Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

GATK4 IlluminaBasecallsToSam - java.lang.NullPointerException

Krithika_SubramanianKrithika_Subramanian BangaloreMember
edited July 2 in Ask the GATK team

Hi GATK Team,

I was trying to run "IlluminaBasecallsToSam" with my data

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/"

And I got an error like this:

Jul 02, 2019 2:15:28 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
[Tue Jul 02 14:15:28 IST 2019] Executing as [email protected] on Linux 3.10.0-514.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_201-b09; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.1.2.0
[Tue Jul 02 14:15:28 IST 2019] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.76 minutes.
Runtime.totalMemory()=1633157120
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
java.lang.NullPointerException
at htsjdk.samtools.util.StringUtil.join(StringUtil.java:54)
at picard.illumina.IlluminaBasecallsToSam.populateWritersFromLibraryParams(IlluminaBasecallsToSam.java:419)
at picard.illumina.IlluminaBasecallsToSam.initialize(IlluminaBasecallsToSam.java:297)
at picard.illumina.IlluminaBasecallsToSam.doWork(IlluminaBasecallsToSam.java:275)
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)

Kindly help me to fix this error

Regards
Krithika S

Answers

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin
  • Krithika_SubramanianKrithika_Subramanian BangaloreMember

    Hi @bhanuGandham

    The above issues resolved by adding "unassinged n n" in library_params.txt file.

    Command used:

    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 --MAX_RECORDS_IN_RAM 1200000

    I have tried both less ("--MAX_RECORDS_IN_RAM 50000" ) and more ("--MAX_RECORDS_IN_RAM 1200000") than default

    But I am getting error "OutOfMemoryError"

    INFO 2019-07-04 20:59:05 BasecallsConverter Read 346,000,000 records. Elapsed time: 08:22:17s. Time for last 1,000,000: 4s. Last read position: /
    INFO 2019-07-04 20:59:06 NewIlluminaBasecallsConverter Finished processing tile 2602
    INFO 2019-07-04 20:59:10 BasecallsConverter Read 347,000,000 records. Elapsed time: 08:22:22s. Time for last 1,000,000: 4s. Last read position: /
    INFO 2019-07-04 20:59:14 BasecallsConverter Read 348,000,000 records. Elapsed time: 08:22:27s. Time for last 1,000,000: 4s. Last read position: /
    INFO 2019-07-04 20:59:19 BasecallsConverter Read 349,000,000 records. Elapsed time: 08:22:32s. Time for last 1,000,000: 4s. Last read position: /
    INFO 2019-07-04 20:59:24 BasecallsConverter Read 350,000,000 records. Elapsed time: 08:22:37s. Time for last 1,000,000: 4s. Last read position: /
    INFO 2019-07-04 20:59:25 NewIlluminaBasecallsConverter Finished processing tile 2645
    INFO 2019-07-04 20:59:28 NewIlluminaBasecallsConverter Finished processing tile 2661
    INFO 2019-07-04 20:59:31 NewIlluminaBasecallsConverter Finished processing tile 2676
    INFO 2019-07-04 20:59:32 NewIlluminaBasecallsConverter Finished processing tile 2674

    Exception: picard.PicardException thrown from the UncaughtExceptionHandler in thread "pool-27-thread-1"
    [Thu Jul 04 20:59:32 IST 2019] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 503.52 minutes.
    Runtime.totalMemory()=21865431040
    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: java.lang.OutOfMemoryError: Java heap space

    Kindly give me your suggestion to resolve this issue.

    Thanks and Regards
    Krithika S

Sign In or Register to comment.