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HaplotypeCaller running error

qihualiangqihualiang UC RiversideMember

Hi I am running HaplotypeCaller and have below error message. Is this related to the same issue here https://github.com/broadinstitute/gatk/issues/5447

Using GATK jar /24-2/home/qliang/0.soft/GATK/gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx4g -jar /24-2/home/qliang/0.soft/GATK/gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar HaplotypeCaller -R Cowpea_Genome_1.0.fasta -I ABCDEF.bam -O output.g.vcf.gz -ERC GVCF
15:36:30.447 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/24-2/home/qliang/0.soft/GATK/gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Jul 22, 2019 3:36:32 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
15:36:32.110 INFO HaplotypeCaller - ------------------------------------------------------------
15:36:32.111 INFO HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.1.2.0
15:36:32.111 INFO HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/
15:36:32.111 INFO HaplotypeCaller - Executing as [email protected] on Linux v4.15.0-54-generic amd64
15:36:32.111 INFO HaplotypeCaller - Java runtime: OpenJDK 64-Bit Server VM v11.0.3+7-Ubuntu-1ubuntu218.04.1
15:36:32.112 INFO HaplotypeCaller - Start Date/Time: July 22, 2019 at 3:36:30 PM PDT
15:36:32.112 INFO HaplotypeCaller - ------------------------------------------------------------
15:36:32.112 INFO HaplotypeCaller - ------------------------------------------------------------
15:36:32.113 INFO HaplotypeCaller - HTSJDK Version: 2.19.0
15:36:32.113 INFO HaplotypeCaller - Picard Version: 2.19.0
15:36:32.113 INFO HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:36:32.113 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:36:32.113 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:36:32.113 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:36:32.113 INFO HaplotypeCaller - Deflater: IntelDeflater
15:36:32.113 INFO HaplotypeCaller - Inflater: IntelInflater
15:36:32.114 INFO HaplotypeCaller - GCS max retries/reopens: 20
15:36:32.114 INFO HaplotypeCaller - Requester pays: disabled
15:36:32.114 INFO HaplotypeCaller - Initializing engine
15:36:32.434 INFO HaplotypeCaller - Shutting down engine
[July 22, 2019 at 3:36:32 PM PDT] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=2149580800
java.lang.NullPointerException
at org.broadinstitute.hellbender.utils.SequenceDictionaryUtils.getContigNames(SequenceDictionaryUtils.java:463)
at org.broadinstitute.hellbender.utils.SequenceDictionaryUtils.getCommonContigsByName(SequenceDictionaryUtils.java:457)
at org.broadinstitute.hellbender.utils.SequenceDictionaryUtils.compareDictionaries(SequenceDictionaryUtils.java:234)
at org.broadinstitute.hellbender.utils.SequenceDictionaryUtils.validateDictionaries(SequenceDictionaryUtils.java:150)
at org.broadinstitute.hellbender.utils.SequenceDictionaryUtils.validateDictionaries(SequenceDictionaryUtils.java:98)
at org.broadinstitute.hellbender.engine.GATKTool.validateSequenceDictionaries(GATKTool.java:760)
at org.broadinstitute.hellbender.engine.GATKTool.onStartup(GATKTool.java:702)
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.onStartup(AssemblyRegionWalker.java:161)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
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)

Answers

  • Tiffany_at_BroadTiffany_at_Broad Cambridge, MAMember, Administrator, Broadie, Moderator admin

    Hi @qihualiang,

    You don't need to worry about that INFO line. I checked with a developer and he said that the warning happens when one of our dependencies has a network error while it's trying to determine if it's running on a google node or not. The issue you are pointing to is really about removing the large bit of stack trace that once came with that INFO line.

    Does this help?

  • qihualiangqihualiang UC RiversideMember

    Thank you Tiffany!
    During my attempt to run HaplotypeCaller, it stopped soon with the above messages. I am not sure where the issue is because other INFO lines do not have explicit error message. Can you or the team help with troubleshooting this?

  • Tiffany_at_BroadTiffany_at_Broad Cambridge, MAMember, Administrator, Broadie, Moderator admin

    Hi @qihualiang we can do our best.
    Where are you running HaplotypeCaller? What is the size of the machine? An example of a successful run on the cloud is here. Notice that your stack trace says Initializing then immediately shutting down which is different from the successful log:
    23:01:43.421 INFO HaplotypeCaller - Initializing engine
    23:01:48.758 INFO IntervalArgumentCollection - Processing 58694888 bp from intervals
    23:01:48.793 INFO HaplotypeCaller - Done initializing engine
    Can you determine if the parameters of the machine you are running on can support this?

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