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Started by upstream project "BIOFORMATS-test-repo" build number 106 originally caused by: Started by upstream project "Trigger" build number 118 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@7 [BIOFORMATS-test-folder@7] $ /bin/bash -xe /tmp/jenkins7703963155942188368.sh + '[' tiff = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_16385_merge_ci -v /uod/idr/repos/curated/tiff:/data -v /uod/idr-scratch/merge-ci/curated/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] 01:22:33,850 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:22:33,852 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 01:22:33,852 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:22:33,853 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:22:33,853 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:22:33,854 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:22:33,854 |-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] 01:22:33,854 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:22:33,855 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:22:33,855 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:22:33,856 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:22:33,856 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:22:34,080 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:22:34,080 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:22:34,111 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:22:34,111 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:22:34,122 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:22:34,122 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:22:34,122 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:22:34,123 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:22:34,123 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 01:22:34,124 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 01:22:34,124 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 269 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-06-29 01:22:34,139] [main] java.version = 11.0.16 [testng] 01:22:34,145 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:22:34,145 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:34,203 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-29_01-22-34.log] [testng] 01:22:34,205 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-06-29 01:22:34,208] [main] testng.directory = /data [testng] [2024-06-29 01:22:34,208] [main] testng.configDirectory = /config [testng] [2024-06-29 01:22:34,222] [main] testng.multiplier = 1.0 [testng] [2024-06-29 01:22:34,224] [main] testng.in-memory = false [testng] [2024-06-29 01:22:34,224] [main] testng.allow-missing = false [testng] [2024-06-29 01:22:34,224] [main] user.language = en [testng] [2024-06-29 01:22:34,224] [main] user.country = ${user.country} [testng] [2024-06-29 01:22:34,224] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-06-29 01:22:41,810] [main] ---------------------------------------- [testng] [2024-06-29 01:22:41,811] [main] Total files: 4426 [testng] [2024-06-29 01:22:41,811] [main] Scan time: 7.586 s (1 ms/file) [testng] [2024-06-29 01:22:41,812] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 722 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-06-29 01:24:48,108] [pool-1-thread-1] Initializing /data/stephane/Copy of listeria + clathrin1_w3Cy5.tif: [testng] 01:24:48,109 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:24:48,110 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:48,111 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-29_01-24-48.log] [testng] 01:24:48,112 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3c0c219 - End of configuration. [testng] [2024-06-29 01:24:48,226] [pool-1-thread-12] Initializing /data/brian/retina/retina_C1_Z033.tif: [testng] 01:24:48,227 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:24:48,227 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:48,228 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-29_01-24-48.log] [testng] 01:24:48,228 |-INFO in ch.qos.logback.core.sift.SiftProcessor@737a6a84 - End of configuration. [testng] [2024-06-29 01:24:48,266] [pool-1-thread-11] Initializing /data/brian/PlantCell/PlantCell_C0_Z006.tif: [testng] 01:24:48,267 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:24:48,267 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:48,267 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-29_01-24-48.log] [testng] 01:24:48,268 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5871d73 - End of configuration. [testng] [2024-06-29 01:24:48,307] [pool-1-thread-10] Initializing /data/josiah/cell-Z11.C0.tiff: [testng] 01:24:48,307 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:24:48,307 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:48,308 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-29_01-24-48.log] [testng] 01:24:48,309 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3160c30a - End of configuration. [testng] [2024-06-29 01:24:48,344] [pool-1-thread-9] Initializing /data/brian/retina/retina_C1_Z057.tif: [testng] 01:24:48,344 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:24:48,344 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:48,345 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-29_01-24-48.log] [testng] 01:24:48,345 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ca56cb9 - End of configuration. [testng] [2024-06-29 01:24:48,396] [pool-1-thread-8] Initializing /data/ascb/bad/CYT-76_PasolliMouse1_4800.tif: [testng] 01:24:48,396 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:24:48,396 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:48,397 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-29_01-24-48.log] [testng] 01:24:48,397 |-INFO in ch.qos.logback.core.sift.SiftProcessor@48b942b0 - End of configuration. [testng] [2024-06-29 01:24:48,451] [pool-1-thread-7] Initializing /data/qa-4833/cjw_tiffs/23273992_Figure 6_NA_NA_22159.TIF: [testng] 01:24:48,451 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:24:48,451 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:48,451 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-29_01-24-48.log] [testng] 01:24:48,452 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68bd2f7d - End of configuration. [testng] [2024-06-29 01:24:48,495] [pool-1-thread-6] Initializing /data/brian/PlantCell/PlantCell_C0_Z007.tif: [testng] 01:24:48,496 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:24:48,496 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:48,496 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-29_01-24-48.log] [testng] 01:24:48,497 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f6d6742 - End of configuration. [testng] [2024-06-29 01:24:48,528] [pool-1-thread-5] Initializing /data/alla/deconvolve6/deconvolve6_Pseudo_Tl000_Zs002.TIF: [testng] 01:24:48,528 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:24:48,529 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:48,529 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-29_01-24-48.log] [testng] 01:24:48,530 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3aeecdf5 - End of configuration. [testng] [2024-06-29 01:24:48,608] [pool-1-thread-4] Initializing /data/josiah/cell-Z21.C1.tiff: [testng] 01:24:48,608 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:24:48,608 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:48,609 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-29_01-24-48.log] [testng] 01:24:48,610 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b2c7565 - End of configuration. [testng] [2024-06-29 01:24:48,654] [pool-1-thread-3] Initializing /data/brian/PlantCell/PlantCell_C1_Z007.tif: [testng] 01:24:48,654 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:24:48,654 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:48,655 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-29_01-24-48.log] [testng] 01:24:48,655 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ba1a2c0 - End of configuration. [testng] [2024-06-29 01:24:48,702] [pool-1-thread-2] Initializing /data/jerome/e346_plt1(m)_F1-6.tif: [testng] 01:24:48,702 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:24:48,702 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:48,703 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-29_01-24-48.log] [testng] 01:24:48,703 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4bbe8858 - End of configuration. [testng] [2024-06-29 01:24:50,897] [pool-1-thread-6] Initializing /data/public/condensation/A1.pattern1.tif: [testng] [2024-06-29 01:24:51,005] [pool-1-thread-5] Initializing /data/josiah/cell-Z21.C0.tiff: [testng] [2024-06-29 01:24:51,034] [pool-1-thread-2] Initializing /data/brian/MFGTMP_080902150001t001B02f73d1.TIF: [testng] [2024-06-29 01:24:51,076] [pool-1-thread-9] Initializing /data/julien/MarjorieCoisy1.TIF: [testng] [2024-06-29 01:24:51,120] [pool-1-thread-11] Initializing /data/lzw/DendriteForks.tif: [testng] [2024-06-29 01:24:51,220] [pool-1-thread-3] Initializing /data/josiah/cell-Z15.C1.tiff: [testng] [2024-06-29 01:24:51,259] [pool-1-thread-12] Initializing /data/brian/retina/retina_C1_Z051.tif: [testng] [2024-06-29 01:24:51,279] [pool-1-thread-10] Initializing /data/julien/Chadisoukkarieh6.TIF: [testng] [2024-06-29 01:24:51,334] [pool-1-thread-4] Initializing /data/stephane/P014.tif: [testng] [2024-06-29 01:24:51,409] [pool-1-thread-1] Initializing /data/samples/tiling-variants/data-layout-64x64-chunky-tiles-16x32.tiff: [testng] [2024-06-29 01:24:51,589] [pool-1-thread-7] Initializing /data/josiah/cell-Z25.C1.tiff: [testng] [2024-06-29 01:24:52,303] [pool-1-thread-12] Initializing /data/public/libtiff/jim___gg.tif: [testng] [2024-06-29 01:24:52,441] [pool-1-thread-1] Initializing /data/brian/retina/retina_C0_Z052.tif: [testng] [2024-06-29 01:24:52,559] [pool-1-thread-5] Initializing /data/brian/PlantCell/PlantCell_C1_Z018.tif: [testng] [2024-06-29 01:24:52,658] [pool-1-thread-3] Initializing /data/marc/ball48_LOCI_RGB_autoscale_10x.tif: [testng] [2024-06-29 01:24:52,836] [pool-1-thread-7] Initializing /data/qa-4745/LIBPB476_Figure 1_H_NA_21879.tiff: [testng] [2024-06-29 01:24:52,979] [pool-1-thread-10] Initializing /data/samples/tiling-variants/data-layout-64x64-planar-tiles-64x48.tiff: [testng] [2024-06-29 01:24:53,092] [pool-1-thread-6] Initializing /data/josiah/cell-Z5.C1.tiff: [testng] [2024-06-29 01:24:53,144] [pool-1-thread-4] Initializing /data/brian/retina/retina_C0_Z059.tif: [testng] [2024-06-29 01:24:53,325] [pool-1-thread-2] Initializing /data/josh/jnb1s1_raw0243.TIF: [testng] [2024-06-29 01:24:53,488] [pool-1-thread-9] Initializing /data/josh/jnb1s1_raw0223.TIF: [testng] [2024-06-29 01:24:53,560] [pool-1-thread-1] Initializing /data/brian/PlantCell/PlantCell_C0_Z028.tif: [testng] [2024-06-29 01:24:53,646] [pool-1-thread-12] Initializing /data/wayne/mBoeglin_lzw/mm_7.1.2.0.tif: [testng] [2024-06-29 01:24:53,733] [pool-1-thread-5] Initializing /data/jayne/Zst_13/WTERZ2_Series13_z000_ch00.tif: [testng] [2024-06-29 01:24:53,880] [pool-1-thread-10] Initializing /data/brian/retina/retina_C1_Z002.tif: [testng] [2024-06-29 01:24:54,235] [pool-1-thread-4] Initializing /data/public/libtiff/ycbcr-cat.tif: [testng] [2024-06-29 01:24:54,327] [pool-1-thread-6] Initializing /data/wayne/Rockies-grayscale.tif: [testng] [2024-06-29 01:24:54,362] [pool-1-thread-11] Initializing /data/ascb/FND-25_PaladeGroup_4800.tif: [testng] [2024-06-29 01:24:54,693] [pool-1-thread-2] Initializing /data/brian/PlantCell/PlantCell_C1_Z004.tif: [testng] [2024-06-29 01:24:54,769] [pool-1-thread-3] Initializing /data/brian/retina/retina_C0_Z016.tif: [testng] [2024-06-29 01:24:54,807] [pool-1-thread-1] Initializing /data/jae/first image.tif: [testng] [2024-06-29 01:24:54,866] [pool-1-thread-10] Initializing /data/julien/Chadisoukkarieh.TIF: [testng] [2024-06-29 01:24:55,202] [pool-1-thread-9] Initializing /data/public/condensation/C4.pattern7.tif: [testng] [2024-06-29 01:24:55,534] [pool-1-thread-4] Initializing /data/wayne/mBoeglin_lzw/mm7.1.2.0_07.tif: [testng] [2024-06-29 01:24:55,592] [pool-1-thread-7] Initializing /data/wayne/Rockies-48bit-rgb.tif: [testng] [2024-06-29 01:24:55,633] [pool-1-thread-6] Initializing /data/martin/head.tif: [testng] [2024-06-29 01:24:55,699] [pool-1-thread-3] Initializing /data/brian/retina/retina_C0_Z018.tif: [testng] [2024-06-29 01:24:55,773] 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/data/brian/retina/retina_C1_Z039.tif: [testng] [2024-06-29 01:27:14,224] [pool-1-thread-7] Initializing /data/alla/deconvolve6/deconvolve6_Pseudo_Tl000_Zs004.TIF: [testng] [2024-06-29 01:27:14,436] [pool-1-thread-2] Initializing /data/brian/retina/retina_C0_Z009.tif: [testng] [2024-06-29 01:27:14,455] [pool-1-thread-9] Initializing /data/brian/retina/retina_C0_Z062.tif: [testng] [2024-06-29 01:27:14,583] [pool-1-thread-12] Initializing /data/samples/melissa/imagej-4gb/4gb-imagej.tif: [testng] [2024-06-29 01:27:14,781] [pool-1-thread-9] Initializing /data/public/libtiff/quad-jpeg.tif: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 38266, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 5 minutes 30 seconds Finished: SUCCESS