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GATK 4 IlluminaBaseCallsToSam Error

Dear GATK Team,

I am getting the following error:

Exception: picard.PicardException thrown from the UncaughtExceptionHandler in thread "pool-4-thread-905"
INFO 2019-07-01 15:41:32 CbclReader Processing tile 2676
INFO 2019-07-01 15:41:32 CbclReader Processing tile 2677
INFO 2019-07-01 15:41:32 CbclReader Processing tile 2678

Exception: picard.PicardException thrown from the UncaughtExceptionHandler in thread "pool-4-thread-919"

Exception: picard.PicardException thrown from the UncaughtExceptionHandler in thread "pool-4-thread-915"

Exception: picard.PicardException thrown from the UncaughtExceptionHandler in thread "pool-4-thread-920"

Exception: picard.PicardException thrown from the UncaughtExceptionHandler in thread "pool-4-thread-917"

Exception: picard.PicardException thrown from the UncaughtExceptionHandler in thread "pool-4-thread-928"

Exception: picard.PicardException thrown from the UncaughtExceptionHandler in thread "pool-4-thread-924"

Exception: picard.PicardException thrown from the UncaughtExceptionHandler in thread "pool-4-thread-921"

Exception: picard.PicardException thrown from the UncaughtExceptionHandler in thread "pool-4-thread-931"

Exception: picard.PicardException thrown from the UncaughtExceptionHandler in thread "pool-4-thread-925"

Exception: picard.PicardException thrown from the UncaughtExceptionHandler in thread "pool-4-thread-927"

Exception: picard.PicardException thrown from the UncaughtExceptionHandler in thread "pool-4-thread-923"

Exception: picard.PicardException thrown from the UncaughtExceptionHandler in thread "pool-4-thread-929"

Exception: picard.PicardException thrown from the UncaughtExceptionHandler in thread "pool-4-thread-926"

Exception: picard.PicardException thrown from the UncaughtExceptionHandler in thread "pool-4-thread-922"

Exception: picard.PicardException thrown from the UncaughtExceptionHandler in thread "pool-4-thread-933"

Exception: picard.PicardException thrown from the UncaughtExceptionHandler in thread "pool-4-thread-934"

Exception: picard.PicardException thrown from the UncaughtExceptionHandler in thread "pool-4-thread-935"

Exception: picard.PicardException thrown from the UncaughtExceptionHandler in thread "pool-4-thread-930"

Exception: picard.PicardException thrown from the UncaughtExceptionHandler in thread "pool-4-thread-932"

Exception: picard.PicardException thrown from the UncaughtExceptionHandler in thread "pool-4-thread-936"

Exception: picard.PicardException thrown from the UncaughtExceptionHandler in thread "pool-3-thread-1"
[Mon Jul 01 15:41:32 IST 2019] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.91 minutes.
Runtime.totalMemory()=9960947712
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
picard.PicardException: Reading executor had exceptions. There were 0 tasks were still running or queued and have been cancelled.
at picard.illumina.NewIlluminaBasecallsConverter.doTileProcessing(NewIlluminaBasecallsConverter.java:170)
at picard.illumina.IlluminaBasecallsToSam.doWork(IlluminaBasecallsToSam.java:276)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:295)
at org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor.instanceMain(PicardCommandLineProgramExecutor.java:25)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:162)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205)
at org.broadinstitute.hellbender.Main.main(Main.java:291)
Caused by: picard.PicardException: Expected cbcl file for surface 1 cycle 319 but it was not found.
at picard.illumina.parser.readers.CbclReader.readSurfaceTile(CbclReader.java:121)
at picard.illumina.parser.readers.CbclReader.(CbclReader.java:102)
at picard.illumina.parser.NewIlluminaDataProvider.(NewIlluminaDataProvider.java:37)
at picard.illumina.parser.IlluminaDataProviderFactory.makeDataProvider(IlluminaDataProviderFactory.java:269)
at picard.illumina.NewIlluminaBasecallsConverter$TileProcessor.run(NewIlluminaBasecallsConverter.java:232)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)

Kindly help us to fix this issues.

Krithika S

Answers

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin
    edited July 1

    Hi @Krithika_Subramanian

    Please post the version of GATK and the exact command you are using and the entire error log.

  • Krithika_SubramanianKrithika_Subramanian BangaloreMember

    Hi @bhanuGandham

    Thank for your response. I have resolved the above issue. Its because of "ReadStructure".

    GATK Package details:
    The Genome Analysis Toolkit (GATK) v4.1.2.0
    HTSJDK Version: 2.19.0
    Picard Version: 2.19.0

    Command:
    "gatk IlluminaBasecallsToSam --BASECALLS_DIR BaseCalls/ --LANE 001 --READ_STRUCTURE 151T8B8B151T --BARCODES_DIR ExtractBarcodes/Lane1/ --LIBRARY_PARAMS library_params.txt --RUN_BARCODE Lane1 --NUM_PROCESSORS 24 --ADAPTERS_TO_CHECK INDEXED --TMP_DIR Temp/"

    But, Now I am getting the below error:

    Exception: picard.PicardException thrown from the UncaughtExceptionHandler in thread "pool-27-thread-934"

    Exception: picard.PicardException thrown from the UncaughtExceptionHandler in thread "pool-27-thread-933"

    Exception: picard.PicardException thrown from the UncaughtExceptionHandler in thread "pool-27-thread-932"

    Exception: picard.PicardException thrown from the UncaughtExceptionHandler in thread "pool-26-thread-1"
    [Tue Jul 02 11:58:37 IST 2019] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 125.45 minutes.
    Runtime.totalMemory()=22076194816
    To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
    picard.PicardException: Reading executor had exceptions. There were 0 tasks were still running or queued and have been cancelled.
    at picard.illumina.NewIlluminaBasecallsConverter.doTileProcessing(NewIlluminaBasecallsConverter.java:170)
    at picard.illumina.IlluminaBasecallsToSam.doWork(IlluminaBasecallsToSam.java:276)
    at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:295)
    at org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor.instanceMain(PicardCommandLineProgramExecutor.java:25)
    at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:162)
    at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205)
    at org.broadinstitute.hellbender.Main.main(Main.java:291)
    Caused by: picard.PicardException: Read records with barcode null, but this barcode was not expected. (Is it referenced in the parameters file?)
    at picard.illumina.NewIlluminaBasecallsConverter$TileProcessor.addRecord(NewIlluminaBasecallsConverter.java:266)
    at picard.illumina.NewIlluminaBasecallsConverter$TileProcessor.run(NewIlluminaBasecallsConverter.java:238)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)

    Regards
    Krithika S

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Thank you posting your solution here @Krithika_Subramanian This will help other users.

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