Started by upstream project "BIOFORMATS-test-repo" build number 249 originally caused by: Started by upstream project "Trigger" build number 273 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder [BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins6578144078896244662.sh + '[' ome-tiff = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_39213_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] 01:14:50,054 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:14:50,055 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 01:14:50,055 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:14:50,056 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:14:50,057 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:14:50,057 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:14:50,057 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:14:50,057 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:14:50,057 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:14:50,058 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:14:50,058 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:14:50,058 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:14:50,281 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:14:50,282 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:14:50,309 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:14:50,309 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:14:50,317 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:14:50,317 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:14:50,317 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:14:50,318 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:14:50,318 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 01:14:50,319 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 01:14:50,319 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 262 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-08 01:14:50,328] [main] java.version = 1.8.0_342 [testng] 01:14:50,332 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:14:50,332 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:14:50,378 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-08_01-14-50.log] [testng] 01:14:50,380 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-11-08 01:14:50,382] [main] testng.directory = /data [testng] [2024-11-08 01:14:50,382] [main] testng.configDirectory = /config [testng] [2024-11-08 01:14:50,394] [main] testng.multiplier = 1.0 [testng] [2024-11-08 01:14:50,395] [main] testng.in-memory = false [testng] [2024-11-08 01:14:50,395] [main] testng.allow-missing = false [testng] [2024-11-08 01:14:50,395] [main] user.language = en [testng] [2024-11-08 01:14:50,395] [main] user.country = ${user.country} [testng] [2024-11-08 01:14:50,395] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-11-08 01:23:09,834] [main] ---------------------------------------- [testng] [2024-11-08 01:23:09,834] [main] Total files: 4771 [testng] [2024-11-08 01:23:09,835] [main] Scan time: 499.439 s (104 ms/file) [testng] [2024-11-08 01:23:09,835] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 1455 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-08 02:13:33,663] [pool-1-thread-1] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X00--Y04/image--L12--S00--U00--V00--J00--X00--Y04--T12--Z00--C00.ome.tif: [testng] 02:13:33,663 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:13:33,664 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:33,665 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-08_02-13-33.log] [testng] 02:13:33,665 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d9a6d7 - End of configuration. [testng] [2024-11-08 02:13:34,315] [pool-1-thread-12] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X00--Y00/image--L03--S00--U00--V00--J00--X00--Y00--T03--Z00--C00.ome.tif: [testng] 02:13:34,316 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:13:34,316 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:34,316 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-08_02-13-34.log] [testng] 02:13:34,317 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1316c829 - End of configuration. [testng] [2024-11-08 02:13:34,950] [pool-1-thread-11] Initializing /data/andor/iQMM_FURA_TIME198_WAVELENGTH0_0.ome.tif: [testng] 02:13:34,950 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:13:34,950 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:34,951 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-08_02-13-34.log] [testng] 02:13:34,951 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1aaefc9e - End of configuration. [testng] [2024-11-08 02:13:35,853] [pool-1-thread-10] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X00--Y06/image--L08--S00--U00--V00--J00--X00--Y06--T08--Z00--C00.ome.tif: [testng] 02:13:35,853 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:13:35,853 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:35,854 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-08_02-13-35.log] [testng] 02:13:35,854 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6ce6a6cc - End of configuration. [testng] [2024-11-08 02:13:36,544] [pool-1-thread-9] Initializing /data/mat/mut393_100x_opt_5_R3D_D3D_CAC_C0.tif: [testng] 02:13:36,544 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:13:36,544 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:36,545 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-08_02-13-36.log] [testng] 02:13:36,545 |-INFO in ch.qos.logback.core.sift.SiftProcessor@557cb00a - End of configuration. [testng] [2024-11-08 02:13:37,827] [pool-1-thread-8] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X04--Y06/image--L11--S00--U00--V00--J00--X04--Y06--T11--Z00--C00.ome.tif: [testng] 02:13:37,827 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:13:37,827 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:37,827 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-08_02-13-37.log] [testng] 02:13:37,828 |-INFO in ch.qos.logback.core.sift.SiftProcessor@47d95df0 - End of configuration. [testng] [2024-11-08 02:13:38,522] [pool-1-thread-7] Initializing /data/oliver/LA_ProtocolCombination_12.10.2009_20_55_46_Marker__1 2.tif: [testng] 02:13:38,523 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:13:38,523 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:38,524 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-08_02-13-38.log] [testng] 02:13:38,525 |-INFO in ch.qos.logback.core.sift.SiftProcessor@87675af - End of configuration. [testng] [2024-11-08 02:13:39,736] [pool-1-thread-6] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X01--Y02/image--L04--S00--U00--V00--J00--X01--Y02--T04--Z00--C00.ome.tif: [testng] 02:13:39,736 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:13:39,736 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:39,737 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-08_02-13-39.log] [testng] 02:13:39,737 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5441d6f2 - End of configuration. [testng] [2024-11-08 02:13:40,416] [pool-1-thread-5] Initializing /data/andor/iQMM_FURA_TIME113_WAVELENGTH1_0.ome.tif: [testng] 02:13:40,416 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:13:40,416 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:40,416 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-08_02-13-40.log] [testng] 02:13:40,417 |-INFO in ch.qos.logback.core.sift.SiftProcessor@20d731d2 - End of configuration. [testng] [2024-11-08 02:13:41,214] [pool-1-thread-4] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X00--Y04/image--L04--S00--U00--V00--J00--X00--Y04--T04--Z00--C00.ome.tif: [testng] 02:13:41,214 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:13:41,214 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:41,215 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-08_02-13-41.log] [testng] 02:13:41,215 |-INFO in ch.qos.logback.core.sift.SiftProcessor@187dcf60 - End of configuration. [testng] [2024-11-08 02:13:42,501] [pool-1-thread-3] Initializing /data/andor/iQMM_FURA_TIME197_WAVELENGTH1_0.ome.tif: [testng] 02:13:42,502 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:13:42,502 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:42,502 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-08_02-13-42.log] [testng] 02:13:42,502 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4179a9 - End of configuration. [testng] [2024-11-08 02:13:43,280] [pool-1-thread-2] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X03--Y03/image--L01--S00--U00--V00--J00--X03--Y03--T01--Z00--C00.ome.tif: [testng] 02:13:43,281 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:13:43,281 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:43,281 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-08_02-13-43.log] [testng] 02:13:43,282 |-INFO in ch.qos.logback.core.sift.SiftProcessor@162550f - End of configuration. [testng] [2024-11-08 02:13:54,835] [pool-1-thread-4] Initializing /data/public/2010-04/multi-channel-z-series.ome.tiff: [testng] [2024-11-08 02:13:55,619] [pool-1-thread-12] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X01--Y00/image--L05--S00--U00--V00--J00--X01--Y00--T05--Z00--C00.ome.tif: [testng] [2024-11-08 02:13:56,413] [pool-1-thread-2] Initializing /data/public/2013-06/tubhiswt-4D/tubhiswt_C0_TP0.ome.tif: [testng] [2024-11-08 02:14:21,212] [pool-1-thread-9] Initializing /data/andor/iQMM_FURA_TIME86_WAVELENGTH1_0.ome.tif: [testng] [2024-11-08 02:14:21,772] [pool-1-thread-8] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X02--Y03/image--L03--S00--U00--V00--J00--X02--Y03--T03--Z00--C00.ome.tif: [testng] [2024-11-08 02:14:22,311] [pool-1-thread-1] Initializing /data/public/2009-09/one-screen-one-plate-four-wells.ome.tiff: [testng] [2024-11-08 02:14:23,051] [pool-1-thread-10] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X03--Y05/image--L14--S00--U00--V00--J00--X03--Y05--T14--Z00--C00.ome.tif: [testng] [2024-11-08 02:14:23,632] [pool-1-thread-6] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X03--Y05/image--L10--S00--U00--V00--J00--X03--Y05--T10--Z00--C00.ome.tif: [testng] [2024-11-08 02:14:24,466] [pool-1-thread-5] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X04--Y01/image--L13--S00--U00--V00--J00--X04--Y01--T13--Z00--C00.ome.tif: [testng] [2024-11-08 02:14:25,021] [pool-1-thread-3] Initializing /data/andor/iQMM_FURA_TIME185_WAVELENGTH0_0.ome.tif: [testng] [2024-11-08 02:14:25,605] [pool-1-thread-11] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X05--Y04/image--L14--S00--U00--V00--J00--X05--Y04--T14--Z00--C00.ome.tif: [testng] [2024-11-08 02:14:26,174] [pool-1-thread-7] Initializing 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[pool-1-thread-1] Initializing /data/andor/iQMM_FURA_TIME6_WAVELENGTH1_0.ome.tif: [testng] [2024-11-08 03:28:54,723] [pool-1-thread-2] Initializing /data/andor/iQMM_FURA_TIME73_WAVELENGTH1_0.ome.tif: [testng] [2024-11-08 03:28:56,761] [pool-1-thread-11] Initializing /data/public/2016-06/sub-resolutions/EM/BGal_000438_frames.ome.tiff: [testng] [2024-11-08 03:28:57,646] [pool-1-thread-9] Initializing /data/andor/iQMM_FURA_TIME0_WAVELENGTH0_0.ome.tif: [testng] [2024-11-08 03:28:58,485] [pool-1-thread-12] Initializing /data/samples/missing-tiffs/test_s0.ome.tiff: [testng] [2024-11-08 03:29:01,710] [pool-1-thread-10] Initializing /data/scott/4.2_roundTrip/exported_4.2.ome.tif: [testng] [2024-11-08 03:29:03,645] [pool-1-thread-3] Initializing /data/sebastian/5x5_T=1_Z=1_CH=3_200pix #1.tif: [testng] [2024-11-08 03:29:04,989] [pool-1-thread-5] 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] [2024-11-08 03:29:05,773] [pool-1-thread-7] Initializing /data/public/2015-01/binaryonly/multifile-Z1.ome.tiff: [testng] [2024-11-08 03:29:06,557] [pool-1-thread-1] Initializing /data/andor/iQMM_FURA_TIME175_WAVELENGTH1_0.ome.tif: [testng] [2024-11-08 03:29:07,279] [pool-1-thread-2] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X02--Y04/image--L08--S00--U00--V00--J00--X02--Y04--T08--Z00--C00.ome.tif: [testng] [2024-11-08 03:29:11,783] [pool-1-thread-9] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X03--Y05/image--L03--S00--U00--V00--J00--X03--Y05--T03--Z00--C00.ome.tif: [testng] 05:17:55,673 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 05:17:55,674 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:17:55,675 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-08_05-17-55.log] [testng] 05:17:55,675 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3c444112 - End of configuration. [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 77115, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 243 minutes 12 seconds Finished: SUCCESS