Diff of the two buildlogs: -- --- b1/build.log 2025-03-08 07:59:19.117070147 +0000 +++ b2/build.log 2025-03-08 08:02:25.380654232 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Apr 10 02:19:24 -12 2026 -I: pbuilder-time-stamp: 1775830764 +I: Current time: Sat Mar 8 21:59:22 +14 2025 +I: pbuilder-time-stamp: 1741420762 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -35,52 +35,84 @@ 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/3303201/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3810798/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Mar 8 07:59 /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/3810798/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3810798/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='a4f3b63a72ed4314bd45ce7db181206b' - 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='3303201' - PS1='# ' - PS2='> ' + INVOCATION_ID=e431dc265dd04eefbc51c9586fb3ed81 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3810798 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.9lWLgjM2/pbuilderrc_KYWt --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.9lWLgjM2/b1 --logfile b1/build.log beast2-mcmc_2.7.6+dfsg-1.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.9lWLgjM2/pbuilderrc_kg5b --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.9lWLgjM2/b2 --logfile b2/build.log beast2-mcmc_2.7.6+dfsg-1.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink03-arm64 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3303201/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3810798/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -462,7 +494,7 @@ Get: 316 http://deb.debian.org/debian trixie/main arm64 libjam-java all 0.1.git20240425.aec45be+dfsg-1 [168 kB] Get: 317 http://deb.debian.org/debian trixie/main arm64 libopenjfx-jni arm64 11.0.11+1-6 [19.7 MB] Get: 318 http://deb.debian.org/debian trixie/main arm64 libopenjfx-java all 11.0.11+1-6 [8941 kB] -Fetched 354 MB in 2s (161 MB/s) +Fetched 354 MB in 1s (290 MB/s) Preconfiguring packages ... Selecting previously unselected package libsystemd-shared:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19914 files and directories currently installed.) @@ -1520,8 +1552,8 @@ Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' -Local time is now: Fri Apr 10 14:20:10 UTC 2026. -Universal Time is now: Fri Apr 10 14:20:10 UTC 2026. +Local time is now: Sat Mar 8 08:00:07 UTC 2025. +Universal Time is now: Sat Mar 8 08:00:07 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:arm64 (1.17.0-2+b1) ... @@ -1985,7 +2017,11 @@ 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/3810798/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/3810798/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 @@ -2155,12 +2191,6 @@ [java] Writing file beast.log [java] Sample null.1 null.2 [java] 1 0.3 0.7 -- - [java] {spec: "test.beast.core.PrimitiveBeastObject", e: "none", i: "0", - [java] p: [ - [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] OK [java] test getCitation [java] test initByName @@ -2171,6 +2201,12 @@ [java] Validation error when initializing object test.beast.core.BEASTInterfaceTest$BEASTi (id null): [java] Failed to set the string value to '1e-1' for beastobject id=null [java] Failed to set the string value to '21474836470' for beastobject id=null + [java] {spec: "test.beast.core.PrimitiveBeastObject", e: "none", i: "0", + [java] p: [ + [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] WARNING: Operator scaleOperator.Species is contained in multiple operator schedules. [java] Operator weighting may not work as expected. [java] =============================================================================== @@ -2197,14 +2233,14 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 0.996 seconds + [java] Total calculation time: 0.938 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] =============================================================================== [java] Citations for this model: [java] @@ -2229,7 +2265,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 1.096 seconds + [java] Total calculation time: 1.094 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 1.4999085326599657 variance: 0.009984682019634223 ESS: 199303.5697419057 @@ -2261,7 +2297,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 0.978 seconds + [java] Total calculation time: 0.969 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: -0.9999141170712793 variance: 0.33333524355317856 ESS: 198672.26933150293 @@ -2293,7 +2329,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 0.945 seconds + [java] Total calculation time: 0.948 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 2.000085882932697 variance: 0.3333352435532261 ESS: 198672.26933142878 @@ -2325,69 +2361,14 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 0.944 seconds + [java] Total calculation time: 0.949 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 1.0000858834576856 variance: 0.3333352435537048 ESS: 198672.26933242727 [java] ------------------------------------------------- [java] - [java] End likelihood: -0.6931471805599453 [java] trace log written to /tmp/bactrian.log - [java] seq1: 3 4 - [java] seq2: 3 4 - [java] seq3: 3 4 - [java] Alignment(null) - [java] 3 taxa - [java] 3 sites - [java] 3 patterns - [java] - [java] Most probable sequences: - [java] ATT - [java] ATC - [java] GCC - [java] Tip likelihoods: - [java] 0.7 0.0 0.3 0.0 ; 0.0 0.3 0.0 0.7 ; 0.0 0.0 0.0 1.0 ; - [java] 0.7 0.0 0.3 0.0 ; 0.0 0.3 0.0 0.7 ; 0.0 1.0 0.0 0.0 ; - [java] 0.4 0.0 0.6 0.0 ; 0.0 0.6 0.0 0.4 ; 0.0 1.0 0.0 0.0 ; - [java] Most likely sequences: - [java] ATT - [java] ATC - [java] GCC - [java] seq1: 3 4 - [java] seq2: 3 4 - [java] seq3: 3 4 - [java] Alignment(null) - [java] 3 taxa - [java] 3 sites - [java] 3 patterns - [java] - [java] Starting frequencies: [0.3333333, 0.3333333, 0.3333333] - [java] freqs = - [java] [0.3333333, 0.3333333, 0.3333333] - [java] - [java] relative rates : - [java] [0.1, 0.0, 0.1, 0.2, 0.0, 0.2] - [java] - [java] - [java] renormalised rate matrix : - [java] [1.0, -2.4928748491937626E-16, -3.386149245429483E-17] - [java] [2.69374457498681E-22, 1.0, -1.9925481744283377E-16] - [java] [3.749348770303284E-12, 6.1384477687519146E-18, 1.0] - [java] - [java] transition prob : - [java] [0.6674871505723157, 0.22927797953210746, 0.10323486989557647, 0.2292779795321076, 0.415400931299253, 0.35532108916863914, 0.10323486989557647, 0.3553210891686388, 0.5414440409357847] - [java] row 0 prob sum = 0.9999999999999996 - [java] row 1 prob sum = 0.9999999999999998 - [java] row 2 prob sum = 0.9999999999999999 - [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 - [java] Pterocnemia_pennata: 85 20 - [java] Alignment(null) - [java] 3 taxa - [java] 85 sites - [java] 32 patterns - [java] + [java] End likelihood: -0.6931471805599453 [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) @@ -2533,42 +2514,61 @@ [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 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] 4.547473508864641E-13 - [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] seq1: 3 4 + [java] seq2: 3 4 + [java] seq3: 3 4 + [java] Alignment(null) + [java] 3 taxa + [java] 3 sites + [java] 3 patterns + [java] + [java] Most probable sequences: + [java] ATT + [java] ATC + [java] GCC + [java] Tip likelihoods: + [java] 0.7 0.0 0.3 0.0 ; 0.0 0.3 0.0 0.7 ; 0.0 0.0 0.0 1.0 ; + [java] 0.7 0.0 0.3 0.0 ; 0.0 0.3 0.0 0.7 ; 0.0 1.0 0.0 0.0 ; + [java] 0.4 0.0 0.6 0.0 ; 0.0 0.6 0.0 0.4 ; 0.0 1.0 0.0 0.0 ; + [java] Most likely sequences: + [java] ATT + [java] ATC + [java] GCC + [java] seq1: 3 4 + [java] seq2: 3 4 + [java] seq3: 3 4 + [java] Alignment(null) + [java] 3 taxa + [java] 3 sites + [java] 3 patterns + [java] + [java] Starting frequencies: [0.3333333, 0.3333333, 0.3333333] + [java] freqs = + [java] [0.3333333, 0.3333333, 0.3333333] + [java] + [java] relative rates : + [java] [0.1, 0.0, 0.1, 0.2, 0.0, 0.2] + [java] + [java] + [java] renormalised rate matrix : + [java] [1.0, -2.4928748491937626E-16, -3.386149245429483E-17] + [java] [2.69374457498681E-22, 1.0, -1.9925481744283377E-16] + [java] [3.749348770303284E-12, 6.1384477687519146E-18, 1.0] + [java] + [java] transition prob : + [java] [0.6674871505723157, 0.22927797953210746, 0.10323486989557647, 0.2292779795321076, 0.415400931299253, 0.35532108916863914, 0.10323486989557647, 0.3553210891686388, 0.5414440409357847] + [java] row 0 prob sum = 0.9999999999999996 + [java] row 1 prob sum = 0.9999999999999998 + [java] row 2 prob sum = 0.9999999999999999 + [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 + [java] Pterocnemia_pennata: 85 20 + [java] Alignment(null) + [java] 3 taxa + [java] 85 sites + [java] 32 patterns + [java] [java] Using BEAGLE version: 4.0.1 (PRE-RELEASE) resource 0: CPU (arm64) [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU [java] human: 772 4 @@ -2655,77 +2655,42 @@ [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_COMPLEX SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU [java] Using BEAGLE version: 4.0.1 (PRE-RELEASE) resource 0: CPU (arm64) [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_COMPLEX SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU - [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 - [java] Alignment(null) - [java] 3 taxa - [java] 85 sites - [java] 32 patterns - [java] - [java] Using BEAGLE version: 4.0.1 (PRE-RELEASE) resource 0: CPU (arm64) - [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU - [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: 4.0.1 (PRE-RELEASE) resource 0: CPU (arm64) - [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU - [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] Using BEAGLE version: 4.0.1 (PRE-RELEASE) resource 0: CPU (arm64) - [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU - [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 - [java] Alignment(null) - [java] 3 taxa - [java] 85 sites - [java] 32 patterns - [java] - [java] Using BEAGLE version: 4.0.1 (PRE-RELEASE) resource 0: CPU (arm64) - [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU - [java] human: 768 4 - [java] chimp: 768 4 - [java] bonobo: 768 4 - [java] gorilla: 768 4 - [java] orangutan: 768 4 - [java] siamang: 768 4 - [java] Alignment(null) - [java] 6 taxa - [java] 768 sites - [java] 69 patterns - [java] - [java] Using BEAGLE version: 4.0.1 (PRE-RELEASE) resource 0: CPU (arm64) - [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU - [java] Using BEAGLE version: 4.0.1 (PRE-RELEASE) resource 0: CPU (arm64) - [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU - [java] human: 768 4 - [java] chimp: 768 4 - [java] bonobo: 768 4 - [java] gorilla: 768 4 - [java] orangutan: 768 4 - [java] siamang: 768 4 - [java] Alignment(null) - [java] 6 taxa - [java] 768 sites - [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 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] 4.547473508864641E-13 + [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] ============================================================================================================== [java] ============================================================================================================== [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == @@ -2897,80 +2862,77 @@ [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 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] 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. == - [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] ============================================================================================================== - [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 8 unique site patterns. - [java] Using rescaling scheme : dynamic - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 8 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] 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 + [java] Alignment(null) + [java] 3 taxa + [java] 85 sites + [java] 32 patterns + [java] + [java] Using BEAGLE version: 4.0.1 (PRE-RELEASE) resource 0: CPU (arm64) + [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU + [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: 4.0.1 (PRE-RELEASE) resource 0: CPU (arm64) + [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU + [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] Using BEAGLE version: 4.0.1 (PRE-RELEASE) resource 0: CPU (arm64) + [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU + [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 + [java] Alignment(null) + [java] 3 taxa + [java] 85 sites + [java] 32 patterns + [java] + [java] Using BEAGLE version: 4.0.1 (PRE-RELEASE) resource 0: CPU (arm64) + [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU + [java] human: 768 4 + [java] chimp: 768 4 + [java] bonobo: 768 4 + [java] gorilla: 768 4 + [java] orangutan: 768 4 + [java] siamang: 768 4 + [java] Alignment(null) + [java] 6 taxa + [java] 768 sites + [java] 69 patterns + [java] + [java] Using BEAGLE version: 4.0.1 (PRE-RELEASE) resource 0: CPU (arm64) + [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU + [java] Using BEAGLE version: 4.0.1 (PRE-RELEASE) resource 0: CPU (arm64) + [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU + [java] human: 768 4 + [java] chimp: 768 4 + [java] bonobo: 768 4 + [java] gorilla: 768 4 + [java] orangutan: 768 4 + [java] siamang: 768 4 + [java] Alignment(null) + [java] 6 taxa + [java] 768 sites + [java] 69 patterns + [java] + [java] Starting frequencies: [0.3390942900867236, 0.24655436447178358, 0.1531393568179342, 0.26121198862355866] [java] Using BEAGLE version: 4.0.1 (PRE-RELEASE) resource 0: CPU (arm64) [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU [java] Using BEAGLE version: 4.0.1 (PRE-RELEASE) resource 0: CPU (arm64) @@ -3148,9 +3110,106 @@ [java] 69 patterns [java] [java] Starting frequencies: [0.3390942900867236, 0.24655436447178358, 0.1531393568179342, 0.26121198862355866] - [java] Using BEAGLE version: 4.0.1 (PRE-RELEASE) resource 0: CPU (arm64) + [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] ============================================================================================================== + [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. == + [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] ============================================================================================================== + [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 8 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 8 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 BEAGLE version: 4.0.1 (PRE-RELEASE) resource 0: CPU (arm64) 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] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU - [java] Using BEAGLE version: 4.0.1 (PRE-RELEASE) resource 0: CPU (arm64) + [java] ============================================================================================================== Using BEAGLE version: 4.0.1 (PRE-RELEASE) resource 0: CPU (arm64) + [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] ============================================================================================================== + [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] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU [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 @@ -3242,6 +3301,7 @@ [java] 768 sites [java] 69 patterns [java] + [java] [java] Starting frequencies: [0.3390942900867236, 0.24655436447178358, 0.1531393568179342, 0.26121198862355866] [java] Using BEAGLE version: 4.0.1 (PRE-RELEASE) resource 0: CPU (arm64) [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU @@ -3312,44 +3372,6 @@ [java] 32 patterns [java] [java] Using BEAGLE version: 4.0.1 (PRE-RELEASE) resource 0: CPU (arm64) - [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU - [java] =============================================================================== - [java] Citations for this model: - [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, - [java] Fábio K. Mendes, Nicola F. Müller, Huw A. Ogilvie, Louis du Plessis, Alex Popinga, Andrew Rambaut, - [java] David Rasmussen, Igor Siveroni, Marc A. Suchard, Chieh-Hsi Wu, Dong Xie, Chi Zhang, Tanja Stadler, - [java] Alexei J. Drummond - [java] BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. - [java] PLoS computational biology 15, no. 4 (2019): e1006650. - [java] - [java] =============================================================================== - [java] Start likelihood: -14.297530455869882 - [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] ============================================================================================================== - [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] ============================================================================================================== @@ -3424,6 +3446,20 @@ [java] Ignoring character uncertainty in tree likelihood. [java] With 32 unique site patterns. [java] Using rescaling scheme : dynamic + [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU + [java] =============================================================================== + [java] Citations for this model: + [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, + [java] Fábio K. Mendes, Nicola F. Müller, Huw A. Ogilvie, Louis du Plessis, Alex Popinga, Andrew Rambaut, + [java] David Rasmussen, Igor Siveroni, Marc A. Suchard, Chieh-Hsi Wu, Dong Xie, Chi Zhang, Tanja Stadler, + [java] Alexei J. Drummond + [java] BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. + [java] PLoS computational biology 15, no. 4 (2019): e1006650. + [java] + [java] =============================================================================== + [java] Start likelihood: -14.297530455869882 [java] End likelihood: -2.101581781210349 [java] [java] Operator Tuning #accept #reject Pr(m) Pr(acc|m) @@ -3436,7 +3472,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 0.633 seconds + [java] Total calculation time: 0.63 seconds [java] =============================================================================== [java] Citations for this model: [java] @@ -3450,6 +3486,7 @@ [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 @@ -3461,7 +3498,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 0.489 seconds + [java] Total calculation time: 0.487 seconds [java] =============================================================================== [java] Citations for this model: [java] @@ -3475,7 +3512,7 @@ [java] [java] =============================================================================== [java] Start likelihood: -21.446295683804824 - [java] End likelihood: 0.008929267909451477 + [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 @@ -3488,7 +3525,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 0.687 seconds + [java] Total calculation time: 0.686 seconds [java] =============================================================================== [java] Citations for this model: [java] @@ -3502,7 +3539,7 @@ [java] [java] =============================================================================== [java] Start likelihood: -21.446295683804824 - [java] End likelihood: -0.5552616722623194 + [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 @@ -3514,7 +3551,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 1.203 seconds + [java] Total calculation time: 0.989 seconds [java] A: 1 4 [java] B: 1 4 [java] C: 1 4 @@ -3523,7 +3560,6 @@ [java] 4 taxa [java] 1 site [java] - [java] End likelihood: -2.422052674651341 [java] Matches: 24.785% [java] Matches: 25.13% [java] A: 1 4 @@ -3562,6 +3598,13 @@ [java] [java] =============================================================================== [java] Start likelihood: 0.6286086594223761 + [java] End likelihood: 3.119201359019653 + [java] Testing mirror distribution + [java] Testing mirror distribution for scaling + [java] kick in + [java] kick in + [java] kick in + [java] Testing mirror distribution [java] [java] Operator Tuning #accept #reject Pr(m) Pr(acc|m) [java] beast.base.inference.operator.kernel.BactrianDeltaExchangeOperator(unknown) 0.46265 69697 930304 1.00000 0.06970 Try setting delta to about 0.231 @@ -3573,14 +3616,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 0.488 seconds - [java] End likelihood: 3.119201359019653 - [java] Testing mirror distribution - [java] Testing mirror distribution for scaling - [java] kick in - [java] kick in - [java] kick in - [java] Testing mirror distribution + [java] Total calculation time: 0.494 seconds [java] Testing t4 s= 1.0013578565664571 [java] Testing bactrian_t4 s= 1.0001051250800803 [java] Testing bactrian_strawhat s= 0.25462688741501555 @@ -3604,28 +3640,129 @@ [java] Testing bactrian_triangle s= 0.9998030418762279 [java] Testing bactrian_box s= 0.9993617332307378 [java] Testing bactrian_box s= 0.9993638943013682 - [java] 0human: 16 4 + [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] 0human: 16 4 at org.junit.platform.console.options.MainCommand.runCommand(MainCommand.java:93) + [java] at org.junit.platform.console.options.MainCommand.call(MainCommand.java:77) + [java] [java] 1chimp: 16 4 [java] Alignment(null) - [java] 2 taxa + [java] 2 taxa at org.junit.platform.console.shadow.picocli.CommandLine.executeUserObject(CommandLine.java:1953) [java] 16 sites [java] 16 patterns [java] [java] 0human: 16 4 [java] 1chimp: 16 4 [java] Alignment(null) + [java] at org.junit.platform.console.shadow.picocli.CommandLine.access$1300(CommandLine.java:145) [java] 2 taxa - [java] 16 sites + [java] + [java] 16 sites at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [java] 16 patterns [java] [java] 0human: 16 4 [java] 1chimp: 16 4 [java] Alignment(null) + [java] [java] 2 taxa [java] 16 sites with weight 12514 - [java] 16 patterns + [java] 16 patterns at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [java] - [java] 0human: 16 4 + [java] + [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.handle(CommandLine.java:2314) + [java] 0human: 16 4 at org.junit.platform.console.shadow.picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [java] 1chimp: 16 4 [java] Alignment(null) [java] 2 taxa @@ -3634,40 +3771,57 @@ [java] [java] 0human: 16 4 [java] 1chimp: 16 4 - [java] Alignment(null) + [java] + [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.execute(CommandLine.java:2316)Alignment(null) + [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] [java] 2 taxa - [java] 16 sites with weight 12514 + [java] at org.junit.platform.console.options.MainCommand.run(MainCommand.java:125) + [java] 16 sites with weight 12514 at org.junit.platform.console.options.CommandFacade.run(CommandFacade.java:36) [java] 16 patterns [java] [java] 0human: 6 4 [java] 1chimp: 6 4 [java] Alignment(null) + [java] at org.junit.platform.console.ConsoleLauncher.run(ConsoleLauncher.java:57) + [java] [java] 2 taxa [java] 6 sites [java] 4 patterns [java] [java] 0human: 6 4 - [java] 1chimp: 6 4 + [java] at org.junit.platform.console.ConsoleLauncher.run(ConsoleLauncher.java:42) + [java] at org.junit.platform.console.ConsoleLauncher.main(ConsoleLauncher.java:35) + [java] 1chimp: 6 4initAndValidate() failed! Cannot handle site weights in FilteredAlignment. Remove "weights" from data input. [java] Alignment(null) [java] 2 taxa [java] 6 sites with weight 111111 [java] 4 patterns [java] + [java] [java] 0human: 16 4 [java] 1chimp: 16 4 - [java] Alignment(null) + [java] Alignment(null)java.lang.IllegalArgumentException: constantSiteWeights should be of the same dimension as the datatype (3!=4) [java] 2 taxa - [java] 16 sites + [java] + [java] at beast.base.evolution.alignment.FilteredAlignment.initAndValidate(Unknown Source) 16 sites + [java] at beast.base.core.BEASTInterface.initByName(Unknown Source) + [java] [java] 16 patterns [java] [java] 0human: 16 4 - [java] 1chimp: 16 4 + [java] 1chimp: 16 4 at test.beast.evolution.alignment.FilteredAlignmentTest.testConstantSites(Unknown Source) [java] Alignment(null) + [java] at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) [java] 2 taxa [java] 16 sites with weight 12514 [java] 16 patterns [java] - [java] 0human: 16 4 + [java] at java.base/java.lang.reflect.Method.invoke(Method.java:580) + [java] + [java] at org.junit.platform.commons.util.ReflectionUtils.invokeMethod(ReflectionUtils.java:728) + [java] 0human: 16 4 at org.junit.jupiter.engine.execution.MethodInvocation.proceed(MethodInvocation.java:60) [java] 1chimp: 16 4 [java] Alignment(null) [java] 2 taxa @@ -3677,76 +3831,93 @@ [java] Filter 2:16:2 [java] 2 taxa [java] 8 sites + [java] at org.junit.jupiter.engine.execution.InvocationInterceptorChain$ValidatingInvocation.proceed(InvocationInterceptorChain.java:131) [java] 8 patterns [java] Filter - [java] 2 taxa + [java] + [java] at org.junit.jupiter.engine.extension.TimeoutExtension.intercept(TimeoutExtension.java:156) [java] 8 sites [java] 8 patterns [java] Filter - [java] 2 taxa [java] 8 sites - [java] 8 patterns + [java] 8 patterns at org.junit.jupiter.engine.extension.TimeoutExtension.interceptTestableMethod(TimeoutExtension.java:147) [java] 0human: 16 4 [java] 1chimp: 16 4 [java] Alignment(null) [java] 2 taxa + [java] at org.junit.jupiter.engine.extension.TimeoutExtension.interceptTestMethod(TimeoutExtension.java:86) [java] 16 sites [java] 16 patterns [java] - [java] Filter - + [java] + [java] Filter - at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker$ReflectiveInterceptorCall.lambda$ofVoidMethod$0(InterceptingExecutableInvoker.java:103) [java] 2 taxa [java] 16 sites + 11241 constant sites [java] 16 patterns [java] Filter -8 [java] 2 taxa + [java] at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker.lambda$invoke$0(InterceptingExecutableInvoker.java:93) [java] 8 sites + 11241 constant sites [java] 10 patterns - [java] Stripping invariant sitesFilter -8 + [java] + [java] Stripping invariant sitesFilter -8 at org.junit.jupiter.engine.execution.InvocationInterceptorChain$InterceptedInvocation.proceed(InvocationInterceptorChain.java:106) [java] 2 taxa [java] 8 sites + 11241 constant sites [java] 10 patterns [java] 0human: 16 4 [java] 1chimp: 16 4 [java] Alignment(null) + [java] at org.junit.jupiter.engine.execution.InvocationInterceptorChain.proceed(InvocationInterceptorChain.java:64) [java] 2 taxa - [java] 16 sites + [java] + [java] 16 sites at org.junit.jupiter.engine.execution.InvocationInterceptorChain.chainAndInvoke(InvocationInterceptorChain.java:45) [java] 12 patterns [java] [java] Filter 3:6:1 [java] 2 taxa [java] 4 sites + [java] [java] 4 patterns [java] human AACC - [java] 1chimp GTAC + [java] 1chimp GTAC at org.junit.jupiter.engine.execution.InvocationInterceptorChain.invoke(InvocationInterceptorChain.java:37) [java] Filter 11:14:1 [java] 2 taxa [java] 4 sites [java] 4 patterns - [java] human GGAA + [java] + [java] human GGAA at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker.invoke(InterceptingExecutableInvoker.java:92) [java] 1chimp GTAC [java] Filter 3:16:4 [java] 2 taxa [java] 4 sites + [java] [java] 3 patterns [java] human ACGA [java] 1chimp GGGG [java] Filter 4:14:3 [java] 2 taxa - [java] 4 sites + [java] 4 sites at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker.invoke(InterceptingExecutableInvoker.java:86) [java] 4 patterns - [java] human ACGA + [java] + [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.lambda$invokeTestMethod$7(TestMethodTestDescriptor.java:218)human ACGA + [java] [java] 1chimp TGCA [java] 0human: 16 4 [java] 1chimp: 16 4 - [java] Alignment(null) + [java] Alignment(null) at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) [java] 2 taxa [java] 16 sites [java] 16 patterns [java] [java] Filter 1 + [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.invokeTestMethod(TestMethodTestDescriptor.java:214) + [java] [java] 2 taxa [java] 1 sites - [java] 1 patterns + [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.execute(TestMethodTestDescriptor.java:139) + [java] 1 patterns at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.execute(TestMethodTestDescriptor.java:69) [java] Filter 2,5 [java] 2 taxa [java] 2 sites @@ -3757,26 +3928,33 @@ [java] 4 patterns [java] 0human: 16 4 [java] 1chimp: 16 4 + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$6(NodeTestTask.java:151) [java] Alignment(null) - [java] 2 taxa + [java] + [java] 2 taxa at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) [java] 16 sites [java] 16 patterns [java] [java] Filter 1-9 [java] 2 taxa + [java] [java] 9 sites [java] 9 patterns [java] Filter 2-9 - [java] 2 taxa + [java] 2 taxa at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:141) [java] 8 sites [java] 8 patterns [java] Filter 10- [java] 2 taxa - [java] 7 sites + [java] at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:137) + [java] + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$9(NodeTestTask.java:139) + [java] 7 sites at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) [java] 7 patterns [java] Filter -10 [java] 2 taxa [java] 10 sites + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) [java] 10 patterns [java] Filter - [java] 2 taxa @@ -3785,19 +3963,24 @@ [java] Filter 2-5,7-10 [java] 2 taxa [java] 8 sites - [java] 8 patterns + [java] + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95)8 patterns + [java] at java.base/java.util.ArrayList.forEach(ArrayList.java:1596) + [java] [java] 0human: 16 4 [java] 1chimp: 16 4 [java] Alignment(null) [java] 2 taxa - [java] 16 sites + [java] 16 sites at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41) [java] 16 patterns [java] [java] Filter 1:16:2 [java] 2 taxa [java] 8 sites [java] 8 patterns - [java] Filter 2:16:2 + [java] + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$6(NodeTestTask.java:155)Filter 2:16:2 + [java] [java] 2 taxa [java] 8 sites [java] 8 patterns @@ -3810,7 +3993,9 @@ [java] 6 sites [java] 6 patterns [java] Filter 2::3 - [java] 2 taxa + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:141)2 taxa + [java] at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:137) [java] 5 sites [java] 5 patterns [java] Filter :: @@ -3824,6 +4009,8 @@ [java] Filter :5: [java] 2 taxa [java] 5 sites + [java] + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$9(NodeTestTask.java:139) [java] 5 patterns [java] Filter 1::3,2::3 [java] 2 taxa @@ -3836,7 +4023,8 @@ [java] t0: 1 4 [java] t1: 1 4 [java] Alignment(null) - [java] 2 taxa + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] 2 taxa at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) [java] 1 site [java] [java] t0 = 0 (10.0) @@ -3849,7 +4037,8 @@ [java] [java] t0 = null (0.0) [java] t1 = 10 (0.0) - [java] t0: 1 4 + [java] + [java] t0: 1 4 at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) [java] t1: 1 4 [java] Alignment(null) [java] 2 taxa @@ -3857,160 +4046,7 @@ [java] [java] t0 = 0 (0.0) [java] t1 = 10 (10.0) - [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$9(NodeTestTask.java:139) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) + [java] [java] at java.base/java.util.ArrayList.forEach(ArrayList.java:1596) [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41) [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$6(NodeTestTask.java:155) @@ -4116,7 +4152,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 0.822 seconds + [java] Total calculation time: 0.828 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 0.9998844142873523 variance: 0.9962228119352534 ESS: 194315.96975231904 @@ -4148,13 +4184,29 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 0.79 seconds + [java] Total calculation time: 0.81 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 1.0017946084516174 variance: 1.7216547315129034 ESS: 25717.88066360503 [java] ------------------------------------------------- [java] [java] End likelihood: -0.8084620917497215 + [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] trace log written to /tmp/bactrian.log [java] Starting frequencies: [0.25, 0.25, 0.25, 0.25] [java] Starting frequencies: [0.25, 0.25, 0.25, 0.25] @@ -4191,22 +4243,6 @@ [java] [java] =============================================================================== [java] Start likelihood: -6.753673320834167 - [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] [java] Operator Tuning #accept #reject Pr(m) Pr(acc|m) [java] beast.base.inference.operator.kernel.BactrianUpDownOperator(unknown) 0.02500 435934 2062466 0.50000 0.17449 @@ -4220,14 +4256,19 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 3.521 seconds + [java] Total calculation time: 3.545 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] 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] 9.094947017729282E-13 + [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 @@ -4527,11 +4568,6 @@ [java] Alignment(null): [taxa, patterns, sites] = [6, 69, 768] [java] TreeLikelihood(null) uses BeerLikelihoodCore4 [java] Alignment(null): [taxa, patterns, sites] = [6, 69, 768] - [java] 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] 9.094947017729282E-13 [java] human: 768 4 [java] chimp: 768 4 [java] bonobo: 768 4 @@ -14452,149 +14488,6 @@ [java] Testing logNormal[M=0.831723454775867 S=7.267288007434337].pdf(0.5889447676204608) [java] Testing logNormal[M=-1.574020679205983 S=2.5371768478656795].pdf(1.4465898798236607) [java] Testing logNormal[M=3.1284114228468685 S=0.7564957947598672].pdf(2.2553823831377486) - [java] Loading package BEAST.app v2.7.6 - [java] Loading package BEAST.app v2.7.6 - [java] Loading package BEAST.base v2.7.6 - [java] java.lang.reflect.InvocationTargetException - [java] at java.base/jdk.internal.reflect.DirectConstructorHandleAccessor.newInstance(DirectConstructorHandleAccessor.java:74) - [java] at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:502) - [java] at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:486) - [java] at beast.base.core.Input.fromString(Unknown Source) - [java] at beast.base.core.InputForAnnotatedConstructor.(Unknown Source) - [java] at beast.base.core.BEASTInterface.listAnnotatedInputs(Unknown Source) - [java] at beast.base.core.BEASTInterface.listInputs(Unknown Source) - [java] at beast.base.core.BEASTObject.getInputs(Unknown Source) - [java] at beast.base.core.BEASTInterface.listActiveBEASTObjects(Unknown Source) - [java] at beast.base.core.BEASTObjectStore.listActiveBEASTObjects(Unknown Source) - [java] at beast.base.parser.ClassToPackageMap.getPackagesAndVersions(Unknown Source) - [java] at beast.base.parser.ClassToPackageMap.getPackagesAndVersions(Unknown Source) - [java] at beast.base.parser.XMLProducer.toXML(Unknown Source) - [java] at beast.base.parser.XMLProducer.toXML(Unknown Source) - [java] at test.beast.util.XMLTest.testAnnotatedConstructor2(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] Caused by: java.lang.NumberFormatException: empty String - [java] at java.base/jdk.internal.math.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:1842) - [java] at java.base/jdk.internal.math.FloatingDecimal.parseDouble(FloatingDecimal.java:110) - [java] at java.base/java.lang.Double.parseDouble(Double.java:792) - [java] at java.base/java.lang.Double.(Double.java:888) - [java] at java.base/jdk.internal.reflect.DirectConstructorHandleAccessor.newInstance(DirectConstructorHandleAccessor.java:62) - [java] ... 109 more - [java] java.lang.reflect.InvocationTargetException - [java] at java.base/jdk.internal.reflect.DirectConstructorHandleAccessor.newInstance(DirectConstructorHandleAccessor.java:74) - [java] at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:502) - [java] at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:486) - [java] at beast.base.core.Input.fromString(Unknown Source) - [java] at beast.base.core.InputForAnnotatedConstructor.(Unknown Source) - [java] at beast.base.core.BEASTInterface.listAnnotatedInputs(Unknown Source) - [java] at beast.base.core.BEASTInterface.listInputs(Unknown Source) - [java] at beast.base.core.BEASTObjectStore.listInputs(Unknown Source) - [java] at beast.base.parser.XMLProducer.beastObjectToXML(Unknown Source) - [java] at beast.base.parser.XMLProducer.toXML(Unknown Source) - [java] at beast.base.parser.XMLProducer.toXML(Unknown Source) - [java] at test.beast.util.XMLTest.testAnnotatedConstructor2(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$0(InterceptingExecutableInvoker.java:103) [java] Testing logNormal[M=3.999595991188766 S=1.759176722134489].pdf(1.624899490571806) [java] Testing logNormal[M=-2.767884555190495 S=0.19762720079634644].pdf(1.8481887339966967) [java] Testing logNormal[M=1.0180320911444385 S=1.4232228281179438].pdf(2.042225307669547) @@ -14724,8 +14617,6 @@ [java] Testing logNormal[M=-0.9057149147895407 S=5.624129537341109].pdf(2.0639649453723092) [java] Testing logNormal[M=-0.9852977315697666 S=6.961750485541527].pdf(0.49252596752092326) [java] Testing logNormal[M=0.014102584652576411 S=5.137062363978048].pdf(2.1556766552252937) - [java] at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker.lambda$invoke$0(InterceptingExecutableInvoker.java:93) - [java] at org.junit.jupiter.engine.execution.InvocationInterceptorChain$InterceptedInvocation.proceed(InvocationInterceptorChain.java:106) [java] Testing logNormal[M=-3.2626406209227876 S=2.7199556985904225].pdf(1.963281927645774) [java] Testing logNormal[M=-2.881970698346983 S=2.1073757670581026].pdf(2.286016230542248) [java] Testing logNormal[M=-4.265351432314139 S=4.513362986375755].pdf(1.3265057595912528) @@ -14964,6 +14855,151 @@ [java] Testing logNormal[M=-2.023496228033016 S=3.9227618715869506].pdf(1.5882725769254962) [java] Testing logNormal[M=-3.577699957972137 S=9.345578106358118].pdf(2.165879097028796) [java] Testing logNormal[M=1.0516748055181635 S=5.484242020370206].pdf(1.6803895137128866) + [java] Loading package BEAST.app v2.7.6 + [java] Loading package BEAST.app v2.7.6 + [java] Loading package BEAST.base v2.7.6 + [java] java.lang.reflect.InvocationTargetException + [java] at java.base/jdk.internal.reflect.DirectConstructorHandleAccessor.newInstance(DirectConstructorHandleAccessor.java:74) + [java] at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:502) + [java] at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:486) + [java] at beast.base.core.Input.fromString(Unknown Source) + [java] at beast.base.core.InputForAnnotatedConstructor.(Unknown Source) + [java] at beast.base.core.BEASTInterface.listAnnotatedInputs(Unknown Source) + [java] at beast.base.core.BEASTInterface.listInputs(Unknown Source) + [java] at beast.base.core.BEASTObject.getInputs(Unknown Source) + [java] at beast.base.core.BEASTInterface.listActiveBEASTObjects(Unknown Source) + [java] at beast.base.core.BEASTObjectStore.listActiveBEASTObjects(Unknown Source) + [java] at beast.base.parser.ClassToPackageMap.getPackagesAndVersions(Unknown Source) + [java] at beast.base.parser.ClassToPackageMap.getPackagesAndVersions(Unknown Source) + [java] at beast.base.parser.XMLProducer.toXML(Unknown Source) + [java] at beast.base.parser.XMLProducer.toXML(Unknown Source) + [java] at test.beast.util.XMLTest.testAnnotatedConstructor2(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] Caused by: java.lang.NumberFormatException: empty String + [java] at java.base/jdk.internal.math.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:1842) + [java] at java.base/jdk.internal.math.FloatingDecimal.parseDouble(FloatingDecimal.java:110) + [java] at java.base/java.lang.Double.parseDouble(Double.java:792) + [java] at java.base/java.lang.Double.(Double.java:888) + [java] at java.base/jdk.internal.reflect.DirectConstructorHandleAccessor.newInstance(DirectConstructorHandleAccessor.java:62) + [java] ... 109 more + [java] java.lang.reflect.InvocationTargetException + [java] at java.base/jdk.internal.reflect.DirectConstructorHandleAccessor.newInstance(DirectConstructorHandleAccessor.java:74) + [java] at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:502) + [java] at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:486) + [java] at beast.base.core.Input.fromString(Unknown Source) + [java] at beast.base.core.InputForAnnotatedConstructor.(Unknown Source) + [java] at beast.base.core.BEASTInterface.listAnnotatedInputs(Unknown Source) + [java] at beast.base.core.BEASTInterface.listInputs(Unknown Source) + [java] at beast.base.core.BEASTObjectStore.listInputs(Unknown Source) + [java] at beast.base.parser.XMLProducer.beastObjectToXML(Unknown Source) + [java] at beast.base.parser.XMLProducer.toXML(Unknown Source) + [java] at beast.base.parser.XMLProducer.toXML(Unknown Source) + [java] at test.beast.util.XMLTest.testAnnotatedConstructor2(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) @@ -15056,6 +15092,12 @@ [java] at java.base/jdk.internal.reflect.DirectConstructorHandleAccessor.newInstance(DirectConstructorHandleAccessor.java:62) [java] ... 106 more [java] adfgad + [java] exception thrown + [java] /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/examples/nexus/Primates.nex (No such file or directory) + [java] Test Nexus Examples in /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/examples/nexus + [java] exception thrown + [java] Cannot read the array length because "" is null + [java] (C:10.0,(B:20.0,A:30.0):10.0):0.0 [java] java.lang.reflect.InvocationTargetException [java] at java.base/jdk.internal.reflect.DirectConstructorHandleAccessor.newInstance(DirectConstructorHandleAccessor.java:74) [java] at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:502) @@ -15395,12 +15437,6 @@ [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] exception thrown - [java] /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/examples/nexus/Primates.nex (No such file or directory) - [java] Test Nexus Examples in /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/examples/nexus - [java] exception thrown - [java] Cannot read the array length because "" is null - [java] (C:10.0,(B:20.0,A:30.0):10.0):0.0 [java] ╷ [java] ├─ JUnit Platform Suite ✔ [java] ├─ JUnit Jupiter ✔ @@ -15545,7 +15581,11 @@ [java] │ │ └─ testIteratorFiltered() ✔ [java] │ ├─ TraitSetTest ✔ [java] │ │ ├─ testDateForward() ✔ + [java] + [java] WARNING: Delegated to the 'execute' command. [java] │ │ ├─ testDateForwardUnspecified() ✔ + [java] This behaviour has been deprecated and will be removed in a future release. + [java] Please use the 'execute' command directly. [java] │ │ └─ testDateBackward() ✔ [java] │ ├─ TreeTest ✔ [java] │ │ └─ testTreeScaling() ✔ @@ -15574,10 +15614,6 @@ [java] │ │ ├─ testAminoAcidLikelihoodIMTRev() ✔ [java] │ │ ├─ testAminoAcidLikelihoodIcpRev() ✔ [java] │ │ ├─ testJC69Likelihood() ✔ - [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. [java] │ │ ├─ testHKY85ILikelihood() ✔ [java] │ │ ├─ testAminoAcidLikelihoodDayhoff() ✔ [java] │ │ ├─ testJC69LikelihoodWithUncertainCharacters() ✔ @@ -15610,7 +15646,7 @@ [java] │ ├─ TreeUtilsTest ✔ [java] │ │ └─ testSortTreeAlphabetically() ✔ [java] │ ├─ RandomTreeTest ✔ - [java] │ │ └─ testCoalescentTimes() 12969 ms ✔ + [java] │ │ └─ testCoalescentTimes() 14573 ms ✔ [java] │ ├─ BirthDeathGernhard08ModelTest ✔ [java] │ │ └─ testJC69Likelihood() ✔ [java] │ ├─ LaplaceDistributionTest ✔ @@ -15667,7 +15703,7 @@ [java] │ └─ logNormalTest() ✔ [java] └─ JUnit Vintage ✔ [java] - [java] Test run finished after 76851 ms + [java] Test run finished after 77901 ms [java] [ 51 containers found ] [java] [ 0 containers skipped ] [java] [ 51 containers started ] @@ -15681,10 +15717,10 @@ [java] [ 207 tests successful ] [java] [ 0 tests failed ] [java] -[junitreport] Processing /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/build/junitreport/TESTS-TestSuites.xml to /tmp/null1484170020 +[junitreport] Processing /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/build/junitreport/TESTS-TestSuites.xml to /tmp/null560365608 [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: 497ms -[junitreport] Deleting: /tmp/null1484170020 +[junitreport] Transform time: 446ms +[junitreport] Deleting: /tmp/null560365608 junit-integration: [java] @@ -15693,16 +15729,12 @@ [java] Loading package BEAST.app v2.7.6 BEAST.app v2.7.6 BEAST.base v2.7.6 [java] Testing 160 classes [java] Done! - [java] Loading package BEAST.app v2.7.6 - [java] Loading package BEAST.app v2.7.6 - [java] Loading package BEAST.base v2.7.6 [java] Test Nexus Examples in /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/examples/nexus [java] exception thrown [java] Cannot read the array length because "" is null - [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. + [java] Loading package BEAST.app v2.7.6 + [java] Loading package BEAST.app v2.7.6 + [java] Loading package BEAST.base v2.7.6 [java] [java] [java] @@ -15728,7 +15760,7 @@ [java] │ └─ testMutualDependencyOfPackageDependencies() ↷ Needs the user dir, which is intentionally void on Debian buildds [java] └─ JUnit Vintage ✔ [java] - [java] Test run finished after 784 ms + [java] Test run finished after 736 ms [java] [ 8 containers found ] [java] [ 0 containers skipped ] [java] [ 8 containers started ] @@ -15742,27 +15774,31 @@ [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/null62167756 + [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/integrationreport/TESTS-TestSuites.xml to /tmp/null39784939 [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: 126ms -[junitreport] Deleting: /tmp/null62167756 +[junitreport] Transform time: 120ms +[junitreport] Deleting: /tmp/null39784939 junit-xmlparsertest: [java] [java] Thanks for using JUnit! Support its development at https://junit.org/sponsoring [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. [java] ╷ [java] ├─ JUnit Platform Suite ✔ [java] ├─ JUnit Jupiter ✔ + [java] + [java] WARNING: Delegated to the 'execute' command. [java] │ └─ XMLParserTest ✔ [java] │ └─ testClassMap() ✔ + [java] This behaviour has been deprecated and will be removed in a future release. + [java] Please use the 'execute' command directly. [java] └─ JUnit Vintage ✔ [java] - [java] Test run finished after 328 ms + [java] Test run finished after 297 ms [java] [ 4 containers found ] [java] [ 0 containers skipped ] [java] [ 4 containers started ] @@ -15776,15 +15812,15 @@ [java] [ 1 tests successful ] [java] [ 0 tests failed ] [java] -[junitreport] Processing /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/build/xmlparserreport/TESTS-TestSuites.xml to /tmp/null331496894 +[junitreport] Processing /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/build/xmlparserreport/TESTS-TestSuites.xml to /tmp/null317614433 [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: 102ms -[junitreport] Deleting: /tmp/null331496894 +[junitreport] Transform time: 122ms +[junitreport] Deleting: /tmp/null317614433 junit: BUILD SUCCESSFUL -Total time: 1 minute 21 seconds +Total time: 1 minute 22 seconds make[1]: Leaving directory '/build/reproducible-path/beast2-mcmc-2.7.6+dfsg' create-stamp debian/debhelper-build-stamp dh_prep @@ -15822,12 +15858,14 @@ 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/3810798/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3810798/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/3303201 and its subdirectories -I: Current time: Fri Apr 10 02:22:16 -12 2026 -I: pbuilder-time-stamp: 1775830936 +I: removing directory /srv/workspace/pbuilder/3810798 and its subdirectories +I: Current time: Sat Mar 8 22:02:23 +14 2025 +I: pbuilder-time-stamp: 1741420943