Started by upstream project "BIOFORMATS-test-repo" build number 26 originally caused by: Started by upstream project "Trigger" build number 29 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@5 [BIOFORMATS-test-folder@5] $ /bin/bash -xe /tmp/jenkins8761021329312075637.sh + '[' ome-tiff = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_3313_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] Could not load field socket from SocketImpl: java.lang.NoSuchFieldException: socket [testng] Could not load field serverSocket from SocketImpl: java.lang.NoSuchFieldException: serverSocket [testng] File leak detector installed [testng] 01:38:05,546 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:38:05,547 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 01:38:05,547 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:38:05,548 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:38:05,548 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:38:05,549 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:38:05,549 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:38:05,549 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:38:05,549 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:38:05,550 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:38:05,550 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:38:05,550 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:38:05,724 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:38:05,724 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:38:05,748 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:38:05,749 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:38:05,755 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:38:05,756 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:38:05,756 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:38:05,756 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:38:05,756 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 01:38:05,758 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 01:38:05,758 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 209 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-04-07 01:38:05,767] [main] java.version = 17.0.2 [testng] 01:38:05,770 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:38:05,770 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:05,814 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-07_01-38-05.log] [testng] 01:38:05,816 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-04-07 01:38:05,817] [main] testng.directory = /data [testng] [2024-04-07 01:38:05,818] [main] testng.configDirectory = /config [testng] [2024-04-07 01:38:05,827] [main] testng.multiplier = 1.0 [testng] [2024-04-07 01:38:05,827] [main] testng.in-memory = false [testng] [2024-04-07 01:38:05,828] [main] testng.allow-missing = false [testng] [2024-04-07 01:38:05,828] [main] user.language = en [testng] [2024-04-07 01:38:05,828] [main] user.country = ${user.country} [testng] [2024-04-07 01:38:05,828] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-04-07 01:41:27,689] [main] ---------------------------------------- [testng] [2024-04-07 01:41:27,689] [main] Total files: 4771 [testng] [2024-04-07 01:41:27,689] [main] Scan time: 201.861 s (42 ms/file) [testng] [2024-04-07 01:41:27,690] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 1455 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-04-07 01:49:11,647] [pool-1-thread-1] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X00--Y00/image--L13--S00--U00--V00--J00--X00--Y00--T13--Z00--C00.ome.tif: [testng] 01:49:11,648 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:49:11,648 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:49:11,649 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-07_01-49-11.log] [testng] 01:49:11,650 |-INFO in ch.qos.logback.core.sift.SiftProcessor@47e4b209 - End of configuration. [testng] [2024-04-07 01:49:11,693] [pool-1-thread-9] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X04--Y02/image--L01--S00--U00--V00--J00--X04--Y02--T01--Z00--C00.ome.tif: [testng] 01:49:11,693 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:49:11,693 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:49:11,694 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-07_01-49-11.log] [testng] 01:49:11,694 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d29f043 - End of configuration. [testng] [2024-04-07 01:49:11,727] [pool-1-thread-8] Initializing /data/chris/Fig6/Fig 6E.ome.tiff: [testng] 01:49:11,728 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:49:11,728 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:49:11,729 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-07_01-49-11.log] [testng] 01:49:11,729 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a0a7692 - End of configuration. [testng] [2024-04-07 01:49:11,779] [pool-1-thread-7] Initializing /data/public/2008-09/dataset-group-project.ome.tiff: [testng] 01:49:11,779 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:49:11,779 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:49:11,781 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-07_01-49-11.log] [testng] 01:49:11,781 |-INFO in ch.qos.logback.core.sift.SiftProcessor@409d7712 - End of configuration. [testng] [2024-04-07 01:49:11,814] [pool-1-thread-6] Initializing /data/oliver/LA_ProtocolCombination_12.10.2009_20_55_46_Marker__1.xml: [testng] 01:49:11,814 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:49:11,814 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:49:11,815 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-07_01-49-11.log] [testng] 01:49:11,815 |-INFO in ch.qos.logback.core.sift.SiftProcessor@92127c6 - End of configuration. [testng] [2024-04-07 01:49:14,173] [pool-1-thread-5] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X01--Y03/image--L02--S00--U00--V00--J00--X01--Y03--T02--Z00--C00.ome.tif: [testng] 01:49:14,174 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:49:14,174 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:49:14,175 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-07_01-49-14.log] [testng] 01:49:14,175 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22f4bd08 - End of configuration. [testng] [2024-04-07 01:49:14,207] [pool-1-thread-4] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X05--Y00/image--L09--S00--U00--V00--J00--X05--Y00--T09--Z00--C00.ome.tif: [testng] 01:49:14,207 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:49:14,207 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:49:14,208 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-07_01-49-14.log] [testng] 01:49:14,208 |-INFO in ch.qos.logback.core.sift.SiftProcessor@46f87f2c - End of configuration. [testng] [2024-04-07 01:49:14,237] [pool-1-thread-3] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X03--Y00/image--L00--S00--U00--V00--J00--X03--Y00--T00--Z00--C00.ome.tif: [testng] 01:49:14,237 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:49:14,237 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:49:14,238 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-07_01-49-14.log] [testng] 01:49:14,238 |-INFO in ch.qos.logback.core.sift.SiftProcessor@643f3ba9 - End of configuration. [testng] [2024-04-07 01:49:14,278] [pool-1-thread-2] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X03--Y00/image--L07--S00--U00--V00--J00--X03--Y00--T07--Z00--C00.ome.tif: [testng] 01:49:14,278 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:49:14,278 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:49:14,279 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-07_01-49-14.log] [testng] 01:49:14,279 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1afb7c20 - End of configuration. [testng] [2024-04-07 01:49:14,311] [pool-1-thread-12] Initializing /data/prairie/SingleImage-12062007-1400-019/SingleImage.tif: [testng] 01:49:14,311 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:49:14,311 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:49:14,312 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-07_01-49-14.log] [testng] 01:49:14,312 |-INFO in ch.qos.logback.core.sift.SiftProcessor@20e4947e - End of configuration. [testng] [2024-04-07 01:49:14,347] [pool-1-thread-11] Initializing /data/andor/iQMM_FURA_TIME182_WAVELENGTH0_0.ome.tif: [testng] 01:49:14,347 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:49:14,347 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:49:14,347 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-07_01-49-14.log] [testng] 01:49:14,348 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f34d5ad - End of configuration. [testng] [2024-04-07 01:49:14,392] [pool-1-thread-10] Initializing /data/andor/iQMM_FURA_TIME107_WAVELENGTH0_0.ome.tif: [testng] 01:49:14,393 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:49:14,393 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:49:14,393 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-07_01-49-14.log] [testng] 01:49:14,393 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4ee844be - End of configuration. [testng] [2024-04-07 01:49:22,422] [pool-1-thread-10] Initializing /data/andor/iQMM_FURA_TIME72_WAVELENGTH1_0.ome.tif: [testng] [2024-04-07 01:49:22,457] [pool-1-thread-5] Initializing /data/andor/iQMM_FURA_TIME153_WAVELENGTH1_0.ome.tif: [testng] [2024-04-07 01:49:22,518] [pool-1-thread-8] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X06--Y05/image--L02--S00--U00--V00--J00--X06--Y05--T02--Z00--C00.ome.tif: [testng] [2024-04-07 01:49:22,548] [pool-1-thread-2] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X06--Y04/image--L07--S00--U00--V00--J00--X06--Y04--T07--Z00--C00.ome.tif: [testng] [2024-04-07 01:49:22,596] [pool-1-thread-4] Initializing /data/andor/iQMM_FURA_TIME15_WAVELENGTH1_0.ome.tif: [testng] [2024-04-07 01:49:22,655] [pool-1-thread-3] Initializing /data/tubhiswtTEST/tubhiswt4D-LZW.ome.tif: [testng] [2024-04-07 01:49:22,766] [pool-1-thread-9] Initializing /data/public/2012-06/modulo/FLIM-ModuloAlongC.ome.tiff: [testng] [2024-04-07 01:49:22,793] [pool-1-thread-11] Initializing /data/andor/iQMM_FURA_TIME194_WAVELENGTH0_0.ome.tif: [testng] [2024-04-07 01:49:22,837] [pool-1-thread-1] Initializing /data/andor/iQMM_FURA_TIME187_WAVELENGTH1_0.ome.tif: [testng] [2024-04-07 01:49:22,883] [pool-1-thread-7] Initializing /data/andor/iQMM_FURA_TIME109_WAVELENGTH1_0.ome.tif: [testng] [2024-04-07 01:49:22,917] [pool-1-thread-12] Initializing /data/ruben/experiment--2009_10_27_15_43_34/slide--S00/chamber--U00--V00/field--X03--Y01/image--L00--S00--U00--V00--J00--X03--Y01--T00--Z00--C00.ome.tif: [testng] [2024-04-07 01:49:24,747] [pool-1-thread-10] Initializing /data/andor/iQMM_FURA_TIME186_WAVELENGTH1_0.ome.tif: [testng] [2024-04-07 01:49:24,807] [pool-1-thread-11] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X03--Y03/image--L07--S00--U00--V00--J00--X03--Y03--T07--Z00--C00.ome.tif: [testng] [2024-04-07 01:49:24,927] [pool-1-thread-7] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X00--Y02/image--L06--S00--U00--V00--J00--X00--Y02--T06--Z00--C00.ome.tif: [testng] [2024-04-07 01:49:24,983] [pool-1-thread-12] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X05--Y05/image--L00--S00--U00--V00--J00--X05--Y05--T00--Z00--C00.ome.tif: [testng] [2024-04-07 01:49:25,092] [pool-1-thread-4] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X03--Y00/image--L04--S00--U00--V00--J00--X03--Y00--T04--Z00--C00.ome.tif: [testng] [2024-04-07 01:49:25,125] [pool-1-thread-5] Initializing /data/public/2008-09/multi-channel-z-series-time-series.ome.tiff: [testng] [2024-04-07 01:49:25,172] [pool-1-thread-2] Initializing /data/andor/iQMM_FURA_TIME189_WAVELENGTH1_0.ome.tif: [testng] [2024-04-07 01:49:25,243] [pool-1-thread-9] Initializing 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Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X03--Y03/image--L03--S00--U00--V00--J00--X03--Y03--T03--Z00--C00.ome.tif: [testng] [2024-04-07 01:55:39,565] [pool-1-thread-11] Initializing /data/andor/iQMM_FURA_TIME17_WAVELENGTH1_0.ome.tif: [testng] [2024-04-07 01:55:39,658] [pool-1-thread-2] Initializing /data/andor/iQMM_FURA_TIME104_WAVELENGTH0_0.ome.tif: [testng] [2024-04-07 01:55:39,734] [pool-1-thread-1] Initializing /data/glen/OMETiff Slidebook donotopen/Capture 2 - Position 1_XY1306537975_Z00_T003_C1.tiff: [testng] [2024-04-07 01:55:40,024] [pool-1-thread-6] Initializing /data/chris/Fig4/Fig 4B.ome.tiff: [testng] [2024-04-07 01:55:40,316] [pool-1-thread-12] Initializing /data/ruben/experiment--2009_10_27_15_43_34/slide--S00/chamber--U00--V00/field--X01--Y02/image--L00--S00--U00--V00--J00--X01--Y02--T00--Z00--C00.ome.tif: [testng] [2024-04-07 01:55:40,461] [pool-1-thread-4] Initializing /data/andor/iQMM_FURA_TIME9_WAVELENGTH1_0.ome.tif: [testng] [2024-04-07 01:55:40,760] [pool-1-thread-2] Initializing /data/public/2009-09/z-series-time-series.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: 28 minutes 14 seconds Finished: SUCCESS