCCCCGGTTTTTTCCAGATACTTACCCAAGCCTTGGCATTAGCACTAATGAAGTTTCTCGTGCGAATGTAACGCAAAAGAAATTTCATCTCTTCTCTGACGTAACGAATGGTCTTGGAAGGTTGCGCTCCCCATGGGTTATCTCCACGTCTGGTGACGTGTGCGCCTATACAGGCAGTTTTTATTTTGGTGTCCCCGTATGTTACACATGAGTGGCAGCTAAGATTGCACGCCACCCTCCCGCTGGCTCGTTGAACTACCCCTAGTCTAGCTGACCAATTATTCGATAAAAATAAGCCGAAGATGAGACTCGACCTAATGCACATTTCGGGTTCTCCTGTAAGTAATCCCATATACACTCCTACGGTAATAGCCGTACAATAAGTCCTCTTCCCTCTAGACTTACAAAGCATGGTCGACTATTTGATGACCAACGCGCGGGGCTATGTGCAAGCTCCACTGGGAGGAACATGGGGTATGGCTCACGCCCGCGAGTGACACTCAGTCAGTGGCGACTGACAGTCCGGGCGTAATCTATTTTCCATCAGTTCGGCTCGCTTATCATTACCGTTTAAGTGCTTTAG + 0 TCCTCCATCACAGCAAGGATGTGAGGAAAGACAACCCAGTACATGGTACGAAGATGATCTCGTCT-TCAACCCGGGGTCGGCACTGC--GCCCAC-A-ATTACGCCGCCCC-CGGTTTTTTCCAGATAC-TTACCCAA-GCCTTGGCATT-AGCACTAAT-GA-AGTTTCTCGTG-CGA-ATGTAACGCAAAAGAAATTTCATCTC-TTCTCT-GACG-TAACGAATGGTCTTGGA-AG-GTTG-CGCTCCCCATG-GGTTA-TC-T-CC-ACGTCTGG-TGACGTGTGCGCCTATACAGG-CAG-TTTTTATTTTGGTGTCCCCGTAT-GTTACACA-TGAG-TGGCAGCT-AAGATTGCACGCCACCCTCCCGCTGGCT--C-GTTG-AA--CTACCCCTAGTCTAGCTGACCAATTA-T-TCGA-TAAA-AATAAGC--CGAAGATGAGACTCGA-CCTAATGCACATTTC-GGGTTCTCC--TGTAAGTAATCCCATATACACTCCTACGGTAATAGCCGTA-C-AATAA-GT-CC-TCTT-CCCTCT-AGACTTACAAAG-CA-T-GGTCGACTATTTGATGACCAACGCGCGGGGCTAT--GTGCAAGCTCCACT-GGGAGGAACATG-GGGT-AT--G-GCTCA-CGCCCGCGAGTGACA--CTCA-GTCAGT-GGCGACTGACAGTCCGGGCGTAATCTATTTTCCATCAGTTCGGCTCGCTTATCATTACCGTT-TAAGTGCTTT-AG 684 + ||| |||||||||||| || ||||||||| ||||||||||||||||||||||||||||||||||| ||||||||||| ||| |||| | |||| | ||||||||||||| || ||||||||||||| |||||||| ||||||||||| ||||||||| || |||| |||||| | | ||||||||| |||| ||||| | ||| |||||| |||| ||||| |||||| ||| || |||| || |||| ||| ||||| || | || ||| |||| || ||| |||| ||||||||| ||| |||||||||||||| |||||||| |||||||| |||| |||||||| ||||||||||||||||| ||||| |||| | |||| || ||||||||||||| || ||| ||||| | |||| |||| || |||| | ||| |||||||||| |||||||||||| | ||||||||| ||||| || ||||||| |||||||| | |||||||||||| | ||||| || || |||| ||| || |||||||| || || | |||||||| ||||||||||||| ||||||||||| | ||||||| |||| ||| |||||||| |||| || | ||| | ||||||| ||||||| | || |||||| ||||||| ||||||||||||||||||||||| |||||| |||||||||||||| |||||||| |||||||||| || + 0 TCCGCCATCACAGCAAAGACGTGAGGAAAAACAACCCAGTACATGGTACGAAGATGATCTCGTCTATCAACCCGGGG-CGG--CTGCTAG-CCACGAGATTACGCCGCCCCTAGG-TTTTTCCAGATACATTACCCAAGGCCTTGGCATTGAGCACTAATCGATAGTTACTCGTGCCAAGATGTAACGC-AAAG-AATTT-A-CTCGTTCTCTCGACGCTAACG-ATGGTCAGGGATAGTGTTGACG-TCCCTATGTGGTTACTCTTCCCTACGCCTGGATG-CGT-TGCG-CTATACAGGACAGTTTTTTATTTTGGTGCCCCCGTATCGTTACACATTGAGTTGGCAGCTGAAGATTGCACGCCACCCCCCCGCGGGCTGACGGTTGTAAGCCTACCCCTAGTCTGGCGGACTAATTATTCTCGAGTAAATAA-AAGCGTC-AAG-TGAGACTCGATTCTAATGCACATTGCGGGGTTCTCCATTGTAA-TATTCCCATA-ACACTCCTGCAGTAATAGCCGTATCTAATAACGTACCTTCTTCCCCACTGAGACTTAC--AGTCATTGGGTCGACTGTTTGATGACCAAC-CGCGGGGCTATAGGGGCAAGCT-CACTGGGGGGGAACATGCGGGTGATGGGCGCTAACCGCCCGC-AGTGACATGCACATGTCAGTCGGCGACT-ACAGTCCGGGCGTAATCTATTTTTCATCAGCTCGGCTCGCTTATC-TTACCGTTATAAGTGCTTTCAG 730 + [D26:A,I30:A,I73:G,D76:G,D80:C,D81:T,D82:G,S85:A->G,I86:C,I86:T,I86:A,I104:C,I106:T,S106:C->A,D107:T,S108:A->G,D110:G,I133:G,D134:G,I221:A,S221:A->G,D222:G,I254:T,S255:T->C,S258:C->T,D259:T,I291:T,D293:T,I324:T,D325:T,I329:T,D330:T,I356:C,D357:C,I367:G,S367:G->A,D368:A,I378:G,S378:G->C,D379:C,I406:T,S407:T->C,D408:C,I425:G,S425:G->T,D426:T,I441:T,D442:T,I467:A,S467:A->T,D468:T,I526:C,S529:C->A,D530:A,I583:A,S583:A->G,D587:G,I598:G,D600:G,I619:G,I619:G,I620:C,D621:G,S623:G->T,S624:C->A,D625:T,S627:A->C,D629:C,I643:T,S643:T->G,D644:G] + 0 TCCGCCATCACAGCAAAGACGTGAGGAAAA-ACAACCCAGTACATGGTACGAAGATGATCTCGTCTATCAACCC-GGGGCGGCTGCTA---GCCACGAGATTACGCCGC-CC-CTAGGTTTTTCCAGATACATTACCCAA-GGCCTTGGCATTGAGCACTAATCGATAGTTACTCGTGCCAAGATGTAACGCAAAGAATTTACTCGTTCTCTCGACGCTAACGATGGTC-AGGGATAGTGTTGACGTCCCTATGTGGTTACTC-TTCCCTACGCCTGGATGCGTTGCGCTATACAGGACAG-TTTTTTATTTTGGTGCCCCCGTATCGTTACACA-TTGAG-TTGGCAGCTGAAGATTGCACGCCACCC-CCCCGCGGGCT-GACGGTTGTAA-GCCTACCCCTAGTCTGGCGGACTAATTA-TTCTCGAGTAAATAAAAGC-GTCAAGTGAGACTCGA-TTCTAATGCACATTGCGGGGTTCTCC-ATTGTAATATTCCCATAACACTCCTGCAGTAATAGCCGTATCTAATAACGTACCTTCTT-CCCCACTGAGACTTACAGTCATTGGGTCGACTGTTTGATGACCAACCGCGGGGCTAT-AGGGGCAAGCTCACT-GGGGGGGAACATGCGGGTGAT--G-GGCGCTAACCGCCCGCAGTGACA-TGCACATGTCAGTCGGCGACTACAGTCCGGGCGTAATCTATTTTTCATCAGCTCGGCTCGCTTATCTTACCGTTATAAGTGCTTTCAG 730 + |||||||||||||||||||||||||| ||| ||||||||||||||||||||||||||||||||||||||||||| ||| ||| || |||||||||||||||||| || | |||||||||||||||||||||| | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||| | || ||||||||||||||||||||||||||||||| || |||||||||||||||||||||||||||||| | ||| | ||||||||||||||||||||||||| | ||||||||| ||||||||| |||||||||||||||||||||||||| | |||||||||||||||| |||||||||||||| | |||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||| |||||||||||||||||||||||||||||||||||||||||||||||||||| ||| |||||||||| || |||||||||||||||||| | | | | | ||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| + 0 TCCGCCATCACAGCAAAGACGTGAGG-AAAAACAACCCAGTACATGGTACGAAGATGATCTCGTCTATCAACCCGGGG-CGG---CTGCTAGCCACGAGATTACGCCGCCCCTA-GG-TTTTTCCAGATACATTACCCAAGG-CCTTGGCATTGAGCACTAATCGATAGTTACTCGTGCCAAGATGTAACGCAAAGAATTTACTCGTTCTCTCGACGCTAACGATGGTCAG-GGATAGTGTTGACGTCCCTATGTGGTTACTCTTCCCT-ACGCCTGGATGCGTTGCGCTATACAGGACAGTTT-TTTATTTTGGTGCCCCCGTATCGTTACACATT-GAGTT-GGCAGCTGAAGATTGCACGCCACCCCC-CCGCGGGCTGA-CGGTTGTAAGC-CTACCCCTAGTCTGGCGGACTAATTATTC-TCGAGTAAATAAAAGCGT-CAAGTGAGACTCGATT-CTAATGCACATTGCGGGGTTCTCCAT-TGTAATATTCCCATAACACTCCTGCAGTAATAGCCGTATCTAATAACGTACCTTCTTCCCCA-CTGAGACTTACAGTCATTGGGTCGACTGTTTGATGACCAACCGCGGGGCTATAGGGG-CAAGCTCACTGGG-GGGGAACATGCGGGTGATGGGCG-CTA-ACC-GCCCGCAGTGACATG-CACATGTCAGTCGGCGACTACAGTCCGGGCGTAATCTATTTTTCATCAGCTCGGCTCGCTTATCTTACCGTTATAAGTGCTTTCAG 730 + com.milaboratory.core.merger.MergerParametersTest > test2 STANDARD_OUT { "qualityMergingAlgorithm": "SumSubtraction", @@ -2979,23 +2479,13 @@ "identityType": "Unweighted" } -com.milaboratory.core.io.sequence.fasta.RandomAccessFastaReaderTest > test1nt STANDARD_ERROR - Indexing milib_326c759082a0fbb2f4959967ff264bbd6632b7093594106240637940121.fasta: 0% - Indexing milib_326c759082a0fbb2f4959967ff264bbd6632b7093594106240637940121.fasta: done - -com.milaboratory.core.io.sequence.fasta.RandomAccessFastaReaderTest > test1 STANDARD_ERROR - Indexing milib_326c759082a0fbb2f4959967ff264bbd6632b7093594106240637940121.fasta: 0% - Indexing milib_326c759082a0fbb2f4959967ff264bbd6632b7093594106240637940121.fasta: done - -com.milaboratory.core.io.sequence.fasta.RandomAccessFastaReaderTest > test2 STANDARD_ERROR - Indexing milib_e2a052d432469e255d0a373ec622d20475dcba0c4532202376860771668.tmp: 0% - Indexing milib_e2a052d432469e255d0a373ec622d20475dcba0c4532202376860771668.tmp: done +com.milaboratory.core.RangeTest > test23e14 STANDARD_OUT + 1000001 + 1010100 + 1000111 + 1000011 -com.milaboratory.core.io.util.IOUtilTest > test111 STANDARD_OUT - 3 - 3 - -2147483648 - -9223372036854775808 + 1000010 com.milaboratory.core.tree.PrimerGenerator > generate SKIPPED @@ -3053,123 +2543,152 @@ ------------------ -com.milaboratory.core.alignment.AlignmentTrimmerTest > testRandom1 STANDARD_OUT - lTrimmed = 1748 - rTrimmed = 1601 - lTrimmed = 2776 - rTrimmed = 2803 - -com.milaboratory.core.alignment.blast.BlastDBBuilderTest > test1 SKIPPED - -com.milaboratory.core.alignment.blast.BlastAlignerTest > test1 SKIPPED - -com.milaboratory.core.alignment.blast.BlastAlignerTest > simpleRandomTestT1 SKIPPED - -com.milaboratory.core.alignment.blast.BlastAlignerTest > simpleRandomTestT2 SKIPPED - -com.milaboratory.core.alignment.blast.BlastAlignerTest > simpleRandomTestT3 SKIPPED - -com.milaboratory.core.alignment.blast.BlastAlignerExtTest > test16SMicrobial1 SKIPPED - -com.milaboratory.core.alignment.blast.BlastAlignerExtTest > test1 SKIPPED - -com.milaboratory.core.alignment.batch.SimpleBatchAlignerTest > test1 STANDARD_OUT - 4 hits. - -com.milaboratory.core.alignment.MultiAlignmentHelperTest > test1 STANDARD_OUT - 8 AGACACAGATACA 20 - ||||||| ||||| - 0 AGACACATATACA 12 - - 0 GATACATTAGACACAGATACA--- 20 - ||||||| ||||| - 0 --------AGACACATATACACAG 15 - - 0 GATACATTAGA---CACAGATACA 20 - ||||||||||| |||||||||| - 5 GATACATTAGAGACCACAGATACA 28 - - 0 GATAC-----ATTAGA---CACAGATACA 20 - ||||| |||||| |||||||||| - 0 GATACGATACATTAGAGACCACAGATACA 28 +com.milaboratory.core.io.sequence.fasta.RandomAccessFastaReaderTest > test1nt STANDARD_ERROR + Indexing milib_f4655911efe6769308d5676d1a1a6665c03a395e17677624757433102313.fasta: 0% + Indexing milib_f4655911efe6769308d5676d1a1a6665c03a395e17677624757433102313.fasta: done - Quality 78778 878777 7778887878 - Subject 0 GATAC-----ATTAGA---CACAGATACA--- 20 - Query0 0 aga---cacaTataca 12 - Query1 0 -------------aga---cacaTatacaCAG 15 - Query2 5 gatac-----attagaGACcacagataca 28 - Query3 0 gatacGATACattagaGACcacagataca 28 +com.milaboratory.core.io.sequence.fasta.RandomAccessFastaReaderTest > test1 STANDARD_ERROR + Indexing milib_f4655911efe6769308d5676d1a1a6665c03a395e17677624757433102313.fasta: 0% + Indexing milib_f4655911efe6769308d5676d1a1a6665c03a395e17677624757433102313.fasta: done - Quality 78778 - Subject 0 GATAC 4 - Query1 0 ----- 0 - Query2 5 gatac 9 - Query3 0 gatac 4 +com.milaboratory.core.io.sequence.fasta.RandomAccessFastaReaderTest > test2 STANDARD_ERROR + Indexing milib_b737b4a22d18e6a3f5b3cd68c18a3016f1844e7e13917634565446873680.tmp: 0% + Indexing milib_b737b4a22d18e6a3f5b3cd68c18a3016f1844e7e13917634565446873680.tmp: done - Quality - Subject 5 ----- 5 - Query1 0 ----- 0 - Query2 10 ----- 10 - Query3 5 GATAC 9 +com.milaboratory.core.io.util.IOUtilTest > test111 STANDARD_OUT + 3 + 3 + -2147483648 + -9223372036854775808 - Quality 87877 - Subject 5 ATTAG 9 - Query0 0 ag 1 - Query1 0 ---ag 1 - Query2 10 attag 14 - Query3 10 attag 14 +com.milaboratory.core.sequence.GeneticCodeTest > generateExtendedGeneticCode SKIPPED - Quality 7 7 - Subject 10 A---C 11 - Query0 2 a---c 3 - Query1 2 a---c 3 - Query2 15 aGACc 19 - Query3 15 aGACc 19 +com.milaboratory.core.sequence.quality.QualityTrimmerTest > testParametersSerialization0 STANDARD_OUT + { + "averageQualityThreshold": 7.0, + "windowSize": 6 + } - Quality 77888 - Subject 12 ACAGA 16 - Query0 4 acaTa 8 - Query1 4 acaTa 8 - Query2 20 acaga 24 - Query3 20 acaga 24 +com.milaboratory.core.sequence.quality.QualityAggregatorTest > test1 STANDARD_OUT + 48 - Quality 7878 - Subject 17 TACA- 20 - Query0 9 taca 12 - Query1 9 tacaC 13 - Query2 25 taca 28 - Query3 25 taca 28 +com.milaboratory.core.sequence.quality.QualityAggregatorTest > test2 STANDARD_OUT + 610 - Quality - Subject 21 -- 21 - Query1 14 AG 15 +com.milaboratory.core.sequence.quality.QualityAggregatorTest > test3 STANDARD_OUT + 2509 - 0 GATAC-----ATTAGA---CACAGATACA--- 20 - 0 ...---....T..... 12 - 0 -------------...---....T.....CAG 15 - 5 .....-----......GAC.......... 28 - 0 .....GATAC......GAC.......... 28 +com.milaboratory.core.sequence.ShortSequenceSetTest > test1 STANDARD_OUT + 99953 elements with 366.06KiB in raw nucleotide entropy serialized into 272.85KiB - 787788787777778887878 - 0 GATACATTAGACACAGATACA 20 +com.milaboratory.core.sequence.AminoAcidAlphabetTest > testCalculateMatches SKIPPED -com.milaboratory.core.alignment.MultiAlignmentHelperTest > test2 STANDARD_OUT - 15 TATAGGGAGAACTCCGATCGACATCG 40 - ||||||||| ||||||||||||||| - 0 TATAGGGAG--CTCCGATCGACATCG 23 +com.milaboratory.core.sequence.AminoAcidSequenceTest > testName STANDARD_OUT + 3 - 56 CGATCC--CGGTGACAAAGCGTTCGGACC 82 - |||||| ||||||||||||||||||||| - 0 CGATCCTTCGGTGACAAAGCGTTCGGACC 28 +com.milaboratory.core.sequence.AminoAcidSequenceTest > testConvertPositionSync1 STANDARD_OUT + FromCenter + 2 + 3 + 4 + 5 + 6 + 7 + 8 + 9 + 10 + 11 + 12 + 13 + 14 + 15 + 16 + 17 + 18 + 19 + FromLeftWithoutIncompleteCodon + 2 + 3 + 4 + 5 + 6 + 7 + 8 + 9 + 10 + 11 + 12 + 13 + 14 + 15 + 16 + 17 + 18 + 19 + FromLeftWithIncompleteCodon + 2 + 3 + 4 + 5 + 6 + 7 + 8 + 9 + 10 + 11 + 12 + 13 + 14 + 15 + 16 + 17 + 18 + 19 + FromRightWithoutIncompleteCodon + 2 + 3 + 4 + 5 + 6 + 7 + 8 + 9 + 10 + 11 + 12 + 13 + 14 + 15 + 16 + 17 + 18 + 19 + FromRightWithIncompleteCodon + 2 + 3 + 4 + 5 + 6 + 7 + 8 + 9 + 10 + 11 + 12 + 13 + 14 + 15 + 16 + 17 + 18 + 19 - 36 CATCGGGTATCGCCCTGGTACG 57 - |||| ||||||||||||||||| - 0 CATCAGGTATCGCCCTGGTACG 21 +com.milaboratory.core.sequence.NucleotideAlphabetTest > testCalculateIntersections SKIPPED - 0 AACGATGGGCGCAAATATAGGGAGAACTCCGATCGACATCGGGTATCGCCCTGGTACGATCC--CGGTGACAAAGCGTTCGGACCTGTCTGGACGCTAGAACGC 101 - 0 tatagggag--ctccgatcgacatcg 23 - 0 cgatccTTcggtgacaaagcgttcggacc 28 - 0 catcAggtatcgccctggtacg 21 +com.milaboratory.core.alignment.AlignerTest > testCalculateScore1 STANDARD_OUT + 4.45us + 4.55us + 3.23us com.milaboratory.core.alignment.AlignmentHelperTest > test1 STANDARD_OUT 0 GAGGTGCAGCTGGTGGAGTCTGGGGGAGGC 29 @@ -3213,71 +2732,65 @@ 267 GACACGGCTGTGTATTACTGTGC 289 -com.milaboratory.core.alignment.AlignerCustomTest > testSemiLocal0 STANDARD_OUT - 29.0 - 2 c----cccTTgaa---tgTtaGTa-----taacta--tct 27 - 0 cAGTTccc--gaaACCtgCta--aGCTCTtaactaCTtct 35 - 29.0 - 2 c----cccTTgaa---tgTtaGTa-----taacta--tct 27 - 0 cAGTTccc--gaaACCtgCta--aGCTCTtaactaCTtct 35 +com.milaboratory.core.alignment.AlignmentIteratorTest > test1 STANDARD_OUT + 0 -ATT-AGACA-- 7 + ||| || | + 0 AATTGGGA-ATT 10 + I0AI3GSA3GDC6I8TI8T -com.milaboratory.core.alignment.AlignmentTest > testInvert STANDARD_OUT - 8 AGACACAGATACA 20 - ||||||| ||||| - 0 AGACACATATACA 12 - 0 AGACACATATACA 12 - ||||||| ||||| - 8 AGACACAGATACA 20 +com.milaboratory.core.alignment.BandedAffineAlignerTest > test11 STANDARD_OUT + 0 --------------------- -1 + 0 ATAAAAAAAAAAACGAGCTAG 20 + 0 --------------------- -1 + 0 ATAAAAAAAAAAACGAGCTAG 20 - 0 GATACATTAGACACAGATACA--- 20 - ||||||| ||||| - 0 --------AGACACATATACACAG 15 - 0 --------AGACACATATACACAG 15 - ||||||| ||||| - 0 GATACATTAGACACAGATACA--- 20 +com.milaboratory.core.alignment.BandedAffineAlignerTest > test23 STANDARD_OUT + 0 atgcggggatgc 11 + 0 atgcggggatgc 11 - 0 GATACATTAGA---CACAGATACA 20 - ||||||||||| |||||||||| - 5 GATACATTAGAGACCACAGATACA 28 - 5 GATACATTAGAGACCACAGATACA 28 - ||||||||||| |||||||||| - 0 GATACATTAGA---CACAGATACA 20 +com.milaboratory.core.alignment.BandedAffineAlignerTest > test1 STANDARD_OUT + 0 at-----------cgagctagTTTTTTTTTTT 20 + 0 atAAAAAAAAAAAcgagctag----------- 20 + 0 at-----------cgagctagTTTTTTTTTTT 20 + 0 atAAAAAAAAAAAcgagctag----------- 20 - 0 GATAC-----ATTAGA---CACAGATACA 20 - ||||| |||||| |||||||||| - 0 GATACGATACATTAGAGACCACAGATACA 28 - 0 GATACGATACATTAGAGACCACAGATACA 28 - ||||| |||||| |||||||||| - 0 GATAC-----ATTAGA---CACAGATACA 20 +com.milaboratory.core.alignment.BandedAffineAlignerTest > test2 STANDARD_OUT + 0 atgcGGGGatgc 11 + 0 atgcTA--atgc 9 + 0 atgcGGGGatgc----------- 11 + 0 atgcTA--atgcTTTTTTTTTTT 20 +com.milaboratory.core.alignment.BandedAffineAlignerTest > test3 STANDARD_OUT + 0 cgtaGGGGcgta 11 + 11 cgta--ATcgta 20 + 0 -----------cgtaGGGGcgta 11 + 0 TTTTTTTTTTTcgtaAT--cgta 20 -com.milaboratory.core.alignment.kaligner1.KMapperTest > testBestOffset2 STANDARD_OUT - -205 +com.milaboratory.core.alignment.BandedAffineAlignerTest > test4 STANDARD_OUT + 0 atgcggggat-gTTTTT 15 + 0 atgcggggatAg----- 11 + 0 atgcggggat-gTTTTTTT 17 + 0 atgcggggatAg------- 11 -com.milaboratory.core.alignment.kaligner1.KAlignerTest > testRandomCorrectness STANDARD_OUT - C=1182;I=0;M=0;ScE=0;R=0.0 AlignmentTime = 920.25us - C=1642;I=1;M=0;ScE=0;R=0.0 AlignmentTime = 501.06us - C=2048;I=0;M=0;ScE=0;R=0.0 AlignmentTime = 233.91us - C=2142;I=0;M=0;ScE=0;R=8.333333333333333E-7 AlignmentTime = 246.61us +com.milaboratory.core.alignment.BandedAffineAlignerTest > test5 STANDARD_OUT + 7 g-taggggcgta 17 + 0 gAtaggggcgta 11 -com.milaboratory.core.alignment.kaligner1.KAlignerTest > testRandom1 STANDARD_OUT - ##teamcity[buildStatisticValue key='kmFound' value='0.9449'] - ##teamcity[buildStatisticValue key='kmWrong' value='1.0E-4'] - ##teamcity[buildStatisticValue key='kmFalse' value='0.0058'] + 0 TTTTTTTg-taggggcgta 17 + 0 -------gAtaggggcgta 11 -com.milaboratory.core.alignment.kaligner1.KAlignerTest > testRandomCorrectnessConcurrent STANDARD_OUT - C=2998;I=0;M=0;ScE=1;R=0.0 AlignmentTime = 280.13us - C=3000;I=0;M=0;ScE=0;R=0.0 AlignmentTime = 309.18us - C=2996;I=0;M=0;ScE=0;R=0.0 AlignmentTime = 307.41us - C=3000;I=0;M=0;ScE=0;R=0.0 AlignmentTime = 353.80us +com.milaboratory.core.alignment.BandedAffineAlignerTest > test6 STANDARD_OUT + 0 0 + 0 0 -com.milaboratory.core.alignment.AlignerTest > testCalculateScore1 STANDARD_OUT - 4.41us - 4.43us - 3.37us +com.milaboratory.core.alignment.BandedAffineAlignerTest > semiGlobalLeft1 STANDARD_OUT + 0 gCccTtgtgatgacccagactccagcctccgtgGAGgCaGctgtgggaggcacagtcaccatcaagtgccaggccagtcagagcattagcaacctcttaGCCTGGTATCAGCAGAAACCAGGGCAGCCTCCCAAGCTCCTGATCTATTATGCATCCGATCTGGcatctggggtctcatcaaggttcaaaggcagtggatctgggacagagtAcactctcaccatcagTggcgtgcagtgtgccgatgctgccacttactac 260 + 1 gAccCtgtgatgacccagactccagcctccgtgTCTgAaCctgtgggaggcacagtcaccatcaagtgccaggccagtcagagcattagcaacctctta-------------------------------------------------------------NNNcatctggggtctcatcaaggttcaaaggcagtggatctgggacagagtTcactctcaccatcagCggcgtgcagtgtgccgatgctgccacttactac 200 + +com.milaboratory.core.alignment.kaligner2.OffsetPacksAccumulatorTest > testScoreCorrection2 SKIPPED com.milaboratory.core.alignment.kaligner2.KAligner2Test > testBoundaries STANDARD_OUT - 4965 + 4957 com.milaboratory.core.alignment.kaligner2.KAligner2Test > caseJ1 STANDARD_OUT 52 @@ -3291,15 +2804,15 @@ com.milaboratory.core.alignment.kaligner2.KAligner2Test > testCase0 SKIPPED com.milaboratory.core.alignment.kaligner2.KAligner2Test > testSimpleRandomTest STANDARD_OUT - Time per query: 2.23ms - Processed queries: 19 + Time per query: 1.92ms + Processed queries: 23 Bad percent: 0.0 - False positive percent: 0.6988277727682597 + False positive percent: 0.7040876197926853 Scoring error percent: 0.0 com.milaboratory.core.alignment.kaligner2.KMapper2Test > test11112 STANDARD_OUT ID: 0 - Score: 1716 + Score: 1620 Cluster 0: Q 27 -> T 15 - -12 Q 30 -> T 18 - -12 @@ -3323,16 +2836,14 @@ Q 156 -> T 98 - -58 Q 159 -> T 101 - -58 Cluster 3: - Q 198 -> T 120 - -78 Q 201 -> T 123 - -78 Q 204 -> T 126 - -78 Q 207 -> T 129 - -78 Q 216 -> T 139 - -77 Q 219 -> T 142 - -77 - Q 231 -> T 153 - -78 + Q 222 -> T 145 - -77 Q 234 -> T 156 - -78 Q 237 -> T 159 - -78 - Q 240 -> T 162 - -78 Cluster 4: Q 246 -> T 178 - -68 Q 249 -> T 181 - -68 @@ -3345,7 +2856,7 @@ com.milaboratory.core.alignment.kaligner2.KMapper2Test > test1111 STANDARD_OUT ID: 0 - Score: 1209 + Score: 1260 Cluster 0: Q 9 -> T 15 - 6 Q 12 -> T 18 - 6 @@ -3357,12 +2868,11 @@ Q 30 -> T 36 - 6 Cluster 1: Q 57 -> T 48 - -9 + Q 60 -> T 51 - -9 Q 69 -> T 61 - -8 Q 78 -> T 69 - -9 Q 81 -> T 72 - -9 Q 84 -> T 75 - -9 - Q 87 -> T 78 - -9 - Q 90 -> T 81 - -9 Cluster 2: Q 123 -> T 89 - -34 Q 126 -> T 92 - -34 @@ -3370,20 +2880,22 @@ Q 132 -> T 98 - -34 Q 135 -> T 101 - -34 Q 150 -> T 116 - -34 + Q 168 -> T 132 - -36 Q 171 -> T 135 - -36 Q 174 -> T 138 - -36 Q 177 -> T 141 - -36 Q 180 -> T 144 - -36 Q 183 -> T 147 - -36 + Q 185 -> T 149 - -36 com.milaboratory.core.alignment.kaligner2.KMapper2Test > testRandom1 STANDARD_OUT - noHits: 222 + noHits: 269 noHits2: 0 noHits3: 0 - wrongTopHit: 40 - wrongTopHitS: 28 - noCorrectHitInList: 19 + wrongTopHit: 36 + wrongTopHitS: 25 + noCorrectHitInList: 14 @@ -3391,13 +2903,13 @@ Timings: DescriptiveStatistics: n: 100000 - min: 16038.0 - max: 9.73475694E8 - mean: 263144.3220599702 - std dev: 5400026.380307346 - median: 194951.5 - skewness: 121.66201239293335 - kurtosis: 16670.90900264126 + min: 12979.0 + max: 4.26172795E8 + mean: 222583.6180099821 + std dev: 3426431.4372672574 + median: 173124.0 + skewness: 98.47286053934224 + kurtosis: 9950.251640753775 @@ -3405,14 +2917,14 @@ Clusters basicSize DescriptiveStatistics: - n: 99738 + n: 99695 min: 1.0 max: 6.0 - mean: 2.8758848182237324 - std dev: 1.106528792823208 + mean: 2.8425798685992345 + std dev: 1.1014567162109217 median: 3.0 - skewness: 0.29497130772348684 - kurtosis: -0.6950967554231662 + skewness: 0.32469019242645786 + kurtosis: -0.6613133739096413 @@ -3420,72 +2932,158 @@ Top Delta DescriptiveStatistics: - n: 99759 + n: 99717 min: -29.0 max: 0.0 - mean: -0.001303140568770635 - std dev: 0.15477816420649226 + mean: -0.0016145692309233084 + std dev: 0.17167148412922448 median: 0.0 - skewness: -136.58433377780725 - kurtosis: 20415.36343338452 + skewness: -121.51883851462306 + kurtosis: 16244.013595552413 -com.milaboratory.core.alignment.kaligner2.OffsetPacksAccumulatorTest > testScoreCorrection2 SKIPPED +com.milaboratory.core.alignment.AlignmentTrimmerTest > testRandom1 STANDARD_OUT + lTrimmed = 1716 + rTrimmed = 1711 + lTrimmed = 2881 + rTrimmed = 2806 -com.milaboratory.core.alignment.BandedAffineAlignerTest > test11 STANDARD_OUT - 0 --------------------- -1 - 0 ATAAAAAAAAAAACGAGCTAG 20 - 0 --------------------- -1 - 0 ATAAAAAAAAAAACGAGCTAG 20 +com.milaboratory.core.alignment.blast.BlastAlignerTest > test1 SKIPPED -com.milaboratory.core.alignment.BandedAffineAlignerTest > test23 STANDARD_OUT - 0 atgcggggatgc 11 - 0 atgcggggatgc 11 +com.milaboratory.core.alignment.blast.BlastAlignerTest > simpleRandomTestT1 SKIPPED -com.milaboratory.core.alignment.BandedAffineAlignerTest > test1 STANDARD_OUT - 0 at-----------cgagctagTTTTTTTTTTT 20 - 0 atAAAAAAAAAAAcgagctag----------- 20 - 0 at-----------cgagctagTTTTTTTTTTT 20 - 0 atAAAAAAAAAAAcgagctag----------- 20 +com.milaboratory.core.alignment.blast.BlastAlignerTest > simpleRandomTestT2 SKIPPED -com.milaboratory.core.alignment.BandedAffineAlignerTest > test2 STANDARD_OUT - 0 atgcGGGGatgc 11 - 0 atgcTA--atgc 9 - 0 atgcGGGGatgc----------- 11 - 0 atgcTA--atgcTTTTTTTTTTT 20 +com.milaboratory.core.alignment.blast.BlastAlignerTest > simpleRandomTestT3 SKIPPED -com.milaboratory.core.alignment.BandedAffineAlignerTest > test3 STANDARD_OUT - 0 cgtaGGGGcgta 11 - 11 cgta--ATcgta 20 - 0 -----------cgtaGGGGcgta 11 - 0 TTTTTTTTTTTcgtaAT--cgta 20 +com.milaboratory.core.alignment.blast.BlastDBBuilderTest > test1 SKIPPED -com.milaboratory.core.alignment.BandedAffineAlignerTest > test4 STANDARD_OUT - 0 atgcggggat-gTTTTT 15 - 0 atgcggggatAg----- 11 - 0 atgcggggat-gTTTTTTT 17 - 0 atgcggggatAg------- 11 +com.milaboratory.core.alignment.blast.BlastAlignerExtTest > test16SMicrobial1 SKIPPED -com.milaboratory.core.alignment.BandedAffineAlignerTest > test5 STANDARD_OUT - 7 g-taggggcgta 17 - 0 gAtaggggcgta 11 +com.milaboratory.core.alignment.blast.BlastAlignerExtTest > test1 SKIPPED - 0 TTTTTTTg-taggggcgta 17 - 0 -------gAtaggggcgta 11 +com.milaboratory.core.alignment.kaligner1.KMapperTest > testBestOffset2 STANDARD_OUT + -205 -com.milaboratory.core.alignment.BandedAffineAlignerTest > test6 STANDARD_OUT - 0 0 - 0 0 +com.milaboratory.core.alignment.kaligner1.KAlignerTest > testRandomCorrectness STANDARD_OUT + C=1182;I=0;M=0;ScE=0;R=0.0 AlignmentTime = 1.47ms + C=1642;I=1;M=0;ScE=0;R=0.0 AlignmentTime = 499.95us + C=2048;I=0;M=0;ScE=0;R=0.0 AlignmentTime = 274.26us + C=2142;I=0;M=0;ScE=0;R=8.333333333333333E-7 AlignmentTime = 270.83us -com.milaboratory.core.alignment.BandedAffineAlignerTest > semiGlobalLeft1 STANDARD_OUT - 0 gCccTtgtgatgacccagactccagcctccgtgGAGgCaGctgtgggaggcacagtcaccatcaagtgccaggccagtcagagcattagcaacctcttaGCCTGGTATCAGCAGAAACCAGGGCAGCCTCCCAAGCTCCTGATCTATTATGCATCCGATCTGGcatctggggtctcatcaaggttcaaaggcagtggatctgggacagagtAcactctcaccatcagTggcgtgcagtgtgccgatgctgccacttactac 260 - 1 gAccCtgtgatgacccagactccagcctccgtgTCTgAaCctgtgggaggcacagtcaccatcaagtgccaggccagtcagagcattagcaacctctta-------------------------------------------------------------NNNcatctggggtctcatcaaggttcaaaggcagtggatctgggacagagtTcactctcaccatcagCggcgtgcagtgtgccgatgctgccacttactac 200 +com.milaboratory.core.alignment.kaligner1.KAlignerTest > testRandom1 STANDARD_OUT + ##teamcity[buildStatisticValue key='kmFound' value='0.9449'] + ##teamcity[buildStatisticValue key='kmWrong' value='1.0E-4'] + ##teamcity[buildStatisticValue key='kmFalse' value='0.0058'] -com.milaboratory.core.alignment.AlignmentIteratorTest > test1 STANDARD_OUT - 0 -ATT-AGACA-- 7 - ||| || | - 0 AATTGGGA-ATT 10 - I0AI3GSA3GDC6I8TI8T +com.milaboratory.core.alignment.kaligner1.KAlignerTest > testRandomCorrectnessConcurrent STANDARD_OUT + C=3000;I=0;M=0;ScE=1;R=0.0 AlignmentTime = 3.14ms + C=2998;I=0;M=1;ScE=2;R=0.0 AlignmentTime = 2.79ms + C=2999;I=0;M=0;ScE=0;R=0.0 AlignmentTime = 325.50us + C=2998;I=0;M=0;ScE=0;R=0.0 AlignmentTime = 308.56us + +com.milaboratory.core.alignment.MultiAlignmentHelperTest > test1 STANDARD_OUT + 8 AGACACAGATACA 20 + ||||||| ||||| + 0 AGACACATATACA 12 + + 0 GATACATTAGACACAGATACA--- 20 + ||||||| ||||| + 0 --------AGACACATATACACAG 15 + + 0 GATACATTAGA---CACAGATACA 20 + ||||||||||| |||||||||| + 5 GATACATTAGAGACCACAGATACA 28 + + 0 GATAC-----ATTAGA---CACAGATACA 20 + ||||| |||||| |||||||||| + 0 GATACGATACATTAGAGACCACAGATACA 28 + + Quality 78778 878777 7778887878 + Subject 0 GATAC-----ATTAGA---CACAGATACA--- 20 + Query0 0 aga---cacaTataca 12 + Query1 0 -------------aga---cacaTatacaCAG 15 + Query2 5 gatac-----attagaGACcacagataca 28 + Query3 0 gatacGATACattagaGACcacagataca 28 + + Quality 78778 + Subject 0 GATAC 4 + Query1 0 ----- 0 + Query2 5 gatac 9 + Query3 0 gatac 4 + + Quality + Subject 5 ----- 5 + Query1 0 ----- 0 + Query2 10 ----- 10 + Query3 5 GATAC 9 + + Quality 87877 + Subject 5 ATTAG 9 + Query0 0 ag 1 + Query1 0 ---ag 1 + Query2 10 attag 14 + Query3 10 attag 14 + + Quality 7 7 + Subject 10 A---C 11 + Query0 2 a---c 3 + Query1 2 a---c 3 + Query2 15 aGACc 19 + Query3 15 aGACc 19 + + Quality 77888 + Subject 12 ACAGA 16 + Query0 4 acaTa 8 + Query1 4 acaTa 8 + Query2 20 acaga 24 + Query3 20 acaga 24 + + Quality 7878 + Subject 17 TACA- 20 + Query0 9 taca 12 + Query1 9 tacaC 13 + Query2 25 taca 28 + Query3 25 taca 28 + + Quality + Subject 21 -- 21 + Query1 14 AG 15 + + 0 GATAC-----ATTAGA---CACAGATACA--- 20 + 0 ...---....T..... 12 + 0 -------------...---....T.....CAG 15 + 5 .....-----......GAC.......... 28 + 0 .....GATAC......GAC.......... 28 + + 787788787777778887878 + 0 GATACATTAGACACAGATACA 20 + +com.milaboratory.core.alignment.MultiAlignmentHelperTest > test2 STANDARD_OUT + 15 TATAGGGAGAACTCCGATCGACATCG 40 + ||||||||| ||||||||||||||| + 0 TATAGGGAG--CTCCGATCGACATCG 23 + + 56 CGATCC--CGGTGACAAAGCGTTCGGACC 82 + |||||| ||||||||||||||||||||| + 0 CGATCCTTCGGTGACAAAGCGTTCGGACC 28 + + 36 CATCGGGTATCGCCCTGGTACG 57 + |||| ||||||||||||||||| + 0 CATCAGGTATCGCCCTGGTACG 21 + + 0 AACGATGGGCGCAAATATAGGGAGAACTCCGATCGACATCGGGTATCGCCCTGGTACGATCC--CGGTGACAAAGCGTTCGGACCTGTCTGGACGCTAGAACGC 101 + 0 tatagggag--ctccgatcgacatcg 23 + 0 cgatccTTcggtgacaaagcgttcggacc 28 + 0 catcAggtatcgccctggtacg 21 + +com.milaboratory.core.alignment.AlignerCustomTest > testSemiLocal0 STANDARD_OUT + 29.0 + 2 c----cccTTgaa---tgTtaGTa-----taacta--tct 27 + 0 cAGTTccc--gaaACCtgCta--aGCTCTtaactaCTtct 35 + 29.0 + 2 c----cccTTgaa---tgTtaGTa-----taacta--tct 27 + 0 cAGTTccc--gaaACCtgCta--aGCTCTtaactaCTtct 35 com.milaboratory.core.alignment.BandedLinearAlignerTest > testCase1 STANDARD_OUT GCGTGAAGACTGCAGGCATTGAGTACGTTACTAGTCCAGTGGGGCCCAACCGTAACATTGCGTGTGACTGGTTGCTTAGCGGGTGACGGCGTTTCAGGTTACGCCCTCTGTGCATCACCGATAGCGTTGTTTGAGCTTTCTAACGTCTCAAACCTGCTTGCGCCCTACGGTTTCTCTATATATACACGAAAGGGGCTGGTCGCAACCTCGCAATTCTATCCCTCCAACCTCCCTCGAATTTTT @@ -3511,1396 +3109,1854 @@ |||||| | 1 AATTGACAG 9 -com.milaboratory.core.sequence.AminoAcidAlphabetTest > testCalculateMatches SKIPPED +com.milaboratory.core.alignment.AlignmentTest > testInvert STANDARD_OUT + 8 AGACACAGATACA 20 + ||||||| ||||| + 0 AGACACATATACA 12 + 0 AGACACATATACA 12 + ||||||| ||||| + 8 AGACACAGATACA 20 -com.milaboratory.core.sequence.AminoAcidSequenceTest > testName STANDARD_OUT - 3 + 0 GATACATTAGACACAGATACA--- 20 + ||||||| ||||| + 0 --------AGACACATATACACAG 15 + 0 --------AGACACATATACACAG 15 + ||||||| ||||| + 0 GATACATTAGACACAGATACA--- 20 -com.milaboratory.core.sequence.AminoAcidSequenceTest > testConvertPositionSync1 STANDARD_OUT - FromCenter - 2 - 3 - 4 - 5 - 6 - 7 - 8 - 9 - 10 - 11 - 12 - 13 - 14 - 15 - 16 - 17 - 18 - 19 - FromLeftWithoutIncompleteCodon - 2 - 3 - 4 - 5 - 6 - 7 - 8 - 9 - 10 - 11 - 12 - 13 - 14 - 15 - 16 - 17 - 18 - 19 - FromLeftWithIncompleteCodon - 2 - 3 - 4 - 5 - 6 - 7 - 8 - 9 - 10 - 11 - 12 - 13 - 14 - 15 - 16 - 17 - 18 - 19 - FromRightWithoutIncompleteCodon - 2 - 3 - 4 - 5 - 6 - 7 - 8 - 9 - 10 - 11 - 12 - 13 - 14 - 15 - 16 - 17 - 18 - 19 - FromRightWithIncompleteCodon - 2 - 3 - 4 - 5 - 6 - 7 - 8 - 9 - 10 - 11 - 12 - 13 - 14 - 15 - 16 - 17 - 18 - 19 + 0 GATACATTAGA---CACAGATACA 20 + ||||||||||| |||||||||| + 5 GATACATTAGAGACCACAGATACA 28 + 5 GATACATTAGAGACCACAGATACA 28 + ||||||||||| |||||||||| + 0 GATACATTAGA---CACAGATACA 20 -com.milaboratory.core.sequence.GeneticCodeTest > generateExtendedGeneticCode SKIPPED + 0 GATAC-----ATTAGA---CACAGATACA 20 + ||||| |||||| |||||||||| + 0 GATACGATACATTAGAGACCACAGATACA 28 + 0 GATACGATACATTAGAGACCACAGATACA 28 + ||||| |||||| |||||||||| + 0 GATAC-----ATTAGA---CACAGATACA 20 -com.milaboratory.core.sequence.ShortSequenceSetTest > test1 STANDARD_OUT - 99952 elements with 366.36KiB in raw nucleotide entropy serialized into 273.22KiB -com.milaboratory.core.sequence.NucleotideAlphabetTest > testCalculateIntersections SKIPPED +com.milaboratory.core.alignment.batch.SimpleBatchAlignerTest > test1 STANDARD_OUT + 4 hits. -com.milaboratory.core.sequence.quality.QualityTrimmerTest > testParametersSerialization0 STANDARD_OUT - { - "averageQualityThreshold": 7.0, - "windowSize": 6 - } +com.milaboratory.primitivio.blocks.PrimitivOBlocksTest > benchmark1 SKIPPED -com.milaboratory.core.sequence.quality.QualityAggregatorTest > test1 STANDARD_OUT - 45 +com.milaboratory.primitivio.blocks.PrimitivOBlocksTest > test1 STANDARD_OUT -com.milaboratory.core.sequence.quality.QualityAggregatorTest > test2 STANDARD_OUT - 613 + ================== + High compression: false + Concurrency: 4 + File size: 6799510 + Write time: 655.77ms -com.milaboratory.core.sequence.quality.QualityAggregatorTest > test3 STANDARD_OUT - 2483 + O. Stats: + Wall clock time: 658.45ms + Total CPU time: 1.15s + User wait time: 511.32ms + Serialization time: 609.66ms (52.82%) + Checksum calculation time: 399.68ms (34.63%) + Compression time: 137.34ms (11.9%) + Total IO delay: 177.59ms + Concurrency overhead: 152.68ms + Uncompressed size: 18.44MiB (~2.08KiB per object) + Output size: 6.48MiB (~748B per object; compression = 35.17%) + IO speed: 36.64MiB/s + Concurrency adjusted uncompressed speed: 38.01MiB/s + Actual uncompressed speed: 28.02MiB/s + Actual speed: 9.85MiB/s + Objects: 9079 + Average object size uncompressed: 2.08KiB + Average object size compressed: 748B + Blocks: 62 (~107.1KiB each) + Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 -com.milaboratory.core.mutations.MutationTest > exportRegexps STANDARD_OUT - S([\QAGCTNRYSWKMBDHV\E])(\d+)([\QAGCTNRYSWKMBDHV\E])|D([\QAGCTNRYSWKMBDHV\E])(\d+)|I(\d+)([\QAGCTNRYSWKMBDHV\E]) - S([\Q*ACDEFGHIKLMNPQRSTVWY_XBJZ\E])(\d+)([\Q*ACDEFGHIKLMNPQRSTVWY_XBJZ\E])|D([\Q*ACDEFGHIKLMNPQRSTVWY_XBJZ\E])(\d+)|I(\d+)([\Q*ACDEFGHIKLMNPQRSTVWY_XBJZ\E]) + I. Stats 1: + Wall clock time: 437.31ms + Total CPU time: 499.77ms + Serialization time: 373.07ms (74.65%) + Checksum calculation time: 47.91ms (9.59%) + Compression time: 71.07ms (14.22%) + Total IO delay: 171.17ms + Input size: 6.48MiB + Decompressed size: 18.44MiB (compression = 35.17%) + IO speed: 37.92MiB/s + Concurrency adjusted uncompressed speed: 110.4MiB/s + Actual uncompressed speed: 42.19MiB/s + Actual speed: 14.84MiB/s + Objects: 9079 + Average object size uncompressed: 2.08KiB + Average object size compressed: 748B + Blocks: 62 (~107.1KiB each) + Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 -com.milaboratory.core.mutations.MutationsTest > testCanonical1 STANDARD_OUT - CCTAAAATGTATCCAAGCACCTGTCCTATTGACACCTTGCTACAAGTCAGTTCTAACAATAGGCTCGCAAATGGTCCTGCTTCGATCCAACCTGCTGACTCAGCAACTACTTCCCCACAGCGGCAACTATACAGAACTCTCACCCAGGATAAGGGCCATTCAGTCACACCGGTCCTAATCGCGCAATCACAATACCGGTGTGATTAATGTTCCTCCTTAGTCCTTATATTTCTTAGGTGCCAGAATCGTGACACAGAGACGTCTGCTCCAACATTAATGACTGATCCAGCAGCACGAGTTCCACCACCCCCTCTACTCCCCACATTAGAGTAGGCTTCTTAGCGTGCGTTCCTATGCAAACTAGCAGTAGACTTGTGGAACCCACGATACGTATTTGGATGCGCGTCAGCATTCCGATCTCAATTGACTCTTTTAATCGGGACCCCTCAGTGCGCAACAATACTGCGCTAGTGGATCTGATGGTGCTCTTGGGCACCAGAATATCGCTGCTTGCC - CCTAAAATGTATCCAGCACCTGTCCTATTGACACCTTTCTACAAGTCAGTTCTAAAATAAGGCCTCTAGCAGATGGTCTTGCTTCGATCCAACCTGCTGACTCTGCAACTACTTTCCCACAGGGCAACTATATAGAACTCTCACCCAGGATAAGGGCTTCGGTCGACACTCGGTCCTAATCGCGCAATCACAATACCGGTGTGATTTATGTTCCTCCTTAGTCCTATATTTCTTATGTCGCCAGAATCGTGACACAGAGACGTCTGCTCCAACATTAATGACTGATCCAGCAGCGCGTTCCACCACCCCCCTACTCCCCACATTAGAGTAGGCTTTTTAGCGGCGTTCCTATGCTAACTAGCAGTAGACTTGTGGAACCCACGATACGTATTTGGATGCGCGTCAGCATTCCGATCTAATTGACTCTTCTAACGGGGCCCCTCAGTCGCAAAATACTGCGGCTAGTGGATCTGATGGTGCTTGGACCAGAATGTCGCTGCTTGCC - CCTAAAGATGTATCCAGCACCTGTTATTGACACCTTTTCTACAGCAGTTCTGAAATAAGGCCTCTAGCAGGTGGTCTTTTATCCAAACCTGCGACTCTGCAACTACTTCTCCAGGGCAACTATATGAATGCTCACCCAGGATAAGGGCTATTGGCCGCACCTCGGTCCTAATCGCGCAAACTAATACCGGTGTGATTTGTGTTCCTCCTTGTCCTATATTTCTTATGTCCCAGAATCGTGCACACAGGAGCGTCTGCTCCATCATTAATGACTGATCAGCAGGCGCGTTCCACCACCCCCCTACTCCCCACATTAGAGTAGCGCTTTTTAGCGGCGTTCCTAGTTTACTAGCAGTAGACTGTGGGACCACGTACGTATTTATGCCGCGTCAGCATTCCGATCTAATTGACTCTTCTAACGGGGCCCCTCAGTCGCTAAATACGCGGCTAGGATCTGATTGGTGCTTGGACCAGAATGTCGCTGCTTGCC - 0 CCTAAAGATGTATCC-AGCACCTGT--TATTGACACCTTTTCTAC-AG-CAGTTCTGA-AATAAGGCCTCTAGCAGGTGGT-CT--TT-TATCCAAACCTGC-GACTCTGCAACTACTT-CTC-CAG-GGCAACTATA-TGAA-TGCTCACCCAGGATAAGGGCTATTGGCCG-CAC-CTCGGTCCTAATCGCGCAA--ACTAATACCGGTGTGATTTGTGTTCCTCCTT-GTCC-TATATTTCTTATGTCCCAGAATCGTGCACACAG-GAGCGTCTGCTCCATCATTAATGACTGAT-CAGCAG-GCGCGTTCCACCACCCCC-CTACTCCCCACATTAGAGTAGCGCTTTTTAGCG-GCGTTCCTA-GTTTACTAGCAGTAGAC-TGTGGGA-CCACG-TACGTATTT--ATGCCGCGTCAGCATTCCGATCT-AATTGACTCTTCTAA-CGGGGCCCCTCAGT-CGCTA-AATAC-GCGGCTA--GGATCTGATTGGTG--CTT-GG-ACCAGAATGTCGCTGCTTGCC 488 - |||||| |||||||| ||||||||| |||||||||| || |||| || ||||||| | ||| ||| ||| ||| |||| || || |||| ||||||| ||||| |||||||||| | | ||| |||||||||| ||| | |||||||||||||||||| ||| | | ||| | ||||||||||||||||| || ||||||||||||||| ||||||||||| |||| ||||||||||| || ||||||||||| |||||| || ||||||||||| |||||||||||||| |||||| || |||||||||||||| ||||||||||||||||||||| |||| |||||| ||||||||| | ||||||||||||| ||||| | ||||| ||||||||| ||| ||||||||||||||||||| ||||||||||| ||| |||| ||||||||| ||| | ||||| || |||| |||||||| ||||| ||| || |||||||| |||||||||||| - 0 CCTAAA-ATGTATCCAAGCACCTGTCCTATTGACACC-TTGCTACAAGTCAGTTCTAACAAT-AGG-CTC--GCAAATGGTCCTGCTTCGATCC-AACCTGCTGACTCAGCAACTACTTCCCCACAGCGGCAACTATACAGAACT-CTCACCCAGGATAAGGGCCATT--CAGTCACAC-CGGTCCTAATCGCGCAATCAC-AATACCGGTGTGATTAATGTTCCTCCTTAGTCCTTATATTTCTTAGGTGCCAGAATCGTG-ACACAGAGA-CGTCTGCTCCAACATTAATGACTGATCCAGCAGCACGAGTTCCACCACCCCCTCTACTCCCCACATTAGAGTAG-GCTTCTTAGCGTGCGTTCCTATGCAAACTAGCAGTAGACTTGTGGAACCCACGATACGTATTTGGATG-CGCGTCAGCATTCCGATCTCAATTGACTCTTTTAATCGGGACCCCTCAGTGCGCAACAATACTGC-GCTAGTGGATCTGA-TGGTGCTCTTGGGCACCAGAATATCGCTGCTTGCC 514 - [I14:A,D15:A,I24:C,D25:C,D36:T,S38:G->T,I39:G,I75:C,D76:C,I78:G,I78:C,S78:G->T,D79:C,I81:C,S81:T->G,D82:C,D83:G,D111:T,S112:C->T,I113:C,I131:C,S131:C->A,D132:A,D155:C,D157:A,S158:T->C,I159:A,S160:C->T,D161:A,D162:G,S163:T->C,S164:C->A,S165:A->G,I166:T,I168:C,I168:A,I186:T,S186:T->C,D187:C,I223:T,D224:T,I285:C,D286:C,I291:G,I291:C,S291:G->A,S293:A->G,S294:C->A,D296:A,D297:G,I354:T,I354:G,S354:T->C,D355:G,S356:C->A,D358:A,I372:T,D373:T,D395:T,S396:G->T,I397:G,I470:G,I470:T,D471:T,D473:G,I485:C,S485:C->T,D486:T] - 0 CCTAAAATGTATCC-AAGCACCTGT-CCTATTGACACCTTG-CTACAAGTCAGTTCTAACAATAGGCTCGCAAATGGT-CCT--GCT-TCGATCCAACCTGCTGACTCAGCAACTACTTC-CCCACAGCGGCAACTATA-CAGAACTCTCACCCAGGATAAGGGCCAT-TCAGTCA-CA--CCGGTCCTAATCGCGCAA-TCACAATACCGGTGTGATTAATGTTCCTCCTTAGTCC-TTATATTTCTTAGGTGCCAGAATCGTGACACAGAGACGTCTGCTCCAACATTAATGACTGAT-CCAGCA--GCACGAGTTCCACCACCCCCTCTACTCCCCACATTAGAGTAGGCTTCTTAGCGTGCGTTCCTA--TGCAAACTAGCAGTAGAC-TTGTGGAACCCACGATACGTATTTG-GATGCGCGTCAGCATTCCGATCTCAATTGACTCTTTTAATCGGGACCCCTCAGTGCGCAACAATACTGCGCTA--GTGGATCTGATGGTG-CTCTTGGGCACCAGAATATCGCTGCTTGCC 514 - |||||||||||||| | |||||||| | |||||||||| | |||||||||||||||||||||||||||||||||||| | | | ||||||||||||||||||||||||||| |||||||||||||||||| |||||||||||||||||||||| | | || |||||||||||||||||| ||||||||||||||||||||||||||||||||||| | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| | |||| | | |||||||||||||||||||||||||||||||||||||||||||||||||||||||| | ||||||||||||| | ||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| | | ||||||||||| |||||||||||||||||||||||||||| - 0 CCTAAAATGTATCCAA-GCACCTGTCC-TATTGACACC-TTGCTACAAGTCAGTTCTAACAATAGGCTCGCAAATGGTCC-TGCT-TCG--ATCCAACCTGCTGACTCAGCAACTACT-TCCCCACAGCGGCAACTATACA-GAACTCTCACCCAGGATAAGGG-C-CATT--CAGTCACACCGGTCCTAATCGCGCAATC-ACAATACCGGTGTGATTAATGTTCCTCCTTAGTCCTT-ATATTTCTTAGGTGCCAGAATCGTGACACAGAGACGTCTGCTCCAACATTAATGACTGATCC-AGCAGCACGAG--TTCCACCACCCCCTCTACTCCCCACATTAGAGTAGGCTTCTTAGCGTGCGTTCCTATGC-AA-ACTAGCAGTAGACTT-GTGGAACCCACGATACGTATT-TGGATGCGCGTCAGCATTCCGATCTCAATTGACTCTTTTAATCGGGACCCCTCAGTGCGCAACAATACTGCGCTAGTG-G-ATCTGATGGTGCT-CTTGGGCACCAGAATATCGCTGCTTGCC 514 + I. Stats 2: + Wall clock time: 811.3ms + Total CPU time: 740.1ms + Serialization time: 485.37ms (65.58%) + Checksum calculation time: 95.78ms (12.94%) + Compression time: 142.41ms (19.24%) + Total IO delay: 352ms + Input size: 12.97MiB + Decompressed size: 36.87MiB (compression = 35.17%) + IO speed: 36.84MiB/s + Concurrency adjusted uncompressed speed: 135.07MiB/s + Actual uncompressed speed: 45.47MiB/s + Actual speed: 15.99MiB/s + Objects: 18158 + Average object size uncompressed: 2.08KiB + Average object size compressed: 748B + Blocks: 124 (~107.1KiB each) + Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 -com.milaboratory.core.mutations.MutationsUtilTest > test1111 STANDARD_OUT - S([\QAGCTNRYSWKMBDHV\E])(\d+)([\QAGCTNRYSWKMBDHV\E])|D([\QAGCTNRYSWKMBDHV\E])(\d+)|I(\d+)([\QAGCTNRYSWKMBDHV\E]) - S([\Q*ACDEFGHIKLMNPQRSTVWY_XBJZ\E])(\d+)([\Q*ACDEFGHIKLMNPQRSTVWY_XBJZ\E])|D([\Q*ACDEFGHIKLMNPQRSTVWY_XBJZ\E])(\d+)|I(\d+)([\Q*ACDEFGHIKLMNPQRSTVWY_XBJZ\E]) + ================== + High compression: false + Concurrency: 4 + File size: 6791878 + Write time: 217.72ms -com.milaboratory.core.mutations.MutationsUtilTest > nt2AAWithMappingManual1 STANDARD_OUT - [I2C::SM0I, I2G::I1A, I2C::I1A, SG2C:SM0I:I1A] + O. Stats: + Wall clock time: 219.34ms + Total CPU time: 263.14ms + User wait time: 171.65ms + Serialization time: 106.97ms (40.65%) + Checksum calculation time: 59ms (22.42%) + Compression time: 92.67ms (35.22%) + Total IO delay: 65.15ms + Concurrency overhead: 10.4ms + Uncompressed size: 18.44MiB (~2.08KiB per object) + Output size: 6.48MiB (~748B per object; compression = 35.13%) + IO speed: 99.65MiB/s + Concurrency adjusted uncompressed speed: 200.4MiB/s + Actual uncompressed speed: 84.19MiB/s + Actual speed: 29.58MiB/s + Objects: 9079 + Average object size uncompressed: 2.08KiB + Average object size compressed: 748B + Blocks: 20 (~331.63KiB each) + Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 -com.milaboratory.core.mutations.MutationsUtilTest > nt2AAWithMappingManual2 STANDARD_OUT - [S0:T->N,D13:V,S14:S->Y,S15:P->R,S16:W->P,S17:Y->G,S18:D->T,S19:P->I,S20:G->P,S21:D->A,S22:K->T,S23:A->K,S24:F->R,S25:G->S,S26:P->D,I27:S] - [-1, -1, 9, 15] + I. Stats 1: + Wall clock time: 258.5ms + Total CPU time: 256.8ms + Serialization time: 106.71ms (41.55%) + Checksum calculation time: 59.03ms (22.99%) + Compression time: 89.22ms (34.74%) + Total IO delay: 67.87ms + Input size: 6.48MiB + Decompressed size: 18.44MiB (compression = 35.13%) + IO speed: 96.68MiB/s + Concurrency adjusted uncompressed speed: 227.62MiB/s + Actual uncompressed speed: 71.46MiB/s + Actual speed: 25.11MiB/s + Objects: 9079 + Average object size uncompressed: 2.08KiB + Average object size compressed: 748B + Blocks: 20 (~331.63KiB each) + Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 -com.milaboratory.core.mutations.MutationsUtilTest > nt2AAWithMappingManual3 STANDARD_OUT - 0 CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTACGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA 295 - |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||| ||||| ||||||||||||||||||||||||||||| ||||||||| ||||||||| ||||||||||||||||||| || ||||| ||| || |||||||||||||| - 0 CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTACGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACATTCTATGCAGAGAAGTTCCAGGGCAGAGTCACCATGACCACAGACGCATCCACGACCACAGCCTATATGGAGCTGAGGAGCCTGACATTTGACG-----GCCACATACTACTGTGCGAGAGA 290 - [S58:N->F,S61:Q->E,S63:L->F,S73:T->A,S76:S->T,S86:R->T,S87:S->F,S89:D->G,D90:T,D91:A,S92:V->H,S93:Y->I,S94:Y->L,S95:C->L,S96:A->C,S97:R->E,S98:_->R] - QVQLVQSGAEVKKPGASVKVSCKASGYTFTSYGISWVRQAPGQGLEWMGWISAYNGNTFYAEKFQGRVTMTTDASTTTAYMELRSLTFDGHILLCER - QVQLVQSGAEVKKPGASVKVSCKASGYTFTSYGISWVRQAPGQGLEWMGWISAYNGNTFYAEKFQGRVTMTTDASTTTAYMELRSLTFDGHILLCER - [S58:N->F,S61:Q->E,S63:L->F,S73:T->A,S76:S->T,S86:R->T,S87:S->F,S89:D->G,D90:T,D91:A,S92:V->H,S93:Y->I,S94:Y->L,S95:C->L,S96:A->C,S97:R->E,S98:_->R] - [0, 0, 1, 2, 3, 4, -1, 5, 6, 7, 7, 8, 8, 8, 10, 10, 11, 12] + I. Stats 2: + Wall clock time: 530.43ms + Total CPU time: 485.31ms + Serialization time: 182.6ms (37.62%) + Checksum calculation time: 120.8ms (24.89%) + Compression time: 179.04ms (36.89%) + Total IO delay: 115.81ms + Input size: 12.95MiB + Decompressed size: 36.87MiB (compression = 35.13%) + IO speed: 112.65MiB/s + Concurrency adjusted uncompressed speed: 245.83MiB/s + Actual uncompressed speed: 69.57MiB/s + Actual speed: 24.44MiB/s + Objects: 18158 + Average object size uncompressed: 2.08KiB + Average object size compressed: 748B + Blocks: 40 (~331.63KiB each) + Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 -com.milaboratory.core.mutations.MutationsUtilTest > nt2AAWithMappingManual4 STANDARD_OUT - [S3:S->M,D4:D,S5:_->I] + ================== + High compression: false + Concurrency: 1 + File size: 6799510 + Write time: 338.17ms -com.milaboratory.core.RangeTest > test23e14 STANDARD_OUT - 1000001 - 1010100 - 1000111 - 1000011 + O. Stats: + Wall clock time: 339.92ms + Total CPU time: 217.9ms + User wait time: 303.45ms + Serialization time: 98.66ms (45.28%) + Checksum calculation time: 47.92ms (21.99%) + Compression time: 63.25ms (29.03%) + Total IO delay: 58.22ms + Concurrency overhead: 26.01ms + Uncompressed size: 18.44MiB (~2.08KiB per object) + Output size: 6.48MiB (~748B per object; compression = 35.17%) + IO speed: 111.8MiB/s + Concurrency adjusted uncompressed speed: 61.05MiB/s + Actual uncompressed speed: 54.39MiB/s + Actual speed: 19.13MiB/s + Objects: 9079 + Average object size uncompressed: 2.08KiB + Average object size compressed: 748B + Blocks: 62 (~107.1KiB each) + Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 + Checksum ok! - 1000010 + I. Stats 1: + Wall clock time: 240.68ms + Total CPU time: 238.76ms + Serialization time: 96.88ms (40.57%) + Checksum calculation time: 54.63ms (22.88%) + Compression time: 82.82ms (34.69%) + Total IO delay: 102.48ms + Input size: 6.48MiB + Decompressed size: 18.44MiB (compression = 35.17%) + IO speed: 63.57MiB/s + Concurrency adjusted uncompressed speed: 54.07MiB/s + Actual uncompressed speed: 76.82MiB/s + Actual speed: 27.02MiB/s + Objects: 9079 + Average object size uncompressed: 2.08KiB + Average object size compressed: 748B + Blocks: 62 (~107.1KiB each) + Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 -com.milaboratory.util.CacheTest > test1 STANDARD_OUT - Cache misses:400 - Cache hits:800 + I. Stats 2: + Wall clock time: 590.7ms + Total CPU time: 506.29ms + Serialization time: 194ms (38.32%) + Checksum calculation time: 136.83ms (27.03%) + Compression time: 157.14ms (31.04%) + Total IO delay: 294.04ms + Input size: 12.97MiB + Decompressed size: 36.87MiB (compression = 35.17%) + IO speed: 44.11MiB/s + Concurrency adjusted uncompressed speed: 46.09MiB/s + Actual uncompressed speed: 62.5MiB/s + Actual speed: 21.98MiB/s + Objects: 18158 + Average object size uncompressed: 2.08KiB + Average object size compressed: 748B + Blocks: 124 (~107.1KiB each) + Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 -com.milaboratory.util.VersionInfoTest > test3 SKIPPED + ================== + High compression: false + Concurrency: 1 + File size: 6791878 + Write time: 270.28ms -com.milaboratory.util.AtomicEnumHistogramTest > test1 STANDARD_OUT - {"labels":["A","B","C","null"],"hist":[1,2,0,1]} + O. Stats: + Wall clock time: 272.93ms + Total CPU time: 202.89ms + User wait time: 241.05ms + Serialization time: 81.59ms (40.21%) + Checksum calculation time: 46.77ms (23.05%) + Compression time: 70.65ms (34.82%) + Total IO delay: 36.12ms + Concurrency overhead: 2.49ms + Uncompressed size: 18.44MiB (~2.08KiB per object) + Output size: 6.48MiB (~748B per object; compression = 35.13%) + IO speed: 179.92MiB/s + Concurrency adjusted uncompressed speed: 76.5MiB/s + Actual uncompressed speed: 67.78MiB/s + Actual speed: 23.81MiB/s + Objects: 9079 + Average object size uncompressed: 2.08KiB + Average object size compressed: 748B + Blocks: 20 (~331.63KiB each) + Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 + Checksum ok! + + I. Stats 1: + Wall clock time: 207.15ms + Total CPU time: 201.64ms + Serialization time: 54.26ms (26.91%) + Checksum calculation time: 63.42ms (31.45%) + Compression time: 82.69ms (41.01%) + Total IO delay: 57.45ms + Input size: 6.48MiB + Decompressed size: 18.44MiB (compression = 35.13%) + IO speed: 113.64MiB/s + Concurrency adjusted uncompressed speed: 71.18MiB/s + Actual uncompressed speed: 89.07MiB/s + Actual speed: 31.29MiB/s + Objects: 9079 + Average object size uncompressed: 2.08KiB + Average object size compressed: 748B + Blocks: 20 (~331.63KiB each) + Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 + + I. Stats 2: + Wall clock time: 482.19ms + Total CPU time: 416.42ms + Serialization time: 128.11ms (30.76%) + Checksum calculation time: 128.95ms (30.97%) + Compression time: 157.11ms (37.73%) + Total IO delay: 107.4ms + Input size: 12.95MiB + Decompressed size: 36.87MiB (compression = 35.13%) + IO speed: 121.07MiB/s + Concurrency adjusted uncompressed speed: 70.5MiB/s + Actual uncompressed speed: 76.5MiB/s + Actual speed: 26.88MiB/s + Objects: 18158 + Average object size uncompressed: 2.08KiB + Average object size compressed: 748B + Blocks: 40 (~331.63KiB each) + Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 + Pending / IO / Serde: 3 / 1 / 0 + Pending / IO / Serde: 2 / 0 / 2 + + ================== + High compression: true + Concurrency: 4 + File size: 4156299 + Write time: 4.26s + + O. Stats: + Wall clock time: 4.26s + Total CPU time: 11.29s + User wait time: 4.03s + Serialization time: 100.32ms (0.89%) + Checksum calculation time: 54.13ms (0.48%) + Compression time: 11.12s (98.56%) + Total IO delay: 115.42ms + Concurrency overhead: 63.97ms + Uncompressed size: 18.44MiB (~2.08KiB per object) + Output size: 3.96MiB (~457B per object; compression = 21.5%) + IO speed: 34.47MiB/s + Concurrency adjusted uncompressed speed: 6.33MiB/s + Actual uncompressed speed: 4.32MiB/s + Actual speed: 952.12KiB/s + Objects: 9079 + Average object size uncompressed: 2.08KiB + Average object size compressed: 457B + Blocks: 62 (~65.47KiB each) + Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 + + I. Stats 1: + Wall clock time: 173.59ms + Total CPU time: 181.26ms + Serialization time: 71.23ms (39.29%) + Checksum calculation time: 47.04ms (25.95%) + Compression time: 58.33ms (32.18%) + Total IO delay: 83.34ms + Input size: 3.96MiB + Decompressed size: 18.44MiB (compression = 21.5%) + IO speed: 47.76MiB/s + Concurrency adjusted uncompressed speed: 279.35MiB/s + Actual uncompressed speed: 106.57MiB/s + Actual speed: 22.91MiB/s + Objects: 9079 + Average object size uncompressed: 2.08KiB + Average object size compressed: 457B + Blocks: 62 (~65.47KiB each) + Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 + + I. Stats 2: + Wall clock time: 380.34ms + Total CPU time: 368.46ms + Serialization time: 147.7ms (40.09%) + Checksum calculation time: 95.65ms (25.96%) + Compression time: 116.56ms (31.63%) + Total IO delay: 158.94ms + Input size: 7.93MiB + Decompressed size: 36.87MiB (compression = 21.5%) + IO speed: 50.17MiB/s + Concurrency adjusted uncompressed speed: 281.48MiB/s + Actual uncompressed speed: 97.04MiB/s + Actual speed: 20.86MiB/s + Objects: 18158 + Average object size uncompressed: 2.08KiB + Average object size compressed: 457B + Blocks: 124 (~65.47KiB each) + Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 + Pending / IO / Serde: 2 / 0 / 2 + Pending / IO / Serde: 2 / 0 / 2 + Pending / IO / Serde: 1 / 0 / 1 + + ================== + High compression: true + Concurrency: 4 + File size: 4098671 + Write time: 6.29s + + O. Stats: + Wall clock time: 6.29s + Total CPU time: 10.43s + User wait time: 5.71s + Serialization time: 78.28ms (0.75%) + Checksum calculation time: 46.83ms (0.45%) + Compression time: 10.3s (98.76%) + Total IO delay: 30.33ms + Concurrency overhead: 4.19ms + Uncompressed size: 18.44MiB (~2.08KiB per object) + Output size: 3.91MiB (~451B per object; compression = 21.2%) + IO speed: 130.29MiB/s + Concurrency adjusted uncompressed speed: 7.04MiB/s + Actual uncompressed speed: 2.93MiB/s + Actual speed: 636.24KiB/s + Objects: 9079 + Average object size uncompressed: 2.08KiB + Average object size compressed: 451B + Blocks: 20 (~200.13KiB each) + Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 + + I. Stats 1: + Wall clock time: 158.87ms + Total CPU time: 161.73ms + Serialization time: 48.47ms (29.97%) + Checksum calculation time: 50.63ms (31.31%) + Compression time: 61.96ms (38.31%) + Total IO delay: 16.79ms + Input size: 3.91MiB + Decompressed size: 18.44MiB (compression = 21.2%) + IO speed: 244.3MiB/s + Concurrency adjusted uncompressed speed: 419.02MiB/s + Actual uncompressed speed: 116.69MiB/s + Actual speed: 24.74MiB/s + Objects: 9079 + Average object size uncompressed: 2.08KiB + Average object size compressed: 451B + Blocks: 20 (~200.13KiB each) + Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 + + I. Stats 2: + Wall clock time: 362.05ms + Total CPU time: 319.47ms + Serialization time: 96.74ms (30.28%) + Checksum calculation time: 97.3ms (30.46%) + Compression time: 124.21ms (38.88%) + Total IO delay: 42.27ms + Input size: 7.82MiB + Decompressed size: 36.87MiB (compression = 21.2%) + IO speed: 186.13MiB/s + Concurrency adjusted uncompressed speed: 409.71MiB/s + Actual uncompressed speed: 101.86MiB/s + Actual speed: 21.6MiB/s + Objects: 18158 + Average object size uncompressed: 2.08KiB + Average object size compressed: 451B + Blocks: 40 (~200.13KiB each) + Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 + Pending / IO / Serde: 0 / 0 / 1 + Pending / IO / Serde: 0 / 0 / 1 + Pending / IO / Serde: 0 / 0 / 1 + Pending / IO / Serde: 0 / 0 / 1 + + ================== + High compression: true + Concurrency: 1 + File size: 4156299 + Write time: 9.51s + + O. Stats: + Wall clock time: 9.51s + Total CPU time: 9.42s + User wait time: 9.48s + Serialization time: 89.83ms (0.95%) + Checksum calculation time: 47.66ms (0.51%) + Compression time: 9.28s (98.45%) + Total IO delay: 42.88ms + Concurrency overhead: 8.17ms + Uncompressed size: 18.44MiB (~2.08KiB per object) + Output size: 3.96MiB (~457B per object; compression = 21.5%) + IO speed: 94.38MiB/s + Concurrency adjusted uncompressed speed: 1.95MiB/s + Actual uncompressed speed: 1.94MiB/s + Actual speed: 426.8KiB/s + Objects: 9079 + Average object size uncompressed: 2.08KiB + Average object size compressed: 457B + Blocks: 62 (~65.47KiB each) + Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 + Checksum ok! + + I. Stats 1: + Wall clock time: 148.66ms + Total CPU time: 167.42ms + Serialization time: 56.86ms (33.97%) + Checksum calculation time: 48.15ms (28.76%) + Compression time: 59.99ms (35.84%) + Total IO delay: 40.46ms + Input size: 3.96MiB + Decompressed size: 18.44MiB (compression = 21.5%) + IO speed: 99.09MiB/s + Concurrency adjusted uncompressed speed: 89.07MiB/s + Actual uncompressed speed: 124.57MiB/s + Actual speed: 26.78MiB/s + Objects: 9079 + Average object size uncompressed: 2.08KiB + Average object size compressed: 457B + Blocks: 62 (~65.47KiB each) + Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 + + I. Stats 2: + Wall clock time: 326.33ms + Total CPU time: 333.38ms + Serialization time: 111.54ms (33.46%) + Checksum calculation time: 95.79ms (28.73%) + Compression time: 119.89ms (35.96%) + Total IO delay: 77.64ms + Input size: 7.93MiB + Decompressed size: 36.87MiB (compression = 21.5%) + IO speed: 102.95MiB/s + Concurrency adjusted uncompressed speed: 89.72MiB/s + Actual uncompressed speed: 113.11MiB/s + Actual speed: 24.32MiB/s + Objects: 18158 + Average object size uncompressed: 2.08KiB + Average object size compressed: 457B + Blocks: 124 (~65.47KiB each) + Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 + Pending / IO / Serde: 0 / 0 / 1 + Pending / IO / Serde: 0 / 0 / 1 + Pending / IO / Serde: 0 / 0 / 1 + Pending / IO / Serde: 0 / 0 / 1 + Pending / IO / Serde: 0 / 0 / 1 + + ================== + High compression: true + Concurrency: 1 + File size: 4098671 + Write time: 10.04s + + O. Stats: + Wall clock time: 10.04s + Total CPU time: 9.98s + User wait time: 10.01s + Serialization time: 78.6ms (0.79%) + Checksum calculation time: 47ms (0.47%) + Compression time: 9.85s (98.64%) + Total IO delay: 26.38ms + Concurrency overhead: 2.04ms + Uncompressed size: 18.44MiB (~2.08KiB per object) + Output size: 3.91MiB (~451B per object; compression = 21.2%) + IO speed: 150.34MiB/s + Concurrency adjusted uncompressed speed: 1.84MiB/s + Actual uncompressed speed: 1.84MiB/s + Actual speed: 398.79KiB/s + Objects: 9079 + Average object size uncompressed: 2.08KiB + Average object size compressed: 451B + Blocks: 20 (~200.13KiB each) + Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 + Checksum ok! + + I. Stats 1: + Wall clock time: 152.77ms + Total CPU time: 151.16ms + Serialization time: 47.39ms (31.35%) + Checksum calculation time: 46.84ms (30.99%) + Compression time: 56.21ms (37.19%) + Total IO delay: 19.27ms + Input size: 3.91MiB + Decompressed size: 18.44MiB (compression = 21.2%) + IO speed: 205.73MiB/s + Concurrency adjusted uncompressed speed: 108.45MiB/s + Actual uncompressed speed: 121.3MiB/s + Actual speed: 25.72MiB/s + Objects: 9079 + Average object size uncompressed: 2.08KiB + Average object size compressed: 451B + Blocks: 20 (~200.13KiB each) + Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 + + I. Stats 2: + Wall clock time: 334.86ms + Total CPU time: 301.16ms + Serialization time: 94.86ms (31.5%) + Checksum calculation time: 93.49ms (31.04%) + Compression time: 111.4ms (36.99%) + Total IO delay: 37.08ms + Input size: 7.82MiB + Decompressed size: 36.87MiB (compression = 21.2%) + IO speed: 211.29MiB/s + Concurrency adjusted uncompressed speed: 109.09MiB/s + Actual uncompressed speed: 110.4MiB/s + Actual speed: 23.41MiB/s + Objects: 18158 + Average object size uncompressed: 2.08KiB + Average object size compressed: 451B + Blocks: 40 (~200.13KiB each) + Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 + +com.milaboratory.primitivio.blocks.PrimitivOBlocksTest > bigBlocks STANDARD_OUT + Pending / IO / Serde / Objs: 0 / 1 / 1 / 2000 + Pending / IO / Serde / Objs: 0 / 1 / 1 / 5000 + Pending / IO / Serde / Objs: 0 / 1 / 1 / 8000 + Pending / IO / Serde / Objs: 3 / 1 / 0 / 12000 + Pending / IO / Serde / Objs: 6 / 1 / 1 / 15000 + Pending / IO / Serde / Objs: 7 / 1 / 0 / 17000 + Pending / IO / Serde / Objs: 7 / 1 / 0 / 18000 + Pending / IO / Serde / Objs: 7 / 1 / 0 / 19000 + Pending / IO / Serde / Objs: 7 / 1 / 0 / 19000 + Pending / IO / Serde / Objs: 7 / 1 / 0 / 20000 + Pending / IO / Serde / Objs: 7 / 1 / 0 / 20000 + Pending / IO / Serde / Objs: 6 / 1 / 0 / 20000 + Pending / IO / Serde / Objs: 6 / 1 / 0 / 20000 + Pending / IO / Serde / Objs: 6 / 1 / 0 / 20000 + Pending / IO / Serde / Objs: 2 / 1 / 0 / 20000 + O. Stats: + Wall clock time: 31.13s + Total CPU time: 9.86s + User wait time: 8.86s + Serialization time: 1.74s (17.69%) + Checksum calculation time: 5.36s (54.4%) + Compression time: 1.4s (14.18%) + Total IO delay: 28.99s + Concurrency overhead: 17.93ms + Uncompressed size: 1.86GiB (~97.66KiB per object) + Output size: 1.86GiB (~97.66KiB per object; compression = 100%) + IO speed: 65.81MiB/s + Concurrency adjusted uncompressed speed: 391.35MiB/s + Actual uncompressed speed: 61.27MiB/s + Actual speed: 61.27MiB/s + Objects: 20000 + Average object size uncompressed: 97.66KiB + Average object size compressed: 97.66KiB + Blocks: 20 (~95.37MiB each) + Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 + +com.milaboratory.test.TestUtil > testLT STANDARD_OUT + Short tests. + No system env properties. com.milaboratory.util.JsonOverriderTest > test1 STANDARD_OUT WARNING: unnecessary override -Ob= with the same value. -com.milaboratory.util.RemoveActionTest > test1 STANDARD_OUT - /tmp/milib_7e62fe9975a57bdec5f84c41d9364e83f2cda5c98344584286744868976 +com.milaboratory.util.NSequenceWithQualityPrintHelperTest > test1 SKIPPED -com.milaboratory.util.RemoveActionTest > test2 STANDARD_OUT - /tmp/milib_1dc000064eb8d6e514ada4eba28e1ca7fca22954251484128020444988.tmp +com.milaboratory.util.sorting.HashSorterTest > testSingleton STANDARD_OUT + /tmp/milib_aee945127b385e425ffc80c643dff33168bef3171153829001150018388 + timeInCollate: 16.1s + timeInCollatorInit: 11.57s + timeAwaitingO: 8.19ms + timeAwaitingI: 2.58s + timeInFinalSorting1: 0ns + timeInFinalSorting2: 45.58ms + timeInFinalSorting3: 141.65ms + /10S (5|27|32): objs=50000 size=3.25MiB + +com.milaboratory.util.sorting.HashSorterTest > test1 STANDARD_OUT + /tmp/milib_53df74567ccc5016930e8a54c698fe4dce829e5f2259518515305100732 + timeInCollate: 40.13s + timeInCollatorInit: 1.97s + timeAwaitingO: 5.59s + timeAwaitingI: 9.63s + timeInFinalSorting1: 5.65s + timeInFinalSorting2: 4.9s + timeInFinalSorting3: 1.83s + /0N (5|27|32): objs=158653 size=8.97MiB + /1N (5|27|32): objs=163310 size=9.3MiB + /2N (5|27|32): objs=150713 size=8.53MiB + /3N (5|27|32): objs=156613 size=8.79MiB + /4N (5|27|32): objs=159098 size=8.96MiB + /5N (5|27|32): objs=151704 size=8.5MiB + /6N (5|27|32): objs=158734 size=9.28MiB + /7N (5|27|32): objs=147555 size=8.19MiB + /8N (5|27|32): objs=156552 size=8.64MiB + /9N (5|27|32): objs=151581 size=8.75MiB + /10N (5|27|32): objs=155437 size=8.79MiB + /11N (5|27|32): objs=160693 size=9.37MiB + /12N (5|27|32): objs=162987 size=9.23MiB + /13N (5|27|32): objs=154226 size=8.74MiB + /14N (5|27|32): objs=152777 size=8.83MiB + /15N (5|27|32): objs=153416 size=8.51MiB + /16N (5|27|32): objs=158301 size=9MiB + /17N (5|27|32): objs=152724 size=8.87MiB + /18N (5|27|32): objs=155107 size=8.75MiB + /19N (5|27|32): objs=158714 size=9.29MiB + /20N (5|27|32): objs=163779 size=9.36MiB + /21N (5|27|32): objs=160918 size=9.24MiB + /22N (5|27|32): objs=158151 size=9.02MiB + /23N (5|27|32): objs=150136 size=8.36MiB + /24N (5|27|32): objs=152732 size=8.68MiB + /25N (5|27|32): objs=154239 size=8.49MiB + /26N (5|27|32): objs=150457 size=8.54MiB + /27N (5|27|32): objs=160777 size=9.28MiB + /28N (5|27|32): objs=151462 size=8.64MiB + /29N (5|27|32): objs=156554 size=8.91MiB + /30N (5|27|32): objs=159846 size=9.32MiB + /31N (5|27|32): objs=162054 size=9.22MiB + /0/0N (2|25|36): objs=27771 size=532.61KiB + /0/1S (2|25|36): objs=174 size=174B + /0/2N (2|25|36): objs=9192 size=45.69KiB + /0/3N (2|25|36): objs=37769 size=784.57KiB + /0/4N (2|25|36): objs=42863 size=1.01MiB + /0/5N (2|25|36): objs=14169 size=87.83KiB + /0/6S (2|25|36): objs=144 size=182B + /0/8S (2|25|36): objs=166 size=139B + /0/9N (2|25|36): objs=439 size=1.66KiB + /0/10S (2|25|36): objs=153 size=324B + /0/11N (2|25|36): objs=7452 size=37.99KiB + /0/12S (2|25|36): objs=176 size=203B + /0/14S (2|25|36): objs=150 size=150B + /0/15N (2|25|36): objs=2278 size=10.27KiB + /0/16S (2|25|36): objs=160 size=125B + /0/17N (2|25|36): 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+com.milaboratory.util.RemoveActionTest > test1 STANDARD_OUT + /tmp/milib_ba90a62062f71f558a0fd59ba70307ae9d6c518111601913460444030730 -com.milaboratory.util.ByteStringTest > testSpeed1 STANDARD_OUT - Time per hash: 667ns - Addition to hash set (per operation): 2.66us - Hash set removal (per operation): 1.35us - a +com.milaboratory.util.RemoveActionTest > test2 STANDARD_OUT + /tmp/milib_22f00791c386cf1288e40b528a13435542d250c016042928911936768415.tmp +Gradle Test Executor 1 finished executing tests. WARNING: A terminally deprecated method in java.lang.System has been called WARNING: System::setSecurityManager has been called by org.gradle.api.internal.tasks.testing.worker.TestWorker (file:/usr/share/gradle/lib/plugins/gradle-testing-base-4.4.1.jar) WARNING: Please consider reporting this to the maintainers of org.gradle.api.internal.tasks.testing.worker.TestWorker WARNING: System::setSecurityManager will be removed in a future release -Gradle Test Executor 1 finished executing tests. -Finished generating test XML results (0.554 secs) into: /build/reproducible-path/milib-2.2.0+dfsg/build/test-results/test +Finished generating test XML results (0.488 secs) into: /build/reproducible-path/milib-2.2.0+dfsg/build/test-results/test Generating HTML test report... -Finished generating test html results (0.617 secs) into: /build/reproducible-path/milib-2.2.0+dfsg/build/reports/tests/test -:test (Thread[Task worker for ':',5,main]) completed. Took 8 mins 29.213 secs. +Finished generating test html results (0.64 secs) into: /build/reproducible-path/milib-2.2.0+dfsg/build/reports/tests/test +:test (Thread[Task worker for ':' Thread 3,5,main]) completed. Took 9 mins 13.464 secs. -BUILD SUCCESSFUL in 9m 15s +BUILD SUCCESSFUL in 9m 54s 5 actionable tasks: 3 executed, 2 up-to-date create-stamp debian/debhelper-build-stamp dh_prep @@ -4931,12 +4987,14 @@ 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/1635/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1635/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/12854 and its subdirectories -I: Current time: Mon Mar 25 04:43:42 -12 2024 -I: pbuilder-time-stamp: 1711385022 +I: removing directory /srv/workspace/pbuilder/1635 and its subdirectories +I: Current time: Tue Mar 26 06:58:32 +14 2024 +I: pbuilder-time-stamp: 1711385912