Diff of the two buildlogs: -- --- b1/build.log 2024-12-11 08:12:16.184050295 +0000 +++ b2/build.log 2024-12-11 08:28:35.899422413 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Dec 10 19:27:13 -12 2024 -I: pbuilder-time-stamp: 1733902033 +I: Current time: Wed Dec 11 22:12:25 +14 2024 +I: pbuilder-time-stamp: 1733904745 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -38,52 +38,84 @@ dpkg-source: info: applying skip_install_BEAST_package.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/6489/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/30433/tmp/hooks/D01_modify_environment starting +debug: Running on virt64b. +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 11 08:12 /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/30433/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/30433/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='72f0a02985214a49bc2ed57b167108f0' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='6489' - PS1='# ' - PS2='> ' + INVOCATION_ID=8b06a86d50c5491cb6c3c336b5ff1342 + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=30433 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.iYGqzUNG/pbuilderrc_7isn --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.iYGqzUNG/b1 --logfile b1/build.log beast2-mcmc_2.7.6+dfsg-1.dsc' - SUDO_GID='113' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.iYGqzUNG/pbuilderrc_HXxa --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.iYGqzUNG/b2 --logfile b2/build.log beast2-mcmc_2.7.6+dfsg-1.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux wbq0 6.1.0-28-armmp #1 SMP Debian 6.1.119-1 (2024-11-22) armv7l GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/6489/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/30433/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -459,7 +491,7 @@ Get: 310 http://deb.debian.org/debian unstable/main armhf libjam-java all 0.1.git20240425.aec45be+dfsg-1 [168 kB] Get: 311 http://deb.debian.org/debian unstable/main armhf libopenjfx-jni armhf 11.0.11+1-4 [18.4 MB] Get: 312 http://deb.debian.org/debian unstable/main armhf libopenjfx-java all 11.0.11+1-4 [8941 kB] -Fetched 336 MB in 38s (8750 kB/s) +Fetched 336 MB in 7s (51.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libapparmor1:armhf. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19680 files and directories currently installed.) @@ -1501,8 +1533,8 @@ Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Wed Dec 11 07:31:48 UTC 2024. -Universal Time is now: Wed Dec 11 07:31:48 UTC 2024. +Local time is now: Wed Dec 11 08:14:29 UTC 2024. +Universal Time is now: Wed Dec 11 08:14:29 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:armhf (1.17.0-2+b1) ... @@ -1952,7 +1984,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/beast2-mcmc-2.7.6+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 > ../beast2-mcmc_2.7.6+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/30433/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/30433/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/beast2-mcmc-2.7.6+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 > ../beast2-mcmc_2.7.6+dfsg-1_source.changes dpkg-buildpackage: info: source package beast2-mcmc dpkg-buildpackage: info: source version 2.7.6+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -1968,7 +2004,7 @@ clean: BUILD SUCCESSFUL -Total time: 5 seconds +Total time: 1 second jh_clean Duplicate specification "unlink|u" for option "u" debian/rules override_dh_clean @@ -2085,7 +2121,7 @@ [jar] Building jar: /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/build/dist/BEAST.app.jar BUILD SUCCESSFUL -Total time: 6 minutes 33 seconds +Total time: 2 minutes 13 seconds make[1]: Leaving directory '/build/reproducible-path/beast2-mcmc-2.7.6+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/beast2-mcmc-2.7.6+dfsg' @@ -2119,15 +2155,12 @@ [java] 768 sites [java] 69 patterns [java] - [java] {spec: "test.beast.core.PrimitiveBeastObject", i: "0", e: "none", + [java] {spec: "test.beast.core.PrimitiveBeastObject", e: "none", i: "0", [java] p: [ - [java] {spec: "test.beast.core.PrimitiveBeastObject", i: "0", e: "none", a: [1.0, 3.0] }, - [java] {spec: "test.beast.core.PrimitiveBeastObject", i: "0", e: "none", a: [3.0, 4.0] } + [java] {spec: "test.beast.core.PrimitiveBeastObject", e: "none", i: "0", a: [1.0, 3.0] }, + [java] {spec: "test.beast.core.PrimitiveBeastObject", e: "none", i: "0", a: [3.0, 4.0] } [java] ] [java] } - [java] Writing file beast.log - [java] Sample null.1 null.2 - [java] 1 0.3 0.7 -- [java] OK [java] test getCitation [java] test initByName @@ -2136,7 +2169,10 @@ [java] test getInputValue [java] test getOutputs [java] Validation error when initializing object test.beast.core.BEASTInterfaceTest$BEASTi (id null): + [java] Writing file beast.log [java] Failed to set the string value to '1e-1' for beastobject id=null + [java] Sample null.1 null.2 + [java] 1 0.3 0.7 -- [java] Failed to set the string value to '21474836470' for beastobject id=null [java] WARNING: Operator scaleOperator.Species is contained in multiple operator schedules. [java] Operator weighting may not work as expected. @@ -2164,14 +2200,14 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 14.256 seconds + [java] Total calculation time: 5.827 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 1.0017946084516174 variance: 1.7216547315129034 ESS: 25717.88066360503 [java] ------------------------------------------------- [java] - [java] End likelihood: -0.8084620917497215 [java] trace log written to /tmp/bactrian.log + [java] End likelihood: -0.8084620917497215 [java] =============================================================================== [java] Citations for this model: [java] @@ -2196,7 +2232,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 15.353 seconds + [java] Total calculation time: 5.783 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 1.4999085326599657 variance: 0.009984682019634223 ESS: 199303.5697419057 @@ -2228,7 +2264,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 14.127 seconds + [java] Total calculation time: 6.31 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: -0.9999141170712793 variance: 0.33333524355317856 ESS: 198672.26933150293 @@ -2260,14 +2296,14 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 12.039 seconds + [java] Total calculation time: 6.053 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 2.000085882932697 variance: 0.3333352435532261 ESS: 198672.26933142878 [java] ------------------------------------------------- [java] - [java] trace log written to /tmp/bactrian.log [java] End likelihood: -0.6931471805599453 + [java] trace log written to /tmp/bactrian.log [java] =============================================================================== [java] Citations for this model: [java] @@ -2292,7 +2328,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 13.154 seconds + [java] Total calculation time: 5.966 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 1.0000858834576856 variance: 0.3333352435537048 ESS: 198672.26933242727 @@ -2343,10 +2379,10 @@ [java] [java] transition prob : [java] [0.6674871505723157, 0.22927797953210746, 0.10323486989557647, 0.2292779795321076, 0.415400931299253, 0.35532108916863914, 0.10323486989557647, 0.3553210891686388, 0.5414440409357847] - [java] Validation error when initializing object beast.base.inference.operator.DeltaExchangeOperator (id null): [java] row 0 prob sum = 0.9999999999999996 [java] row 1 prob sum = 0.9999999999999998 [java] row 2 prob sum = 0.9999999999999999 + [java] Validation error when initializing object beast.base.inference.operator.DeltaExchangeOperator (id null): [java] java.lang.IllegalArgumentException: Input 'weight' must be specified. [java] at beast.base.core.Input.validate(Unknown Source) [java] at beast.base.core.BEASTInterface.validateInputs(Unknown Source) @@ -2447,6 +2483,11 @@ [java] at org.junit.platform.console.ConsoleLauncher.run(ConsoleLauncher.java:57) [java] at org.junit.platform.console.ConsoleLauncher.run(ConsoleLauncher.java:42) [java] at org.junit.platform.console.ConsoleLauncher.main(ConsoleLauncher.java:35) + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [java] ============================================================================================================== + [java] ============================================================================================================== [java] Starting frequencies: [0.074, 0.025, 0.054, 0.054, 0.047, 0.074, 0.026, 0.068, 0.058, 0.099, 0.025, 0.045, 0.039, 0.034, 0.052, 0.057, 0.051, 0.073, 0.013, 0.032] [java] Struthio_camelus: 85 20 [java] Rhea_americana: 85 20 @@ -2456,22 +2497,26 @@ [java] 85 sites [java] 32 patterns [java] - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: EIGEN_COMPLEX [java] Ignoring ambiguities in tree likelihood. [java] Ignoring character uncertainty in tree likelihood. [java] With 32 unique site patterns. [java] Using rescaling scheme : dynamic + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: EIGEN_COMPLEX [java] WARNING: found multiple entries for a site that occurs multiple times and is ascertained for. This may indicate some sites should be removed. Regardless, these sites will be ignored in the likelihood calculation. [java] WARNING: found multiple entries for a site that occurs multiple times and is ascertained for. This may indicate some sites should be removed. Regardless, these sites will be ignored in the likelihood calculation. [java] WARNING: found multiple entries for a site that occurs multiple times and is ascertained for. This may indicate some sites should be removed. Regardless, these sites will be ignored in the likelihood calculation. [java] WARNING: found multiple entries for a site that occurs multiple times and is ascertained for. This may indicate some sites should be removed. Regardless, these sites will be ignored in the likelihood calculation. - [java] human: 772 4 + [java] ============================================================================================================== + [java] ==============================================================================================================human: 772 4 + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 69 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] [java] chimp: 772 4 [java] bonobo: 772 4 [java] gorilla: 772 4 @@ -2494,6 +2539,10 @@ [java] Ignoring character uncertainty in tree likelihood. [java] With 69 unique site patterns. [java] Using rescaling scheme : dynamic + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 69 unique site patterns. + [java] Using rescaling scheme : dynamic [java] human: 768 4 [java] chimp: 768 4 [java] bonobo: 768 4 @@ -2506,19 +2555,6 @@ [java] 69 patterns [java] [java] Starting frequencies: [0.3390942900867236, 0.24655436447178358, 0.1531393568179342, 0.26121198862355866] - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 69 unique site patterns. - [java] Using rescaling scheme : dynamic - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 69 unique site patterns. - [java] Using rescaling scheme : dynamic [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_SINGLE COMPUTATION_SYNCH SCALING_MANUAL [java] Using BEAGLE version: 3.1.2 resource 0: CPU @@ -2544,15 +2580,6 @@ [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: EIGEN_COMPLEX [java] Starting frequencies: [0.0866, 0.0193, 0.057, 0.0581, 0.0384, 0.0833, 0.0244, 0.0485, 0.062, 0.0862, 0.0195, 0.0391, 0.0458, 0.0367, 0.044, 0.0695, 0.061, 0.0709, 0.0144, 0.0353] - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 32 unique site patterns. - [java] Using rescaling scheme : dynamic [java] Struthio_camelus: 85 20 [java] Rhea_americana: 85 20 [java] Pterocnemia_pennata: 85 20 @@ -2563,6 +2590,15 @@ [java] [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: EIGEN_COMPLEX + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 32 unique site patterns. + [java] Using rescaling scheme : dynamic [java] human: 768 4 [java] chimp: 768 4 [java] bonobo: 768 4 @@ -2605,6 +2641,10 @@ [java] 50 patterns [java] [java] Starting frequencies: [1.0, 0.0] + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: PRECISION_DOUBLE EIGEN_REAL EIGEN_COMPLEX + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: PRECISION_DOUBLE EIGEN_REAL EIGEN_COMPLEX [java] ============================================================================================================== [java] ============================================================================================================== [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == @@ -2618,20 +2658,12 @@ [java] Ignoring character uncertainty in tree likelihood. [java] With 50 unique site patterns. [java] Using rescaling scheme : dynamic - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_DOUBLE EIGEN_REAL EIGEN_COMPLEX - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_DOUBLE EIGEN_REAL EIGEN_COMPLEX - [java] Starting frequencies: [0.077, 0.02, 0.052, 0.062, 0.04, 0.074, 0.023, 0.052, 0.059, 0.091, 0.024, 0.043, 0.051, 0.041, 0.051, 0.069, 0.059, 0.066, 0.014, 0.032] [java] ============================================================================================================== [java] ============================================================================================================== [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == [java] ============================================================================================================== [java] ============================================================================================================== - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 32 unique site patterns. - [java] Using rescaling scheme : dynamic + [java] Starting frequencies: [0.077, 0.02, 0.052, 0.062, 0.04, 0.074, 0.023, 0.052, 0.059, 0.091, 0.024, 0.043, 0.051, 0.041, 0.051, 0.069, 0.059, 0.066, 0.014, 0.032] [java] Struthio_camelus: 85 20 [java] Rhea_americana: 85 20 [java] Pterocnemia_pennata: 85 20 @@ -2642,12 +2674,20 @@ [java] [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: EIGEN_COMPLEX + [java] Starting frequencies: [0.0866, 0.0193, 0.057, 0.0581, 0.0384, 0.0833, 0.0244, 0.0485, 0.062, 0.0862, 0.0195, 0.0391, 0.0458, 0.0367, 0.044, 0.0695, 0.061, 0.0709, 0.0144, 0.0353] + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 32 unique site patterns. + [java] Using rescaling scheme : dynamic [java] ============================================================================================================== [java] ============================================================================================================== [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == [java] ============================================================================================================== [java] ============================================================================================================== - [java] Starting frequencies: [0.0866, 0.0193, 0.057, 0.0581, 0.0384, 0.0833, 0.0244, 0.0485, 0.062, 0.0862, 0.0195, 0.0391, 0.0458, 0.0367, 0.044, 0.0695, 0.061, 0.0709, 0.0144, 0.0353] + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 32 unique site patterns. + [java] Using rescaling scheme : dynamic [java] Struthio_camelus: 85 20 [java] Rhea_americana: 85 20 [java] Pterocnemia_pennata: 85 20 @@ -2658,10 +2698,6 @@ [java] [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: EIGEN_COMPLEX - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 32 unique site patterns. - [java] Using rescaling scheme : dynamic [java] Starting frequencies: [0.07207207207207206, 0.006006006006006005, 0.019019019019019014, 0.02402402402402402, 0.061061061061061045, 0.05605605605605604, 0.02802802802802802, 0.08808808808808806, 0.023023023023023018, 0.16816816816816815, 0.05405405405405404, 0.039039039039039033, 0.05405405405405404, 0.02502502502502502, 0.019019019019019014, 0.07207207207207206, 0.08608608608608606, 0.04304304304304303, 0.029029029029029024, 0.033033033033033024] [java] Struthio_camelus: 85 20 [java] Rhea_americana: 85 20 @@ -2671,8 +2707,6 @@ [java] 85 sites [java] 32 patterns [java] - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: EIGEN_COMPLEX [java] ============================================================================================================== [java] ============================================================================================================== [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == @@ -2682,6 +2716,8 @@ [java] Ignoring character uncertainty in tree likelihood. [java] With 32 unique site patterns. [java] Using rescaling scheme : dynamic + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: EIGEN_COMPLEX [java] Starting frequencies: [0.076, 0.009, 0.037, 0.049, 0.051, 0.084, 0.025, 0.081, 0.05, 0.101, 0.022, 0.041, 0.043, 0.038, 0.062, 0.062, 0.054, 0.066, 0.018, 0.031] [java] Struthio_camelus: 85 20 [java] Rhea_americana: 85 20 @@ -2691,13 +2727,13 @@ [java] 85 sites [java] 32 patterns [java] + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: EIGEN_COMPLEX [java] ============================================================================================================== [java] ============================================================================================================== [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == [java] ============================================================================================================== [java] ============================================================================================================== - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: EIGEN_COMPLEX [java] Ignoring ambiguities in tree likelihood. [java] Ignoring character uncertainty in tree likelihood. [java] With 32 unique site patterns. @@ -2715,6 +2751,8 @@ [java] [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_SINGLE COMPUTATION_SYNCH SCALING_MANUAL + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: PRECISION_SINGLE COMPUTATION_SYNCH SCALING_MANUAL [java] ============================================================================================================== [java] ============================================================================================================== [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == @@ -2728,8 +2766,6 @@ [java] Ignoring character uncertainty in tree likelihood. [java] With 69 unique site patterns. [java] Using rescaling scheme : dynamic - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_SINGLE COMPUTATION_SYNCH SCALING_MANUAL [java] human: 768 4 [java] chimp: 768 4 [java] bonobo: 768 4 @@ -2768,15 +2804,6 @@ [java] 85 sites [java] 32 patterns [java] - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 32 unique site patterns. - [java] Using rescaling scheme : dynamic [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: EIGEN_COMPLEX [java] seq1: 3 4 @@ -2787,6 +2814,15 @@ [java] 3 sites [java] 3 patterns [java] + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 32 unique site patterns. + [java] Using rescaling scheme : dynamic [java] seq1: 3 4 [java] seq2: 3 4 [java] seq3: 3 4 @@ -2802,7 +2838,7 @@ [java] [java] Tree A: [java] Without tip likelihoods: - [java] Using BEAGLE version: 3.1.2 resource 0: CPU============================================================================================================== + [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_SINGLE PRECISION_DOUBLE [java] -11.85320233632878 [java] With tip likelihoods: @@ -2810,18 +2846,27 @@ [java] with instance flags: PRECISION_SINGLE PRECISION_DOUBLE [java] -11.85320233632878 [java] Without tip likelihoods: - [java] [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_SINGLE PRECISION_DOUBLE [java] -11.85320233632878 [java] With tip likelihoods: - [java] ============================================================================================================== [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_SINGLE PRECISION_DOUBLE - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. ==-12.069603116476458 + [java] -12.069603116476458 [java] [java] Tree B: - [java] + [java] Without tip likelihoods: + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: PRECISION_SINGLE PRECISION_DOUBLE + [java] -12.421114302827698 + [java] With tip likelihoods: + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: PRECISION_SINGLE PRECISION_DOUBLE + [java] -12.421114302827698 + [java] Without tip likelihoods: + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == [java] ============================================================================================================== [java] ============================================================================================================== [java] Ignoring ambiguities in tree likelihood. @@ -2850,11 +2895,6 @@ [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == [java] ============================================================================================================== [java] ============================================================================================================== - [java] Without tip likelihoods: - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_SINGLE PRECISION_DOUBLE - [java] -12.421114302827698 - [java] With tip likelihoods: [java] Ignoring ambiguities in tree likelihood. [java] Ignoring character uncertainty in tree likelihood. [java] With 3 unique site patterns. @@ -2862,20 +2902,7 @@ [java] Ignoring ambiguities in tree likelihood. [java] Using character uncertainty in tree likelihood. [java] With 3 unique site patterns. - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_SINGLE PRECISION_DOUBLE - [java] -12.421114302827698 - [java] Without tip likelihoods: - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_SINGLE PRECISION_DOUBLE - [java] -12.421114302827698 - [java] With tip likelihoods: - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_SINGLE PRECISION_DOUBLE - [java] -11.621056623105131 Using rescaling scheme : none - [java] - [java] Testing alignment doubling: - [java] + [java] Using rescaling scheme : none [java] ============================================================================================================== [java] ============================================================================================================== [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == @@ -2889,6 +2916,24 @@ [java] Using character uncertainty in tree likelihood. [java] With 3 unique site patterns. [java] Using rescaling scheme : none + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 6 unique site patterns. + [java] Using rescaling scheme : none + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: PRECISION_SINGLE PRECISION_DOUBLE + [java] -12.421114302827698 + [java] With tip likelihoods: + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: PRECISION_SINGLE PRECISION_DOUBLE + [java] -11.621056623105131 + [java] + [java] Testing alignment doubling: [java] seq1: 6 4 [java] seq2: 6 4 [java] seq3: 6 4 @@ -2909,19 +2954,6 @@ [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH [java] -23.242113246210263 - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 6 unique site patterns. - [java] Using rescaling scheme : none - [java] Ignoring ambiguities in tree likelihood. - [java] Using character uncertainty in tree likelihood. - [java] With 6 unique site patterns. - [java] Using rescaling scheme : none [java] German_ST: 64 4 [java] Dutch_List: 64 4 [java] English_ST: 64 4 @@ -2931,10 +2963,10 @@ [java] 64 patterns [java] [java] Starting frequencies: [0.2, 0.3, 0.4, 0.1] - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: SCALING_MANUAL - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: SCALING_MANUAL + [java] Ignoring ambiguities in tree likelihood. + [java] Using character uncertainty in tree likelihood. + [java] With 6 unique site patterns. + [java] Using rescaling scheme : none [java] ============================================================================================================== [java] ============================================================================================================== [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == @@ -2948,6 +2980,10 @@ [java] Ignoring character uncertainty in tree likelihood. [java] With 64 unique site patterns. [java] Using rescaling scheme : dynamic + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: SCALING_MANUAL + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: SCALING_MANUAL [java] Starting frequencies: [0.087, 0.033, 0.047, 0.05, 0.04, 0.089, 0.034, 0.037, 0.08, 0.085, 0.015, 0.04, 0.051, 0.038, 0.041, 0.07, 0.058, 0.065, 0.01, 0.03] [java] Struthio_camelus: 85 20 [java] Rhea_americana: 85 20 @@ -2980,6 +3016,10 @@ [java] 69 patterns [java] [java] Starting frequencies: [0.3390942900867236, 0.24655436447178358, 0.1531393568179342, 0.26121198862355866] + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: PRECISION_SINGLE COMPUTATION_SYNCH SCALING_MANUAL + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: PRECISION_SINGLE COMPUTATION_SYNCH SCALING_MANUAL [java] ============================================================================================================== [java] ============================================================================================================== [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == @@ -2989,10 +3029,6 @@ [java] Ignoring character uncertainty in tree likelihood. [java] With 69 unique site patterns. [java] Using rescaling scheme : dynamic - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_SINGLE COMPUTATION_SYNCH SCALING_MANUAL - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_SINGLE COMPUTATION_SYNCH SCALING_MANUAL [java] Ignoring ambiguities in tree likelihood. [java] Ignoring character uncertainty in tree likelihood. [java] With 69 unique site patterns. @@ -3009,21 +3045,8 @@ [java] 69 patterns [java] [java] Starting frequencies: [0.3390942900867236, 0.24655436447178358, 0.1531393568179342, 0.26121198862355866] - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 69 unique site patterns. - [java] Using rescaling scheme : dynamic [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_SINGLE COMPUTATION_SYNCH SCALING_MANUAL - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 69 unique site patterns. - [java] Using rescaling scheme : dynamic [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_SINGLE COMPUTATION_SYNCH SCALING_MANUAL [java] human: 768 4 @@ -3037,7 +3060,6 @@ [java] 768 sites [java] 69 patterns [java] - [java] Starting frequencies: [0.25, 0.25, 0.25, 0.25] [java] ============================================================================================================== [java] ============================================================================================================== [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == @@ -3047,14 +3069,20 @@ [java] Ignoring character uncertainty in tree likelihood. [java] With 69 unique site patterns. [java] Using rescaling scheme : dynamic + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 69 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] Starting frequencies: [0.25, 0.25, 0.25, 0.25] [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_SINGLE COMPUTATION_SYNCH SCALING_MANUAL [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_SINGLE COMPUTATION_SYNCH SCALING_MANUAL - [java] Using ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 69 unique site patterns. - [java] Using rescaling scheme : dynamic [java] human: 768 4 [java] chimp: 768 4 [java] bonobo: 768 4 @@ -3067,10 +3095,14 @@ [java] 69 patterns [java] [java] Starting frequencies: [0.3390942900867236, 0.24655436447178358, 0.1531393568179342, 0.26121198862355866] - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_SINGLE COMPUTATION_SYNCH SCALING_MANUAL - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_SINGLE COMPUTATION_SYNCH SCALING_MANUAL + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 69 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] Using ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 69 unique site patterns. + [java] Using rescaling scheme : dynamic [java] ============================================================================================================== [java] ============================================================================================================== [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == @@ -3084,6 +3116,10 @@ [java] Ignoring character uncertainty in tree likelihood. [java] With 69 unique site patterns. [java] Using rescaling scheme : dynamic + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: PRECISION_SINGLE COMPUTATION_SYNCH SCALING_MANUAL + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: PRECISION_SINGLE COMPUTATION_SYNCH SCALING_MANUAL [java] Starting frequencies: [0.074, 0.025, 0.054, 0.054, 0.047, 0.074, 0.026, 0.068, 0.058, 0.099, 0.025, 0.045, 0.039, 0.034, 0.052, 0.057, 0.051, 0.073, 0.013, 0.032] [java] Struthio_camelus: 85 20 [java] Rhea_americana: 85 20 @@ -3093,8 +3129,6 @@ [java] 85 sites [java] 32 patterns [java] - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: EIGEN_COMPLEX [java] ============================================================================================================== [java] ============================================================================================================== [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == @@ -3104,6 +3138,8 @@ [java] Ignoring character uncertainty in tree likelihood. [java] With 32 unique site patterns. [java] Using rescaling scheme : dynamic + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: EIGEN_COMPLEX [java] German_ST: 8 2 [java] Dutch_List: 8 2 [java] English_ST: 8 2 @@ -3112,10 +3148,12 @@ [java] 8 sites [java] 8 patterns [java] - [java] Starting frequencies: [0.683, 0.317]============================================================================================================== + [java] Starting frequencies: [0.683, 0.317] [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: COMPUTATION_ASYNCH - [java] + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: COMPUTATION_ASYNCH + [java] ============================================================================================================== [java] ============================================================================================================== [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == [java] ============================================================================================================== @@ -3128,8 +3166,6 @@ [java] Ignoring character uncertainty in tree likelihood. [java] With 8 unique site patterns. [java] Using rescaling scheme : dynamic - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: COMPUTATION_ASYNCH [java] human: 768 4 [java] chimp: 768 4 [java] bonobo: 768 4 @@ -3146,19 +3182,6 @@ [java] with instance flags: PRECISION_SINGLE COMPUTATION_SYNCH SCALING_MANUAL [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_SINGLE COMPUTATION_SYNCH SCALING_MANUAL - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 69 unique site patterns. - [java] Using rescaling scheme : dynamic - [java] Using ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 69 unique site patterns. - [java] Using rescaling scheme : dynamic [java] German_ST: 5051 4 [java] Dutch_List: 5051 4 [java] English_ST: 5051 4 @@ -3172,19 +3195,6 @@ [java] 5051 sites with weight 565 [java] 50 patterns [java] - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 50 unique site patterns. - [java] Using rescaling scheme : dynamic - [java] Using ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 50 unique site patterns. - [java] Using rescaling scheme : dynamic [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_DOUBLE EIGEN_REAL EIGEN_COMPLEX [java] Using BEAGLE version: 3.1.2 resource 0: CPU @@ -3203,13 +3213,27 @@ [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == [java] ============================================================================================================== [java] ============================================================================================================== - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: EIGEN_COMPLEX [java] Ignoring ambiguities in tree likelihood. [java] Ignoring character uncertainty in tree likelihood. - [java] With 32 unique site patterns. + [java] With 69 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] Using ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 69 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 50 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] Using ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 50 unique site patterns. [java] Using rescaling scheme : dynamic - [java] Starting frequencies: [0.076, 0.009, 0.037, 0.049, 0.051, 0.084, 0.025, 0.081, 0.05, 0.101, 0.022, 0.041, 0.043, 0.038, 0.062, 0.062, 0.054, 0.066, 0.018, 0.031] [java] ============================================================================================================== [java] ============================================================================================================== [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == @@ -3219,6 +3243,9 @@ [java] Ignoring character uncertainty in tree likelihood. [java] With 32 unique site patterns. [java] Using rescaling scheme : dynamic + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: EIGEN_COMPLEX + [java] Starting frequencies: [0.076, 0.009, 0.037, 0.049, 0.051, 0.084, 0.025, 0.081, 0.05, 0.101, 0.022, 0.041, 0.043, 0.038, 0.062, 0.062, 0.054, 0.066, 0.018, 0.031] [java] Struthio_camelus: 85 20 [java] Rhea_americana: 85 20 [java] Pterocnemia_pennata: 85 20 @@ -3241,23 +3268,10 @@ [java] 69 patterns [java] [java] Starting frequencies: [0.3390942900867236, 0.24655436447178358, 0.1531393568179342, 0.26121198862355866] - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 69 unique site patterns. - [java] Using rescaling scheme : dynamic [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_SINGLE COMPUTATION_SYNCH SCALING_MANUAL [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_SINGLE COMPUTATION_SYNCH SCALING_MANUAL - [java] Using ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 69 unique site patterns. - [java] Using rescaling scheme : dynamic [java] Starting frequencies: [0.077, 0.02, 0.052, 0.062, 0.04, 0.074, 0.023, 0.052, 0.059, 0.091, 0.024, 0.043, 0.051, 0.041, 0.051, 0.069, 0.059, 0.066, 0.014, 0.032] [java] Struthio_camelus: 85 20 [java] Rhea_americana: 85 20 @@ -3267,6 +3281,30 @@ [java] 85 sites [java] 32 patterns [java] + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: EIGEN_COMPLEX + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 32 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 69 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] Using ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 69 unique site patterns. + [java] Using rescaling scheme : dynamic [java] ============================================================================================================== [java] ============================================================================================================== [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == @@ -3276,9 +3314,18 @@ [java] Ignoring character uncertainty in tree likelihood. [java] With 32 unique site patterns. [java] Using rescaling scheme : dynamic + [java] Starting frequencies: [0.0866, 0.0193, 0.057, 0.0581, 0.0384, 0.0833, 0.0244, 0.0485, 0.062, 0.0862, 0.0195, 0.0391, 0.0458, 0.0367, 0.044, 0.0695, 0.061, 0.0709, 0.0144, 0.0353] + [java] Struthio_camelus: 85 20 + [java] Rhea_americana: 85 20 + [java] Pterocnemia_pennata: 85 20 + [java] Alignment(null) + [java] 3 taxa + [java] 85 sites + [java] 32 patterns + [java] [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: EIGEN_COMPLEX - [java] Starting frequencies: [0.0866, 0.0193, 0.057, 0.0581, 0.0384, 0.0833, 0.0244, 0.0485, 0.062, 0.0862, 0.0195, 0.0391, 0.0458, 0.0367, 0.044, 0.0695, 0.061, 0.0709, 0.0144, 0.0353] + [java] Starting frequencies: [0.07207207207207206, 0.006006006006006005, 0.019019019019019014, 0.02402402402402402, 0.061061061061061045, 0.05605605605605604, 0.02802802802802802, 0.08808808808808806, 0.023023023023023018, 0.16816816816816815, 0.05405405405405404, 0.039039039039039033, 0.05405405405405404, 0.02502502502502502, 0.019019019019019014, 0.07207207207207206, 0.08608608608608606, 0.04304304304304303, 0.029029029029029024, 0.033033033033033024] [java] Struthio_camelus: 85 20 [java] Rhea_americana: 85 20 [java] Pterocnemia_pennata: 85 20 @@ -3298,15 +3345,6 @@ [java] Ignoring character uncertainty in tree likelihood. [java] With 32 unique site patterns. [java] Using rescaling scheme : dynamic - [java] Starting frequencies: [0.07207207207207206, 0.006006006006006005, 0.019019019019019014, 0.02402402402402402, 0.061061061061061045, 0.05605605605605604, 0.02802802802802802, 0.08808808808808806, 0.023023023023023018, 0.16816816816816815, 0.05405405405405404, 0.039039039039039033, 0.05405405405405404, 0.02502502502502502, 0.019019019019019014, 0.07207207207207206, 0.08608608608608606, 0.04304304304304303, 0.029029029029029024, 0.033033033033033024] - [java] Struthio_camelus: 85 20 - [java] Rhea_americana: 85 20 - [java] Pterocnemia_pennata: 85 20 - [java] Alignment(null) - [java] 3 taxa - [java] 85 sites - [java] 32 patterns - [java] [java] ============================================================================================================== [java] ============================================================================================================== [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == @@ -3316,8 +3354,15 @@ [java] Ignoring character uncertainty in tree likelihood. [java] With 32 unique site patterns. [java] Using rescaling scheme : dynamic - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: EIGEN_COMPLEX + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 32 unique site patterns. + [java] Using rescaling scheme : dynamic [java] Starting frequencies: [0.076, 0.009, 0.037, 0.049, 0.051, 0.084, 0.025, 0.081, 0.05, 0.101, 0.022, 0.041, 0.043, 0.038, 0.062, 0.062, 0.054, 0.066, 0.018, 0.031] [java] Struthio_camelus: 85 20 [java] Rhea_americana: 85 20 @@ -3327,17 +3372,8 @@ [java] 85 sites [java] 32 patterns [java] - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: EIGEN_COMPLEX - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 32 unique site patterns. - [java] Using rescaling scheme : dynamic [java] Starting frequencies: [0.074, 0.025, 0.054, 0.054, 0.047, 0.074, 0.026, 0.068, 0.058, 0.099, 0.025, 0.045, 0.039, 0.034, 0.052, 0.057, 0.051, 0.073, 0.013, 0.032] [java] Struthio_camelus: 85 20 [java] Rhea_americana: 85 20 @@ -3347,15 +3383,6 @@ [java] 85 sites [java] 32 patterns [java] - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 32 unique site patterns. - [java] Using rescaling scheme : dynamic [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: EIGEN_COMPLEX [java] Starting frequencies: [0.087, 0.033, 0.047, 0.05, 0.04, 0.089, 0.034, 0.037, 0.08, 0.085, 0.015, 0.04, 0.051, 0.038, 0.041, 0.07, 0.058, 0.065, 0.01, 0.03] @@ -3376,10 +3403,19 @@ [java] Ignoring character uncertainty in tree likelihood. [java] With 32 unique site patterns. [java] Using rescaling scheme : dynamic + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [java] ============================================================================================================== + [java] ============================================================================================================== [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: EIGEN_COMPLEX [java] =============================================================================== [java] Citations for this model: + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 32 unique site patterns. + [java] Using rescaling scheme : dynamic [java] [java] Bouckaert, Remco, Timothy G. Vaughan, Joëlle Barido-Sottani, Sebastián Duchêne, Mathieu Fourment, [java] Alexandra Gavryushkina, Joseph Heled, Graham Jones, Denise Kühnert, Nicola De Maio, Michael Matschiner, @@ -3391,6 +3427,7 @@ [java] [java] =============================================================================== [java] Start likelihood: -14.297530455869882 + [java] End likelihood: -2.101581781210349 [java] [java] Operator Tuning #accept #reject Pr(m) Pr(acc|m) [java] kernel.BactrianScaleOperator(unknown) 2.30772 308831 691170 1.00000 0.30883 @@ -3402,8 +3439,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 22.941 seconds - [java] End likelihood: -2.101581781210349 + [java] Total calculation time: 7.682 seconds [java] =============================================================================== [java] Citations for this model: [java] @@ -3417,6 +3453,7 @@ [java] [java] =============================================================================== [java] Start likelihood: -7.148765227934941 + [java] End likelihood: 0.008929267909451477 [java] [java] Operator Tuning #accept #reject Pr(m) Pr(acc|m) [java] kernel.BactrianScaleOperator(unknown) 2.31053 307447 692554 1.00000 0.30745 @@ -3428,8 +3465,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 13.711 seconds - [java] End likelihood: 0.008929267909451477 + [java] Total calculation time: 6.187 seconds [java] =============================================================================== [java] Citations for this model: [java] @@ -3443,6 +3479,7 @@ [java] [java] =============================================================================== [java] Start likelihood: -21.446295683804824 + [java] End likelihood: -0.5552616722623194 [java] [java] Operator Tuning #accept #reject Pr(m) Pr(acc|m) [java] kernel.BactrianScaleOperator(unknown) 1.33125 153295 347047 0.50000 0.30638 @@ -3455,8 +3492,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 22.622 seconds - [java] End likelihood: -0.5552616722623194 + [java] Total calculation time: 7.151 seconds [java] =============================================================================== [java] Citations for this model: [java] @@ -3470,7 +3506,6 @@ [java] [java] =============================================================================== [java] Start likelihood: -21.446295683804824 - [java] End likelihood: -2.422052674651341 [java] [java] Operator Tuning #accept #reject Pr(m) Pr(acc|m) [java] kernel.BactrianScaleOperator(unknown) 1.23542 303560 696441 1.00000 0.30356 @@ -3482,7 +3517,8 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 22.579 seconds + [java] Total calculation time: 10.57 seconds + [java] End likelihood: -2.422052674651341 [java] A: 1 4 [java] B: 1 4 [java] C: 1 4 @@ -3541,7 +3577,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 5.776 seconds + [java] Total calculation time: 3.294 seconds [java] Testing mirror distribution [java] Testing mirror distribution for scaling [java] kick in @@ -3571,6 +3607,227 @@ [java] Testing bactrian_triangle s= 0.9998030418762279 [java] Testing bactrian_box s= 0.9993617332307378 [java] Testing bactrian_box s= 0.9993638943013682 + [java] Number of weights (4) does not match sequence length (16) + [java] [11232, 2, 3, 4, 1123, 2, 3, 4, 112, 2, 3, 4, 11, 2, 3, 4] + [java] 0human AAAACCCCGGGGTTTT + [java] 1chimp ACGTACGTACGTACGT + [java] [11232, 2, 4, 3, 1123, 2, 3, 4, 11, 2, 3, 4, 112, 2, 3, 4] + [java] AAAACCCCTTTTGGGG + [java] ACTGACGTACGTACGT + [java] [101000, 10000, 1, 110] + [java] GGGAAA + [java] AGGACA + [java] java.lang.RuntimeException: Cannot handle site weights in FilteredAlignment. Remove "weights" from data input. + [java] at beast.base.evolution.alignment.FilteredAlignment.calcPatterns(Unknown Source) + [java] at beast.base.evolution.alignment.FilteredAlignment.initAndValidate(Unknown Source) + [java] at beast.base.core.BEASTInterface.initByName(Unknown Source) + [java] at test.beast.evolution.alignment.FilteredAlignmentTest.testWeightedSites(Unknown Source) + [java] at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) + [java] at java.base/java.lang.reflect.Method.invoke(Method.java:580) + [java] at org.junit.platform.commons.util.ReflectionUtils.invokeMethod(ReflectionUtils.java:728) + [java] at org.junit.jupiter.engine.execution.MethodInvocation.proceed(MethodInvocation.java:60) + [java] at org.junit.jupiter.engine.execution.InvocationInterceptorChain$ValidatingInvocation.proceed(InvocationInterceptorChain.java:131) + [java] at org.junit.jupiter.engine.extension.TimeoutExtension.intercept(TimeoutExtension.java:156) + [java] at org.junit.jupiter.engine.extension.TimeoutExtension.interceptTestableMethod(TimeoutExtension.java:147) + [java] at org.junit.jupiter.engine.extension.TimeoutExtension.interceptTestMethod(TimeoutExtension.java:86) + [java] at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker$ReflectiveInterceptorCall.lambda$ofVoidMethod$0(InterceptingExecutableInvoker.java:103) + [java] at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker.lambda$invoke$0(InterceptingExecutableInvoker.java:93) + [java] at org.junit.jupiter.engine.execution.InvocationInterceptorChain$InterceptedInvocation.proceed(InvocationInterceptorChain.java:106) + [java] at org.junit.jupiter.engine.execution.InvocationInterceptorChain.proceed(InvocationInterceptorChain.java:64) + [java] at org.junit.jupiter.engine.execution.InvocationInterceptorChain.chainAndInvoke(InvocationInterceptorChain.java:45) + [java] at org.junit.jupiter.engine.execution.InvocationInterceptorChain.invoke(InvocationInterceptorChain.java:37) + [java] at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker.invoke(InterceptingExecutableInvoker.java:92) + [java] at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker.invoke(InterceptingExecutableInvoker.java:86) + [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.lambda$invokeTestMethod$7(TestMethodTestDescriptor.java:218) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.invokeTestMethod(TestMethodTestDescriptor.java:214) + [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.execute(TestMethodTestDescriptor.java:139) + [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.execute(TestMethodTestDescriptor.java:69) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$6(NodeTestTask.java:151) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:141) + [java] at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:137) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$9(NodeTestTask.java:139) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) + [java] at java.base/java.util.ArrayList.forEach(ArrayList.java:1596) + [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$6(NodeTestTask.java:155) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:141) + [java] at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:137) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$9(NodeTestTask.java:139) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) + [java] at java.base/java.util.ArrayList.forEach(ArrayList.java:1596) + [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$6(NodeTestTask.java:155) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:141) + [java] at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:137) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$9(NodeTestTask.java:139) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) + [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.submit(SameThreadHierarchicalTestExecutorService.java:35) + [java] at org.junit.platform.engine.support.hierarchical.HierarchicalTestExecutor.execute(HierarchicalTestExecutor.java:57) + [java] at org.junit.platform.engine.support.hierarchical.HierarchicalTestEngine.execute(HierarchicalTestEngine.java:54) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:198) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:169) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:93) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.lambda$execute$0(EngineExecutionOrchestrator.java:58) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.withInterceptedStreams(EngineExecutionOrchestrator.java:141) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:57) + [java] at org.junit.platform.launcher.core.DefaultLauncher.execute(DefaultLauncher.java:103) + [java] at org.junit.platform.launcher.core.DefaultLauncher.execute(DefaultLauncher.java:85) + [java] at org.junit.platform.launcher.core.DelegatingLauncher.execute(DelegatingLauncher.java:47) + [java] at org.junit.platform.launcher.core.SessionPerRequestLauncher.execute(SessionPerRequestLauncher.java:63) + [java] at org.junit.platform.console.tasks.ConsoleTestExecutor.executeTests(ConsoleTestExecutor.java:102) + [java] at org.junit.platform.console.tasks.ConsoleTestExecutor.lambda$execute$1(ConsoleTestExecutor.java:71) + [java] at org.junit.platform.console.tasks.CustomContextClassLoaderExecutor.invoke(CustomContextClassLoaderExecutor.java:35) + [java] at org.junit.platform.console.tasks.ConsoleTestExecutor.execute(ConsoleTestExecutor.java:71) + [java] at org.junit.platform.console.options.ExecuteTestsCommand.execute(ExecuteTestsCommand.java:61) + [java] at org.junit.platform.console.options.ExecuteTestsCommand.execute(ExecuteTestsCommand.java:27) + [java] at org.junit.platform.console.options.BaseCommand.call(BaseCommand.java:74) + [java] at org.junit.platform.console.shadow.picocli.CommandLine.executeUserObject(CommandLine.java:1953) + [java] at org.junit.platform.console.shadow.picocli.CommandLine.access$1300(CommandLine.java:145) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.handle(CommandLine.java:2352) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.handle(CommandLine.java:2314) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.execute(CommandLine.java:2316) + [java] at org.junit.platform.console.shadow.picocli.CommandLine.execute(CommandLine.java:2078) + [java] at org.junit.platform.console.options.MainCommand.runCommand(MainCommand.java:137) + [java] at org.junit.platform.console.options.MainCommand.runCommand(MainCommand.java:129) + [java] at org.junit.platform.console.options.MainCommand.runCommand(MainCommand.java:93) + [java] at org.junit.platform.console.options.MainCommand.call(MainCommand.java:77) + [java] at org.junit.platform.console.shadow.picocli.CommandLine.executeUserObject(CommandLine.java:1953) + [java] at org.junit.platform.console.shadow.picocli.CommandLine.access$1300(CommandLine.java:145) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.handle(CommandLine.java:2352) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.handle(CommandLine.java:2314) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.execute(CommandLine.java:2316) + [java] at org.junit.platform.console.shadow.picocli.CommandLine.execute(CommandLine.java:2078) + [java] at org.junit.platform.console.options.MainCommand.runCommand(MainCommand.java:137) + [java] at org.junit.platform.console.options.MainCommand.run(MainCommand.java:125) + [java] at org.junit.platform.console.options.CommandFacade.run(CommandFacade.java:36) + [java] at org.junit.platform.console.ConsoleLauncher.run(ConsoleLauncher.java:57) + [java] at org.junit.platform.console.ConsoleLauncher.run(ConsoleLauncher.java:42) + [java] at org.junit.platform.console.ConsoleLauncher.main(ConsoleLauncher.java:35) + [java] initAndValidate() failed! Cannot handle site weights in FilteredAlignment. Remove "weights" from data input. + [java] java.lang.IllegalArgumentException: constantSiteWeights should be of the same dimension as the datatype (3!=4) + [java] at beast.base.evolution.alignment.FilteredAlignment.initAndValidate(Unknown Source) + [java] at beast.base.core.BEASTInterface.initByName(Unknown Source) + [java] at test.beast.evolution.alignment.FilteredAlignmentTest.testConstantSites(Unknown Source) + [java] at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) + [java] at java.base/java.lang.reflect.Method.invoke(Method.java:580) + [java] at org.junit.platform.commons.util.ReflectionUtils.invokeMethod(ReflectionUtils.java:728) + [java] at org.junit.jupiter.engine.execution.MethodInvocation.proceed(MethodInvocation.java:60) + [java] at org.junit.jupiter.engine.execution.InvocationInterceptorChain$ValidatingInvocation.proceed(InvocationInterceptorChain.java:131) + [java] at org.junit.jupiter.engine.extension.TimeoutExtension.intercept(TimeoutExtension.java:156) + [java] at org.junit.jupiter.engine.extension.TimeoutExtension.interceptTestableMethod(TimeoutExtension.java:147) + [java] at org.junit.jupiter.engine.extension.TimeoutExtension.interceptTestMethod(TimeoutExtension.java:86) + [java] at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker$ReflectiveInterceptorCall.lambda$ofVoidMethod$0(InterceptingExecutableInvoker.java:103) + [java] at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker.lambda$invoke$0(InterceptingExecutableInvoker.java:93) + [java] at org.junit.jupiter.engine.execution.InvocationInterceptorChain$InterceptedInvocation.proceed(InvocationInterceptorChain.java:106) + [java] at org.junit.jupiter.engine.execution.InvocationInterceptorChain.proceed(InvocationInterceptorChain.java:64) + [java] at org.junit.jupiter.engine.execution.InvocationInterceptorChain.chainAndInvoke(InvocationInterceptorChain.java:45) + [java] at org.junit.jupiter.engine.execution.InvocationInterceptorChain.invoke(InvocationInterceptorChain.java:37) + [java] at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker.invoke(InterceptingExecutableInvoker.java:92) + [java] at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker.invoke(InterceptingExecutableInvoker.java:86) + [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.lambda$invokeTestMethod$7(TestMethodTestDescriptor.java:218) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.invokeTestMethod(TestMethodTestDescriptor.java:214) + [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.execute(TestMethodTestDescriptor.java:139) + [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.execute(TestMethodTestDescriptor.java:69) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$6(NodeTestTask.java:151) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:141) + [java] at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:137) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$9(NodeTestTask.java:139) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) + [java] at java.base/java.util.ArrayList.forEach(ArrayList.java:1596) + [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$6(NodeTestTask.java:155) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:141) + [java] at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:137) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$9(NodeTestTask.java:139) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) + [java] at java.base/java.util.ArrayList.forEach(ArrayList.java:1596) + [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$6(NodeTestTask.java:155) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:141) + [java] at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:137) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$9(NodeTestTask.java:139) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) + [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.submit(SameThreadHierarchicalTestExecutorService.java:35) + [java] at org.junit.platform.engine.support.hierarchical.HierarchicalTestExecutor.execute(HierarchicalTestExecutor.java:57) + [java] at org.junit.platform.engine.support.hierarchical.HierarchicalTestEngine.execute(HierarchicalTestEngine.java:54) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:198) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:169) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:93) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.lambda$execute$0(EngineExecutionOrchestrator.java:58) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.withInterceptedStreams(EngineExecutionOrchestrator.java:141) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:57) + [java] at org.junit.platform.launcher.core.DefaultLauncher.execute(DefaultLauncher.java:103) + [java] at org.junit.platform.launcher.core.DefaultLauncher.execute(DefaultLauncher.java:85) + [java] at org.junit.platform.launcher.core.DelegatingLauncher.execute(DelegatingLauncher.java:47) + [java] at org.junit.platform.launcher.core.SessionPerRequestLauncher.execute(SessionPerRequestLauncher.java:63) + [java] at org.junit.platform.console.tasks.ConsoleTestExecutor.executeTests(ConsoleTestExecutor.java:102) + [java] at org.junit.platform.console.tasks.ConsoleTestExecutor.lambda$execute$1(ConsoleTestExecutor.java:71) + [java] at org.junit.platform.console.tasks.CustomContextClassLoaderExecutor.invoke(CustomContextClassLoaderExecutor.java:35) + [java] at org.junit.platform.console.tasks.ConsoleTestExecutor.execute(ConsoleTestExecutor.java:71) + [java] at org.junit.platform.console.options.ExecuteTestsCommand.execute(ExecuteTestsCommand.java:61) + [java] at org.junit.platform.console.options.ExecuteTestsCommand.execute(ExecuteTestsCommand.java:27) + [java] at org.junit.platform.console.options.BaseCommand.call(BaseCommand.java:74) + [java] at org.junit.platform.console.shadow.picocli.CommandLine.executeUserObject(CommandLine.java:1953) + [java] at org.junit.platform.console.shadow.picocli.CommandLine.access$1300(CommandLine.java:145) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.handle(CommandLine.java:2352) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.handle(CommandLine.java:2314) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.execute(CommandLine.java:2316) + [java] at org.junit.platform.console.shadow.picocli.CommandLine.execute(CommandLine.java:2078) + [java] at org.junit.platform.console.options.MainCommand.runCommand(MainCommand.java:137) + [java] at org.junit.platform.console.options.MainCommand.runCommand(MainCommand.java:129) + [java] at org.junit.platform.console.options.MainCommand.runCommand(MainCommand.java:93) + [java] at org.junit.platform.console.options.MainCommand.call(MainCommand.java:77) + [java] at org.junit.platform.console.shadow.picocli.CommandLine.executeUserObject(CommandLine.java:1953) + [java] at org.junit.platform.console.shadow.picocli.CommandLine.access$1300(CommandLine.java:145) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.handle(CommandLine.java:2352) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.handle(CommandLine.java:2314) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.execute(CommandLine.java:2316) + [java] at org.junit.platform.console.shadow.picocli.CommandLine.execute(CommandLine.java:2078) + [java] at org.junit.platform.console.options.MainCommand.runCommand(MainCommand.java:137) + [java] at org.junit.platform.console.options.MainCommand.run(MainCommand.java:125) + [java] at org.junit.platform.console.options.CommandFacade.run(CommandFacade.java:36) + [java] at org.junit.platform.console.ConsoleLauncher.run(ConsoleLauncher.java:57) + [java] at org.junit.platform.console.ConsoleLauncher.run(ConsoleLauncher.java:42) + [java] at org.junit.platform.console.ConsoleLauncher.main(ConsoleLauncher.java:35) + [java] initAndValidate() failed! constantSiteWeights should be of the same dimension as the datatype (3!=4) + [java] [11233, 1, 1, 1, 1, 3, 1, 1, 1, 1, 4, 1, 1, 1, 1, 5] + [java] [11233, 1, 1, 1, 1, 3, 1, 1, 3, 4] + [java] <0> <1> <2> <3> removed 6 sites + [java] [11232, 1, 1, 1, 1, 2, 1, 1, 3, 4] + [java] t0=0 + [java] t1=10 + [java] t1=10 + [java] WARNING: no trait specified for t0: Assumed to be 10.0 + [java] t0=0 + [java] t1=10 [java] 0human: 16 4 [java] 1chimp: 16 4 [java] Alignment(null) @@ -3661,7 +3918,7 @@ [java] 16 patterns [java] [java] Filter - - [java] Number of weights (4) does not match sequence length (16)2 taxa + [java] 2 taxa [java] 16 sites + 11241 constant sites [java] 16 patterns [java] Filter -8 @@ -3683,99 +3940,12 @@ [java] 2 taxa [java] 4 sites [java] 4 patterns - [java] - [java] [11232, 2, 3, 4, 1123, 2, 3, 4, 112, 2, 3, 4, 11, 2, 3, 4] - [java] 0human AAAACCCCGGGGTTTT - [java] 1chimp ACGTACGTACGTACGT - [java] [11232, 2, 4, 3, 1123, 2, 3, 4, 11, 2, 3, 4, 112, 2, 3, 4] - [java] AAAACCCCTTTTGGGG - [java] ACTGACGTACGTACGT - [java] [101000, 10000, 1, 110] - [java] GGGAAA - [java] AGGACA - [java] java.lang.RuntimeException: Cannot handle site weights in FilteredAlignment. Remove "weights" from data input. - [java] at beast.base.evolution.alignment.FilteredAlignment.calcPatterns(Unknown Source) - [java] at beast.base.evolution.alignment.FilteredAlignment.initAndValidate(Unknown Source) - [java] at beast.base.core.BEASTInterface.initByName(Unknown Source) - [java] at test.beast.evolution.alignment.FilteredAlignmentTest.testWeightedSites(Unknown Source) - [java] at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) - [java] at java.base/java.lang.reflect.Method.invoke(Method.java:580) - [java] at org.junit.platform.commons.util.ReflectionUtils.invokeMethod(ReflectionUtils.java:728) - [java] at org.junit.jupiter.engine.execution.MethodInvocation.proceed(MethodInvocation.java:60) - [java] at org.junit.jupiter.engine.execution.InvocationInterceptorChain$ValidatingInvocation.proceed(InvocationInterceptorChain.java:131) - [java] at org.junit.jupiter.engine.extension.TimeoutExtension.intercept(TimeoutExtension.java:156) - [java] at org.junit.jupiter.engine.extension.TimeoutExtension.interceptTestableMethod(TimeoutExtension.java:147) - [java] at org.junit.jupiter.engine.extension.TimeoutExtension.interceptTestMethod(TimeoutExtension.java:86) - [java] at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker$ReflectiveInterceptorCall.lambda$ofVoidMethod$0(InterceptingExecutableInvoker.java:103) - [java] at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker.lambda$invoke$0(InterceptingExecutableInvoker.java:93) - [java] at org.junit.jupiter.engine.execution.InvocationInterceptorChain$InterceptedInvocation.proceed(InvocationInterceptorChain.java:106) - [java] at org.junit.jupiter.engine.execution.InvocationInterceptorChain.proceed(InvocationInterceptorChain.java:64) - [java] at org.junit.jupiter.engine.execution.InvocationInterceptorChain.chainAndInvoke(InvocationInterceptorChain.java:45) - [java] at org.junit.jupiter.engine.execution.InvocationInterceptorChain.invoke(InvocationInterceptorChain.java:37) - [java] at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker.invoke(InterceptingExecutableInvoker.java:92) - [java] at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker.invoke(InterceptingExecutableInvoker.java:86) - [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.lambda$invokeTestMethod$7(TestMethodTestDescriptor.java:218) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.invokeTestMethod(TestMethodTestDescriptor.java:214) - [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.execute(TestMethodTestDescriptor.java:139) - [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.execute(TestMethodTestDescriptor.java:69) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$6(NodeTestTask.java:151) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:141) - [java] at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:137) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$9(NodeTestTask.java:139) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) - [java] at java.base/java.util.ArrayList.forEach(ArrayList.java:1596) - [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$6(NodeTestTask.java:155) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:141) - [java] at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:137) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$9(NodeTestTask.java:139) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) - [java] at java.base/java.util.ArrayList.forEach(ArrayList.java:1596) - [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$6(NodeTestTask.java:155) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:141) - [java] at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:137) [java] human AACC [java] 1chimp GTAC [java] Filter 11:14:1 [java] 2 taxa [java] 4 sites [java] 4 patterns - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$9(NodeTestTask.java:139) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) - [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.submit(SameThreadHierarchicalTestExecutorService.java:35) - [java] at org.junit.platform.engine.support.hierarchical.HierarchicalTestExecutor.execute(HierarchicalTestExecutor.java:57) - [java] at org.junit.platform.engine.support.hierarchical.HierarchicalTestEngine.execute(HierarchicalTestEngine.java:54) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:198) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:169) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:93) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.lambda$execute$0(EngineExecutionOrchestrator.java:58) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.withInterceptedStreams(EngineExecutionOrchestrator.java:141) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:57) - [java] at org.junit.platform.launcher.core.DefaultLauncher.execute(DefaultLauncher.java:103) - [java] at org.junit.platform.launcher.core.DefaultLauncher.execute(DefaultLauncher.java:85) - [java] at org.junit.platform.launcher.core.DelegatingLauncher.execute(DelegatingLauncher.java:47) - [java] at org.junit.platform.launcher.core.SessionPerRequestLauncher.execute(SessionPerRequestLauncher.java:63) - [java] at org.junit.platform.console.tasks.ConsoleTestExecutor.executeTests(ConsoleTestExecutor.java:102) - [java] at org.junit.platform.console.tasks.ConsoleTestExecutor.lambda$execute$1(ConsoleTestExecutor.java:71) - [java] at org.junit.platform.console.tasks.CustomContextClassLoaderExecutor.invoke(CustomContextClassLoaderExecutor.java:35) - [java] at org.junit.platform.console.tasks.ConsoleTestExecutor.execute(ConsoleTestExecutor.java:71) - [java] at org.junit.platform.console.options.ExecuteTestsCommand.execute(ExecuteTestsCommand.java:61) - [java] at org.junit.platform.console.options.ExecuteTestsCommand.execute(ExecuteTestsCommand.java:27) - [java] at org.junit.platform.console.options.BaseCommand.call(BaseCommand.java:74) - [java] at org.junit.platform.console.shadow.picocli.CommandLine.executeUserObject(CommandLine.java:1953) - [java] at org.junit.platform.console.shadow.picocli.CommandLine.access$1300(CommandLine.java:145) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [java] human GGAA [java] 1chimp GTAC [java] Filter 3:16:4 @@ -3900,105 +4070,6 @@ [java] Alignment(null) [java] 2 taxa [java] 1 site - [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.handle(CommandLine.java:2352) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.handle(CommandLine.java:2314) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.execute(CommandLine.java:2316) - [java] at org.junit.platform.console.shadow.picocli.CommandLine.execute(CommandLine.java:2078) - [java] at org.junit.platform.console.options.MainCommand.runCommand(MainCommand.java:137) - [java] at org.junit.platform.console.options.MainCommand.runCommand(MainCommand.java:129) - [java] at org.junit.platform.console.options.MainCommand.runCommand(MainCommand.java:93) - [java] at org.junit.platform.console.options.MainCommand.call(MainCommand.java:77) - [java] at org.junit.platform.console.shadow.picocli.CommandLine.executeUserObject(CommandLine.java:1953) - [java] at org.junit.platform.console.shadow.picocli.CommandLine.access$1300(CommandLine.java:145) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.handle(CommandLine.java:2352) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.handle(CommandLine.java:2314) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.execute(CommandLine.java:2316) - [java] at org.junit.platform.console.shadow.picocli.CommandLine.execute(CommandLine.java:2078) - [java] at org.junit.platform.console.options.MainCommand.runCommand(MainCommand.java:137) - [java] at org.junit.platform.console.options.MainCommand.run(MainCommand.java:125) - [java] at org.junit.platform.console.options.CommandFacade.run(CommandFacade.java:36) - [java] at org.junit.platform.console.ConsoleLauncher.run(ConsoleLauncher.java:57) - [java] at org.junit.platform.console.ConsoleLauncher.run(ConsoleLauncher.java:42) - [java] at org.junit.platform.console.ConsoleLauncher.main(ConsoleLauncher.java:35) - [java] initAndValidate() failed! Cannot handle site weights in FilteredAlignment. Remove "weights" from data input. - [java] java.lang.IllegalArgumentException: constantSiteWeights should be of the same dimension as the datatype (3!=4) - [java] at beast.base.evolution.alignment.FilteredAlignment.initAndValidate(Unknown Source) - [java] at beast.base.core.BEASTInterface.initByName(Unknown Source) - [java] at test.beast.evolution.alignment.FilteredAlignmentTest.testConstantSites(Unknown Source) - [java] at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) - [java] at java.base/java.lang.reflect.Method.invoke(Method.java:580) - [java] at org.junit.platform.commons.util.ReflectionUtils.invokeMethod(ReflectionUtils.java:728) - [java] at org.junit.jupiter.engine.execution.MethodInvocation.proceed(MethodInvocation.java:60) - [java] at org.junit.jupiter.engine.execution.InvocationInterceptorChain$ValidatingInvocation.proceed(InvocationInterceptorChain.java:131) - [java] at org.junit.jupiter.engine.extension.TimeoutExtension.intercept(TimeoutExtension.java:156) - [java] at org.junit.jupiter.engine.extension.TimeoutExtension.interceptTestableMethod(TimeoutExtension.java:147) - [java] at org.junit.jupiter.engine.extension.TimeoutExtension.interceptTestMethod(TimeoutExtension.java:86) - [java] at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker$ReflectiveInterceptorCall.lambda$ofVoidMethod$0(InterceptingExecutableInvoker.java:103) - [java] at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker.lambda$invoke$0(InterceptingExecutableInvoker.java:93) - [java] at org.junit.jupiter.engine.execution.InvocationInterceptorChain$InterceptedInvocation.proceed(InvocationInterceptorChain.java:106) - [java] at org.junit.jupiter.engine.execution.InvocationInterceptorChain.proceed(InvocationInterceptorChain.java:64) - [java] at org.junit.jupiter.engine.execution.InvocationInterceptorChain.chainAndInvoke(InvocationInterceptorChain.java:45) - [java] at org.junit.jupiter.engine.execution.InvocationInterceptorChain.invoke(InvocationInterceptorChain.java:37) - [java] at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker.invoke(InterceptingExecutableInvoker.java:92) - [java] at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker.invoke(InterceptingExecutableInvoker.java:86) - [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.lambda$invokeTestMethod$7(TestMethodTestDescriptor.java:218) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.invokeTestMethod(TestMethodTestDescriptor.java:214) - [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.execute(TestMethodTestDescriptor.java:139) - [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.execute(TestMethodTestDescriptor.java:69) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$6(NodeTestTask.java:151) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:141) - [java] at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:137) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$9(NodeTestTask.java:139) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) - [java] at java.base/java.util.ArrayList.forEach(ArrayList.java:1596) - [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$6(NodeTestTask.java:155) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:141) - [java] at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:137) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$9(NodeTestTask.java:139) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) - [java] at java.base/java.util.ArrayList.forEach(ArrayList.java:1596) - [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$6(NodeTestTask.java:155) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:141) - [java] at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:137) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$9(NodeTestTask.java:139) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) - [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.submit(SameThreadHierarchicalTestExecutorService.java:35) - [java] at org.junit.platform.engine.support.hierarchical.HierarchicalTestExecutor.execute(HierarchicalTestExecutor.java:57) - [java] at org.junit.platform.engine.support.hierarchical.HierarchicalTestEngine.execute(HierarchicalTestEngine.java:54) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:198) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:169) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:93) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.lambda$execute$0(EngineExecutionOrchestrator.java:58) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.withInterceptedStreams(EngineExecutionOrchestrator.java:141) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:57) - [java] at org.junit.platform.launcher.core.DefaultLauncher.execute(DefaultLauncher.java:103) - [java] at org.junit.platform.launcher.core.DefaultLauncher.execute(DefaultLauncher.java:85) - [java] at org.junit.platform.launcher.core.DelegatingLauncher.execute(DelegatingLauncher.java:47) - [java] at org.junit.platform.launcher.core.SessionPerRequestLauncher.execute(SessionPerRequestLauncher.java:63) - [java] at org.junit.platform.console.tasks.ConsoleTestExecutor.executeTests(ConsoleTestExecutor.java:102) - [java] at org.junit.platform.console.tasks.ConsoleTestExecutor.lambda$execute$1(ConsoleTestExecutor.java:71) - [java] at org.junit.platform.console.tasks.CustomContextClassLoaderExecutor.invoke(CustomContextClassLoaderExecutor.java:35) - [java] at org.junit.platform.console.tasks.ConsoleTestExecutor.execute(ConsoleTestExecutor.java:71) - [java] at org.junit.platform.console.options.ExecuteTestsCommand.execute(ExecuteTestsCommand.java:61) - [java] at org.junit.platform.console.options.ExecuteTestsCommand.execute(ExecuteTestsCommand.java:27) - [java] at org.junit.platform.console.options.BaseCommand.call(BaseCommand.java:74) - [java] at org.junit.platform.console.shadow.picocli.CommandLine.executeUserObject(CommandLine.java:1953) - [java] at org.junit.platform.console.shadow.picocli.CommandLine.access$1300(CommandLine.java:145) [java] [java] t0 = null (0.0) [java] t1 = 10 (0.0) @@ -4010,41 +4081,6 @@ [java] [java] t0 = 0 (0.0) [java] t1 = 10 (10.0) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.handle(CommandLine.java:2352) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.handle(CommandLine.java:2314) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.execute(CommandLine.java:2316) - [java] at org.junit.platform.console.shadow.picocli.CommandLine.execute(CommandLine.java:2078) - [java] at org.junit.platform.console.options.MainCommand.runCommand(MainCommand.java:137) - [java] at org.junit.platform.console.options.MainCommand.runCommand(MainCommand.java:129) - [java] at org.junit.platform.console.options.MainCommand.runCommand(MainCommand.java:93) - [java] at org.junit.platform.console.options.MainCommand.call(MainCommand.java:77) - [java] at org.junit.platform.console.shadow.picocli.CommandLine.executeUserObject(CommandLine.java:1953) - [java] at org.junit.platform.console.shadow.picocli.CommandLine.access$1300(CommandLine.java:145) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.handle(CommandLine.java:2352) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.handle(CommandLine.java:2314) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.execute(CommandLine.java:2316) - [java] at org.junit.platform.console.shadow.picocli.CommandLine.execute(CommandLine.java:2078) - [java] at org.junit.platform.console.options.MainCommand.runCommand(MainCommand.java:137) - [java] at org.junit.platform.console.options.MainCommand.run(MainCommand.java:125) - [java] at org.junit.platform.console.options.CommandFacade.run(CommandFacade.java:36) - [java] at org.junit.platform.console.ConsoleLauncher.run(ConsoleLauncher.java:57) - [java] at org.junit.platform.console.ConsoleLauncher.run(ConsoleLauncher.java:42) - [java] at org.junit.platform.console.ConsoleLauncher.main(ConsoleLauncher.java:35) - [java] initAndValidate() failed! constantSiteWeights should be of the same dimension as the datatype (3!=4) - [java] [11233, 1, 1, 1, 1, 3, 1, 1, 1, 1, 4, 1, 1, 1, 1, 5] - [java] [11233, 1, 1, 1, 1, 3, 1, 1, 3, 4] - [java] <0> <1> <2> <3> removed 6 sites - [java] [11232, 1, 1, 1, 1, 2, 1, 1, 3, 4] - [java] t0=0 - [java] t1=10 - [java] t1=10 - [java] WARNING: no trait specified for t0: Assumed to be 10.0 - [java] t0=0 - [java] t1=10 [java] Distribution lower = 0, upper = 6 windowSize = 1 Average deviation: 2957 [java] Distribution lower = 0, upper = 6 windowSize = 2 Average deviation: 2179 [java] Distribution lower = 0, upper = 6 windowSize = 3 Average deviation: 3318 @@ -4083,14 +4119,14 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 20.277 seconds + [java] Total calculation time: 7.411 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 0.9998844142873523 variance: 0.9962228119352534 ESS: 194315.96975231904 [java] ------------------------------------------------- [java] - [java] trace log written to /tmp/bactrian.log [java] End likelihood: -0.9585015029579629 + [java] trace log written to /tmp/bactrian.log [java] =============================================================================== [java] Citations for this model: [java] @@ -4115,14 +4151,30 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 9.83 seconds + [java] Total calculation time: 3.741 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 1.0017946084516174 variance: 1.7216547315129034 ESS: 25717.88066360503 [java] ------------------------------------------------- [java] - [java] trace log written to /tmp/bactrian.log [java] End likelihood: -0.8084620917497215 + [java] trace log written to /tmp/bactrian.log + [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. + [java] Expected: [0.05870763770495499, 0.4129812075958677, 0.06575499966675094, 0.46255615503242636] + [java] Calculat: [0.058707637705059205, 0.41298120759660106, 0.06575499966686761, 0.46255615503324765, 0.05870763770505924, 0.4129812075966013, 0.06575499966686764, 0.4625561550332479, 0.05870763770505928, 0.41298120759660156, 0.0657549996668677, 0.4625561550332482, 0.05870763770505928, 0.41298120759660156, 0.0657549996668677, 0.4625561550332482] + [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. + [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. + [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. + [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. + [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. + [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. + [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. + [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. + [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. + [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. + [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. + [java] Expected: [0.1584087537031632, 0.01389998976971136, 0.7609221549346824, 0.06676910159244315] + [java] Calculat: [0.15840875370312343, 0.013899989769708488, 0.7609221549344917, 0.06676910159242638, 0.1584087537031232, 0.013899989769708469, 0.7609221549344906, 0.0667691015924263, 0.15840875370312313, 0.01389998976970846, 0.7609221549344901, 0.06676910159242626, 0.15840875370312307, 0.013899989769708455, 0.7609221549344899, 0.06676910159242623] [java] Starting frequencies: [0.25, 0.25, 0.25, 0.25] [java] Starting frequencies: [0.25, 0.25, 0.25, 0.25] [java] Starting frequencies: [0.25, 0.25, 0.25, 0.25] @@ -4133,14 +4185,6 @@ [java] Starting frequencies: [0.25, 0.25, 0.25, 0.25] [java] Starting frequencies: [0.25, 0.25, 0.25, 0.25] [java] Starting frequencies: [0.25, 0.25, 0.25, 0.25] - [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. - [java] Expected: [0.05870763770495499, 0.4129812075958677, 0.06575499966675094, 0.46255615503242636] - [java] Calculat: [0.058707637705059205, 0.41298120759660106, 0.06575499966686761, 0.46255615503324765, 0.05870763770505924, 0.4129812075966013, 0.06575499966686764, 0.4625561550332479, 0.05870763770505928, 0.41298120759660156, 0.0657549996668677, 0.4625561550332482, 0.05870763770505928, 0.41298120759660156, 0.0657549996668677, 0.4625561550332482] - [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. - [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. - [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. - [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. - [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. [java] Starting frequencies: [0.25, 0.25, 0.25, 0.25] [java] Starting frequencies: [0.25, 0.25, 0.25, 0.25] [java] Starting frequencies: [0.25, 0.25, 0.25, 0.25] @@ -4153,14 +4197,6 @@ [java] Starting frequencies: [0.25, 0.25, 0.25, 0.25] [java] Starting frequencies: [0.25, 0.25, 0.25, 0.25] [java] Starting frequencies: [0.25, 0.25, 0.25, 0.25] - [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. - [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. - [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. - [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. - [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. - [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. - [java] Expected: [0.1584087537031632, 0.01389998976971136, 0.7609221549346824, 0.06676910159244315] - [java] Calculat: [0.15840875370312343, 0.013899989769708488, 0.7609221549344917, 0.06676910159242638, 0.1584087537031232, 0.013899989769708469, 0.7609221549344906, 0.0667691015924263, 0.15840875370312313, 0.01389998976970846, 0.7609221549344901, 0.06676910159242626, 0.15840875370312307, 0.013899989769708455, 0.7609221549344899, 0.06676910159242623] [java] =============================================================================== [java] Citations for this model: [java] @@ -4187,14 +4223,14 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 48.013 seconds + [java] Total calculation time: 14.707 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 0.999687438963848 variance: 1.6815511765072393 ESS: 106131.3927120149 [java] ------------------------------------------------- [java] - [java] trace log written to /tmp/bactrian.log [java] End likelihood: -0.20113760213898557 + [java] trace log written to /tmp/bactrian.log [java] Starting frequencies: [0.074, 0.025, 0.054, 0.054, 0.047, 0.074, 0.026, 0.068, 0.058, 0.099, 0.025, 0.045, 0.039, 0.034, 0.052, 0.057, 0.051, 0.073, 0.013, 0.032] [java] Struthio_camelus: 85 20 [java] Rhea_americana: 85 20 @@ -4206,6 +4242,10 @@ [java] [java] TreeLikelihood(null) uses BeerLikelihoodCore [java] Alignment(null): [taxa, patterns, sites] = [3, 32, 85] + [java] WARNING: found multiple entries for a site that occurs multiple times and is ascertained for. This may indicate some sites should be removed. Regardless, these sites will be ignored in the likelihood calculation. + [java] WARNING: found multiple entries for a site that occurs multiple times and is ascertained for. This may indicate some sites should be removed. Regardless, these sites will be ignored in the likelihood calculation. + [java] WARNING: found multiple entries for a site that occurs multiple times and is ascertained for. This may indicate some sites should be removed. Regardless, these sites will be ignored in the likelihood calculation. + [java] WARNING: found multiple entries for a site that occurs multiple times and is ascertained for. This may indicate some sites should be removed. Regardless, these sites will be ignored in the likelihood calculation. [java] human: 772 4 [java] chimp: 772 4 [java] bonobo: 772 4 @@ -4220,10 +4260,6 @@ [java] Starting frequencies: [0.25, 0.25, 0.25, 0.25] [java] TreeLikelihood(null) uses BeerLikelihoodCore4 [java] Alignment(null): [taxa, patterns, sites] = [6, 69, 145] - [java] WARNING: found multiple entries for a site that occurs multiple times and is ascertained for. This may indicate some sites should be removed. Regardless, these sites will be ignored in the likelihood calculation. - [java] WARNING: found multiple entries for a site that occurs multiple times and is ascertained for. This may indicate some sites should be removed. Regardless, these sites will be ignored in the likelihood calculation. - [java] WARNING: found multiple entries for a site that occurs multiple times and is ascertained for. This may indicate some sites should be removed. Regardless, these sites will be ignored in the likelihood calculation. - [java] WARNING: found multiple entries for a site that occurs multiple times and is ascertained for. This may indicate some sites should be removed. Regardless, these sites will be ignored in the likelihood calculation. [java] human: 768 4 [java] chimp: 768 4 [java] bonobo: 768 4 @@ -4262,6 +4298,7 @@ [java] [java] TreeLikelihood(null) uses BeerLikelihoodCore [java] Alignment(null): [taxa, patterns, sites] = [3, 32, 85] + [java] 9.094947017729282E-13 [java] human: 768 4 [java] chimp: 768 4 [java] bonobo: 768 4 @@ -4278,7 +4315,6 @@ [java] Alignment(null): [taxa, patterns, sites] = [6, 69, 768] [java] TreeLikelihood(null) uses BeerLikelihoodCore4 [java] Alignment(null): [taxa, patterns, sites] = [6, 69, 768] - [java] 9.094947017729282E-13 [java] German_ST: 5051 2 [java] Dutch_List: 5051 2 [java] English_ST: 5051 2 @@ -4686,6 +4722,16 @@ [java] [java] TreeLikelihood(null) uses BeerLikelihoodCore [java] Alignment(null): [taxa, patterns, sites] = [3, 32, 85] + [java] t 0=0 + [java] t 1=1 + [java] t 2=2 + [java] t 3=3 + [java] t 4=4 + [java] t 5=5 + [java] t 6=6 + [java] t 7=7 + [java] t 8=8 + [java] t 9=9 [java] Starting frequencies: [0.074, 0.025, 0.054, 0.054, 0.047, 0.074, 0.026, 0.068, 0.058, 0.099, 0.025, 0.045, 0.039, 0.034, 0.052, 0.057, 0.051, 0.073, 0.013, 0.032] [java] Struthio_camelus: 85 20 [java] Rhea_americana: 85 20 @@ -4722,18 +4768,8 @@ [java] t 5: 1 4 [java] t 6: 1 4 [java] t 7: 1 4 - [java] t 8: 1 4t 0=0 + [java] t 8: 1 4 [java] t 9: 1 4 - [java] - [java] t 1=1 - [java] t 2=2 - [java] t 3=3 - [java] t 4=4 - [java] t 5=5 - [java] t 6=6 - [java] t 7=7 - [java] t 8=8 - [java] t 9=9 [java] Alignment(null) [java] 10 taxa [java] 1 site @@ -15392,13 +15428,13 @@ [java] │ │ ├─ testJSON() ✔ [java] │ │ ├─ testInnerClass() ✔ [java] │ │ └─ testPrimitiveInput() ✔ + [java] │ ├─ BEASTInterfaceTest ✔ + [java] │ │ ├─ testInputType() ✔ + [java] │ │ └─ testBEASTi() ✔ [java] │ ├─ LoggerTest ✔ [java] │ │ ├─ testFileLog() ✔ [java] │ │ ├─ testScreenLog() ✔ [java] │ │ └─ isLoggingToStdout() ✔ - [java] │ ├─ BEASTInterfaceTest ✔ - [java] │ │ ├─ testInputType() ✔ - [java] │ │ └─ testBEASTi() ✔ [java] │ ├─ BooleanParameterListTest ✔ [java] │ │ └─ test1() ✔ [java] │ ├─ InputTest ✔ @@ -15408,6 +15444,8 @@ [java] │ │ └─ testScientificNotationIntTooLarge() ✔ [java] │ ├─ IntegerParameterListTest ✔ [java] │ │ └─ test1() ✔ + [java] │ ├─ SumTest ✔ + [java] │ │ └─ testSum() ✔ [java] │ ├─ OperatorScheduleTest ✔ [java] │ │ ├─ testOperatorScheduleMultiNestedByPercentageAndRelativeWeight() ✔ [java] │ │ ├─ testOperatorScheduleNestedByPercentage() ✔ @@ -15417,18 +15455,16 @@ [java] │ │ ├─ testOperatorScheduleNestedByRelativeWeight() ✔ [java] │ │ ├─ testOperatorSchedulePlain() ✔ [java] │ │ └─ testOperatorScheduleNestedByRelativeWeight2() ✔ - [java] │ ├─ SumTest ✔ - [java] │ │ └─ testSum() ✔ [java] │ ├─ BactrianIntervalOperatorTest ✔ - [java] │ │ ├─ testLogNormalDistribution() 96591 ms ✔ - [java] │ │ ├─ testNormalDistribution() 91948 ms ✔ - [java] │ │ ├─ testUniformDistributionZeroUpperBound() 111864 ms ✔ - [java] │ │ ├─ testUniformDistribution() 92113 ms ✔ - [java] │ │ └─ testUniformDistributionZeroLowerBound() 86602 ms ✔ - [java] │ ├─ UncertainAlignmentTest ✔ - [java] │ │ └─ testUncertainAlignment() ✔ + [java] │ │ ├─ testLogNormalDistribution() 29462 ms ✔ + [java] │ │ ├─ testNormalDistribution() 33577 ms ✔ + [java] │ │ ├─ testUniformDistributionZeroUpperBound() 29294 ms ✔ + [java] │ │ ├─ testUniformDistribution() 26011 ms ✔ + [java] │ │ └─ testUniformDistributionZeroLowerBound() 27339 ms ✔ [java] │ ├─ DataTypeDeEncodeTest ✔ [java] │ │ └─ testDataTypeDeEncode() ✔ + [java] │ ├─ UncertainAlignmentTest ✔ + [java] │ │ └─ testUncertainAlignment() ✔ [java] │ ├─ GeneralSubstitutionModelTest ✔ [java] │ │ └─ getTransitionProbabilities() ✔ [java] │ ├─ DeltaExchangeOperatorTest ✔ @@ -15473,15 +15509,15 @@ [java] │ │ └─ testAminoAcidLikelihoodGIDayhoff() ✔ [java] │ ├─ BactrianScaleOperatorTest ✔ [java] │ │ ├─ testNormalDistribution() ✔ - [java] │ │ ├─ testTwoDimensionalDistribution() 23775 ms ✔ - [java] │ │ ├─ testLogNormalDistribution() 14020 ms ✔ - [java] │ │ ├─ testScaleAllDistribution() 23184 ms ✔ - [java] │ │ ├─ testScaleAllIndependentlylDistribution() 23132 ms ✔ + [java] │ │ ├─ testTwoDimensionalDistribution() ✔ + [java] │ │ ├─ testLogNormalDistribution() ✔ + [java] │ │ ├─ testScaleAllDistribution() ✔ + [java] │ │ ├─ testScaleAllIndependentlylDistribution() 10763 ms ✔ [java] │ │ └─ testTreeScaling() ✔ [java] │ ├─ ExchangeOperatorTest ✔ - [java] │ │ ├─ testNarrowExchange4Taxa() 115571 ms ✔ - [java] │ │ ├─ testNarrowExchange5Taxa() 84016 ms ✔ - [java] │ │ └─ testNarrowExchange6Taxa() 56037 ms ✔ + [java] │ │ ├─ testNarrowExchange4Taxa() 33002 ms ✔ + [java] │ │ ├─ testNarrowExchange5Taxa() 24457 ms ✔ + [java] │ │ └─ testNarrowExchange6Taxa() 30276 ms ✔ [java] │ ├─ BactrianDeltaExchangeOperatorTest ✔ [java] │ │ ├─ testNormalDistribution() ✔ [java] │ │ ├─ testLogNormalDistribution() ✔ @@ -15501,7 +15537,7 @@ [java] │ │ ├─ testMultiDimensionalMirrorfKernelDistribution() ✔ [java] │ │ ├─ testMultiDimensionalMirrorfKernelDistributionScaler() ✔ [java] │ │ ├─ testMirrorfKernelDistribution() ✔ - [java] │ │ └─ testBactrianKernelDistribution() 19173 ms ✔ + [java] │ │ └─ testBactrianKernelDistribution() ✔ [java] │ ├─ FilteredAlignmentTest ✔ [java] │ │ ├─ testWeightedSites() ✔ [java] │ │ ├─ testFilteredFileredAlignment() ✔ @@ -15517,17 +15553,17 @@ [java] │ ├─ TreeTest ✔ [java] │ │ └─ testTreeScaling() ✔ [java] │ ├─ IntRandomWalkOperatorTest ✔ - [java] │ │ ├─ testIntRandomWalkDistribution3x6() 30534 ms ✔ - [java] │ │ ├─ testIntRandomWalkDistribution3x10() 83109 ms ✔ - [java] │ │ └─ testIntRandomWalkDistribution6x10() 156955 ms ✔ + [java] │ │ ├─ testIntRandomWalkDistribution3x6() 15270 ms ✔ + [java] │ │ ├─ testIntRandomWalkDistribution3x10() 41476 ms ✔ + [java] │ │ └─ testIntRandomWalkDistribution6x10() 59193 ms ✔ [java] │ ├─ BactrianRandomWalkOperatorTest ✔ - [java] │ │ ├─ testNormalDistribution() 69528 ms ✔ - [java] │ │ └─ testLogNormalDistribution() 57228 ms ✔ + [java] │ │ ├─ testNormalDistribution() 22977 ms ✔ + [java] │ │ └─ testLogNormalDistribution() 19702 ms ✔ [java] │ ├─ BinaryCovarionModelTest ✔ [java] │ │ └─ testEquilibriumFrequencies() ✔ [java] │ ├─ BactrianUpDownOperatorTest ✔ [java] │ │ ├─ testNormalDistribution() ✔ - [java] │ │ └─ testLogNormalDistribution() 187801 ms ✔ + [java] │ │ └─ testLogNormalDistribution() 53573 ms ✔ [java] │ ├─ TreeLikelihoodTest ✔ [java] │ │ ├─ testAminoAcidLikelihoodGIBlosum62() ✔ [java] │ │ ├─ testAscertainedJC69Likelihood() ✔ @@ -15573,15 +15609,15 @@ [java] │ ├─ TreeUtilsTest ✔ [java] │ │ └─ testSortTreeAlphabetically() ✔ [java] │ ├─ RandomTreeTest ✔ - [java] │ │ └─ testCoalescentTimes() 170194 ms ✔ + [java] │ │ └─ testCoalescentTimes() 58278 ms ✔ [java] │ ├─ BirthDeathGernhard08ModelTest ✔ [java] │ │ └─ testJC69Likelihood() ✔ [java] │ ├─ LaplaceDistributionTest ✔ - [java] │ │ ├─ testPdf() 29746 ms ✔ + [java] │ │ ├─ testPdf() ✔ [java] │ │ ├─ testMean() ✔ - [java] │ │ ├─ testCDFAndQuantile() 15819 ms ✔ + [java] │ │ ├─ testCDFAndQuantile() ✔ [java] │ │ ├─ testLogPdf() ✔ - [java] │ │ └─ testMedian() 16271 ms ✔ + [java] │ │ └─ testMedian() ✔ [java] │ ├─ MRCAPriorTest ✔ [java] │ │ ├─ testMRCATimePrior() ✔ [java] │ │ └─ testSingleMonophyleticConstraint() ✔ @@ -15594,7 +15630,7 @@ [java] │ │ ├─ testMeanOfNormal() ✔ [java] │ │ └─ testMeanOfGamma() ✔ [java] │ ├─ LogNormalDistributionModelTest ✔ - [java] │ │ ├─ testPDF() 17851 ms ✔ + [java] │ │ ├─ testPDF() ✔ [java] │ │ ├─ testCalcLogP2() ✔ [java] │ │ ├─ testCalcLogP3() ✔ [java] │ │ └─ testCalcLogP() ✔ @@ -15627,10 +15663,10 @@ [java] │ │ ├─ testTranslateBlock2() ✔ [java] │ │ └─ testTranslateBlock() ✔ [java] │ └─ RandomizerTest ✔ - [java] │ └─ logNormalTest() 15161 ms ✔ + [java] │ └─ logNormalTest() ✔ [java] └─ JUnit Vintage ✔ [java] - [java] Test run finished after 1730890 ms + [java] Test run finished after 578978 ms [java] [ 51 containers found ] [java] [ 0 containers skipped ] [java] [ 51 containers started ] @@ -15648,10 +15684,10 @@ [java] WARNING: Delegated to the 'execute' command. [java] This behaviour has been deprecated and will be removed in a future release. [java] Please use the 'execute' command directly. -[junitreport] Processing /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/build/junitreport/TESTS-TestSuites.xml to /tmp/null966580067 +[junitreport] Processing /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/build/junitreport/TESTS-TestSuites.xml to /tmp/null1210722496 [junitreport] Loading stylesheet ile:/usr/share/ant/lib/ant-junit.jar!/org/apache/tools/ant/taskdefs/optional/junit/xsl/junit-frames.xsl -[junitreport] Transform time: 6697ms -[junitreport] Deleting: /tmp/null966580067 +[junitreport] Transform time: 2209ms +[junitreport] Deleting: /tmp/null1210722496 junit-integration: [java] @@ -15695,7 +15731,7 @@ [java] │ └─ testMutualDependencyOfPackageDependencies() ↷ Needs the user dir, which is intentionally void on Debian buildds [java] └─ JUnit Vintage ✔ [java] - [java] Test run finished after 11625 ms + [java] Test run finished after 3122 ms [java] [ 8 containers found ] [java] [ 0 containers skipped ] [java] [ 8 containers started ] @@ -15709,10 +15745,10 @@ [java] [ 9 tests successful ] [java] [ 0 tests failed ] [java] -[junitreport] Processing /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/build/integrationreport/TESTS-TestSuites.xml to /tmp/null1141583014 +[junitreport] Processing /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/build/integrationreport/TESTS-TestSuites.xml to /tmp/null831805955 [junitreport] Loading stylesheet ile:/usr/share/ant/lib/ant-junit.jar!/org/apache/tools/ant/taskdefs/optional/junit/xsl/junit-frames.xsl -[junitreport] Transform time: 4284ms -[junitreport] Deleting: /tmp/null1141583014 +[junitreport] Transform time: 834ms +[junitreport] Deleting: /tmp/null831805955 junit-xmlparsertest: [java] @@ -15725,33 +15761,33 @@ [java] │ └─ testClassMap() ✔ [java] └─ JUnit Vintage ✔ [java] - [java] Test run finished after 3664 ms + [java] Test run finished after 1139 ms [java] [ 4 containers found ] [java] [ 0 containers skipped ] [java] [ 4 containers started ] [java] [ 0 containers aborted ] [java] [ 4 containers successful ] - [java] - [java] WARNING: Delegated to the 'execute' command. [java] [ 0 containers failed ] [java] [ 1 tests found ] [java] [ 0 tests skipped ] - [java] [ 1 tests started ] This behaviour has been deprecated and will be removed in a future release. + [java] [ 1 tests started ] [java] [ 0 tests aborted ] [java] [ 1 tests successful ] [java] [ 0 tests failed ] [java] [java] + [java] WARNING: Delegated to the 'execute' command. + [java] This behaviour has been deprecated and will be removed in a future release. [java] Please use the 'execute' command directly. -[junitreport] Processing /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/build/xmlparserreport/TESTS-TestSuites.xml to /tmp/null237393130 +[junitreport] Processing /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/build/xmlparserreport/TESTS-TestSuites.xml to /tmp/null1674236176 [junitreport] Loading stylesheet ile:/usr/share/ant/lib/ant-junit.jar!/org/apache/tools/ant/taskdefs/optional/junit/xsl/junit-frames.xsl -[junitreport] Transform time: 1707ms -[junitreport] Deleting: /tmp/null237393130 +[junitreport] Transform time: 426ms +[junitreport] Deleting: /tmp/null1674236176 junit: BUILD SUCCESSFUL -Total time: 30 minutes 9 seconds +Total time: 10 minutes 3 seconds make[1]: Leaving directory '/build/reproducible-path/beast2-mcmc-2.7.6+dfsg' create-stamp debian/debhelper-build-stamp dh_prep @@ -15780,8 +15816,8 @@ dpkg-gencontrol: warning: Depends field of package beast2-mcmc-examples: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums dh_builddeb -dpkg-deb: building package 'beast2-mcmc-examples' in '../beast2-mcmc-examples_2.7.6+dfsg-1_all.deb'. dpkg-deb: building package 'beast2-mcmc' in '../beast2-mcmc_2.7.6+dfsg-1_all.deb'. +dpkg-deb: building package 'beast2-mcmc-examples' in '../beast2-mcmc-examples_2.7.6+dfsg-1_all.deb'. dpkg-genbuildinfo --build=binary -O../beast2-mcmc_2.7.6+dfsg-1_armhf.buildinfo dpkg-genchanges --build=binary -O../beast2-mcmc_2.7.6+dfsg-1_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -15789,12 +15825,14 @@ 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/30433/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/30433/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/6489 and its subdirectories -I: Current time: Tue Dec 10 20:11:59 -12 2024 -I: pbuilder-time-stamp: 1733904719 +I: removing directory /srv/workspace/pbuilder/30433 and its subdirectories +I: Current time: Wed Dec 11 22:28:10 +14 2024 +I: pbuilder-time-stamp: 1733905690