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Started by upstream project "BIOFORMATS-test-repo" build number 129 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@10 [BIOFORMATS-test-folder@10] $ /bin/bash -xe /tmp/jenkins15086538940377749282.sh + '[' leica-lif = slidebook ']' ++ date +%u + '[' 1 -le 1 ']' + DOCKER_ARGS='-Dtestng.memory=15g -Dtestng.threadCount=12 -Duser.language=fr -Duser.country=FR' + sudo docker run --rm --name BIOFORMATS-test-folder_20304_merge_ci -v /uod/idr/repos/curated/leica-lif:/data -v /uod/idr-scratch/merge-ci/curated/leica-lif:/config snoopycrimecop/bioformats:merge_ci -Dtestng.memory=15g -Dtestng.threadCount=12 -Duser.language=fr -Duser.country=FR 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] 15:01:41,818 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 15:01:41,820 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 15:01:41,820 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 15:01:41,822 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 15:01:41,822 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 15:01:41,822 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 15:01:41,823 |-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] 15:01:41,823 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 15:01:41,824 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 15:01:41,824 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 15:01:41,824 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 15:01:41,824 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 15:01:42,061 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 15:01:42,061 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 15:01:42,091 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 15:01:42,092 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 15:01:42,101 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 15:01:42,101 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 15:01:42,101 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 15:01:42,102 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 15:01:42,102 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 15:01:42,103 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 15:01:42,103 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 279 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-22 15:01:42,114] [main] java.version = 1.8.0_342 [testng] 15:01:42,118 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 15:01:42,118 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:01:42,166 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-22_15-01-42.log] [testng] 15:01:42,168 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-07-22 15:01:42,170] [main] testng.directory = /data [testng] [2024-07-22 15:01:42,170] [main] testng.configDirectory = /config [testng] [2024-07-22 15:01:42,184] [main] testng.multiplier = 1.0 [testng] [2024-07-22 15:01:42,184] [main] testng.in-memory = false [testng] [2024-07-22 15:01:42,184] [main] testng.allow-missing = false [testng] [2024-07-22 15:01:42,184] [main] user.language = fr [testng] [2024-07-22 15:01:42,184] [main] user.country = FR [testng] [2024-07-22 15:01:42,184] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-07-22 15:05:33,964] [main] ---------------------------------------- [testng] [2024-07-22 15:05:33,964] [main] Total files: 402 [testng] [2024-07-22 15:05:33,964] [main] Scan time: 231.779 s (576 ms/file) [testng] [2024-07-22 15:05:33,964] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 266 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-22 15:07:09,652] [pool-1-thread-1] Initializing /data/kota/int_ok.lif: [testng] 15:07:09,652 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 15:07:09,652 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:07:09,653 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-22_15-07-09.log] [testng] 15:07:09,654 |-INFO in ch.qos.logback.core.sift.SiftProcessor@17715945 - End of configuration. [testng] [2024-07-22 15:07:09,695] [pool-1-thread-12] Initializing /data/andrew/New XZY LIF Upload/XZY Stacks.lif: [testng] 15:07:09,695 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 15:07:09,695 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:07:09,695 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-22_15-07-09.log] [testng] 15:07:09,696 |-INFO in ch.qos.logback.core.sift.SiftProcessor@40bcac08 - End of configuration. [testng] [2024-07-22 15:07:09,741] [pool-1-thread-11] Initializing /data/qa-4791/TestFlorianDescription2.lif: [testng] 15:07:09,741 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 15:07:09,741 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:07:09,742 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-22_15-07-09.log] [testng] 15:07:09,743 |-INFO in ch.qos.logback.core.sift.SiftProcessor@587166ec - End of configuration. [testng] [2024-07-22 15:07:09,755] [pool-1-thread-10] Initializing /data/andrew/Series 68 TIFFs/Series068_t6_y6.tif: [testng] 15:07:09,755 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 15:07:09,755 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:07:09,756 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-22_15-07-09.log] [testng] 15:07:09,756 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2fdab854 - End of configuration. [testng] [2024-07-22 15:07:09,793] [pool-1-thread-9] Initializing /data/andrew/Series 68 TIFFs/Series068_t6_y4.tif: [testng] 15:07:09,793 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 15:07:09,793 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:07:09,794 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-22_15-07-09.log] [testng] 15:07:09,794 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6873d858 - End of configuration. [testng] [2024-07-22 15:07:09,833] [pool-1-thread-8] Initializing /data/public/seanwarren/150519_FRAP_test_ROIs_chromagreen/FRAP002_5um.png: [testng] 15:07:09,833 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 15:07:09,833 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:07:09,834 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-22_15-07-09.log] [testng] 15:07:09,834 |-INFO in ch.qos.logback.core.sift.SiftProcessor@701da349 - End of configuration. [testng] [2024-07-22 15:07:09,847] [pool-1-thread-7] Initializing /data/melissa/roi-test-1.xml: [testng] 15:07:09,847 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 15:07:09,847 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:07:09,848 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-22_15-07-09.log] [testng] 15:07:09,849 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1db6b47d - End of configuration. [testng] [2024-07-22 15:07:09,890] [pool-1-thread-6] Initializing /data/sebastian/sebHaase2.lif: [testng] 15:07:09,890 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 15:07:09,890 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:07:09,891 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-22_15-07-09.log] [testng] 15:07:09,891 |-INFO in ch.qos.logback.core.sift.SiftProcessor@40c7b72a - End of configuration. [testng] [2024-07-22 15:07:09,941] [pool-1-thread-5] Initializing /data/public/seanwarren/150519_FRAP_test_ROIs_chromagreen/FRAP003_10um.png: [testng] 15:07:09,941 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 15:07:09,941 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:07:09,942 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-22_15-07-09.log] [testng] 15:07:09,942 |-INFO in ch.qos.logback.core.sift.SiftProcessor@e0c11ab - End of configuration. [testng] [2024-07-22 15:07:09,953] [pool-1-thread-4] Initializing /data/pki/20111116preCK50.lif: [testng] 15:07:09,954 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 15:07:09,954 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:07:09,954 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-22_15-07-09.log] [testng] 15:07:09,955 |-INFO in ch.qos.logback.core.sift.SiftProcessor@28d3f9c9 - End of configuration. [testng] [2024-07-22 15:07:10,031] [pool-1-thread-3] Initializing /data/andrew/Series 68 TIFFs/Series068_t5_y0.tif: [testng] 15:07:10,032 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 15:07:10,032 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:07:10,032 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-22_15-07-10.log] [testng] 15:07:10,033 |-INFO in ch.qos.logback.core.sift.SiftProcessor@42a19f02 - End of configuration. [testng] [2024-07-22 15:07:10,088] [pool-1-thread-2] Initializing /data/andrew/Series 68 Multi from Importer.tif: [testng] 15:07:10,088 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 15:07:10,088 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:07:10,089 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-22_15-07-10.log] [testng] 15:07:10,090 |-INFO in ch.qos.logback.core.sift.SiftProcessor@656d0f1b - End of configuration. [testng] [2024-07-22 15:07:13,146] [pool-1-thread-11] Initializing /data/andrew/Series 68 TIFFs/Series068_t9_y5.tif: [testng] [2024-07-22 15:07:13,176] [pool-1-thread-12] Initializing /data/andrew/New XZY LIF Upload/Right Order/XZY Stacks Right Order Ch2.avi: [testng] [2024-07-22 15:07:13,446] [pool-1-thread-7] Initializing /data/tony/Celegeansexp01.lif: [testng] [2024-07-22 15:07:13,911] [pool-1-thread-3] Initializing /data/andrew/New XZY LIF Upload/Wrong Order/XZY Stacks Wrong Order Ch2.avi: [testng] [2024-07-22 15:07:13,946] [pool-1-thread-10] Initializing /data/jcb/201007044/Figure 4D - F505.lif: [testng] [2024-07-22 15:07:13,964] [pool-1-thread-9] Initializing /data/dirk/Mag-test.lif: [testng] [2024-07-22 15:07:14,227] [pool-1-thread-6] Initializing /data/melissa/Series001_z0.tif: [testng] [2024-07-22 15:07:14,273] [pool-1-thread-8] Initializing /data/andrew/Series 68 TIFFs/Series068_t7_y5.tif: [testng] [2024-07-22 15:07:14,310] [pool-1-thread-5] Initializing /data/tony/OPN_cy3_dapi_trab.lif: [testng] [2024-07-22 15:07:14,351] [pool-1-thread-12] Initializing /data/andrew/Series 68 TIFFs/Series068_t7_y7.tif: [testng] [2024-07-22 15:07:14,562] [pool-1-thread-11] Initializing /data/andrew/Series 68 TIFFs/Series068_t0_y1.tif: [testng] [2024-07-22 15:07:14,671] [pool-1-thread-10] Initializing /data/public/seanwarren/150519_FRAP_test_ROIs_chromagreen/FRAP001_2_5um.png: [testng] [2024-07-22 15:07:14,919] [pool-1-thread-3] Initializing /data/qa-7273/5-17 Hypoxia.lif: [testng] [2024-07-22 15:07:15,379] [pool-1-thread-6] Initializing /data/andrew/FRAP_Test_250708.lif: [testng] [2024-07-22 15:07:15,756] [pool-1-thread-9] Initializing /data/jerome/E346_316.lif: [testng] [2024-07-22 15:07:15,914] [pool-1-thread-8] Initializing /data/oliver/Single Channel Measurements.lif: [testng] [2024-07-22 15:07:15,997] [pool-1-thread-1] Initializing /data/stefan/Experiment.lif: [testng] [2024-07-22 15:07:16,202] [pool-1-thread-12] Initializing /data/andrew/Series 68 TIFFs/Series068_t5_y3.tif: [testng] [2024-07-22 15:07:16,284] [pool-1-thread-5] Initializing /data/christian/20090323fluoresceinRPMI.lif: [testng] [2024-07-22 15:07:16,389] [pool-1-thread-10] Initializing /data/andrew/Series 68 TIFFs/Series068_t8_y6.tif: [testng] [2024-07-22 15:07:16,430] [pool-1-thread-11] Initializing /data/fabrice/09-10-23 Tete de mouche.lif: [testng] [2024-07-22 15:07:17,225] [pool-1-thread-11] Initializing /data/qa-10980/Day 2 Chitin Kan.lif: [testng] [2024-07-22 15:07:17,349] [pool-1-thread-5] Initializing /data/romain/tile 002.lif: [testng] [2024-07-22 15:07:17,427] [pool-1-thread-12] Initializing /data/alex/2010-11-29-test-for-OME.lif: [testng] [2024-07-22 15:07:17,677] [pool-1-thread-10] Initializing /data/vytas/Series008_t000_ch00.tif: [testng] [2024-07-22 15:07:18,504] [pool-1-thread-1] Initializing /data/schek/Experiment_001.lif: [testng] [2024-07-22 15:07:18,697] [pool-1-thread-12] Initializing /data/andrew/Series 68 TIFFs/Series068_t2_y4.tif: [testng] [2024-07-22 15:07:19,997] [pool-1-thread-12] Initializing /data/jcb/JCB 201203109/FIG 2D STAT3-EYFP CNTF.lif: [testng] [2024-07-22 15:07:20,253] [pool-1-thread-7] Initializing /data/stefan/spe.lif: [testng] [2024-07-22 15:07:21,200] [pool-1-thread-2] Initializing /data/andrew/Series 68 TIFFs/Series068_t9_y2.tif: [testng] [2024-07-22 15:07:21,261] [pool-1-thread-12] Initializing /data/vytas/LIFtest.lif: [testng] [2024-07-22 15:07:21,283] [pool-1-thread-7] Initializing /data/andrew/Series 68 TIFFs/Series068_t2_y2.tif: [testng] [2024-07-22 15:07:21,442] [pool-1-thread-9] Initializing /data/andrew/Series 68 TIFFs/Series068_t8_y1.tif: [testng] [2024-07-22 15:07:21,758] [pool-1-thread-12] Initializing /data/jerome/E345_312.lif: [testng] [2024-07-22 15:07:21,854] [pool-1-thread-2] Initializing /data/andrew/Series 68 TIFFs/Series068_t8_y0.tif: [testng] [2024-07-22 15:07:22,259] [pool-1-thread-7] Initializing /data/leon/leon002.lif: [testng] [2024-07-22 15:07:22,358] [pool-1-thread-9] Initializing /data/melissa/roi-test-1.lif: [testng] [2024-07-22 15:07:22,748] [pool-1-thread-2] Initializing /data/andrew/LIF Lambda/Montage of Alexa 488 Lambda.tif: [testng] [2024-07-22 15:07:22,785] [pool-1-thread-7] Initializing /data/matthias/ms-first tests.lif: [testng] [2024-07-22 15:07:23,063] [pool-1-thread-9] Initializing /data/andrew/LIF Lambda/Lambda 1.lif: [testng] [2024-07-22 15:07:23,513] [pool-1-thread-2] Initializing /data/andrew/Series 68 TIFFs/Series068_t3_y6.tif: [testng] [2024-07-22 15:07:23,562] [pool-1-thread-8] Initializing /data/pki/RA4 P3 x63.lif: [testng] [2024-07-22 15:07:24,289] [pool-1-thread-10] Initializing /data/andrew/Series 68 TIFFs/Series068_t7_y4.tif: [testng] [2024-07-22 15:07:24,521] [pool-1-thread-1] Initializing /data/andrew/New XZY LIF Upload/Right Order/XZY Stacks Right Order Ch1.avi: [testng] [2024-07-22 15:07:24,917] [pool-1-thread-2] Initializing /data/andrew/Series 68 TIFFs/Series068_t2_y8.tif: [testng] [2024-07-22 15:07:25,142] 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[2024-07-22 15:08:20,134] [pool-1-thread-3] Initializing /data/fabrice/new/UL66 bicolore stacks + merge.lif: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 14098, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 9 minutes 26 seconds Finished: SUCCESS