Started by upstream project "BIOFORMATS-test-repo" build number 3 originally caused by: Started by upstream project "Trigger" build number 4 originally caused by: Started by timer 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/jenkins7766533457987091311.sh + '[' ome-tiff = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_359_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 [javac] warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] 1 warning test-automated: [testng] WARNING: An illegal reflective access operation has occurred [testng] WARNING: Illegal reflective access by org.kohsuke.file_leak_detector.Listener (file:/home/build/.m2/repository/org/kohsuke/file-leak-detector/1.18/file-leak-detector-1.18-jar-with-dependencies.jar) to field java.net.SocketImpl.socket [testng] WARNING: Please consider reporting this to the maintainers of org.kohsuke.file_leak_detector.Listener [testng] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [testng] WARNING: All illegal access operations will be denied in a future release [testng] File leak detector installed [testng] 00:45:53,686 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:45:53,688 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 00:45:53,688 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:45:53,689 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:45:53,690 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:45:53,690 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:45:53,690 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:45:53,690 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:45:53,691 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:45:53,692 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:45:53,692 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:45:53,692 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:45:53,860 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:45:53,861 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:45:53,883 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:45:53,883 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:45:53,888 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:45:53,889 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:45:53,889 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:45:53,889 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:45:53,889 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 00:45:53,890 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 00:45:53,890 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 199 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-16 00:45:53,899] [main] java.version = 11.0.16 [testng] 00:45:53,902 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:45:53,902 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:45:53,944 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-16_00-45-53.log] [testng] 00:45:53,946 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-03-16 00:45:53,948] [main] testng.directory = /data [testng] [2024-03-16 00:45:53,948] [main] testng.configDirectory = /config [testng] [2024-03-16 00:45:53,958] [main] testng.multiplier = 1.0 [testng] [2024-03-16 00:45:53,959] [main] testng.in-memory = false [testng] [2024-03-16 00:45:53,960] [main] testng.allow-missing = false [testng] [2024-03-16 00:45:53,960] [main] user.language = en [testng] [2024-03-16 00:45:53,960] [main] user.country = ${user.country} [testng] [2024-03-16 00:45:53,960] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-03-16 00:49:27,885] [main] ---------------------------------------- [testng] [2024-03-16 00:49:27,885] [main] Total files: 4771 [testng] [2024-03-16 00:49:27,885] [main] Scan time: 213.925 s (44 ms/file) [testng] [2024-03-16 00:49:27,886] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 1455 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-16 01:02:32,861] [pool-1-thread-1] Initializing /data/ruben/experiment--2009_10_27_15_43_34/slide--S00/chamber--U00--V00/field--X02--Y00/image--L00--S00--U00--V00--J00--X02--Y00--T00--Z00--C00.ome.tif: [testng] 01:02:32,863 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:02:32,863 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:32,866 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-16_01-02-32.log] [testng] 01:02:32,866 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50e07de0 - End of configuration. [testng] [2024-03-16 01:02:33,147] [pool-1-thread-12] Initializing /data/jason/test1.ome.tif: [testng] 01:02:33,147 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:02:33,147 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:33,148 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-16_01-02-33.log] [testng] 01:02:33,148 |-INFO in ch.qos.logback.core.sift.SiftProcessor@44445794 - End of configuration. [testng] [2024-03-16 01:02:34,436] [pool-1-thread-11] Initializing /data/andor/iQMM_FURA_TIME170_WAVELENGTH0_0.ome.tif: [testng] 01:02:34,437 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:02:34,437 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:34,437 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-16_01-02-34.log] [testng] 01:02:34,438 |-INFO in ch.qos.logback.core.sift.SiftProcessor@20e4d8f8 - End of configuration. [testng] [2024-03-16 01:02:34,675] [pool-1-thread-10] Initializing /data/sebastian/5x5_T=1_Z=1_CH=3_200pix #1.tif: [testng] 01:02:34,675 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:02:34,675 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:34,676 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-16_01-02-34.log] [testng] 01:02:34,676 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1df7b109 - End of configuration. [testng] [2024-03-16 01:02:35,224] [pool-1-thread-9] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X04--Y00/image--L06--S00--U00--V00--J00--X04--Y00--T06--Z00--C00.ome.tif: [testng] 01:02:35,225 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:02:35,225 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:35,225 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-16_01-02-35.log] [testng] 01:02:35,225 |-INFO in ch.qos.logback.core.sift.SiftProcessor@628d84f2 - End of configuration. [testng] [2024-03-16 01:02:35,418] [pool-1-thread-8] Initializing /data/bk/img_bk_20110701.ome.tif: [testng] 01:02:35,418 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:02:35,418 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:35,419 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-16_01-02-35.log] [testng] 01:02:35,419 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68fc260d - End of configuration. [testng] [2024-03-16 01:02:35,652] [pool-1-thread-7] Initializing /data/oliver/DIV0Ctrl-2_1.tif: [testng] 01:02:35,652 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:02:35,652 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:35,653 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-16_01-02-35.log] [testng] 01:02:35,653 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34b7cdfb - End of configuration. [testng] [2024-03-16 01:02:36,793] [pool-1-thread-6] Initializing /data/heinrich/16614250 100x overview confo.ome.tif: [testng] 01:02:36,793 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:02:36,793 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:36,794 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-16_01-02-36.log] [testng] 01:02:36,794 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5fbbbdea - End of configuration. [testng] [2024-03-16 01:02:36,936] [pool-1-thread-5] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X01--Y01/image--L06--S00--U00--V00--J00--X01--Y01--T06--Z00--C00.ome.tif: [testng] 01:02:36,936 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:02:36,937 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:36,937 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-16_01-02-36.log] [testng] 01:02:36,938 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e2ffab9 - End of configuration. [testng] [2024-03-16 01:02:37,089] [pool-1-thread-4] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X04--Y05/image--L13--S00--U00--V00--J00--X04--Y05--T13--Z00--C00.ome.tif: [testng] 01:02:37,089 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:02:37,089 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:37,089 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-16_01-02-37.log] [testng] 01:02:37,090 |-INFO in ch.qos.logback.core.sift.SiftProcessor@54cefbf - End of configuration. [testng] [2024-03-16 01:02:37,280] [pool-1-thread-3] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X02--Y05/image--L04--S00--U00--V00--J00--X02--Y05--T04--Z00--C00.ome.tif: [testng] 01:02:37,280 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:02:37,280 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:37,281 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-16_01-02-37.log] [testng] 01:02:37,281 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3c2598f - End of configuration. [testng] [2024-03-16 01:02:37,606] [pool-1-thread-2] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X02--Y05/image--L11--S00--U00--V00--J00--X02--Y05--T11--Z00--C00.ome.tif: [testng] 01:02:37,607 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:02:37,607 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:37,607 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-16_01-02-37.log] [testng] 01:02:37,608 |-INFO in ch.qos.logback.core.sift.SiftProcessor@66d0b770 - End of configuration. [testng] [2024-03-16 01:02:45,514] [pool-1-thread-6] Initializing /data/andor/iQMM_FURA_TIME60_WAVELENGTH1_0.ome.tif: [testng] [2024-03-16 01:02:45,704] [pool-1-thread-7] Initializing /data/andor/iQMM_FURA_TIME175_WAVELENGTH1_0.ome.tif: [testng] [2024-03-16 01:02:45,835] [pool-1-thread-5] Initializing /data/public/2016-06/modulo/FLIM-ModuloAlongC.ome.tiff: [testng] [2024-03-16 01:02:46,356] [pool-1-thread-3] Initializing /data/andor/iQMM_FURA_TIME141_WAVELENGTH1_0.ome.tif: [testng] [2024-03-16 01:02:46,680] [pool-1-thread-8] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X06--Y03/image--L06--S00--U00--V00--J00--X06--Y03--T06--Z00--C00.ome.tif: [testng] [2024-03-16 01:02:46,790] [pool-1-thread-9] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X06--Y02/image--L11--S00--U00--V00--J00--X06--Y02--T11--Z00--C00.ome.tif: [testng] [2024-03-16 01:02:46,887] [pool-1-thread-1] Initializing /data/andor/iQMM_FURA_TIME148_WAVELENGTH1_0.ome.tif: [testng] [2024-03-16 01:02:46,981] [pool-1-thread-4] Initializing /data/samples/missing-planes/test.companion.ome: [testng] [2024-03-16 01:02:47,058] [pool-1-thread-2] Initializing /data/public/2010-04/single-image.ome.tiff: [testng] [2024-03-16 01:02:47,157] [pool-1-thread-11] Initializing /data/andor/iQMM_FURA_TIME182_WAVELENGTH0_0.ome.tif: [testng] [2024-03-16 01:02:47,268] [pool-1-thread-12] Initializing /data/andor/iQMM_FURA_TIME174_WAVELENGTH1_0.ome.tif: [testng] [2024-03-16 01:02:49,128] [pool-1-thread-5] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X03--Y01/image--L11--S00--U00--V00--J00--X03--Y01--T11--Z00--C00.ome.tif: [testng] [2024-03-16 01:02:49,819] [pool-1-thread-2] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X00--Y00/image--L11--S00--U00--V00--J00--X00--Y00--T11--Z00--C00.ome.tif: [testng] [2024-03-16 01:02:50,040] [pool-1-thread-3] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X05--Y03/image--L04--S00--U00--V00--J00--X05--Y03--T04--Z00--C00.ome.tif: [testng] [2024-03-16 01:02:50,625] [pool-1-thread-8] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X02--Y05/image--L08--S00--U00--V00--J00--X02--Y05--T08--Z00--C00.ome.tif: [testng] [2024-03-16 01:02:50,838] [pool-1-thread-9] Initializing /data/andor/iQMM_FURA_TIME177_WAVELENGTH1_0.ome.tif: [testng] [2024-03-16 01:02:50,979] [pool-1-thread-12] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X03--Y01/image--L08--S00--U00--V00--J00--X03--Y01--T08--Z00--C00.ome.tif: [testng] [2024-03-16 01:02:51,108] [pool-1-thread-11] Initializing /data/oliver/LA_ProtocolCombination_12.10.2009_20_55_46_Marker__1.tif: [testng] [2024-03-16 01:02:54,698] [pool-1-thread-10] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X02--Y05/image--L03--S00--U00--V00--J00--X02--Y05--T03--Z00--C00.ome.tif: [testng] [2024-03-16 01:02:54,780] [pool-1-thread-7] Initializing /data/andor/iQMM_FURA_TIME173_WAVELENGTH1_0.ome.tif: [testng] [2024-03-16 01:02:54,856] [pool-1-thread-6] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X01--Y05/image--L12--S00--U00--V00--J00--X01--Y05--T12--Z00--C00.ome.tif: [testng] [2024-03-16 01:02:54,946] [pool-1-thread-1] Initializing /data/andor/iQMM_FURA_TIME194_WAVELENGTH0_0.ome.tif: [testng] [2024-03-16 01:02:56,311] [pool-1-thread-5] Initializing /data/ruben/experiment--2009_10_27_15_43_34/slide--S00/chamber--U00--V00/field--X03--Y00/image--L00--S00--U00--V00--J00--X03--Y00--T00--Z00--C00.ome.tif: [testng] [2024-03-16 01:02:56,594] [pool-1-thread-3] Initializing 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/data/public/2007-06/Iron-Plate.ome.tiff: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 77115, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 66 minutes 51 seconds Finished: SUCCESS