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Started by upstream project "BIOFORMATS-test-repo" build number 379 originally caused by: Started by upstream project "Trigger" build number 401 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3 [BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins11504732724418364185.sh + '[' samples = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_59927_merge_ci -v /uod/idr/repos/curated/samples:/data -v /uod/idr-scratch/merge-ci/curated/samples:/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] 00:45:44,708 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 00:45:44,709 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - No custom configurators were discovered as a service. [testng] 00:45:44,709 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:45:44,710 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:45:44,711 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:45:44,711 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:45:44,711 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:45:44,711 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:45:44,712 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:45:44,712 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:45:44,713 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:45:44,713 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:45:44,880 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:45:44,880 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:45:44,902 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:45:44,902 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:45:44,907 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:45:44,907 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:45:44,907 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:45:44,908 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:45:44,908 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@65c7a252 - End of configuration. [testng] 00:45:44,909 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@38cee291 - Registering current configuration as safe fallback point [testng] 00:45:44,909 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 197 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-03-15 00:45:44,918] [main] java.version = 11.0.16 [testng] 00:45:44,921 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:45:44,921 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:45:44,963 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-15_00-45-44.log] [testng] 00:45:44,964 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13d73f29 - End of configuration. [testng] [2025-03-15 00:45:44,966] [main] testng.directory = /data [testng] [2025-03-15 00:45:44,967] [main] testng.configDirectory = /config [testng] [2025-03-15 00:45:44,976] [main] testng.multiplier = 1.0 [testng] [2025-03-15 00:45:44,978] [main] testng.in-memory = false [testng] [2025-03-15 00:45:44,978] [main] testng.allow-missing = false [testng] [2025-03-15 00:45:44,978] [main] user.language = en [testng] [2025-03-15 00:45:44,978] [main] user.country = ${user.country} [testng] [2025-03-15 00:45:44,978] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-03-15 00:47:58,998] [main] ---------------------------------------- [testng] [2025-03-15 00:47:58,998] [main] Total files: 165 [testng] [2025-03-15 00:47:58,999] [main] Scan time: 134.02 s (812 ms/file) [testng] [2025-03-15 00:47:58,999] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 60 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-03-15 00:50:06,670] [pool-1-thread-1] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] 00:50:06,671 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:50:06,671 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:50:06,673 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-15_00-50-06.log] [testng] 00:50:06,674 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5abe10d8 - End of configuration. [testng] [2025-03-15 00:50:06,804] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne2.ppm: [testng] 00:50:06,804 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:50:06,804 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:50:06,805 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-15_00-50-06.log] [testng] 00:50:06,805 |-INFO in ch.qos.logback.core.sift.SiftProcessor@626f6e39 - End of configuration. [testng] [2025-03-15 00:50:06,917] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] 00:50:06,918 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:50:06,918 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:50:06,918 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-15_00-50-06.log] [testng] 00:50:06,919 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3614ea80 - End of configuration. [testng] [2025-03-15 00:50:07,227] [pool-1-thread-10] Initializing /data/openjpeg/Bretagne1.j2k: [testng] 00:50:07,227 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:50:07,227 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:50:07,228 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-15_00-50-07.log] [testng] 00:50:07,228 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4a9a7e02 - End of configuration. [testng] [2025-03-15 00:50:07,878] [pool-1-thread-9] Initializing /data/ome/compressed2ChZ.lsm: [testng] 00:50:07,878 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:50:07,878 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:50:07,879 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-15_00-50-07.log] [testng] 00:50:07,880 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7f203429 - End of configuration. [testng] [2025-03-15 00:50:08,407] [pool-1-thread-8] Initializing /data/openjpeg/Cevennes2.jp2: [testng] 00:50:08,408 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:50:08,408 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:50:08,408 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-15_00-50-08.log] [testng] 00:50:08,409 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3e8fdded - End of configuration. [testng] [2025-03-15 00:50:08,977] [pool-1-thread-7] Initializing /data/ome/anusgfpzs.lsm: [testng] 00:50:08,977 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:50:08,977 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:50:08,978 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-15_00-50-08.log] [testng] 00:50:08,978 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1bdbb442 - End of configuration. [testng] [2025-03-15 00:50:09,762] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes2.ppm: [testng] 00:50:09,762 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:50:09,762 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:50:09,763 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-15_00-50-09.log] [testng] 00:50:09,763 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1794a274 - End of configuration. [testng] [2025-03-15 00:50:09,900] [pool-1-thread-5] Initializing /data/ome/Adultmidsection.lsm: [testng] 00:50:09,901 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:50:09,901 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:50:09,901 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-15_00-50-09.log] [testng] 00:50:09,901 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36bf33f3 - End of configuration. [testng] [2025-03-15 00:50:10,604] [pool-1-thread-4] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] 00:50:10,604 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:50:10,604 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:50:10,605 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-15_00-50-10.log] [testng] 00:50:10,605 |-INFO in ch.qos.logback.core.sift.SiftProcessor@46a20d29 - End of configuration. [testng] [2025-03-15 00:50:10,729] [pool-1-thread-3] Initializing /data/ome/CHOBI_d3d.dv: [testng] 00:50:10,729 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:50:10,729 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:50:10,730 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-15_00-50-10.log] [testng] 00:50:10,730 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ee51c98 - End of configuration. [testng] [2025-03-15 00:50:11,095] [pool-1-thread-2] Initializing /data/openjpeg/Cevennes2.bmp: [testng] 00:50:11,095 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:50:11,095 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:50:11,096 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-15_00-50-11.log] [testng] 00:50:11,096 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4979bb79 - End of configuration. [testng] [2025-03-15 00:50:13,990] [pool-1-thread-6] Initializing /data/openjpeg/Rome.ppm: [testng] [2025-03-15 00:50:14,107] [pool-1-thread-2] Initializing /data/ome/cb_1.r3d: [testng] [2025-03-15 00:50:14,844] [pool-1-thread-3] Initializing /data/openjpeg/Facade.bmp: [testng] [2025-03-15 00:50:15,084] [pool-1-thread-12] Initializing /data/openjpeg/Facade.pnm: [testng] [2025-03-15 00:50:15,736] [pool-1-thread-4] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2025-03-15 00:50:16,302] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2025-03-15 00:50:16,458] [pool-1-thread-1] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2025-03-15 00:50:17,317] [pool-1-thread-6] Initializing /data/ome/embryo.lsm: [testng] [2025-03-15 00:50:18,634] [pool-1-thread-2] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2025-03-15 00:50:18,801] [pool-1-thread-9] Initializing /data/ome/011B1_Morph.HTD: [testng] [2025-03-15 00:50:20,204] [pool-1-thread-8] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2025-03-15 00:50:21,279] [pool-1-thread-10] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2025-03-15 00:50:23,140] [pool-1-thread-5] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2025-03-15 00:50:23,946] [pool-1-thread-7] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2025-03-15 00:50:24,768] [pool-1-thread-12] Initializing /data/TAABA/TAABA.pattern: [testng] [2025-03-15 00:50:53,311] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2025-03-15 00:50:53,427] [pool-1-thread-3] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2025-03-15 00:50:54,957] [pool-1-thread-11] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2025-03-15 00:50:55,273] [pool-1-thread-2] Initializing /data/ARFTest/ARFTest.arf: [testng] [2025-03-15 00:50:56,309] [pool-1-thread-1] Initializing /data/ome/worm.tiff: [testng] [2025-03-15 00:50:57,864] [pool-1-thread-6] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2025-03-15 00:50:58,453] [pool-1-thread-5] Initializing /data/openjpeg/Rome.jp2: [testng] [2025-03-15 00:50:58,900] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2025-03-15 00:50:58,997] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2025-03-15 00:50:59,202] [pool-1-thread-4] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2025-03-15 00:51:00,007] [pool-1-thread-11] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2025-03-15 00:51:00,788] [pool-1-thread-3] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2025-03-15 00:51:01,287] [pool-1-thread-2] Initializing /data/ome/tiffany.color.tiff: [testng] [2025-03-15 00:51:02,905] [pool-1-thread-3] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2025-03-15 00:51:03,141] [pool-1-thread-7] Initializing /data/openjpeg/Rome.bmp: [testng] [2025-03-15 00:51:03,249] [pool-1-thread-8] Initializing /data/ome/654Atemp.stk: [testng] [2025-03-15 00:51:04,343] [pool-1-thread-4] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2025-03-15 00:51:05,427] [pool-1-thread-3] Initializing /data/ome/C1.lsm: [testng] [2025-03-15 00:51:06,282] [pool-1-thread-7] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2025-03-15 00:51:07,084] [pool-1-thread-5] Initializing /data/sdub/sdub.pattern: [testng] [2025-03-15 00:51:14,311] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2025-03-15 00:51:14,899] [pool-1-thread-1] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2025-03-15 00:51:17,138] [pool-1-thread-4] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2025-03-15 00:51:17,515] [pool-1-thread-1] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] [2025-03-15 00:51:18,545] [pool-1-thread-3] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2025-03-15 00:51:20,147] [pool-1-thread-2] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2025-03-15 00:51:21,616] [pool-1-thread-10] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2025-03-15 00:51:22,662] [pool-1-thread-7] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2025-03-15 00:51:25,224] [pool-1-thread-8] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2025-03-15 00:51:26,952] [pool-1-thread-4] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2025-03-15 00:51:29,658] [pool-1-thread-8] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2025-03-15 00:51:30,783] [pool-1-thread-1] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] [2025-03-15 00:51:33,313] [pool-1-thread-10] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 3180, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 7 minutes 59 seconds Finished: SUCCESS