Diff of the two buildlogs: -- --- b1/build.log 2024-12-03 06:03:59.546076469 +0000 +++ b2/build.log 2024-12-03 06:11:50.528766217 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Jan 5 00:22:56 -12 2026 -I: pbuilder-time-stamp: 1767615776 +I: Current time: Tue Dec 3 20:04:02 +14 2024 +I: pbuilder-time-stamp: 1733205842 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -31,54 +31,86 @@ 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/114724/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/18774/tmp/hooks/D01_modify_environment starting +debug: Running on ionos12-i386. +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 Dec 3 06:04 /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/18774/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/18774/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='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=22 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='i386' + 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]="32" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=10 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='f3b6ec96e9004b6ea071e709d468c0a7' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='114724' - PS1='# ' - PS2='> ' + INVOCATION_ID=4ab56f347062444d9689566136ce644d + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=18774 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.lym8Atvq/pbuilderrc_1ZZa --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.lym8Atvq/b1 --logfile b1/build.log milib_2.2.0+dfsg-1.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.lym8Atvq/pbuilderrc_UYBT --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.lym8Atvq/b2 --logfile b2/build.log milib_2.2.0+dfsg-1.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos16-i386 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/114724/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/18774/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -530,7 +562,7 @@ Get: 380 http://deb.debian.org/debian trixie/main i386 libmockito-java all 3.3.0-2 [510 kB] Get: 381 http://deb.debian.org/debian trixie/main i386 libredberry-pipe-java all 1.0.0~alpha0-3 [62.7 kB] Get: 382 http://deb.debian.org/debian trixie/main i386 libtrove3-java all 3.0.3-5 [2146 kB] -Fetched 350 MB in 5s (74.9 MB/s) +Fetched 350 MB in 7s (49.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libapparmor1:i386. (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 ... 19950 files and directories currently installed.) @@ -1794,8 +1826,8 @@ Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' -Local time is now: Mon Jan 5 12:23:40 UTC 2026. -Universal Time is now: Mon Jan 5 12:23:40 UTC 2026. +Local time is now: Tue Dec 3 06:05:10 UTC 2024. +Universal Time is now: Tue Dec 3 06:05:10 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:i386 (1.17.0-2+b1) ... @@ -2311,7 +2343,11 @@ 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/18774/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/18774/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 @@ -2346,7 +2382,7 @@ 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=22 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=10 jar openjdk version "21.0.5" 2024-10-15 OpenJDK Runtime Environment (build 21.0.5+11-Debian-1) OpenJDK Server VM (build 21.0.5+11-Debian-1, mixed mode, sharing) @@ -2354,18 +2390,18 @@ 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-21-openjdk-i386/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 0.789 secs. -The client will now receive all logging from the daemon (pid: 123145). The daemon log file: /build/reproducible-path/milib-2.2.0+dfsg/.gradle/daemon/4.4.1/daemon-123145.out.log +An attempt to start the daemon took 4.388 secs. +The client will now receive all logging from the daemon (pid: 34675). The daemon log file: /build/reproducible-path/milib-2.2.0+dfsg/.gradle/daemon/4.4.1/daemon-34675.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 22 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@ad85ca -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@ad85ca -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@fd7234 +Using 10 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@189b9fc +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@189b9fc +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@d60f22 Starting Build Compiling initialization script '/build/reproducible-path/milib-2.2.0+dfsg/.gradle/init.d/init.gradle' using SubsetScriptTransformer. -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@5e97d8 +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@19a2a6b Compiling initialization script '/build/reproducible-path/milib-2.2.0+dfsg/.gradle/init.d/init.gradle' using BuildScriptTransformer. 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) @@ -2382,15 +2418,15 @@ Linking the generated javadoc to the system JDK API documentation All projects evaluated. Selected primary task 'jar' 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@88094a +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@1b76ca4 Tasks to be executed: [task ':compileJava', task ':processResources', task ':classes', task ':debianMavenPom', task ':jar'] -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@fd7234 -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@1f7be3c -Creating new cache for outputFiles, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@140236 -:compileJava (Thread[#57,Task worker for ':' Thread 2,5,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@d60f22 +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@1f80832 +Creating new cache for outputFiles, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@1099784 +:compileJava (Thread[#52,Task worker for ':' Thread 3,5,main]) started. :compileJava -Putting task artifact state for task ':compileJava' into context took 0.003 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@602182 +Putting task artifact state for task ':compileJava' into context took 0.006 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@ec4836 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 @@ -2463,7 +2499,7 @@ at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at java.base/java.lang.Thread.run(Thread.java:1583) -Up-to-date check for task ':compileJava' took 2.031 secs. It is not up-to-date because: +Up-to-date check for task ':compileJava' took 3.809 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. @@ -2487,37 +2523,37 @@ Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 7 warnings -:compileJava (Thread[#57,Task worker for ':' Thread 2,5,main]) completed. Took 6.783 secs. -:processResources (Thread[#57,Task worker for ':' Thread 2,5,main]) started. +:compileJava (Thread[#52,Task worker for ':' Thread 3,5,main]) completed. Took 13.938 secs. +:processResources (Thread[#52,Task worker for ':' Thread 3,5,main]) started. :processResources Putting task artifact state for task ':processResources' into context took 0.0 secs. -Up-to-date check for task ':processResources' took 0.005 secs. It is not up-to-date because: +Up-to-date check for task ':processResources' took 0.016 secs. It is not up-to-date because: No history is available. -:processResources (Thread[#57,Task worker for ':' Thread 2,5,main]) completed. Took 0.027 secs. -:classes (Thread[#57,Task worker for ':' Thread 2,5,main]) started. +:processResources (Thread[#52,Task worker for ':' Thread 3,5,main]) completed. Took 0.052 secs. +:classes (Thread[#52,Task worker for ':' Thread 3,5,main]) started. :classes Skipping task ':classes' as it has no actions. -:classes (Thread[#57,Task worker for ':' Thread 2,5,main]) completed. Took 0.0 secs. -:debianMavenPom (Thread[#57,Task worker for ':' Thread 2,5,main]) started. +:classes (Thread[#52,Task worker for ':' Thread 3,5,main]) completed. Took 0.001 secs. +:debianMavenPom (Thread[#52,Task worker for ':' Thread 3,5,main]) started. :debianMavenPom Putting task artifact state for task ':debianMavenPom' into context took 0.0 secs. Up-to-date check for task ':debianMavenPom' took 0.0 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[#57,Task worker for ':' Thread 2,5,main]) completed. Took 0.068 secs. -:jar (Thread[#57,Task worker for ':' Thread 2,5,main]) started. +:debianMavenPom (Thread[#52,Task worker for ':' Thread 3,5,main]) completed. Took 0.115 secs. +:jar (Thread[#52,Task worker for ':' Thread 3,5,main]) started. :jar Putting task artifact state for task ':jar' into context took 0.0 secs. -Up-to-date check for task ':jar' took 0.015 secs. It is not up-to-date because: +Up-to-date check for task ':jar' took 0.031 secs. It is not up-to-date because: No history is available. -:jar (Thread[#57,Task worker for ':' Thread 2,5,main]) completed. Took 0.188 secs. +:jar (Thread[#52,Task worker for ':' Thread 3,5,main]) completed. Took 0.309 secs. -BUILD SUCCESSFUL in 11s +BUILD SUCCESSFUL in 30s 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=22 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=10 test openjdk version "21.0.5" 2024-10-15 OpenJDK Runtime Environment (build 21.0.5+11-Debian-1) OpenJDK Server VM (build 21.0.5+11-Debian-1, mixed mode, sharing) @@ -2525,17 +2561,17 @@ 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-21-openjdk-i386/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 0.851 secs. -The client will now receive all logging from the daemon (pid: 123358). The daemon log file: /build/reproducible-path/milib-2.2.0+dfsg/.gradle/daemon/4.4.1/daemon-123358.out.log +An attempt to start the daemon took 1.625 secs. +The client will now receive all logging from the daemon (pid: 35587). The daemon log file: /build/reproducible-path/milib-2.2.0+dfsg/.gradle/daemon/4.4.1/daemon-35587.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 22 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@1db7c11 -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@1db7c11 -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@1b86439 +Using 10 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@6cc44c +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@6cc44c +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@1a994dd 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@3370e5 +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@199087a 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' @@ -2549,15 +2585,15 @@ 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@b9deef +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@a11478 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@1b86439 -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@151d1ca -Creating new cache for outputFiles, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@14dbc33 -:compileJava (Thread[#58,Task worker for ':' Thread 3,5,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@1a994dd +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@77022d +Creating new cache for outputFiles, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@18f6cd9 +:compileJava (Thread[#50,Task worker for ':',5,main]) started. :compileJava -Putting task artifact state for task ':compileJava' into context took 0.003 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@a9fa5b +Putting task artifact state for task ':compileJava' into context took 0.009 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@1c2fc0c 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 @@ -2582,21 +2618,21 @@ 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 0.537 secs). +Skipping task ':compileJava' as it is up-to-date (took 0.986 secs). :compileJava UP-TO-DATE -:compileJava (Thread[#58,Task worker for ':' Thread 3,5,main]) completed. Took 0.568 secs. -:processResources (Thread[#58,Task worker for ':' Thread 3,5,main]) started. +:compileJava (Thread[#50,Task worker for ':',5,main]) completed. Took 1.035 secs. +:processResources (Thread[#50,Task worker for ':',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 0.004 secs). +Skipping task ':processResources' as it is up-to-date (took 0.009 secs). :processResources UP-TO-DATE -:processResources (Thread[#58,Task worker for ':' Thread 3,5,main]) completed. Took 0.007 secs. -:classes (Thread[#58,Task worker for ':' Thread 3,5,main]) started. +:processResources (Thread[#50,Task worker for ':',5,main]) completed. Took 0.012 secs. +:classes (Thread[#50,Task worker for ':',5,main]) started. :classes Skipping task ':classes' as it has no actions. :classes UP-TO-DATE -:classes (Thread[#58,Task worker for ':' Thread 3,5,main]) completed. Took 0.0 secs. -:compileTestJava (Thread[#58,Task worker for ':' Thread 3,5,main]) started. +:classes (Thread[#50,Task worker for ':',5,main]) completed. Took 0.0 secs. +:compileTestJava (Thread[#50,Task worker for ':',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 @@ -2612,7 +2648,7 @@ 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 1.417 secs. It is not up-to-date because: +Up-to-date check for task ':compileTestJava' took 2.813 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. @@ -2624,1325 +2660,615 @@ Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 3 warnings -:compileTestJava (Thread[#58,Task worker for ':' Thread 3,5,main]) completed. Took 4.617 secs. -:processTestResources (Thread[#58,Task worker for ':' Thread 3,5,main]) started. +:compileTestJava (Thread[#50,Task worker for ':',5,main]) completed. Took 8.943 secs. +:processTestResources (Thread[#50,Task worker for ':',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 0.007 secs. It is not up-to-date because: +Up-to-date check for task ':processTestResources' took 0.016 secs. It is not up-to-date because: No history is available. -:processTestResources (Thread[#58,Task worker for ':' Thread 3,5,main]) completed. Took 0.029 secs. -:testClasses (Thread[#58,Task worker for ':' Thread 3,5,main]) started. +:processTestResources (Thread[#50,Task worker for ':',5,main]) completed. Took 0.068 secs. +:testClasses (Thread[#50,Task worker for ':',5,main]) started. :testClasses Skipping task ':testClasses' as it has no actions. -:testClasses (Thread[#58,Task worker for ':' Thread 3,5,main]) completed. Took 0.0 secs. -:test (Thread[#58,Task worker for ':' Thread 3,5,main]) started. +:testClasses (Thread[#50,Task worker for ':',5,main]) completed. Took 0.0 secs. +:test (Thread[#50,Task worker for ':',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 0.646 secs. It is not up-to-date because: +Up-to-date check for task ':test' took 1.143 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-21-openjdk-i386/bin/java -Dorg.gradle.native=false @/tmp/gradle-worker-classpath86193963267502284txt -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-21-openjdk-i386/bin/java -Dorg.gradle.native=false @/tmp/gradle-worker-classpath17363679144084749349txt -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.util.NSequenceWithQualityPrintHelperTest > test1 SKIPPED +com.milaboratory.primitivio.blocks.PrimitivOBlocksTest > benchmark1 SKIPPED -com.milaboratory.util.IntCombinationsTest > test1 STANDARD_OUT - [0, 1] - [0, 2] - [1, 2] +com.milaboratory.primitivio.blocks.PrimitivOBlocksTest > test1 STANDARD_OUT -com.milaboratory.util.RemoveActionTest > test1 STANDARD_OUT - /tmp/milib_ecfc04c189e9a236eb83836d4b5bc73609a89afd3093461952267744387 + ================== + High compression: false + Concurrency: 4 + File size: 6799510 + Write time: 381.42ms -com.milaboratory.util.RemoveActionTest > test2 STANDARD_OUT - /tmp/milib_8afabb1459c760f64c81a20c25ffa161159dd1b011949848697222186729.tmp + O. Stats: + Wall clock time: 392.3ms + Total CPU time: 694.56ms + User wait time: 303.48ms + Serialization time: 263.66ms (37.96%) + Checksum calculation time: 358.85ms (51.67%) + Compression time: 61.39ms (8.84%) + Total IO delay: 40.04ms + Concurrency overhead: 11.86ms + Uncompressed size: 18.44MiB (~2.08KiB per object) + Output size: 6.48MiB (~748B per object; compression = 35.17%) + IO speed: 162.11MiB/s + Concurrency adjusted uncompressed speed: 94.55MiB/s + Actual uncompressed speed: 47.03MiB/s + Actual speed: 16.54MiB/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.VersionInfoTest > test3 SKIPPED + I. Stats 1: + Wall clock time: 204.94ms + Total CPU time: 251.35ms + Serialization time: 161.33ms (64.18%) + Checksum calculation time: 8.91ms (3.55%) + Compression time: 76.4ms (30.39%) + Total IO delay: 50.28ms + Input size: 6.48MiB + Decompressed size: 18.44MiB (compression = 35.17%) + IO speed: 129.69MiB/s + Concurrency adjusted uncompressed speed: 245.83MiB/s + Actual uncompressed speed: 90.38MiB/s + Actual speed: 31.79MiB/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.JsonOverriderTest > test1 STANDARD_OUT - WARNING: unnecessary override -Ob= with the same value. + I. Stats 2: + Wall clock time: 360.82ms + Total CPU time: 411.37ms + Serialization time: 241.08ms (58.6%) + Checksum calculation time: 17.26ms (4.19%) + Compression time: 143.83ms (34.96%) + Total IO delay: 74.57ms + Input size: 12.97MiB + Decompressed size: 36.87MiB (compression = 35.17%) + IO speed: 175.26MiB/s + Concurrency adjusted uncompressed speed: 304.74MiB/s + Actual uncompressed speed: 102.43MiB/s + Actual speed: 36.03MiB/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.AtomicEnumHistogramTest > test1 STANDARD_OUT - {"labels":["A","B","C","null"],"hist":[1,2,0,1]} + ================== + High compression: false + Concurrency: 4 + File size: 6791878 + Write time: 190.93ms -com.milaboratory.util.CacheTest > test1 STANDARD_OUT - Cache misses:400 - Cache hits:800 + O. Stats: + Wall clock time: 191.82ms + Total CPU time: 258.42ms + User wait time: 148.13ms + Serialization time: 170.31ms (65.9%) + Checksum calculation time: 8.84ms (3.42%) + Compression time: 63.72ms (24.66%) + Total IO delay: 26.7ms + Concurrency overhead: 1.31ms + Uncompressed size: 18.44MiB (~2.08KiB per object) + Output size: 6.48MiB (~748B per object; compression = 35.13%) + IO speed: 249.12MiB/s + Concurrency adjusted uncompressed speed: 256.07MiB/s + Actual uncompressed speed: 96.53MiB/s + Actual speed: 33.91MiB/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.util.ByteStringTest > testSpeed1 STANDARD_OUT - Time per hash: 110ns - Addition to hash set (per operation): 291ns - Hash set removal (per operation): 210ns - a + I. Stats 1: + Wall clock time: 117.89ms + Total CPU time: 159.75ms + Serialization time: 74.14ms (46.41%) + Checksum calculation time: 8.16ms (5.11%) + Compression time: 76.75ms (48.04%) + Total IO delay: 11.78ms + Input size: 6.48MiB + Decompressed size: 18.44MiB (compression = 35.13%) + IO speed: 588.84MiB/s + Concurrency adjusted uncompressed speed: 438.97MiB/s + Actual uncompressed speed: 157.58MiB/s + Actual speed: 55.36MiB/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.util.sorting.HashSorterTest > testSingleton STANDARD_OUT - /tmp/milib_20ccfb5f1d36a2641396754fa2b783e6180b544c4342258902458810248 - timeInCollate: 3.36s - timeInCollatorInit: 2.34s - timeAwaitingO: 2.99ms - timeAwaitingI: 504.9ms - timeInFinalSorting1: 0ns - timeInFinalSorting2: 11.85ms - timeInFinalSorting3: 52.06ms - /27S (5|27|32): objs=50000 size=2.9MiB + I. Stats 2: + Wall clock time: 274.17ms + Total CPU time: 323.35ms + Serialization time: 149.7ms (46.3%) + Checksum calculation time: 16.43ms (5.08%) + Compression time: 155.7ms (48.15%) + Total IO delay: 22.65ms + Input size: 12.95MiB + Decompressed size: 36.87MiB (compression = 35.13%) + IO speed: 588.84MiB/s + Concurrency adjusted uncompressed speed: 428.77MiB/s + Actual uncompressed speed: 134.58MiB/s + Actual speed: 47.28MiB/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.util.sorting.HashSorterTest > test1 STANDARD_OUT - /tmp/milib_c75755eed57dabbd859a803e9a3e67daf538d25914575747956584127454 - timeInCollate: 8.44s - timeInCollatorInit: 641.49ms - timeAwaitingO: 300.89ms - timeAwaitingI: 2.12s - timeInFinalSorting1: 1.18s - timeInFinalSorting2: 422.17ms - timeInFinalSorting3: 537.89ms - /0N (5|27|32): objs=150367 size=8.4MiB - /1N (5|27|32): objs=151613 size=8.61MiB - /2N (5|27|32): objs=159585 size=9.13MiB - /3N (5|27|32): objs=157716 size=9.02MiB - /4N (5|27|32): objs=151885 size=8.64MiB - /5N (5|27|32): objs=155936 size=8.84MiB - /6N (5|27|32): objs=152082 size=8.6MiB - /7N (5|27|32): objs=159215 size=8.97MiB - /8N (5|27|32): objs=158209 size=8.91MiB - /9N (5|27|32): objs=146436 size=7.94MiB - /10N (5|27|32): objs=159254 size=9.26MiB - /11N (5|27|32): objs=156867 size=8.74MiB - /12N (5|27|32): objs=160503 size=9.27MiB - /13N (5|27|32): objs=159758 size=9.02MiB - /14N (5|27|32): objs=154406 size=8.61MiB - /15N (5|27|32): objs=154516 size=8.78MiB - /16N (5|27|32): objs=161166 size=9.22MiB - /17N (5|27|32): objs=161892 size=9.3MiB - /18N (5|27|32): objs=163683 size=9.61MiB - /19N (5|27|32): objs=162205 size=9.07MiB - /20N (5|27|32): objs=155509 size=8.88MiB - /21N (5|27|32): objs=165679 size=9.55MiB - /22N (5|27|32): objs=157177 size=9.08MiB - /23N (5|27|32): objs=149352 size=8.4MiB - /24N (5|27|32): objs=160420 size=9.24MiB - /25N (5|27|32): objs=152951 size=8.34MiB - /26N (5|27|32): objs=153146 size=8.16MiB - /27N (5|27|32): objs=148781 size=8.22MiB - /28N (5|27|32): objs=159020 size=8.88MiB - /29N (5|27|32): objs=151380 size=8.37MiB - /30N (5|27|32): objs=154748 size=8.67MiB - /31N (5|27|32): objs=154543 size=8.76MiB - /0/0N (2|25|36): objs=39217 size=854.89KiB - /0/1N (2|25|36): objs=36607 size=727.56KiB - /0/2N (2|25|36): objs=31899 size=551.63KiB - /0/3S (2|25|36): objs=166 size=337B - /0/5S (2|25|36): objs=162 size=195B - /0/6N (2|25|36): objs=1122 size=4.63KiB - /0/7S (2|25|36): objs=124 size=315B - /0/8N (2|25|36): objs=2766 size=12.64KiB - /0/9S (2|25|36): objs=164 size=299B - /0/10N (2|25|36): objs=1695 size=7.07KiB - /0/11N (2|25|36): objs=1042 size=4.07KiB - /0/12S (2|25|36): objs=156 size=222B - /0/13N (2|25|36): objs=3121 size=13.57KiB - /0/14S (2|25|36): objs=135 size=308B - /0/15N (2|25|36): objs=288 size=969B - /0/16S (2|25|36): objs=144 size=186B - /0/17N (2|25|36): objs=5432 size=24.91KiB - 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/31/10S (2|25|36): objs=154 size=236B - /31/11N (2|25|36): objs=10025 size=55.89KiB - /31/12S (2|25|36): objs=172 size=302B - /31/13N (2|25|36): objs=2884 size=12.2KiB - /31/14S (2|25|36): objs=167 size=223B - /31/15N (2|25|36): objs=5468 size=24.5KiB - /31/16S (2|25|36): objs=166 size=150B - /31/18S (2|25|36): objs=128 size=123B - /31/19N (2|25|36): objs=858 size=3.37KiB - /31/20S (2|25|36): objs=160 size=173B - /31/21N (2|25|36): objs=1054 size=4.38KiB - /31/22S (2|25|36): objs=141 size=239B - /31/23N (2|25|36): objs=1057 size=4.39KiB - /31/24S (2|25|36): objs=172 size=330B - /31/25N (2|25|36): objs=1019 size=4.12KiB - /31/26S (2|25|36): objs=137 size=276B - /31/27N (2|25|36): objs=3726 size=16.78KiB - /31/28S (2|25|36): objs=155 size=249B - /31/29S (2|25|36): objs=167 size=171B - /31/30S (2|25|36): objs=160 size=322B - /31/31N (2|25|36): objs=749 size=2.98KiB - /31/32S (2|25|36): objs=187 size=270B - /31/33S (2|25|36): objs=168 size=289B - /31/34S (2|25|36): objs=120 size=112B - /31/35N (2|25|36): objs=447 size=1.64KiB + ================== + High compression: false + Concurrency: 1 + File size: 6799510 + Write time: 214.6ms -com.milaboratory.util.sorting.HashSorterTest > test2 SKIPPED + O. Stats: + Wall clock time: 215.98ms + Total CPU time: 165.52ms + User wait time: 193.2ms + Serialization time: 79.18ms (47.84%) + Checksum calculation time: 8.05ms (4.86%) + Compression time: 60.17ms (36.35%) + Total IO delay: 24.16ms + Concurrency overhead: 4.46ms + Uncompressed size: 18.44MiB (~2.08KiB per object) + Output size: 6.48MiB (~748B per object; compression = 35.17%) + IO speed: 270.19MiB/s + Concurrency adjusted uncompressed speed: 95.04MiB/s + Actual uncompressed speed: 85.75MiB/s + Actual speed: 30.16MiB/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! -com.milaboratory.util.sorting.SortingUtilTest > test1 STANDARD_OUT - Collation: 75.42ms - Sorting: 72.26ms - 1 - 217 - 41496 - 99530 - 99999 + I. Stats 1: + Wall clock time: 115.11ms + Total CPU time: 169.96ms + Serialization time: 79.74ms (46.92%) + Checksum calculation time: 8.07ms (4.75%) + Compression time: 79.39ms (46.71%) + Total IO delay: 13.86ms + Input size: 6.48MiB + Decompressed size: 18.44MiB (compression = 35.17%) + IO speed: 498.81MiB/s + Concurrency adjusted uncompressed speed: 100.75MiB/s + Actual uncompressed speed: 160.32MiB/s + Actual speed: 56.39MiB/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.io.sequence.fasta.RandomAccessFastaReaderTest > test1nt STANDARD_ERROR - Indexing milib_bfa559506255b5565688716a4f5634dd44a7b7e3532103409809413561.fasta: 0% - Indexing milib_bfa559506255b5565688716a4f5634dd44a7b7e3532103409809413561.fasta: done + I. Stats 2: + Wall clock time: 236.95ms + Total CPU time: 339.55ms + Serialization time: 159.6ms (47%) + Checksum calculation time: 15.97ms (4.7%) + Compression time: 156.98ms (46.23%) + Total IO delay: 24.85ms + Input size: 12.97MiB + Decompressed size: 36.87MiB (compression = 35.17%) + IO speed: 540.38MiB/s + Concurrency adjusted uncompressed speed: 101.3MiB/s + Actual uncompressed speed: 156.25MiB/s + Actual speed: 54.95MiB/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.io.sequence.fasta.RandomAccessFastaReaderTest > test1 STANDARD_ERROR - Indexing milib_bfa559506255b5565688716a4f5634dd44a7b7e3532103409809413561.fasta: 0% - Indexing milib_bfa559506255b5565688716a4f5634dd44a7b7e3532103409809413561.fasta: done + ================== + High compression: false + Concurrency: 1 + File size: 6791878 + Write time: 220.4ms -com.milaboratory.core.io.sequence.fasta.RandomAccessFastaReaderTest > test2 STANDARD_ERROR - Indexing milib_c4eec1d801e5d3f225c46cbd7da998ff114ede0a445510861062310811.tmp: 0% - Indexing milib_c4eec1d801e5d3f225c46cbd7da998ff114ede0a445510861062310811.tmp: done + O. Stats: + Wall clock time: 221.65ms + Total CPU time: 177.01ms + User wait time: 200.4ms + Serialization time: 95.52ms (53.96%) + Checksum calculation time: 8.17ms (4.62%) + Compression time: 59.65ms (33.7%) + Total IO delay: 21.4ms + Concurrency overhead: 943.02us + Uncompressed size: 18.44MiB (~2.08KiB per object) + Output size: 6.48MiB (~748B per object; compression = 35.13%) + IO speed: 308.44MiB/s + Concurrency adjusted uncompressed speed: 92.65MiB/s + Actual uncompressed speed: 83.42MiB/s + Actual speed: 29.31MiB/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! -com.milaboratory.core.io.util.IOUtilTest > test111 STANDARD_OUT - 3 - 3 - -2147483648 - -9223372036854775808 + I. Stats 1: + Wall clock time: 114.4ms + Total CPU time: 158.65ms + Serialization time: 73.09ms (46.07%) + Checksum calculation time: 8.26ms (5.2%) + Compression time: 76.77ms (48.39%) + Total IO delay: 9.07ms + Input size: 6.48MiB + Decompressed size: 18.44MiB (compression = 35.13%) + IO speed: 719.69MiB/s + Concurrency adjusted uncompressed speed: 110.4MiB/s + Actual uncompressed speed: 161.73MiB/s + Actual speed: 56.82MiB/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.tree.SequenceTreeMapTest > testCase9 STANDARD_OUT - Hit 1 - 0 ac-gacTtgactg 11 - 0 acTgac-tgactg 11 + I. Stats 2: + Wall clock time: 247.06ms + Total CPU time: 315.51ms + Serialization time: 144.45ms (45.79%) + Checksum calculation time: 16.6ms (5.26%) + Compression time: 153.5ms (48.65%) + Total IO delay: 17.2ms + Input size: 12.95MiB + Decompressed size: 36.87MiB (compression = 35.13%) + IO speed: 762.03MiB/s + Concurrency adjusted uncompressed speed: 111.07MiB/s + Actual uncompressed speed: 149.29MiB/s + Actual speed: 52.45MiB/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: 1 / 0 / 3 - Hit 2 - 0 ac-gactTgactg 11 - 0 acTgact-gactg 11 + ================== + High compression: true + Concurrency: 4 + File size: 4156299 + Write time: 2.06s + O. Stats: + Wall clock time: 2.06s + Total CPU time: 5.41s + User wait time: 1.93s + Serialization time: 78.66ms (1.46%) + Checksum calculation time: 8.12ms (0.15%) + Compression time: 5.3s (98.1%) + Total IO delay: 20.41ms + Concurrency overhead: 4.54ms + Uncompressed size: 18.44MiB (~2.08KiB per object) + Output size: 3.96MiB (~457B per object; compression = 21.5%) + IO speed: 198.19MiB/s + Concurrency adjusted uncompressed speed: 13.56MiB/s + Actual uncompressed speed: 8.95MiB/s + Actual speed: 1.93MiB/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 -com.milaboratory.core.tree.SequenceTreeMapTest > optimalityAndScopeTest STANDARD_OUT - --NW alignments-- - CASSLAPGATN-KLFF - CASS-APGATNEKLFF + I. Stats 1: + Wall clock time: 67.41ms + Total CPU time: 103.32ms + Serialization time: 39.58ms (38.31%) + Checksum calculation time: 8.1ms (7.84%) + Compression time: 53.93ms (52.2%) + Total IO delay: 11.71ms + Input size: 3.96MiB + Decompressed size: 18.44MiB (compression = 21.5%) + IO speed: 360.34MiB/s + Concurrency adjusted uncompressed speed: 658.46MiB/s + Actual uncompressed speed: 275.18MiB/s + Actual speed: 59.16MiB/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 - CASSLAPGATN-KLFF - CASSLAPG-TNEKLFF + I. Stats 2: + Wall clock time: 159.27ms + Total CPU time: 203.8ms + Serialization time: 76.55ms (37.56%) + Checksum calculation time: 15.89ms (7.8%) + Compression time: 107.63ms (52.81%) + Total IO delay: 39.56ms + Input size: 7.93MiB + Decompressed size: 36.87MiB (compression = 21.5%) + IO speed: 203.27MiB/s + Concurrency adjusted uncompressed speed: 614.56MiB/s + Actual uncompressed speed: 231.91MiB/s + Actual speed: 49.86MiB/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 - CASSLAPGATN-KLfF - CASSLAPG-TNEKLyF + ================== + High compression: true + Concurrency: 4 + File size: 4098671 + Write time: 3.27s - --STM alignments-- - CASSLAPGATN-KLFF - CASS-APGATNEKLFF + O. Stats: + Wall clock time: 3.27s + Total CPU time: 5.41s + User wait time: 2.96s + Serialization time: 59.05ms (1.09%) + Checksum calculation time: 7.95ms (0.15%) + Compression time: 5.34s (98.66%) + Total IO delay: 16.08ms + Concurrency overhead: 1.89ms + Uncompressed size: 18.44MiB (~2.08KiB per object) + Output size: 3.91MiB (~451B per object; compression = 21.2%) + IO speed: 244.3MiB/s + Concurrency adjusted uncompressed speed: 13.58MiB/s + Actual uncompressed speed: 5.65MiB/s + Actual speed: 1.2MiB/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 - CASSLAPGATN-KLFF - CASSLAPG-TNEKLFF + I. Stats 1: + Wall clock time: 79.38ms + Total CPU time: 101.47ms + Serialization time: 34.4ms (33.9%) + Checksum calculation time: 8.18ms (8.06%) + Compression time: 58.59ms (57.74%) + Total IO delay: 10.17ms + Input size: 3.91MiB + Decompressed size: 18.44MiB (compression = 21.2%) + IO speed: 390.88MiB/s + Concurrency adjusted uncompressed speed: 682.85MiB/s + Actual uncompressed speed: 233.38MiB/s + Actual speed: 49.48MiB/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 - CASSlAPGATN-KLFF - CASSa-PGATNEKLFF + I. Stats 2: + Wall clock time: 169.47ms + Total CPU time: 202.11ms + Serialization time: 69.75ms (34.51%) + Checksum calculation time: 16.27ms (8.05%) + Compression time: 115.47ms (57.13%) + Total IO delay: 16.7ms + Input size: 7.82MiB + Decompressed size: 36.87MiB (compression = 21.2%) + IO speed: 488.6MiB/s + Concurrency adjusted uncompressed speed: 682.85MiB/s + Actual uncompressed speed: 218.19MiB/s + Actual speed: 46.26MiB/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 - CASSLAPGaTN-KLFF - CASSLAPGt-NEKLFF + ================== + High compression: true + Concurrency: 1 + File size: 4156299 + Write time: 5.15s - CASSlAPGATN-KLFF - CA-SsAPGATNEKLFF + O. Stats: + Wall clock time: 5.15s + Total CPU time: 5.1s + User wait time: 5.13s + Serialization time: 50.41ms (0.99%) + Checksum calculation time: 8.02ms (0.16%) + Compression time: 5.04s (98.75%) + Total IO delay: 21.52ms + Concurrency overhead: 3.54ms + Uncompressed size: 18.44MiB (~2.08KiB per object) + Output size: 3.96MiB (~457B per object; compression = 21.5%) + IO speed: 188.75MiB/s + Concurrency adjusted uncompressed speed: 3.6MiB/s + Actual uncompressed speed: 3.58MiB/s + Actual speed: 788.13KiB/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! - CASSlAPGATN-KLFF - CAS-sAPGATNEKLFF + I. Stats 1: + Wall clock time: 81.67ms + Total CPU time: 90.32ms + Serialization time: 31.85ms (35.26%) + Checksum calculation time: 7.82ms (8.65%) + Compression time: 49.47ms (54.77%) + Total IO delay: 29.74ms + Input size: 3.96MiB + Decompressed size: 18.44MiB (compression = 21.5%) + IO speed: 136.68MiB/s + Concurrency adjusted uncompressed speed: 153.64MiB/s + Actual uncompressed speed: 227.62MiB/s + Actual speed: 48.94MiB/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 - CASSLAPGATNk-LFF - CASS-APGATNeKLFF + I. Stats 2: + Wall clock time: 155.18ms + Total CPU time: 180.7ms + Serialization time: 63.35ms (35.06%) + Checksum calculation time: 15.64ms (8.66%) + Compression time: 98.81ms (54.68%) + Total IO delay: 41.85ms + Input size: 7.93MiB + Decompressed size: 36.87MiB (compression = 21.5%) + IO speed: 193.35MiB/s + Concurrency adjusted uncompressed speed: 166.1MiB/s + Actual uncompressed speed: 237.9MiB/s + Actual speed: 51.15MiB/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 - CASSLAPGaTN-KLFF - CASSLAP-gTNEKLFF + ================== + High compression: true + Concurrency: 1 + File size: 4098671 + Write time: 5.55s - CASSLAPGATNk-LFF - CASSLAPG-TNeKLFF + O. Stats: + Wall clock time: 5.55s + Total CPU time: 5.52s + User wait time: 5.53s + Serialization time: 61.54ms (1.12%) + Checksum calculation time: 8.76ms (0.16%) + Compression time: 5.44s (98.64%) + Total IO delay: 16.56ms + Concurrency overhead: 1.19ms + Uncompressed size: 18.44MiB (~2.08KiB per object) + Output size: 3.91MiB (~451B per object; compression = 21.2%) + IO speed: 244.3MiB/s + Concurrency adjusted uncompressed speed: 3.33MiB/s + Actual uncompressed speed: 3.32MiB/s + Actual speed: 721.32KiB/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! - CASSLAPGATN-KLfF - CASSLAPG-TNEKLyF + I. Stats 1: + Wall clock time: 85.72ms + Total CPU time: 102.68ms + Serialization time: 35.23ms (34.31%) + Checksum calculation time: 8.13ms (7.92%) + Compression time: 58.97ms (57.43%) + Total IO delay: 23.2ms + Input size: 3.91MiB + Decompressed size: 18.44MiB (compression = 21.2%) + IO speed: 169.95MiB/s + Concurrency adjusted uncompressed speed: 147.5MiB/s + Actual uncompressed speed: 216.9MiB/s + Actual speed: 45.99MiB/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: 192.33ms + Total CPU time: 208.58ms + Serialization time: 76.65ms (36.75%) + Checksum calculation time: 16.88ms (8.09%) + Compression time: 114.37ms (54.83%) + Total IO delay: 36.88ms + Input size: 7.82MiB + Decompressed size: 36.87MiB (compression = 21.2%) + IO speed: 217.16MiB/s + Concurrency adjusted uncompressed speed: 150.51MiB/s + Actual uncompressed speed: 192.05MiB/s + Actual speed: 40.72MiB/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.core.tree.PrimerGenerator > generate SKIPPED +com.milaboratory.primitivio.blocks.PrimitivOBlocksTest > bigBlocks STANDARD_OUT + Pending / IO / Serde / Objs: 0 / 1 / 0 / 2000 + Pending / IO / Serde / Objs: 0 / 0 / 1 / 5000 + Pending / IO / Serde / Objs: 0 / 0 / 1 / 9000 + Pending / IO / Serde / Objs: 0 / 1 / 0 / 13000 + Pending / IO / Serde / Objs: 0 / 0 / 1 / 15000 + Pending / IO / Serde / Objs: 0 / 1 / 0 / 18000 + O. Stats: + Wall clock time: 13.5s + Total CPU time: 6.33s + User wait time: 119.58us + Serialization time: 1.33s (20.93%) + Checksum calculation time: 1.12s (17.75%) + Compression time: 1.88s (29.71%) + Total IO delay: 5.84s + Concurrency overhead: 3.22ms + Uncompressed size: 1.86GiB (~97.66KiB per object) + Output size: 1.86GiB (~97.66KiB per object; compression = 100%) + IO speed: 326.45MiB/s + Concurrency adjusted uncompressed speed: 1.22GiB/s + Actual uncompressed speed: 141.28MiB/s + Actual speed: 141.28MiB/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.core.sequence.quality.QualityTrimmerTest > testParametersSerialization0 STANDARD_OUT - { - "averageQualityThreshold": 7.0, - "windowSize": 6 - } +com.milaboratory.test.TestUtil > testLT STANDARD_OUT + Short tests. + No system env properties. + +com.milaboratory.core.sequence.ShortSequenceSetTest > test1 STANDARD_OUT + 99952 elements with 366.22KiB in raw nucleotide entropy serialized into 272.98KiB + +com.milaboratory.core.sequence.NucleotideAlphabetTest > testCalculateIntersections SKIPPED com.milaboratory.core.sequence.quality.QualityAggregatorTest > test1 STANDARD_OUT - 37 + 48 com.milaboratory.core.sequence.quality.QualityAggregatorTest > test2 STANDARD_OUT - 615 + 648 com.milaboratory.core.sequence.quality.QualityAggregatorTest > test3 STANDARD_OUT - 2573 + 2460 -com.milaboratory.core.sequence.ShortSequenceSetTest > test1 STANDARD_OUT - 99941 elements with 366.41KiB in raw nucleotide entropy serialized into 273.22KiB +com.milaboratory.core.sequence.quality.QualityTrimmerTest > testParametersSerialization0 STANDARD_OUT + { + "averageQualityThreshold": 7.0, + "windowSize": 6 + } + +com.milaboratory.core.sequence.AminoAcidAlphabetTest > testCalculateMatches SKIPPED + +com.milaboratory.core.sequence.GeneticCodeTest > generateExtendedGeneticCode SKIPPED com.milaboratory.core.sequence.AminoAcidSequenceTest > testName STANDARD_OUT 3 @@ -4044,23 +3370,25 @@ 18 19 -com.milaboratory.core.sequence.GeneticCodeTest > generateExtendedGeneticCode SKIPPED +com.milaboratory.core.motif.BitapPatternTest > ttt STANDARD_OUT + 0 ATTWCCGACA 9 + ||| |||| + 20 ATTT--GACA 27 + [S3:W->T,D4:C,D5:C] + 24 + -26 -com.milaboratory.core.sequence.AminoAcidAlphabetTest > testCalculateMatches SKIPPED +com.milaboratory.core.RangeTest > test23e14 STANDARD_OUT + 1000001 + 1010100 + 1000111 + 1000011 -com.milaboratory.core.sequence.NucleotideAlphabetTest > testCalculateIntersections SKIPPED + 1000010 -com.milaboratory.core.mutations.MutationsTest > testCanonical1 STANDARD_OUT - GCGTTTAGTGCATTCTAAGGATGCGGCACGGGGGTGCATTCATCGGCACCGGGACTCCCACTGCTCCGATATTTTTTTGTCGTTGATCCGACTGCACTAGAGATTCTCAACTAATTGTACGATCGGAATCGCGCGCCGTCTCACGGCGGCGGAATCCACTAGGTTTCAGGTAGCCACACAAGTGTTACTGTTGACACGCCATCTTGCGGTAATTCCGAGTTTCGTGTATACAGATACCTCCCAGAACGGGACACGCGAGACGGTCGCACGCAGACGGTTGGACCACTGCCCTTGATCTGCGGTAAAGCGGGTAGGGTGACCATATAACGGATCAGTTGTGCCTCACGATAAGCCTGCTAGCCACGAAGTCAGTGAGGAACTAGTAGTATATGCAAGCACGAACCGAGGCAGCGGCCGACCTTAAAACATCTTTGGCACA - GCGTTTAGTGCATTCTAAGGATGCGGCACGGGGGTGCATTCATCGGCACCGGGATCCACTGCCTCCGATATTTTTTTGTCGTTGATCCGACTGCACTAGAGATCTCAACTAATTGACGATCGGAATCCGCGCCGTCTCACGGTGCGGAATCCACAGGTTCAGCGTAGCCCACAATGTGTTACTTACTACGCCATCTTGCGGTAATTCCGAGTTTCGTTATACAGTTCCTCGCCCGTACGGGACACGCGAGACGGTCGCACACAGACAGTTGGACCACTGCCTTGATCTGCCGTAAAGCGGTAGTGACCTAAACGGATTAGTTGTGCCTCACGATAGCGCTTCTAGTCACGAAGTCAGTGAGGACATGTTGTATAGCAGTACGACCGAGGCAGCGGCCGACCGTTAAAACATTTGGCAA - GCGTTAGTGCATTCTAAGGATGTCTGCACGGTGGTGCATTCATCGGCACGGGACCACTGCCTCCGATATTTTTTGTGCCTTGACCGACTCACTAGAGTCTCAACTAATTGACGATCGGAATCCGCGCCGTCTCACGGTGCGTAATCCACAGGTTCAACGTAGTCCACAATGTGTTACTTACTACGCCATCTTGCGGTAATTCGAGTTCGTTATACAGTTCCTCGCCCGTACGGGACACGCGATGACGGCTCGCACCAGACAGTTGGGTCCGCTGCCTTTGATCTGCCGTAAAGCTGTAGTGACCTAACGGATTAGTTGTGCCTCCACGATAGCGCTTCTAGTTACGATCTCAGTGAGACATGTGATAGCAGTACGACCGAGGCAGCGGCCGACCCGTTAAAACATTTGGGA - 0 GCG-TTAGTGCATTCTAAGGATGTCTGCACGGTGGTGCATTCATCGGCA-CGGGA---CCACTGCCTCCGATA-TTTTTTGTGCCTTGA-CCGACT-CACTAGAG--TCTCAACTAATTG-ACGATCGGAATC-CGCGCCGTCTCACGG-TGCGTAATCCAC-AGG-TTCAACGTAGTCCACA-ATGTGTTAC--TT-ACTACGCCATCTTGCGGTAATT-CGAG-TTCGT-TATACAG-TTCCTCGCCCGTACGGGACACGCGATGACGGCTCGCAC-CAGACAGTTGGGTCCGCTGCCTTTGATCTGCCGTAAAGC-TGTA--GTGACC---TAACGGATTAGTTGTGCCTCCACGAT-AGCGCTTCTAGTTACGATCTCAGTGA-G-AC-A-T-GTGATA-GC-AGTACG-ACCGAGGCAGCGGCCGACCCGTTAAAACA--TTTGG--GA 410 - ||| ||||||||||||||||||| | |||||| |||||||||||||||| ||||| |||||| |||||||| |||||||| | |||| |||||| |||||||| ||||||||||||| |||||||||||| ||||||||||||||| ||| ||||||| ||| ||| | |||| ||||| | ||||||| || || ||||||||||||||||||| |||| ||||| ||||||| | |||| || | ||||||||||||| ||||| |||||| ||||| ||| || || ||||| ||||||||| ||||||| ||| |||||| |||||||| |||||||||| |||||| ||| || |||| |||| ||||||| | || | | || ||| || || ||| ||||||||||||||||| || |||||||| ||||| | - 0 GCGTTTAGTGCATTCTAAGGATG-CGGCACGGGGGTGCATTCATCGGCACCGGGACTCCCACTG-CTCCGATATTTTTTTGT-CGTTGATCCGACTGCACTAGAGATTCTCAACTAATTGTACGATCGGAATCGCGCGCCGTCTCACGGCGGCGGAATCCACTAGGTTTC-AGGTAG-CCACACAAGTGTTACTGTTGAC-ACGCCATCTTGCGGTAATTCCGAGTTTCGTGTATACAGATACCTC-CCAGAACGGGACACGCGA-GACGG-TCGCACGCAGACGGTT-GGACCACTGCCCTTGATCTGCGGTAAAGCGGGTAGGGTGACCATATAACGGATCAGTTGTGCCT-CACGATAAGC-CTGCTAGCCACGAAGTCAGTGAGGAACTAGTAGT-ATATGCAAGCACGAACCGAGGCAGCGGCCGA-CC-TTAAAACATCTTTGGCACA 438 - [I3:T,D5:T,I54:C,I54:T,D55:T,D58:C,I71:T,D75:T,I102:A,S102:A->T,D104:T,I146:C,S146:C->G,D147:G,I163:T,D164:T,D167:A,S168:G->A,I169:G,D173:C,D175:A,I180:C,I181:A,I188:T,S188:T->G,D189:G,I214:C,D215:C,I219:T,D221:T,D279:G,S281:A->G,I282:A,D288:C,S291:T->C,I293:T,I300:G,D301:G,I308:G,D309:G,I313:G,D315:G,I321:A,I321:T,D324:T,D326:A,I349:A,D350:A,D366:A,S367:G->A,I368:G,I375:G,S376:G->A,D378:A,I382:G,I382:T,I382:A,D384:A,D385:G,D386:T,I400:A,D401:A,I428:T,I428:C,D429:C,D431:T,I435:C,I435:A,D437:C,D438:A] - 0 GCG-TTTAGTGCATTCTAAGGATGCGGCACGGGGGTGCATTCATCGGCACCGGGA--CTCCCACTGCTCCGATA-TTTTTTTGTCGTTGATCCGACTGCACTAGAG-ATTCTCAACTAATTGTACGATCGGAATCGCGCGCCGTCTCACGG-CGGCGGAATCCACTAGG-TTTCAG-GTAGCCACACA-A-GTGTTAC-TGTTGACACGCCATCTTGCGGTAATT-CCGAG-TTTCGTGTATACAGATACCTCCCAGAACGGGACACGCGAGACGGTCGCACGCAGACGGTTGGA-CCACTGCCCTT-GATCTGC-GGTAAAGC-GGGTA-GGGTGACC--ATATAACGGATCAGTTGTGCCTCACGAT-AAGCCTGCTAGCCACGAAG-TCAGTGA-GGAACTA---GTAGTATATGCAAGCACG-AACCGAGGCAGCGGCCGACCTTAAAACA--TCTTTGG--CACA 438 - ||| || |||||||||||||||||||||||||||||||||||||||||||||||| | || |||||||||||| |||| |||||||||||||||||||||||||| | ||||||||||||||||||||||||||||||||||||||||| ||||||||||||||| | || |||| | |||| | ||||||| |||||||||||||||||||||||| | ||| || ||||||||||||||||||||||||||||||||||||||||||||||||||||||||| | |||||| || | ||||||| | |||||| | ||| || ||||| ||| | |||||||||||||||||||||| | ||||||||||||||| ||||||| | | ||| || ||||||||||||| | |||||||||||||||||||||||||| | | ||| || - 0 GCGTTT-AGTGCATTCTAAGGATGCGGCACGGGGGTGCATTCATCGGCACCGGGACTC-CC-ACTGCTCCGATATTTTT-TTGTCGTTGATCCGACTGCACTAGAGATT-CTCAACTAATTGTACGATCGGAATCGCGCGCCGTCTCACGGCG-GCGGAATCCACTAGGTT-TC-AGGTAG-C-CACACAAGTGTTACTG-TTGACACGCCATCTTGCGGTAATTCC-GAGTTT-CGTGTATACAGATACCTCCCAGAACGGGACACGCGAGACGGTCGCACGCAGACGGTT-GGACCACTG-CCCTTGATCTGCGG-TAAAGCGG-GTAGGG-TGACCATATA-A-CGGATCAGTTGTGCCTCACGATAA-GCCTGCTAGCCACGA-AGTCAGTGAGGAA-CTAGTAGT---ATATGCAAGCACGAA-CCGAGGCAGCGGCCGACCTTAAAACATCT-T-TGGCACA-- 438 +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.MutationsUtilTest > test1111 STANDARD_OUT S([\QAGCTNRYSWKMBDHV\E])(\d+)([\QAGCTNRYSWKMBDHV\E])|D([\QAGCTNRYSWKMBDHV\E])(\d+)|I(\d+)([\QAGCTNRYSWKMBDHV\E]) @@ -4086,77 +3414,210 @@ 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 + GAGACTTAAACACAAGCGCTAAACCACCTGGCCCGAGACGGACTAACGTTCCCGTTCGCGGTCATCGTCGACCCGGCTTACTACCCGGGATGTTGTTGCATTTCACCCTGAGTGCCAGGTAGGAGCCTGAGCATAGAAATCCTTCGCGGCGGCTTTATTGTTTAAATGGTGCACACACGGCCTAGTTTCAAAGCTACTTGGGCGTTGGACCACATTTCGCTGGTGGCGCACAAGCGCTTGAGGAGCACAGAAGAAATGTCTATATGAGGGCCACTAGCTGTGGACCTTACTGCTATTGCGAAACGGCCGCAGGTAGGTTACCTTCTCGCATGTTATCTGTTCATCCAAGTGCGTGCTTACCGGTCTCTTGTTCAACTAAAAGACTTCTTATGGTCTTTAGATCAGGATCAAGACGGTGCGTGTTAGGGCGTAGCTGGATAAAAACAGTGGGCTCTCCATTACCCTGAAACGAAGACGGGTCCGCCCACCCTCCATGGACGGGTATACGAAGTGAATTCGTCTAACGGCGGTCAAATCCTGCTGTACCCAATAAGTGAAACGCTCGAGCAAAACTGGTCCACTAGATGCTTTTGTTCGCAACAAACGTGCATATCCTCTGCCTATTACTTTTATCGATTGAAACTTAGGTATGACACTGCACGTACCCGTAAAAAGCCCATGGTTAGGCTCGCCTATCCCGGACAATCTTGAAAGTGCACATACCTGTAAAGACCCCACGATGCAGCGTCTATTCGGGGTACGCCGAAT + GAGATTAAACACAGCGCTAACGCACCTGGCCCGAGACGGGACTATACGTCCTGTTCGGGTCATCCTCGCACCCGGCTCTGCTACCCGGAATTGTTGTTGCATTTCACCCTAGTGCCAGTAGGAGCTGAGCATAGAAACCTTCGCGGGTTTTATTGTTTAAATGGTGTACACACGGCCTAGTTTCAAAGCTACTTGGGCGTTGGACACATTTCGCGGGGCCACAAGCTGCTCGAGGAGCTCGAGAAATGTCTATATGGGCCACTAGCTGTGACCTTACTGCTTGGAAACGGCCGCAGGTAGGTTACTTCTCGCATTTATCTGTTCATCCAAGTGCTGCTTACCTGTCCTCTTGTTCAACTAAAAGACCTCTTATGGTCTTTTAGATCAGGACAAGACGTGCTGTTAGGCGTTGTGGAAAAACAGTGGGCTCTCCCATTACCCTGAAACGAAGACGGGTCCGCCCACCCTGCAGGACGGGACACGAAGTGAATTCTCTAACGGCCGGTCAAATCGTGCTGTACCCAATGAGTGGACGCTCGAGCAAACTGGTCCACTAGATGCTTTAGTTCGCGACAAACGTGATATCCTCTGCCTATTACTTTATCGATTTGAATCTTAGTATGACACTGCATGACCCGTAAAAAGCCCATGTTAGGCTCGCCTATCCCGGACAATCTTGAAAGTGCACATACCTGTAAAGACCCCACGATGCAGCGTCTGTTCGGGTACGCCGAACT + GAGTTAAGACAGCGCAACGCGAGCCTGGCCGAGACGGGACTATACGTCCTTTCGGGTCATCCTCGCACCGGCTCTCTACCCGGAATGTCTGTTGCATTTCACCCTAGTGCAGTAGGAGCTGAGCGTAAAACCTTCGCGGGTTTTATGTTAATGGTGTACACACGGCTAGTTTCAAGCTATTGGGCGTTGGACACAATTCGCGGGCCACAAGCTGCTCGGAGGAGCTCGAGAAATGTCTATTGGGGCCACTAGCTGTGATCTTACTGCTTTGAAACGCGTGGTAGGTTACTTCTCGCATTTATTCGTTCTCCAAGTGCTGCTCACCTGTCCTCCTGTCAACTAAAGACCTTTTATGGCTTTTGATCAGGACAAGACGTGCTGTAGACGTTGTGGGAAAAACAGTGGGCTCTCCATTACCCTGAAACGAAGACGGGTCCGCCCACCCTGCGGAACGGGACACGAAGGAATTCTCAAACGGCCGGTAAATCGTTTTGTACCCAATGAGTGGACGCTCTGAGGCAAACTGGCCCACTAGATGCTTTAGTCGCGACAAACGTGATATCCTCCGCCTATTGACTTATCGATTTGAATCTTAGTATGACACTGCTGACCCGTAAAAAGTCCATGTTGGGCTCGCCTCCGGACATTTGAAAGTGCACATCCTGTTAAGACCCCACGATTATCGTCTGTTCAGTACGCCGAAT + 0 GAG--TT-AAGAC-AGCGC--AACGCGAGCCTGG-CCGAGACGGGACTATACG-T-CCTTTCG-GGTCATCCTCG-CACCGGCTCT-CTACCCGGAATGTCTGTTGCATTTCACCCT-AGTG-CA-GTAGGAG-CTGAGCGTA-AAA-CCTTCGC-G-GGTTTTA-TG-TT-AATGGTGTACACACGG-CTAGTTTC-AAGCTA-TTGGGCGTTGGA-CACAATTCGC--G-GGC-CACAAGCTGCTCGGAGGAGCTC-G-AGAAATGTCTAT-TG-GGGCCACTAGCTGT-GATCTTACTGCT-TT--GAAAC-G-CG-TGGTAGGTTA-CTTCTCGCAT-TTAT-TCGTTC-TCCAAGTGC-TGCTCACCTGTCCTCCTG-TCAACT-AAAGACCTT-TTATGG-CTTTTGATCAGGA-CAAGAC-GTGC-TG-TA-GACGTTG-TGG-GAAAAACAGTGGGCTCTCCATTACCCTGAAACGAAGACGGGTCCGCCCACCCTGC--GGAACGGG-ACACGAAG-GAATTC-TCAAACGGCCGGT-AAATCGTTTTGTACCCAATGAGTG-GACGCTCTGAGGC-AAACTGGCCCACTAGATGCTTTAG-TCGCGACAAACGTG-ATATCCTCCGCCTATTGAC--TTATCGATTTGAATCTTA-GTATGACACTGC-TG-ACCCGTAAAAAGTCCAT-GTTGGGCTCGCC--T-CCGGAC-AT-TTGAAAGTGCACAT-CCTGTTAAGACCCCACGAT-TATCGTCTGTTC--AGTACGCCGAAT 703 + ||| || || || ||||| ||| | | ||||| ||||||| |||||| ||| | || |||| ||||||| ||| | |||||| | |||||||| |||| |||||||||||||||| |||| || ||||||| |||||| || ||| ||||||| | || |||| || || ||||||| |||||||| |||||||| |||||| |||||||||||| |||| ||||| | ||| ||||||| ||| ||||||| | | |||||||||||| || |||||||||||||| || ||||||||| || ||||| | || ||||||||| |||||||||| |||| | |||| ||||||||| |||| ||| || ||| || |||||| ||||| ||| |||||| |||| |||||||| |||||| |||| || || | ||| | ||| |||||||||||||||||||||||||||||||||||||||||||||||||||| | || ||||| | |||||| |||||| || ||||| |||| ||||| | |||||||||| |||| |||||| || || ||||||| |||||||||||||| | |||| ||||||||| |||||||| ||||||| || ||||||| ||||| |||| |||||||||||| | |||||||||||| |||| ||| |||||||| | |||||| || |||||||||||||| ||||| ||||||||||||| | ||||| ||| ||||||||||| + 0 GAGACTTAAACACAAGCGCTAAAC-C-A-CCTGGCCCGAGAC-GGACTA-ACGTTCCCGTTCGCGGTCATCGTCGAC-CCGGCT-TACTACCCGGGATGT-TGTTGCATTTCACCCTGAGTGCCAGGTAGGAGCCTGAGCATAGAAATCCTTCGCGGCGGCTTTATTGTTTAAATGGTGCACACACGGCCTAGTTTCAAAGCTACTTGGGCGTTGGACCACATTTCGCTGGTGGCGCACAAGC-GCT-TGAGGAGCACAGAAGAAATGTCTATATGAGGGCCACTAGCTGTGGACCTTACTGCTATTGCGAAACGGCCGCAGGTAGGTTACCTTCTCGCATGTTATCT-GTTCATCCAAGTGCGTGCTTACCGGT-CTCTTGTTCAACTAAAAGA-CTTCTTATGGTCTTTAGATCAGGATCAAGACGGTGCGTGTTAGGGCGTAGCTGGATAAAAACAGTGGGCTCTCCATTACCCTGAAACGAAGACGGGTCCGCCCACCCTCCATGG-ACGGGTATACGAAGTGAATTCGTCTAACGG-CGGTCAAATCCTGCTGTACCCAATAAGTGAAACGCTC-GA-GCAAAACTGGTCCACTAGATGCTTTTGTTCGCAACAAACGTGCATATCCTCTGCCTATT-ACTTTTATCGA-TTGAAACTTAGGTATGACACTGCACGTACCCGTAAAAAGCCCATGGTTAGGCTCGCCTATCCCGGACAATCTTGAAAGTGCACATACCTGTAAAGACCCCACGATGCAGCGTCTATTCGGGGTACGCCGAAT 767 + [I3:A,S3:A->C,D4:C,I7:A,S9:A->C,D10:C,I13:A,D14:A,I19:T,S19:T->A,D21:A,I31:C,D32:C,I48:T,S49:T->C,S52:C->G,S53:G->T,D54:T,I70:A,S70:A->C,D73:C,I114:C,D115:C,I117:G,D118:G,I125:C,D126:C,I135:G,S135:G->A,S138:A->T,D139:T,I147:G,I148:C,D149:C,D151:G,I160:T,S162:T->A,D164:A,I189:A,D191:A,I209:C,D210:C,I213:A,S213:A->T,D214:T,I220:T,S220:T->G,I222:T,D223:T,D224:G,D238:T,S239:G->T,I240:G,D265:G,D266:A,I268:A,I269:G,I281:G,S282:G->A,D283:A,D295:T,S297:G->T,I298:G,I304:G,S305:G->C,D307:C,I377:A,D380:A,D383:C,S384:T->C,S386:C->T,I387:C,I414:G,D415:G,I422:T,D423:T,I435:G,I436:A,S436:G->T,D437:A,D438:T,D442:A,I444:A,I493:A,S493:A->T,D494:T,I556:A,D557:A,I568:A,D571:A,D589:T,I592:T,I593:T,D594:T,I627:T,D629:T,I646:G,D647:G,I680:G,D681:G,I693:T,S693:T->A,D694:A,I696:C,D698:C,I703:A,S704:A->T,S705:T->C,D706:C,I754:G,D755:G] + 0 GAG-ACTT-AAACAC-AAGCGC-TAAACCACCTGG-CCCGAGACGGACTAACG-TTCCCGTTCGCGGTCATCGTCG-ACCCGGCTTACTACCCGGGATGTTGTTGCATTTCACCCTGAGTG-CCA-GGTAGGAG-CCTGAGCATA-GAAATCCTTCGC-G-GCGGCTTTATTG-TTTAAATGGTGCACACACGGCCTAGTTTC-AAAGCTACTTGGGCGTTGGA-CCAC-ATTTCGC-TG-GTGGCGCACAAGCGCTTG-AGGAGCACAGAAGAAATGTCTATATGAG-G-GCCACTAGCTGT-GGACCTTACTGCTATTG-CGAAAC-GGCCGCAGGTAGGTTACCTTCTCGCATGTTATCTGTTCATCCAAGTGCGTGCTTACCGGTCTCTTGTTCAACT-AAAAGACTTC-TTATGGTCTTTAGATCAGGATCAAGAC-GGTGCGTG-TTAGGGCGTAGCT-G-GATAAAAA-CAGTGGGCTCTCCATTACCCTGAAACGAAGACGGGTCCGCCCACCCTCC-ATGGACGGGTATACGAAGTGAATTCGTCTAACGGCGGTCAAATCCTGCTGTACCCAATAAGTG-AAACGCTCGAGC-AAAACTGGTCCACTAGATGCTTTT-G-TTCGCAACAAACGTGCATATCCTCTGCCTATTAC-TTTTATCGATTGAAACTTA-GGTATGACACTGCACGTACCCGTAAAAAGCCCAT-GGTTAGGCTCGCC-TAT-CCCGGAC-AATCTTGAAAGTGCACATACCTGTAAAGACCCCACGATGCAGCGTCTATTC-GGGGTACGCCGAAT 767 + ||| || || || | |||| | ||||||||| | ||||||||||||||| | || ||||||||||||||| || |||||||||||||||||||||||||||||||||||||||| | | | |||||| | |||||||| || ||||||| | | | |||||||| || | |||||||||||||||||||||||| || ||||||||||||||||| | || ||||| | | ||||||||||||| ||||||||||||||||||||||||| | | |||||||||||| | ||||||||||| | |||||| | | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||| || | ||||||||||||||||||||||||||| | |||||| | ||||||||||| | ||| | ||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| | |||||||||| ||| ||||||||||||||||| || | | |||||||||||||||||||||||||||||||| || |||||||||||||||| | |||||||||||||||||||||||||||||||| | ||||||||||| | || |||| | ||||||||||||||||||||||||||||||||||||||||||||||| | |||||||||||| + 0 GAGAC-TTAAAC-ACAA-GCGCTAA-ACCACCTGGCC-CGAGACGGACTAACGTTCCCGT-TCGCGGTCATCGTCGACCC-GGCTTACTACCCGGGATGTTGTTGCATTTCACCCTGAGTGCC-AGG-TAGGAGCC-TGAGCATAGAAAT-CCTTCGCGGCG-G-CTTTATTGTTTAA-ATGGTGCACACACGGCCTAGTTTCAAA-GCTACTTGGGCGTTGGACC-ACAT-TTCGCTGGTG--GCGCACAAGCGCT-TGAGGAGCACAGAAGAAATGTCTATAT--GAGGGCCACTAGCTGTGGA-CCTTACTGCTA-TTGCGAAACGGCC-GCAGGTAGGTTACCTTCTCGCATGTTATCTGTTCATCCAAGTGCGTGCTTACCGGTCTCTTGTTCAACTAAAA-GA-CTTCTTATGGTCTTTAGATCAGGATCAAGACGG-TGCGTGTT-AGGGCGTAGCTGGAT--AAA-AACAGTGGGCTCTCCATTACCCTGAAACGAAGACGGGTCCGCCCACCCTCCAT-GGACGGGTATACGAAGTGAATTCGTCTAACGGCGGTCAAATCCTGCTGTACCCAATAAGTGAA-ACGCTCGAGCAAAA-CTGGTCCACTAGATGCT-TTTGTT-CGCAACAAACGTGCATATCCTCTGCCTATTACTTT-TATCGATTGAAACTTAGG-TATGACACTGCACGTACCCGTAAAAAGCCCATGG-TTAGGCTCGCCTA-TCCC-GGACAATC-TTGAAAGTGCACATACCTGTAAAGACCCCACGATGCAGCGTCTATTCGG-GGTACGCCGAAT 767 -com.milaboratory.core.merger.MergerParametersTest > test2 STANDARD_OUT - { - "qualityMergingAlgorithm": "SumSubtraction", - "partsLayout": "Collinear", - "minimalOverlap": 15, - "maxQuality": 50, - "minimalIdentity": 0.8, - "identityType": "Unweighted" - } +com.milaboratory.core.alignment.kaligner2.KAligner2Test > testBoundaries STANDARD_OUT + 4964 -com.milaboratory.core.RangeTest > test23e14 STANDARD_OUT - 1000001 - 1010100 - 1000111 - 1000011 +com.milaboratory.core.alignment.kaligner2.KAligner2Test > caseJ1 STANDARD_OUT + 52 + 0 TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAGGA 51 + ||||||||||||||||||||||||||||||||||||||||||||||||||| + 55 TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAGGG 106 + [S51:A->G] + (0->52) + (55->107) - 1000010 +com.milaboratory.core.alignment.kaligner2.KAligner2Test > testCase0 SKIPPED -com.milaboratory.core.motif.BitapPatternTest > ttt STANDARD_OUT - 0 ATTWCCGACA 9 - ||| |||| - 20 ATTT--GACA 27 - [S3:W->T,D4:C,D5:C] - 24 - -26 +com.milaboratory.core.alignment.kaligner2.KAligner2Test > testSimpleRandomTest STANDARD_OUT + Time per query: 803.86us + Processed queries: 53 + Bad percent: 0.0 + False positive percent: 0.5624388653407238 + Scoring error percent: 1.8867924528301887 -com.milaboratory.core.alignment.AlignmentHelperTest > test1 STANDARD_OUT - 0 GAGGTGCAGCTGGTGGAGTCTGGGGGAGGC 29 - |||||||||||||||||||||||||||||| - 0 GAGGTGCAGCTGGTGGAGTCTGGGGGAGGC 29 +com.milaboratory.core.alignment.kaligner2.OffsetPacksAccumulatorTest > testScoreCorrection2 SKIPPED - 30 TTGGT-ACAGCCTGGGGGGTCCCTGAGACT 58 - |||| | |||||||||||||| |||||| - 30 CTGGTCA-AGCCTGGGGGGTCCATGAGACA 58 +com.milaboratory.core.alignment.kaligner2.KMapper2Test > test11112 STANDARD_OUT + ID: 0 + Score: 1716 + Cluster 0: + Q 27 -> T 15 - -12 + Q 30 -> T 18 - -12 + Q 36 -> T 25 - -11 + Q 39 -> T 28 - -11 + Q 42 -> T 31 - -11 + Q 45 -> T 34 - -11 + Q 48 -> T 37 - -11 + Q 51 -> T 40 - -11 + Cluster 1: + Q 84 -> T 50 - -34 + Q 87 -> T 53 - -34 + Q 90 -> T 56 - -34 + Q 93 -> T 59 - -34 + Q 96 -> T 62 - -34 + Q 99 -> T 65 - -34 + Q 114 -> T 82 - -32 + Cluster 2: + Q 150 -> T 92 - -58 + Q 153 -> T 95 - -58 + 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 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 + Q 252 -> T 184 - -68 + Q 255 -> T 187 - -68 + Q 258 -> T 190 - -68 + Q 261 -> T 193 - -68 + Q 262 -> T 194 - -68 - 59 CTCCTGTGCAGCCTCTGGATTCACCTTCAG 88 - |||||||||||||||||||||| ||||||| - 59 CTCCTGTGCAGCCTCTGGATTCCCCTTCAG 88 - 89 TAGC-TATAGCATGAACTGGGTCCGCCAGG 117 - || | ||||||||||||||||||||||||| - 89 TA-CTTATAGCATGAACTGGGTCCGCCAGG 117 +com.milaboratory.core.alignment.kaligner2.KMapper2Test > test1111 STANDARD_OUT + ID: 0 + Score: 1212 + Cluster 0: + Q 9 -> T 15 - 6 + Q 12 -> T 18 - 6 + Q 15 -> T 21 - 6 + Q 18 -> T 24 - 6 + Q 21 -> T 27 - 6 + Q 24 -> T 30 - 6 + Q 27 -> T 33 - 6 + 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 + Cluster 2: + Q 123 -> T 89 - -34 + Q 126 -> T 92 - -34 + Q 129 -> T 95 - -34 + Q 132 -> T 98 - -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 - 118 CTCCAGGGAAGGGGCTGGAGTGGGTTTCAT 147 - ||||||||||||||||||||||||| |||| - 118 CTCCAGGGAAGGGGCTGGAGTGGGTCTCAT 147 - 148 ACATTAGTAGTAGTAGTAG-TACCATATAC 176 - |||||||||| ||||||| || |||||| - 148 CCATTAGTAGTGGTAGTAGTTA-CATATAT 176 +com.milaboratory.core.alignment.kaligner2.KMapper2Test > testRandom1 STANDARD_OUT + noHits: 305 + noHits2: 0 + noHits3: 0 + wrongTopHit: 44 + wrongTopHitS: 33 + noCorrectHitInList: 24 + + + + + Timings: + DescriptiveStatistics: + n: 100000 + min: 10521.0 + max: 3.26413413E8 + mean: 135369.55471999952 + std dev: 2138648.428341139 + median: 107389.5 + skewness: 106.53713053470115 + kurtosis: 12221.629529657328 + + + + + + Clusters basicSize + DescriptiveStatistics: + n: 99651 + min: 1.0 + max: 6.0 + mean: 2.862359635126588 + std dev: 1.1018851007553552 + median: 3.0 + skewness: 0.2992413472127956 + kurtosis: -0.6737932642501048 - 177 TACGCAGACTCTGTGAAGGGCCGATTCACC 206 - ||||||||||| |||||||||||||||||| - 177 TACGCAGACTCCGTGAAGGGCCGATTCACC 206 - 207 ATCTCCAGAGACAATGCCAAGAACTCACTG 236 - |||||||||||||| ||||||||||||||| - 207 ATCTCCAGAGACAACGCCAAGAACTCACTG 236 - 237 TATCTGCAAATGAACAGCCTGAGAGACGAG 266 - ||||||||||||||||||||||||| |||| - 237 TATCTGCAAATGAACAGCCTGAGAGCCGAG 266 - 267 GACACGGCTGTGTATTACTGTGC 289 - ||||||||||||||||||||||| - 267 GACACGGCTGTGTATTACTGTGC 289 + Top Delta + DescriptiveStatistics: + n: 99671 + min: -19.0 + max: 0.0 + mean: -0.0011036309458110172 + std dev: 0.12077633398704204 + median: 0.0 + skewness: -116.43667581233203 + kurtosis: 14281.584480823189 + + +com.milaboratory.core.alignment.batch.SimpleBatchAlignerTest > test1 STANDARD_OUT + 4 hits. + +com.milaboratory.core.alignment.blast.BlastDBBuilderTest > test1 SKIPPED + +com.milaboratory.core.alignment.blast.BlastAlignerExtTest > test16SMicrobial1 SKIPPED + +com.milaboratory.core.alignment.blast.BlastAlignerExtTest > 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.kaligner1.KMapperTest > testBestOffset2 STANDARD_OUT + -205 + +com.milaboratory.core.alignment.kaligner1.KAlignerTest > testRandomCorrectness STANDARD_OUT + C=1182;I=0;M=0;ScE=0;R=0.0 AlignmentTime = 434.11us + C=1642;I=1;M=0;ScE=0;R=0.0 AlignmentTime = 248.91us + C=2048;I=0;M=0;ScE=0;R=0.0 AlignmentTime = 234.97us + C=2142;I=0;M=0;ScE=0;R=8.333333333333333E-7 AlignmentTime = 139.20us + +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.kaligner1.KAlignerTest > testRandomCorrectnessConcurrent STANDARD_OUT + C=3000;I=0;M=0;ScE=0;R=0.0 AlignmentTime = 315.75us + C=2997;I=0;M=0;ScE=0;R=0.0 AlignmentTime = 153.37us + C=2999;I=0;M=0;ScE=0;R=0.0 AlignmentTime = 156.40us + C=2997;I=0;M=1;ScE=0;R=0.0 AlignmentTime = 214.81us com.milaboratory.core.alignment.BandedAffineAlignerTest > test11 STANDARD_OUT 0 --------------------- -1 @@ -4207,50 +3668,6 @@ 0 gCccTtgtgatgacccagactccagcctccgtgGAGgCaGctgtgggaggcacagtcaccatcaagtgccaggccagtcagagcattagcaacctcttaGCCTGGTATCAGCAGAAACCAGGGCAGCCTCCCAAGCTCCTGATCTATTATGCATCCGATCTGGcatctggggtctcatcaaggttcaaaggcagtggatctgggacagagtAcactctcaccatcagTggcgtgcagtgtgccgatgctgccacttactac 260 1 gAccCtgtgatgacccagactccagcctccgtgTCTgAaCctgtgggaggcacagtcaccatcaagtgccaggccagtcagagcattagcaacctctta-------------------------------------------------------------NNNcatctggggtctcatcaaggttcaaaggcagtggatctgggacagagtTcactctcaccatcagCggcgtgcagtgtgccgatgctgccacttactac 200 -com.milaboratory.core.alignment.BandedLinearAlignerTest > testCase1 STANDARD_OUT - GCGTGAAGACTGCAGGCATTGAGTACGTTACTAGTCCAGTGGGGCCCAACCGTAACATTGCGTGTGACTGGTTGCTTAGCGGGTGACGGCGTTTCAGGTTACGCCCTCTGTGCATCACCGATAGCGTTGTTTGAGCTTTCTAACGTCTCAAACCTGCTTGCGCCCTACGGTTTCTCTATATATACACGAAAGGGGCTGGTCGCAACCTCGCAATTCTATCCCTCCAACCTCCCTCGAATTTTT - AAAGCGTGAAGACTTGCAGGCATTGGTACGTTATTAGTCCAGTGGGGCCACAACCGTAACATTGCGTGTGACTGGTGCTTAGCGGGTGACGGCGTTCAGGTTACGCCCTCTGTGCATCACCGATTAGCGTTGTCTGAGCTTTCTAACGTCTCAAACCTGCTTGCGCCCTACGGTTTCTCTATAGTATCACGAAAGGGTCTGGTCGCAACCTCGCAATTCTATCCCTCCAACCTCCCTTGAATTTTTCTA - -com.milaboratory.core.alignment.BandedLinearAlignerTest > testGlobal1 STANDARD_OUT - 1 AATTGACA 8 - |||||| - 0 TATTGACT 7 - -com.milaboratory.core.alignment.BandedLinearAlignerTest > testGlobal2 STANDARD_OUT - 1 AATTGACAG 9 - |||||| | - 0 TATTGAC-G 7 - -com.milaboratory.core.alignment.BandedLinearAlignerTest > testGlobal3 STANDARD_OUT - 0 TATTGACT 7 - |||||| - 1 AATTGACA 8 - -com.milaboratory.core.alignment.BandedLinearAlignerTest > testGlobal4 STANDARD_OUT - 0 TATTGAC-G 7 - |||||| | - 1 AATTGACAG 9 - -com.milaboratory.core.alignment.kaligner1.KMapperTest > testBestOffset2 STANDARD_OUT - -205 - -com.milaboratory.core.alignment.kaligner1.KAlignerTest > testRandomCorrectness STANDARD_OUT - C=1182;I=0;M=0;ScE=0;R=0.0 AlignmentTime = 241.69us - C=1642;I=1;M=0;ScE=0;R=0.0 AlignmentTime = 123.68us - C=2048;I=0;M=0;ScE=0;R=0.0 AlignmentTime = 131.73us - C=2142;I=0;M=0;ScE=0;R=8.333333333333333E-7 AlignmentTime = 83.82us - -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.kaligner1.KAlignerTest > testRandomCorrectnessConcurrent STANDARD_OUT - C=3000;I=0;M=0;ScE=0;R=0.0 AlignmentTime = 93.12us - C=2999;I=0;M=0;ScE=0;R=0.0 AlignmentTime = 97.41us - C=2999;I=0;M=0;ScE=0;R=8.333333333333333E-7 AlignmentTime = 100.39us - C=3000;I=0;M=0;ScE=0;R=8.333333333333333E-7 AlignmentTime = 100.20us - com.milaboratory.core.alignment.MultiAlignmentHelperTest > test1 STANDARD_OUT 8 AGACACAGATACA 20 ||||||| ||||| @@ -4346,187 +3763,88 @@ 0 cgatccTTcggtgacaaagcgttcggacc 28 0 catcAggtatcgccctggtacg 21 -com.milaboratory.core.alignment.AlignmentTrimmerTest > testRandom1 STANDARD_OUT - lTrimmed = 1743 - rTrimmed = 1682 - lTrimmed = 2818 - rTrimmed = 2826 - -com.milaboratory.core.alignment.batch.SimpleBatchAlignerTest > test1 STANDARD_OUT - 4 hits. - -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.kaligner2.KAligner2Test > testBoundaries STANDARD_OUT - 4960 - -com.milaboratory.core.alignment.kaligner2.KAligner2Test > caseJ1 STANDARD_OUT - 52 - 0 TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAGGA 51 - ||||||||||||||||||||||||||||||||||||||||||||||||||| - 55 TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAGGG 106 - [S51:A->G] - (0->52) - (55->107) - -com.milaboratory.core.alignment.kaligner2.KAligner2Test > testCase0 SKIPPED - -com.milaboratory.core.alignment.kaligner2.KAligner2Test > testSimpleRandomTest STANDARD_OUT - Time per query: 489.82us - Processed queries: 84 - Bad percent: 0.0 - False positive percent: 0.535077288941736 - Scoring error percent: 1.1904761904761905 - -com.milaboratory.core.alignment.kaligner2.OffsetPacksAccumulatorTest > testScoreCorrection2 SKIPPED - -com.milaboratory.core.alignment.kaligner2.KMapper2Test > test11112 STANDARD_OUT - ID: 0 - Score: 1767 - Cluster 0: - Q 27 -> T 15 - -12 - Q 30 -> T 18 - -12 - Q 39 -> T 28 - -11 - Q 42 -> T 31 - -11 - Q 45 -> T 34 - -11 - Q 48 -> T 37 - -11 - Q 51 -> T 40 - -11 - Cluster 1: - Q 84 -> T 50 - -34 - Q 87 -> T 53 - -34 - Q 90 -> T 56 - -34 - Q 93 -> T 59 - -34 - Q 96 -> T 62 - -34 - Q 99 -> T 65 - -34 - Q 111 -> T 79 - -32 - Q 114 -> T 82 - -32 - Cluster 2: - Q 150 -> T 92 - -58 - Q 153 -> T 95 - -58 - 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 222 -> T 145 - -77 - Q 231 -> T 153 - -78 - 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 - Q 252 -> T 184 - -68 - Q 255 -> T 187 - -68 - Q 258 -> T 190 - -68 - Q 261 -> T 193 - -68 - Q 262 -> T 194 - -68 - +com.milaboratory.core.alignment.AlignmentHelperTest > test1 STANDARD_OUT + 0 GAGGTGCAGCTGGTGGAGTCTGGGGGAGGC 29 + |||||||||||||||||||||||||||||| + 0 GAGGTGCAGCTGGTGGAGTCTGGGGGAGGC 29 -com.milaboratory.core.alignment.kaligner2.KMapper2Test > test1111 STANDARD_OUT - ID: 0 - Score: 1308 - Cluster 0: - Q 9 -> T 15 - 6 - Q 12 -> T 18 - 6 - Q 15 -> T 21 - 6 - Q 18 -> T 24 - 6 - Q 21 -> T 27 - 6 - Q 24 -> T 30 - 6 - Q 27 -> T 33 - 6 - 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 - Cluster 2: - Q 123 -> T 89 - -34 - Q 126 -> T 92 - -34 - Q 129 -> T 95 - -34 - 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 + 30 TTGGT-ACAGCCTGGGGGGTCCCTGAGACT 58 + |||| | |||||||||||||| |||||| + 30 CTGGTCA-AGCCTGGGGGGTCCATGAGACA 58 + 59 CTCCTGTGCAGCCTCTGGATTCACCTTCAG 88 + |||||||||||||||||||||| ||||||| + 59 CTCCTGTGCAGCCTCTGGATTCCCCTTCAG 88 -com.milaboratory.core.alignment.kaligner2.KMapper2Test > testRandom1 STANDARD_OUT - noHits: 293 - noHits2: 0 - noHits3: 0 - wrongTopHit: 38 - wrongTopHitS: 30 - noCorrectHitInList: 19 + 89 TAGC-TATAGCATGAACTGGGTCCGCCAGG 117 + || | ||||||||||||||||||||||||| + 89 TA-CTTATAGCATGAACTGGGTCCGCCAGG 117 + 118 CTCCAGGGAAGGGGCTGGAGTGGGTTTCAT 147 + ||||||||||||||||||||||||| |||| + 118 CTCCAGGGAAGGGGCTGGAGTGGGTCTCAT 147 + 148 ACATTAGTAGTAGTAGTAG-TACCATATAC 176 + |||||||||| ||||||| || |||||| + 148 CCATTAGTAGTGGTAGTAGTTA-CATATAT 176 + 177 TACGCAGACTCTGTGAAGGGCCGATTCACC 206 + ||||||||||| |||||||||||||||||| + 177 TACGCAGACTCCGTGAAGGGCCGATTCACC 206 - Timings: - DescriptiveStatistics: - n: 100000 - min: 5157.0 - max: 1.37083958E8 - mean: 82268.18267999802 - std dev: 1294625.3011856067 - median: 65868.5 - skewness: 100.05619912046262 - kurtosis: 10023.461347890367 + 207 ATCTCCAGAGACAATGCCAAGAACTCACTG 236 + |||||||||||||| ||||||||||||||| + 207 ATCTCCAGAGACAACGCCAAGAACTCACTG 236 + 237 TATCTGCAAATGAACAGCCTGAGAGACGAG 266 + ||||||||||||||||||||||||| |||| + 237 TATCTGCAAATGAACAGCCTGAGAGCCGAG 266 + 267 GACACGGCTGTGTATTACTGTGC 289 + ||||||||||||||||||||||| + 267 GACACGGCTGTGTATTACTGTGC 289 +com.milaboratory.core.alignment.AlignmentTrimmerTest > testRandom1 STANDARD_OUT + lTrimmed = 1740 + rTrimmed = 1678 + lTrimmed = 2772 + rTrimmed = 2760 - Clusters basicSize - DescriptiveStatistics: - n: 99669 - min: 1.0 - max: 6.0 - mean: 2.8821097833829907 - std dev: 1.1051710081999218 - median: 3.0 - skewness: 0.2782272869754176 - kurtosis: -0.7016470045571506 +com.milaboratory.core.alignment.AlignmentIteratorTest > test1 STANDARD_OUT + 0 -ATT-AGACA-- 7 + ||| || | + 0 AATTGGGA-ATT 10 + I0AI3GSA3GDC6I8TI8T +com.milaboratory.core.alignment.BandedLinearAlignerTest > testCase1 STANDARD_OUT + GCGTGAAGACTGCAGGCATTGAGTACGTTACTAGTCCAGTGGGGCCCAACCGTAACATTGCGTGTGACTGGTTGCTTAGCGGGTGACGGCGTTTCAGGTTACGCCCTCTGTGCATCACCGATAGCGTTGTTTGAGCTTTCTAACGTCTCAAACCTGCTTGCGCCCTACGGTTTCTCTATATATACACGAAAGGGGCTGGTCGCAACCTCGCAATTCTATCCCTCCAACCTCCCTCGAATTTTT + AAAGCGTGAAGACTTGCAGGCATTGGTACGTTATTAGTCCAGTGGGGCCACAACCGTAACATTGCGTGTGACTGGTGCTTAGCGGGTGACGGCGTTCAGGTTACGCCCTCTGTGCATCACCGATTAGCGTTGTCTGAGCTTTCTAACGTCTCAAACCTGCTTGCGCCCTACGGTTTCTCTATAGTATCACGAAAGGGTCTGGTCGCAACCTCGCAATTCTATCCCTCCAACCTCCCTTGAATTTTTCTA +com.milaboratory.core.alignment.BandedLinearAlignerTest > testGlobal1 STANDARD_OUT + 1 AATTGACA 8 + |||||| + 0 TATTGACT 7 +com.milaboratory.core.alignment.BandedLinearAlignerTest > testGlobal2 STANDARD_OUT + 1 AATTGACAG 9 + |||||| | + 0 TATTGAC-G 7 +com.milaboratory.core.alignment.BandedLinearAlignerTest > testGlobal3 STANDARD_OUT + 0 TATTGACT 7 + |||||| + 1 AATTGACA 8 - Top Delta - DescriptiveStatistics: - n: 99688 - min: -26.0 - max: 0.0 - mean: -0.0016250702190833777 - std dev: 0.17096448080906662 - median: 0.0 - skewness: -114.7836183261857 - kurtosis: 13953.240609850001 +com.milaboratory.core.alignment.BandedLinearAlignerTest > testGlobal4 STANDARD_OUT + 0 TATTGAC-G 7 + |||||| | + 1 AATTGACAG 9 +com.milaboratory.core.alignment.AlignerTest > testCalculateScore1 STANDARD_OUT + 3.05us + 3.32us + 3.52us com.milaboratory.core.alignment.AlignerCustomTest > testSemiLocal0 STANDARD_OUT 29.0 @@ -4566,585 +3884,1308 @@ 0 GATAC-----ATTAGA---CACAGATACA 20 -com.milaboratory.core.alignment.AlignerTest > testCalculateScore1 STANDARD_OUT - 1.30us - 1.30us - 1.30us - -com.milaboratory.core.alignment.AlignmentIteratorTest > test1 STANDARD_OUT - 0 -ATT-AGACA-- 7 - ||| || | - 0 AATTGGGA-ATT 10 - I0AI3GSA3GDC6I8TI8T - -com.milaboratory.test.TestUtil > testLT STANDARD_OUT - Short tests. - No system env properties. +com.milaboratory.core.io.sequence.fasta.RandomAccessFastaReaderTest > test1nt STANDARD_ERROR + Indexing milib_5fcae5d3c1bc4655dd34fa7528d8c7f4c260bd4112216977192676847371.fasta: 0% + Indexing milib_5fcae5d3c1bc4655dd34fa7528d8c7f4c260bd4112216977192676847371.fasta: done -com.milaboratory.primitivio.blocks.PrimitivOBlocksTest > benchmark1 SKIPPED +com.milaboratory.core.io.sequence.fasta.RandomAccessFastaReaderTest > test1 STANDARD_ERROR + Indexing milib_5fcae5d3c1bc4655dd34fa7528d8c7f4c260bd4112216977192676847371.fasta: 0% + Indexing milib_5fcae5d3c1bc4655dd34fa7528d8c7f4c260bd4112216977192676847371.fasta: done -com.milaboratory.primitivio.blocks.PrimitivOBlocksTest > test1 STANDARD_OUT +com.milaboratory.core.io.sequence.fasta.RandomAccessFastaReaderTest > test2 STANDARD_ERROR + Indexing milib_8e1fbeeb8141ae5324cfd3149142d276e290d47e3733359207235940483.tmp: 0% + Indexing milib_8e1fbeeb8141ae5324cfd3149142d276e290d47e3733359207235940483.tmp: done - ================== - High compression: false - Concurrency: 4 - File size: 6799510 - Write time: 75.13ms +com.milaboratory.core.io.util.IOUtilTest > test111 STANDARD_OUT + 3 + 3 + -2147483648 + -9223372036854775808 - O. Stats: - Wall clock time: 75.46ms - Total CPU time: 139.04ms - User wait time: 55.48ms - Serialization time: 92.81ms (66.75%) - Checksum calculation time: 3.55ms (2.55%) - Compression time: 39.39ms (28.33%) - Total IO delay: 11.99ms - Concurrency overhead: 3.15ms - Uncompressed size: 18.44MiB (~2.08KiB per object) - Output size: 6.48MiB (~748B per object; compression = 35.17%) - IO speed: 589.5MiB/s - Concurrency adjusted uncompressed speed: 460.92MiB/s - Actual uncompressed speed: 245.83MiB/s - Actual speed: 86.46MiB/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.tree.PrimerGenerator > generate SKIPPED - I. Stats 1: - Wall clock time: 55.08ms - Total CPU time: 106.55ms - Serialization time: 64.38ms (60.42%) - Checksum calculation time: 3.56ms (3.34%) - Compression time: 37.26ms (34.97%) - Total IO delay: 6.19ms - Input size: 6.48MiB - Decompressed size: 18.44MiB (compression = 35.17%) - IO speed: 1.06GiB/s - Concurrency adjusted uncompressed speed: 658.46MiB/s - Actual uncompressed speed: 335.22MiB/s - Actual speed: 117.9MiB/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.tree.SequenceTreeMapTest > testCase9 STANDARD_OUT + Hit 1 + 0 ac-gacTtgactg 11 + 0 acTgac-tgactg 11 - I. Stats 2: - Wall clock time: 125.69ms - Total CPU time: 212.36ms - Serialization time: 127.84ms (60.2%) - Checksum calculation time: 7.15ms (3.36%) - Compression time: 75.1ms (35.36%) - Total IO delay: 11.97ms - Input size: 12.97MiB - Decompressed size: 36.87MiB (compression = 35.17%) - IO speed: 1.15GiB/s - Concurrency adjusted uncompressed speed: 658.46MiB/s - Actual uncompressed speed: 294.99MiB/s - Actual speed: 103.75MiB/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 + Hit 2 + 0 ac-gactTgactg 11 + 0 acTgact-gactg 11 - ================== - High compression: false - Concurrency: 4 - File size: 6791878 - Write time: 58.33ms - O. Stats: - Wall clock time: 58.56ms - Total CPU time: 75.01ms - User wait time: 46.37ms - Serialization time: 32.38ms (43.17%) - Checksum calculation time: 3.82ms (5.09%) - Compression time: 35.96ms (47.95%) - Total IO delay: 10.21ms - Concurrency overhead: 586.47us - Uncompressed size: 18.44MiB (~2.08KiB per object) - Output size: 6.48MiB (~748B per object; compression = 35.13%) - IO speed: 647.72MiB/s - Concurrency adjusted uncompressed speed: 877.95MiB/s - Actual uncompressed speed: 317.88MiB/s - Actual speed: 111.68MiB/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.tree.SequenceTreeMapTest > optimalityAndScopeTest STANDARD_OUT + --NW alignments-- + CASSLAPGATN-KLFF + CASS-APGATNEKLFF - I. Stats 1: - Wall clock time: 44.68ms - Total CPU time: 61.34ms - Serialization time: 20.8ms (33.92%) - Checksum calculation time: 3.44ms (5.6%) - Compression time: 36.93ms (60.2%) - Total IO delay: 4.64ms - Input size: 6.48MiB - Decompressed size: 18.44MiB (compression = 35.13%) - IO speed: 1.58GiB/s - Concurrency adjusted uncompressed speed: 1.13GiB/s - Actual uncompressed speed: 419.02MiB/s - Actual speed: 147.21MiB/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 + CASSLAPGATN-KLFF + CASSLAPG-TNEKLFF - I. Stats 2: - Wall clock time: 91.91ms - Total CPU time: 117.95ms - Serialization time: 37.05ms (31.41%) - Checksum calculation time: 6.93ms (5.87%) - Compression time: 73.67ms (62.46%) - Total IO delay: 8.48ms - Input size: 12.95MiB - Decompressed size: 36.87MiB (compression = 35.13%) - IO speed: 1.58GiB/s - Concurrency adjusted uncompressed speed: 1.16GiB/s - Actual uncompressed speed: 405.21MiB/s - Actual speed: 142.36MiB/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 + CASSLAPGATN-KLfF + CASSLAPG-TNEKLyF - ================== - High compression: false - Concurrency: 1 - File size: 6799510 - Write time: 83.64ms + --STM alignments-- + CASSLAPGATN-KLFF + CASS-APGATNEKLFF - O. Stats: - Wall clock time: 84.28ms - Total CPU time: 64.48ms - User wait time: 75.74ms - Serialization time: 23.22ms (36.01%) - Checksum calculation time: 3.42ms (5.3%) - Compression time: 34.54ms (53.56%) - Total IO delay: 10.18ms - Concurrency overhead: 1.3ms - Uncompressed size: 18.44MiB (~2.08KiB per object) - Output size: 6.48MiB (~748B per object; compression = 35.17%) - IO speed: 648.45MiB/s - Concurrency adjusted uncompressed speed: 245.83MiB/s - Actual uncompressed speed: 219.49MiB/s - Actual speed: 77.2MiB/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! + CASSLAPGATN-KLFF + CASSLAPG-TNEKLFF - I. Stats 1: - Wall clock time: 37.59ms - Total CPU time: 57.33ms - Serialization time: 17.08ms (29.8%) - Checksum calculation time: 3.38ms (5.9%) - Compression time: 36.22ms (63.18%) - Total IO delay: 5.2ms - Input size: 6.48MiB - Decompressed size: 18.44MiB (compression = 35.17%) - IO speed: 1.27GiB/s - Concurrency adjusted uncompressed speed: 297.37MiB/s - Actual uncompressed speed: 498.29MiB/s - Actual speed: 175.26MiB/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 + CASSlAPGATN-KLFF + CASSa-PGATNEKLFF - I. Stats 2: - Wall clock time: 75.07ms - Total CPU time: 114.53ms - Serialization time: 33.8ms (29.51%) - Checksum calculation time: 6.8ms (5.93%) - Compression time: 72.43ms (63.24%) - Total IO delay: 9.77ms - Input size: 12.97MiB - Decompressed size: 36.87MiB (compression = 35.17%) - IO speed: 1.41GiB/s - Concurrency adjusted uncompressed speed: 297.37MiB/s - Actual uncompressed speed: 491.65MiB/s - Actual speed: 172.92MiB/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 + CASSLAPGaTN-KLFF + CASSLAPGt-NEKLFF - ================== - High compression: false - Concurrency: 1 - File size: 6791878 - Write time: 84.71ms + CASSlAPGATN-KLFF + CA-SsAPGATNEKLFF - O. Stats: - Wall clock time: 85.36ms - Total CPU time: 68.38ms - User wait time: 76.73ms - Serialization time: 26.08ms (38.13%) - Checksum calculation time: 3.4ms (4.97%) - Compression time: 35.42ms (51.8%) - Total IO delay: 8.19ms - Concurrency overhead: 432us - Uncompressed size: 18.44MiB (~2.08KiB per object) - Output size: 6.48MiB (~748B per object; compression = 35.13%) - IO speed: 809.65MiB/s - Concurrency adjusted uncompressed speed: 239.44MiB/s - Actual uncompressed speed: 216.9MiB/s - Actual speed: 76.2MiB/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! + CASSlAPGATN-KLFF + CAS-sAPGATNEKLFF - I. Stats 1: - Wall clock time: 44.17ms - Total CPU time: 61.57ms - Serialization time: 17.03ms (27.67%) - Checksum calculation time: 3.56ms (5.79%) - Compression time: 40.84ms (66.33%) - Total IO delay: 4.58ms - Input size: 6.48MiB - Decompressed size: 18.44MiB (compression = 35.13%) - IO speed: 1.58GiB/s - Concurrency adjusted uncompressed speed: 279.35MiB/s - Actual uncompressed speed: 419.02MiB/s - Actual speed: 147.21MiB/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 + CASSLAPGATNk-LFF + CASS-APGATNeKLFF - I. Stats 2: - Wall clock time: 90.4ms - Total CPU time: 117.14ms - Serialization time: 32.55ms (27.79%) - Checksum calculation time: 6.93ms (5.92%) - Compression time: 77.39ms (66.07%) - Total IO delay: 8.23ms - Input size: 12.95MiB - Decompressed size: 36.87MiB (compression = 35.13%) - IO speed: 1.58GiB/s - Concurrency adjusted uncompressed speed: 294.99MiB/s - Actual uncompressed speed: 409.71MiB/s - Actual speed: 143.94MiB/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 + CASSLAPGaTN-KLFF + CASSLAP-gTNEKLFF - ================== - High compression: true - Concurrency: 4 - File size: 4156299 - Write time: 1.03s + CASSLAPGATNk-LFF + CASSLAPG-TNeKLFF - O. Stats: - Wall clock time: 1.03s - Total CPU time: 2.71s - User wait time: 964.18ms - Serialization time: 25.56ms (0.94%) - Checksum calculation time: 3.5ms (0.13%) - Compression time: 2.68s (98.8%) - Total IO delay: 9.14ms - Concurrency overhead: 1.82ms - Uncompressed size: 18.44MiB (~2.08KiB per object) - Output size: 3.96MiB (~457B per object; compression = 21.5%) - IO speed: 440.42MiB/s - Concurrency adjusted uncompressed speed: 27.07MiB/s - Actual uncompressed speed: 17.99MiB/s - Actual speed: 3.87MiB/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 + CASSLAPGATN-KLfF + CASSLAPG-TNEKLyF - I. Stats 1: - Wall clock time: 28.18ms - Total CPU time: 53.4ms - Serialization time: 16.05ms (30.05%) - Checksum calculation time: 3.49ms (6.54%) - Compression time: 33.16ms (62.09%) - Total IO delay: 4.09ms - Input size: 3.96MiB - Decompressed size: 18.44MiB (compression = 21.5%) - IO speed: 990.94MiB/s - Concurrency adjusted uncompressed speed: 1.29GiB/s - Actual uncompressed speed: 658.46MiB/s - Actual speed: 141.56MiB/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: 63.54ms - Total CPU time: 106.76ms - Serialization time: 32.3ms (30.26%) - Checksum calculation time: 6.95ms (6.51%) - Compression time: 66.08ms (61.9%) - Total IO delay: 7.86ms - Input size: 7.93MiB - Decompressed size: 36.87MiB (compression = 21.5%) - IO speed: 1.11GiB/s - Concurrency adjusted uncompressed speed: 1.29GiB/s - Actual uncompressed speed: 585.3MiB/s - Actual speed: 125.83MiB/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 +com.milaboratory.core.merger.MergerParametersTest > test2 STANDARD_OUT + { + "qualityMergingAlgorithm": "SumSubtraction", + "partsLayout": "Collinear", + "minimalOverlap": 15, + "maxQuality": 50, + "minimalIdentity": 0.8, + "identityType": "Unweighted" + } - ================== - High compression: true - Concurrency: 4 - File size: 4098671 - Write time: 1.77s +com.milaboratory.util.sorting.HashSorterTest > testSingleton STANDARD_OUT + /tmp/milib_1cee13d1ea786176eea1d2c4a46a04e177294cc913623794190397590086 + timeInCollate: 6.75s + timeInCollatorInit: 4.64s + timeAwaitingO: 2.34ms + timeAwaitingI: 902.93ms + timeInFinalSorting1: 0ns + timeInFinalSorting2: 31.05ms + timeInFinalSorting3: 49.21ms + /22S (5|27|32): objs=50000 size=2.95MiB - O. Stats: - Wall clock time: 1.77s - Total CPU time: 2.92s - User wait time: 1.6s - Serialization time: 25.18ms (0.86%) - Checksum calculation time: 3.45ms (0.12%) - Compression time: 2.89s (98.92%) - Total IO delay: 7.21ms - Concurrency overhead: 745.04us - Uncompressed size: 18.44MiB (~2.08KiB per object) - Output size: 3.91MiB (~451B per object; compression = 21.2%) - IO speed: 558.4MiB/s - Concurrency adjusted uncompressed speed: 25.19MiB/s - Actual uncompressed speed: 10.43MiB/s - Actual speed: 2.21MiB/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 +com.milaboratory.util.sorting.HashSorterTest > test1 STANDARD_OUT + /tmp/milib_4525180773a57f8109afabf226ddca93ef1267a67881329241565259226 + timeInCollate: 33.51s + timeInCollatorInit: 6.6s + timeAwaitingO: 749.68ms + timeAwaitingI: 10.18s + timeInFinalSorting1: 5.17s + timeInFinalSorting2: 1.15s 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(2|25|36): objs=167 size=240B + /31/35N (2|25|36): objs=3754 size=17.78KiB - I. Stats 1: - Wall clock time: 36.31ms - Total CPU time: 52.34ms - Serialization time: 15.69ms (29.97%) - Checksum calculation time: 3.52ms (6.73%) - Compression time: 32.98ms (63.01%) - Total IO delay: 3.09ms - Input size: 3.91MiB - Decompressed size: 18.44MiB (compression = 21.2%) - IO speed: 1.27GiB/s - Concurrency adjusted uncompressed speed: 1.38GiB/s - Actual uncompressed speed: 512.14MiB/s - Actual speed: 108.58MiB/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 +com.milaboratory.util.sorting.HashSorterTest > test2 SKIPPED - I. Stats 2: - Wall clock time: 79.41ms - Total CPU time: 104.28ms - Serialization time: 31.15ms (29.87%) - Checksum calculation time: 6.95ms (6.66%) - Compression time: 65.91ms (63.21%) - Total IO delay: 5.82ms - Input size: 7.82MiB - Decompressed size: 36.87MiB (compression = 21.2%) - IO speed: 1.53GiB/s - Concurrency adjusted uncompressed speed: 1.33GiB/s - Actual uncompressed speed: 466.76MiB/s - Actual speed: 98.96MiB/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 +com.milaboratory.util.sorting.SortingUtilTest > test1 STANDARD_OUT + Collation: 194.14ms + Sorting: 128.05ms + 1 + 217 + 41419 + 99532 + 99996 - ================== - High compression: true - Concurrency: 1 - File size: 4156299 - Write time: 2.73s +com.milaboratory.util.AtomicEnumHistogramTest > test1 STANDARD_OUT + {"labels":["A","B","C","null"],"hist":[1,2,0,1]} - O. Stats: - Wall clock time: 2.73s - Total CPU time: 2.71s - User wait time: 2.72s - Serialization time: 24.26ms (0.89%) - Checksum calculation time: 3.43ms (0.13%) - Compression time: 2.68s (98.85%) - Total IO delay: 9.1ms - Concurrency overhead: 1.56ms - Uncompressed size: 18.44MiB (~2.08KiB per object) - Output size: 3.96MiB (~457B per object; compression = 21.5%) - IO speed: 440.42MiB/s - Concurrency adjusted uncompressed speed: 6.77MiB/s - Actual uncompressed speed: 6.75MiB/s - Actual speed: 1.45MiB/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! +com.milaboratory.util.VersionInfoTest > test3 SKIPPED - I. Stats 1: - Wall clock time: 33.93ms - Total CPU time: 52.98ms - Serialization time: 16.1ms (30.39%) - Checksum calculation time: 3.46ms (6.53%) - Compression time: 32.99ms (62.27%) - Total IO delay: 4.21ms - Input size: 3.96MiB - Decompressed size: 18.44MiB (compression = 21.5%) - IO speed: 990.94MiB/s - Concurrency adjusted uncompressed speed: 323.45MiB/s - Actual uncompressed speed: 558.69MiB/s - Actual speed: 120.11MiB/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 +com.milaboratory.util.ByteStringTest > testSpeed1 STANDARD_OUT + Time per hash: 231ns + Addition to hash set (per operation): 686ns + Hash set removal (per operation): 412ns + a - I. Stats 2: - Wall clock time: 68.02ms - Total CPU time: 106.18ms - Serialization time: 32.15ms (30.28%) - Checksum calculation time: 6.89ms (6.49%) - Compression time: 66.09ms (62.24%) - Total IO delay: 7.87ms - Input size: 7.93MiB - Decompressed size: 36.87MiB (compression = 21.5%) - IO speed: 1.11GiB/s - Concurrency adjusted uncompressed speed: 323.45MiB/s - Actual uncompressed speed: 542.26MiB/s - Actual speed: 116.58MiB/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 +com.milaboratory.util.CacheTest > test1 STANDARD_OUT + Cache misses:400 + Cache hits:800 - ================== - High compression: true - Concurrency: 1 - File size: 4098671 - Write time: 2.91s +com.milaboratory.util.IntCombinationsTest > test1 STANDARD_OUT + [0, 1] + [0, 2] + [1, 2] - O. Stats: - Wall clock time: 2.91s - Total CPU time: 2.9s - User wait time: 2.91s - Serialization time: 28.9ms (1%) - Checksum calculation time: 3.39ms (0.12%) - Compression time: 2.86s (98.79%) - Total IO delay: 9.35ms - Concurrency overhead: 461.67us - Uncompressed size: 18.44MiB (~2.08KiB per object) - Output size: 3.91MiB (~451B per object; compression = 21.2%) - IO speed: 434.31MiB/s - Concurrency adjusted uncompressed speed: 6.34MiB/s - Actual uncompressed speed: 6.33MiB/s - Actual speed: 1.34MiB/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! +com.milaboratory.util.RemoveActionTest > test1 STANDARD_OUT + /tmp/milib_c5e80b897846656ecd0cb29f27082e0dd495e2941154820859730360261 - I. Stats 1: - Wall clock time: 41.22ms - Total CPU time: 58.41ms - Serialization time: 17.96ms (30.75%) - Checksum calculation time: 4.16ms (7.12%) - Compression time: 36.18ms (61.94%) - Total IO delay: 3.25ms - Input size: 3.91MiB - Decompressed size: 18.44MiB (compression = 21.2%) - IO speed: 1.27GiB/s - Concurrency adjusted uncompressed speed: 302.24MiB/s - Actual uncompressed speed: 449.68MiB/s - Actual speed: 95.34MiB/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 +com.milaboratory.util.RemoveActionTest > test2 STANDARD_OUT + /tmp/milib_be308eef6e21946473e74df53a53e544235bc2c410586744590159706727.tmp - I. Stats 2: - Wall clock time: 89.01ms - Total CPU time: 116.86ms - Serialization time: 35.62ms (30.48%) - Checksum calculation time: 8.31ms (7.11%) - Compression time: 72.64ms (62.16%) - Total IO delay: 6.17ms - Input size: 7.82MiB - Decompressed size: 36.87MiB (compression = 21.2%) - IO speed: 1.27GiB/s - Concurrency adjusted uncompressed speed: 299.79MiB/s - Actual uncompressed speed: 414.31MiB/s - Actual speed: 87.84MiB/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.util.NSequenceWithQualityPrintHelperTest > test1 SKIPPED -com.milaboratory.primitivio.blocks.PrimitivOBlocksTest > bigBlocks STANDARD_OUT - Pending / IO / Serde / Objs: 1 / 1 / 1 / 7000 - Pending / IO / Serde / Objs: 6 / 1 / 1 / 16000 - Pending / IO / Serde / Objs: 6 / 1 / 1 / 19000 - Pending / IO / Serde / Objs: 6 / 1 / 0 / 20000 - Pending / IO / Serde / Objs: 4 / 1 / 0 / 20000 - Pending / IO / Serde / Objs: 2 / 1 / 0 / 20000 - O. Stats: - Wall clock time: 12.61s - Total CPU time: 3.51s - User wait time: 2.35s - Serialization time: 1.22s (34.66%) - Checksum calculation time: 417.42ms (11.88%) - Compression time: 964.4ms (27.45%) - Total IO delay: 11.7s - Concurrency overhead: 1.36ms - Uncompressed size: 1.86GiB (~97.66KiB per object) - Output size: 1.86GiB (~97.66KiB per object; compression = 100%) - IO speed: 163.02MiB/s - Concurrency adjusted uncompressed speed: 1002.34MiB/s - Actual uncompressed speed: 151.32MiB/s - Actual speed: 151.32MiB/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.util.JsonOverriderTest > test1 STANDARD_OUT + WARNING: unnecessary override -Ob= with the same value. Gradle Test Executor 1 finished executing tests. -Finished generating test XML results (0.224 secs) into: /build/reproducible-path/milib-2.2.0+dfsg/build/test-results/test +Finished generating test XML results (0.105 secs) into: /build/reproducible-path/milib-2.2.0+dfsg/build/test-results/test Generating HTML test report... -Finished generating test html results (0.338 secs) into: /build/reproducible-path/milib-2.2.0+dfsg/build/reports/tests/test -:test (Thread[#58,Task worker for ':' Thread 3,5,main]) completed. Took 2 mins 38.1 secs. +Finished generating test html results (0.156 secs) into: /build/reproducible-path/milib-2.2.0+dfsg/build/reports/tests/test +:test (Thread[#50,Task worker for ':',5,main]) completed. Took 5 mins 10.77 secs. -BUILD SUCCESSFUL in 2m 47s +BUILD SUCCESSFUL in 5m 28s 5 actionable tasks: 3 executed, 2 up-to-date create-stamp debian/debhelper-build-stamp dh_prep @@ -5176,12 +5217,14 @@ 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/18774/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/18774/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/114724 and its subdirectories -I: Current time: Mon Jan 5 00:26:58 -12 2026 -I: pbuilder-time-stamp: 1767616018 +I: removing directory /srv/workspace/pbuilder/18774 and its subdirectories +I: Current time: Tue Dec 3 20:11:49 +14 2024 +I: pbuilder-time-stamp: 1733206309