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[ERROR] make_acnv_pon

Hi,
I want to build a ACNV PoN from ~1000 WGS sample. I have ran "make_acnv_pon" for many times. But, all of them are failed due to different Java issues. I have no idea how to change the arguments. So, I really need your help. Thanks a lot!

The workspaces includes "575b23ea-cc5e-4395-ba6b-1ab31c37b709", "
80e88912-cacc-4ac6-b9e2-1b83cb2337ca", "1c5dca3d-4f34-4ff7-bec3-cde4315f8ead", "358ff882-e05c-4ecf-af33-727e2009f43c", "
663e7a52-e88f-4e00-9eb0-1e48196bd7c6"

Best,
Chunyang

Best Answer

Answers

  • Tiffany_at_BroadTiffany_at_Broad Cambridge, MAMember, Broadie, Moderator

    Hi @cbao , what is the java issue? Can you copy and paste it? If it is related to the version of Java you will need to have Java 1.8 installed on the Docker image. What docker image are you using?

    Thanks,
    Tiffany

  • cbaocbao Member, Broadie

    Issue 1:
    17/09/25 05:31:31 INFO SparkContext: Successfully stopped SparkContext [September 25, 2017 5:31:31 AM UTC] org.broadinstitute.hellbender.tools.exome.CreatePanelOfNormals done. Elapsed time: 154.35 minutes. Runtime.totalMemory()=10077863936 Exception in thread "main" java.lang.OutOfMemoryError: Java heap space at java.util.Arrays.copyOf(Arrays.java:3181) at java.util.ArrayList.grow(ArrayList.java:261) at java.util.ArrayList.ensureExplicitCapacity(ArrayList.java:235) at java.util.ArrayList.ensureCapacityInternal(ArrayList.java:227) at java.util.ArrayList.add(ArrayList.java:458) at com.opencsv.CSVParser.parseLine(CSVParser.java:383) at com.opencsv.CSVParser.parseLineMulti(CSVParser.java:299) at com.opencsv.CSVReader.readNext(CSVReader.java:275) at org.broadinstitute.hellbender.utils.tsv.TableReader.fetchNextRecord(TableReader.java:346) at org.broadinstitute.hellbender.utils.tsv.TableReader.readRecord(TableReader.java:307) at org.broadinstitute.hellbender.tools.exome.ReadCountCollectionUtils.readCounts(ReadCountCollectionUtils.java:271) at org.broadinstitute.hellbender.tools.exome.ReadCountCollectionUtils.parse(ReadCountCollectionUtils.java:253) at org.broadinstitute.hellbender.utils.hdf5.HDF5PoNCreator.readReadCountsFromFile(HDF5PoNCreator.java:602) at org.broadinstitute.hellbender.utils.hdf5.HDF5PoNCreator.createPoN(HDF5PoNCreator.java:87) at org.broadinstitute.hellbender.tools.exome.CreatePanelOfNormals.runPipeline(CreatePanelOfNormals.java:244) at org.broadinstitute.hellbender.utils.SparkToggleCommandLineProgram.doWork(SparkToggleCommandLineProgram.java:39) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:98) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:146) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:165) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:66) at org.broadinstitute.hellbender.Main.main(Main.java:81) 17/09/25 05:31:31 INFO ShutdownHookManager: Shutdown hook called 17/09/25 05:31:31 INFO ShutdownHookManager: Deleting directory /cromwell_root/tmp.Dch87u/root/spark-bdae0c8e-5a7f-4f7f-9f5a-20510601f439

    Issue 2:
    17/09/26 16:14:12 INFO SparkContext: Successfully stopped SparkContext 17/09/26 16:14:12 INFO OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped! [September 26, 2017 4:14:12 PM UTC] org.broadinstitute.hellbender.tools.exome.CreatePanelOfNormals done. Elapsed time: 10.78 minutes. Runtime.totalMemory()=9845604352 Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded at org.broadinstitute.hellbender.tools.exome.ReadCountsReader.lambda$countExtractor$14(ReadCountsReader.java:291) at org.broadinstitute.hellbender.tools.exome.ReadCountsReader$$Lambda$75/1427892726.apply(Unknown Source) at org.broadinstitute.hellbender.tools.exome.ReadCountsReader.extractRecordWithTargetNameAndIntervalExtractorsAndTargetCollection(ReadCountsReader.java:278) at org.broadinstitute.hellbender.tools.exome.ReadCountsReader.lambda$composeRecordExtractor$9(ReadCountsReader.java:187) at org.broadinstitute.hellbender.tools.exome.ReadCountsReader$$Lambda$76/321192242.apply(Unknown Source) at org.broadinstitute.hellbender.tools.exome.ReadCountsReader.createRecord(ReadCountsReader.java:284) at org.broadinstitute.hellbender.tools.exome.ReadCountsReader.createRecord(ReadCountsReader.java:23) at org.broadinstitute.hellbender.utils.tsv.TableReader.fetchNextRecord(TableReader.java:351) at org.broadinstitute.hellbender.utils.tsv.TableReader.readRecord(TableReader.java:307) at org.broadinstitute.hellbender.tools.exome.ReadCountCollectionUtils.readCounts(ReadCountCollectionUtils.java:271) at org.broadinstitute.hellbender.tools.exome.ReadCountCollectionUtils.parse(ReadCountCollectionUtils.java:253) at org.broadinstitute.hellbender.utils.hdf5.HDF5PoNCreator.readReadCountsFromFile(HDF5PoNCreator.java:602) at org.broadinstitute.hellbender.utils.hdf5.HDF5PoNCreator.createPoN(HDF5PoNCreator.java:87) at org.broadinstitute.hellbender.tools.exome.CreatePanelOfNormals.runPipeline(CreatePanelOfNormals.java:244) at org.broadinstitute.hellbender.utils.SparkToggleCommandLineProgram.doWork(SparkToggleCommandLineProgram.java:39) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:98) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:146) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:165) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:66) at org.broadinstitute.hellbender.Main.main(Main.java:81) 17/09/26 16:14:12 INFO ShutdownHookManager: Shutdown hook called 17/09/26 16:14:12 INFO ShutdownHookManager: Deleting directory /cromwell_root/tmp.dRF59O/root/spark-d88de260-815d-4530-97f8-e48ef9658daa

  • cbaocbao Member, Broadie

    Thanks, @Tiffany_at_Broad
    I am using a public WDL called "make_acnv_pon".

    Best,
    Chunyang

  • Tiffany_at_BroadTiffany_at_Broad Cambridge, MAMember, Broadie, Moderator
    edited October 2017

    Hi @cbao ,

    After looking at the stderr, I see an issue "java.lang.OutOfMemoryError: Java heap space"

    This article explains how to adjust the java heap space. You may need to clone the public WDL and adjust the JVM parameters "-Xmx " in the command.

    Have you tested increasing the memGB attribute in the method configuration too? I am not exactly sure what is going on here, but maybe this will help?

    Unfortunately, we do not support public WDLs that other people create. I am tagging the author, @amaro , who may be able to assist.

    Let us know how you progress!
    Tiffany

  • cbaocbao Member, Broadie
    Accepted Answer
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