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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

Using GATK jar /24-2/home/qliang/0.soft/GATK/gatk-
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- HaplotypeCaller -R Cowpea_Genome_1.0.fasta -I ABCDEF.bam -O output.g.vcf.gz -ERC GVCF
15:36:30.447 INFO NativeLibraryLoader - Loading from jar:file:/24-2/home/qliang/0.soft/GATK/gatk-!/com/intel/gkl/native/
Jul 22, 2019 3:36:32 PM 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
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] done. Elapsed time: 0.03 minutes.
at org.broadinstitute.hellbender.utils.SequenceDictionaryUtils.getContigNames(
at org.broadinstitute.hellbender.utils.SequenceDictionaryUtils.getCommonContigsByName(
at org.broadinstitute.hellbender.utils.SequenceDictionaryUtils.compareDictionaries(
at org.broadinstitute.hellbender.utils.SequenceDictionaryUtils.validateDictionaries(
at org.broadinstitute.hellbender.utils.SequenceDictionaryUtils.validateDictionaries(
at org.broadinstitute.hellbender.engine.GATKTool.validateSequenceDictionaries(
at org.broadinstitute.hellbender.engine.GATKTool.onStartup(
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.onStartup(
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(
at org.broadinstitute.hellbender.Main.runCommandLineProgram(
at org.broadinstitute.hellbender.Main.mainEntry(
at org.broadinstitute.hellbender.Main.main(


  • 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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