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GATK v4.0.1.1 HaplotypeCaller

I am using GATK v4.0.1.1 HaplotypeCaller for variant analysis. (paired-end DNA sequenced data mapped to the reference using BWA mem).

The command I used;
“gatk HaplotypeCaller –R Reference.fna –I input.bam –O output.vcf”

It runs for a while (couple of seconds) but does not produce an output. No error message was given. Am I doing this right? Any help is appreciated.


  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭


    What do you mean "does not produce an output"? Can you post the entire log output (all the lines after the tool starts to run)?


  • Hi Sheila,
    After running the command there's no output file to be found. Any advice would be appreciated.
    Thank you!

    Here is the entire log output;

    [[email protected] project]$ /local/cluster/bin/gatk HaplotypeCaller -R Reference_genome.fna -I GH-50-a_aln_pairs_mapped_sorted.bam -O GH-50-a_GATK_output.vcf
    Using GATK jar /local/cluster/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=1 -jar /local/cluster/gatk- HaplotypeCaller -R Reference_genome.fna -I GH-50-a_aln_pairs_mapped_sorted.bam -O GH-50-a_GATK_output.vcf
    18:50:41.895 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/local/cluster/gatk-!/com/intel/gkl/native/libgkl_compression.so
    18:50:42.173 INFO HaplotypeCaller - ------------------------------------------------------------
    18:50:42.174 INFO HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.0.1.1
    18:50:42.174 INFO HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/
    18:50:42.175 INFO HaplotypeCaller - Executing as [email protected] on Linux v3.10.0-327.el7.x86_64 amd64
    18:50:42.175 INFO HaplotypeCaller - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_71-b15
    18:50:42.176 INFO HaplotypeCaller - Start Date/Time: February 19, 2018 6:50:41 PM PST
    18:50:42.176 INFO HaplotypeCaller - ------------------------------------------------------------
    18:50:42.176 INFO HaplotypeCaller - ------------------------------------------------------------
    18:50:42.177 INFO HaplotypeCaller - HTSJDK Version: 2.14.1
    18:50:42.177 INFO HaplotypeCaller - Picard Version: 2.17.2
    18:50:42.177 INFO HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 1
    18:50:42.177 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
    18:50:42.178 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
    18:50:42.178 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
    18:50:42.178 INFO HaplotypeCaller - Deflater: IntelDeflater
    18:50:42.178 INFO HaplotypeCaller - Inflater: IntelInflater
    18:50:42.178 INFO HaplotypeCaller - GCS max retries/reopens: 20
    18:50:42.178 INFO HaplotypeCaller - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes
    18:50:42.179 INFO HaplotypeCaller - Initializing engine
    18:50:43.288 INFO HaplotypeCaller - Done initializing engine
    18:50:43.393 INFO HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output
    18:50:44.112 INFO HaplotypeCaller - Shutting down engine
    [February 19, 2018 6:50:44 PM PST] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 0.04 minutes.
    java.lang.IllegalArgumentException: samples cannot be empty
    at org.broadinstitute.hellbender.utils.Utils.validateArg(Utils.java:681)
    at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReferenceConfidenceModel.(ReferenceConfidenceModel.java:161)
    at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine.initialize(HaplotypeCallerEngine.java:182)
    at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine.(HaplotypeCallerEngine.java:160)
    at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine.(HaplotypeCallerEngine.java:151)
    at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller.onTraversalStart(HaplotypeCaller.java:197)
    at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:891)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:136)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:179)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:198)
    at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:153)
    at org.broadinstitute.hellbender.Main.mainEntry(Main.java:195)
    at org.broadinstitute.hellbender.Main.main(Main.java:277)
    14.625u 1.297s 0:05.17 307.7% 0+0k 0+1184io 0pf+0w

  • SkyWarriorSkyWarrior TurkeyMember ✭✭✭
    edited February 2018

    There is no output because there is an error.

    java.lang.IllegalArgumentException: samples cannot be empty

    This is an error statement.

    There seems to be a problem with the command or with your input files.

  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭
    edited February 2018


    Indeed @SkyWarrior is correct. Can you run ValidateSamFile on your input BAM file.


  • RaziRazi Member

    I want to create Gvcf files for Fst estimate. I use version

    This is my command:
    gatk HaplotypeCaller -R ref.fasta -I input.bam --genotyping_mode DISCOVERY -stand_emit_conf 10 -stand_call_conf 30 -ERC GVCF -variant_index_type LINEAR -variant_index_parameter 128000 -o out.vcf

    But, I got this error:
    A USER ERROR has occurred: genotyping_mode is not a recognized option!

    What should I do? What's wrong? Would you please advice me?


  • RaziRazi Member
    Regarding my last question, I changed the command to:

    gatk HaplotypeCaller -R ref.fasta -I input.bam -ERC GVCF -O out.g.vcf

    Now, it is working. Do you think is there any other problem? I don't like surprise after the long-running time. I like to have the right files as input for Fst!

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin


    Looks good to me. That is the basic haplotypecaller command so it should work.

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