Started by upstream project "BIOFORMATS-test-repo" build number 38 originally caused by: Started by upstream project "Trigger" build number 44 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@4 [BIOFORMATS-test-folder@4] $ /bin/bash -xe /tmp/jenkins10361599964498093007.sh + '[' ome-tiff = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_5281_merge_ci -v /uod/idr/repos/curated/ome-tiff:/data -v /uod/idr-scratch/merge-ci/curated/ome-tiff:/config snoopycrimecop/bioformats:merge_ci -Dtestng.memory=15g -Dtestng.threadCount=12 Buildfile: /bio-formats-build/bioformats/components/test-suite/build.xml [echo] isSnapshot = true init-title: [echo] ----------=========== bio-formats-testing-framework ===========---------- init-timestamp: init: copy-resources: compile: [resolver:resolve] Resolving artifacts compile-tests: [resolver:resolve] Resolving artifacts [javac] Compiling 1 source file to /bio-formats-build/bioformats/components/test-suite/test test-automated: [testng] File leak detector installed [testng] 09:22:24,502 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 09:22:24,504 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 09:22:24,504 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 09:22:24,505 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 09:22:24,506 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 09:22:24,506 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 09:22:24,506 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 09:22:24,506 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 09:22:24,506 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 09:22:24,507 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 09:22:24,507 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 09:22:24,507 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 09:22:24,746 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 09:22:24,746 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 09:22:24,775 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 09:22:24,775 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 09:22:24,784 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 09:22:24,784 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 09:22:24,784 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 09:22:24,785 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 09:22:24,785 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 09:22:24,786 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 09:22:24,786 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 280 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-04-19 09:22:24,796] [main] java.version = 1.8.0_342 [testng] 09:22:24,800 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 09:22:24,800 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:22:24,848 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-19_09-22-24.log] [testng] 09:22:24,849 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-04-19 09:22:24,852] [main] testng.directory = /data [testng] [2024-04-19 09:22:24,852] [main] testng.configDirectory = /config [testng] [2024-04-19 09:22:24,865] [main] testng.multiplier = 1.0 [testng] [2024-04-19 09:22:24,865] [main] testng.in-memory = false [testng] [2024-04-19 09:22:24,866] [main] testng.allow-missing = false [testng] [2024-04-19 09:22:24,866] [main] user.language = en [testng] [2024-04-19 09:22:24,866] [main] user.country = ${user.country} [testng] [2024-04-19 09:22:24,866] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-04-19 09:24:44,891] [main] ---------------------------------------- [testng] [2024-04-19 09:24:44,891] [main] Total files: 4771 [testng] [2024-04-19 09:24:44,891] [main] Scan time: 140.025 s (29 ms/file) [testng] [2024-04-19 09:24:44,891] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 1455 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-04-19 09:32:18,605] [pool-1-thread-1] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X00--Y06/image--L03--S00--U00--V00--J00--X00--Y06--T03--Z00--C00.ome.tif: [testng] 09:32:18,606 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 09:32:18,606 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:32:18,607 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-19_09-32-18.log] [testng] 09:32:18,607 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21b0d5d1 - End of configuration. [testng] [2024-04-19 09:32:18,649] [pool-1-thread-9] Initializing /data/peter/LA_ProtocolCombination_23.01.2012_16_29_52_1.ome.tif: [testng] 09:32:18,650 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 09:32:18,650 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:32:18,650 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-19_09-32-18.log] [testng] 09:32:18,651 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2c985011 - End of configuration. [testng] [2024-04-19 09:32:18,944] [pool-1-thread-8] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X05--Y01/image--L01--S00--U00--V00--J00--X05--Y01--T01--Z00--C00.ome.tif: [testng] 09:32:18,944 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 09:32:18,944 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:32:18,945 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-19_09-32-18.log] [testng] 09:32:18,945 |-INFO in ch.qos.logback.core.sift.SiftProcessor@748a49c2 - End of configuration. [testng] [2024-04-19 09:32:18,975] [pool-1-thread-7] Initializing /data/public/2007-06/single-channel.ome.tif: [testng] 09:32:18,975 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 09:32:18,975 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:32:18,976 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-19_09-32-18.log] [testng] 09:32:18,976 |-INFO in ch.qos.logback.core.sift.SiftProcessor@400d9bf - End of configuration. [testng] [2024-04-19 09:32:18,996] [pool-1-thread-6] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X01--Y03/image--L10--S00--U00--V00--J00--X01--Y03--T10--Z00--C00.ome.tif: [testng] 09:32:18,996 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 09:32:18,996 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:32:18,997 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-19_09-32-18.log] [testng] 09:32:18,997 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3353caea - End of configuration. [testng] [2024-04-19 09:32:19,024] [pool-1-thread-5] Initializing /data/andor/iQMM_FURA_TIME123_WAVELENGTH0_0.ome.tif: [testng] 09:32:19,025 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 09:32:19,025 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:32:19,025 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-19_09-32-19.log] [testng] 09:32:19,025 |-INFO in ch.qos.logback.core.sift.SiftProcessor@b0083b8 - End of configuration. [testng] [2024-04-19 09:32:19,075] [pool-1-thread-4] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X00--Y05/image--L10--S00--U00--V00--J00--X00--Y05--T10--Z00--C00.ome.tif: [testng] 09:32:19,075 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 09:32:19,075 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:32:19,076 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-19_09-32-19.log] [testng] 09:32:19,077 |-INFO in ch.qos.logback.core.sift.SiftProcessor@60775743 - End of configuration. [testng] [2024-04-19 09:32:19,114] [pool-1-thread-3] Initializing /data/andor/iQMM_FURA_TIME26_WAVELENGTH0_0.ome.tif: [testng] 09:32:19,114 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 09:32:19,114 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:32:19,115 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-19_09-32-19.log] [testng] 09:32:19,115 |-INFO in ch.qos.logback.core.sift.SiftProcessor@49f9f9f6 - End of configuration. [testng] [2024-04-19 09:32:19,147] [pool-1-thread-2] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X03--Y04/image--L07--S00--U00--V00--J00--X03--Y04--T07--Z00--C00.ome.tif: [testng] 09:32:19,147 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 09:32:19,147 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:32:19,147 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-19_09-32-19.log] [testng] 09:32:19,148 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12bb46f3 - End of configuration. [testng] [2024-04-19 09:32:19,175] [pool-1-thread-12] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X00--Y01/image--L08--S00--U00--V00--J00--X00--Y01--T08--Z00--C00.ome.tif: [testng] 09:32:19,175 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 09:32:19,175 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:32:19,176 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-19_09-32-19.log] [testng] 09:32:19,176 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12d88f64 - End of configuration. [testng] [2024-04-19 09:32:19,210] [pool-1-thread-11] Initializing /data/andor/iQMM_FURA_TIME26_WAVELENGTH1_0.ome.tif: [testng] 09:32:19,210 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 09:32:19,210 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:32:19,211 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-19_09-32-19.log] [testng] 09:32:19,211 |-INFO in ch.qos.logback.core.sift.SiftProcessor@65ff04fa - End of configuration. [testng] [2024-04-19 09:32:19,277] [pool-1-thread-10] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X01--Y00/image--L14--S00--U00--V00--J00--X01--Y00--T14--Z00--C00.ome.tif: [testng] 09:32:19,278 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 09:32:19,278 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:32:19,278 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-19_09-32-19.log] [testng] 09:32:19,278 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4502b01 - End of configuration. [testng] [2024-04-19 09:32:30,565] [pool-1-thread-9] Initializing /data/public/2012-06/bioformats-artificial/multi-channel-4D-series.ome.tif: [testng] [2024-04-19 09:32:30,616] [pool-1-thread-8] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X04--Y03/image--L04--S00--U00--V00--J00--X04--Y03--T04--Z00--C00.ome.tif: [testng] [2024-04-19 09:32:30,658] [pool-1-thread-12] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X01--Y01/image--L10--S00--U00--V00--J00--X01--Y01--T10--Z00--C00.ome.tif: [testng] [2024-04-19 09:32:30,698] [pool-1-thread-3] Initializing /data/public/2016-06/binaryonly/multifile-Z1.ome.tiff: [testng] [2024-04-19 09:32:30,710] [pool-1-thread-5] Initializing /data/andor/iQMM_FURA_TIME96_WAVELENGTH0_0.ome.tif: [testng] [2024-04-19 09:32:30,747] [pool-1-thread-4] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X02--Y04/image--L09--S00--U00--V00--J00--X02--Y04--T09--Z00--C00.ome.tif: [testng] [2024-04-19 09:32:30,777] [pool-1-thread-11] Initializing /data/public/2010-06/multi-channel-z-series-time-series.ome.tiff: [testng] [2024-04-19 09:32:30,800] [pool-1-thread-6] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X04--Y00/image--L05--S00--U00--V00--J00--X04--Y00--T05--Z00--C00.ome.tif: [testng] [2024-04-19 09:32:30,831] [pool-1-thread-1] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X04--Y00/image--L01--S00--U00--V00--J00--X04--Y00--T01--Z00--C00.ome.tif: [testng] [2024-04-19 09:32:30,863] [pool-1-thread-7] Initializing /data/andor/iQMM_FURA_TIME194_WAVELENGTH1_0.ome.tif: [testng] [2024-04-19 09:32:31,085] [pool-1-thread-2] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X05--Y06/image--L05--S00--U00--V00--J00--X05--Y06--T05--Z00--C00.ome.tif: [testng] [2024-04-19 09:32:31,124] [pool-1-thread-10] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X03--Y03/image--L07--S00--U00--V00--J00--X03--Y03--T07--Z00--C00.ome.tif: [testng] [2024-04-19 09:32:32,165] [pool-1-thread-8] Initializing /data/andor/iQMM_FURA_TIME90_WAVELENGTH1_0.ome.tif: [testng] [2024-04-19 09:32:32,429] [pool-1-thread-12] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X03--Y06/image--L13--S00--U00--V00--J00--X03--Y06--T13--Z00--C00.ome.tif: [testng] [2024-04-19 09:32:32,459] [pool-1-thread-2] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X03--Y03/image--L11--S00--U00--V00--J00--X03--Y03--T11--Z00--C00.ome.tif: [testng] [2024-04-19 09:32:32,484] [pool-1-thread-11] Initializing 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09:38:46,419] [pool-1-thread-10] Initializing /data/andor/iQMM_FURA_TIME83_WAVELENGTH0_0.ome.tif: [testng] [2024-04-19 09:38:46,551] [pool-1-thread-5] Initializing /data/ruben/experiment--2009_10_27_15_43_34/slide--S00/chamber--U00--V00/field--X04--Y00/image--L00--S00--U00--V00--J00--X04--Y00--T00--Z00--C00.ome.tif: [testng] [2024-04-19 09:38:46,627] [pool-1-thread-4] Initializing /data/andor/iQMM_FURA_TIME109_WAVELENGTH1_0.ome.tif: [testng] [2024-04-19 09:38:46,740] [pool-1-thread-2] Initializing /data/tubhiswtTEST/tubhiswt4D-J2K.ome.tif: [testng] [2024-04-19 09:38:47,487] [pool-1-thread-11] Initializing /data/public/2016-06/bioformats-artificial/4D-series.ome.btf: [testng] [2024-04-19 09:38:47,568] [pool-1-thread-8] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X05--Y02/image--L06--S00--U00--V00--J00--X05--Y02--T06--Z00--C00.ome.tif: [testng] [2024-04-19 09:38:47,833] [pool-1-thread-10] Initializing /data/andor/iQMM_FURA_TIME185_WAVELENGTH0_0.ome.tif: [testng] [2024-04-19 09:38:48,264] [pool-1-thread-4] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X02--Y05/image--L14--S00--U00--V00--J00--X02--Y05--T14--Z00--C00.ome.tif: [testng] [2024-04-19 09:38:48,867] [pool-1-thread-5] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X03--Y06/image--L09--S00--U00--V00--J00--X03--Y06--T09--Z00--C00.ome.tif: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 77115, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 26 minutes 12 seconds Finished: SUCCESS