BaseRecalibrator stops working after 0.01 minutes; no error message

jreevejreeve Member
edited October 2018 in Ask the GATK team

I'm trying to run BQSR on a .bam file using an known set of SNPs I downloaded from Dyrad ( I'm able to BaseRecalibrator working, but it stops immediately after initialising. I don't even have an empty output file. Any ideas where the problem might lie?

My Code:
./gatk BaseRecalibrator -R reference_genome.fa -I file1.bam --known-sites Stickleback_SNPs.vcf -O file1_recal.table

Output Log:
19:07:12.026 INFO NativeLibraryLoader - Loading from jar:file:/data/programs/gatk-!/com/intel/gkl/native/
19:07:12.135 INFO BaseRecalibrator - ------------------------------------------------------------
19:07:12.135 INFO BaseRecalibrator - The Genome Analysis Toolkit (GATK) v4.0.4.0
19:07:12.135 INFO BaseRecalibrator - For support and documentation go to
19:07:12.136 INFO BaseRecalibrator - Executing as [email protected] on Linux v3.10.0-862.9.1.el7.x86_64 amd64
19:07:12.136 INFO BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_181-b13
19:07:12.136 INFO BaseRecalibrator - Start Date/Time: October 3, 2018 7:07:12 MDT PM
19:07:12.136 INFO BaseRecalibrator - ------------------------------------------------------------
19:07:12.136 INFO BaseRecalibrator - ------------------------------------------------------------
19:07:12.137 INFO BaseRecalibrator - HTSJDK Version: 2.14.3
19:07:12.137 INFO BaseRecalibrator - Picard Version: 2.18.2
19:07:12.137 INFO BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:07:12.137 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:07:12.137 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:07:12.137 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:07:12.137 INFO BaseRecalibrator - Deflater: IntelDeflater
19:07:12.137 INFO BaseRecalibrator - Inflater: IntelInflater
19:07:12.137 INFO BaseRecalibrator - GCS max retries/reopens: 20
19:07:12.137 INFO BaseRecalibrator - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from
19:07:12.137 INFO BaseRecalibrator - Initializing engine
19:07:12.571 INFO FeatureManager - Using codec VCFCodec to read file file:///data/home/james/stickleback_LD/BQSR_SNPs_Fang2018.vcf
19:07:12.584 INFO BaseRecalibrator - Shutting down engine
[October 3, 2018 7:07:12 MDT PM] done. Elapsed time: 0.01 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.ReadWalker.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(

Best Answer


  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin


    Sorry about the delayed response as I was out sick.
    I need a little more information before resolving this issue. Have you been able to repeat this issue? Are you running this command on a NFS?


  • jreevejreeve Member


    This issue is repeating each time I run BaseRecalibrator and now the same thing is happening for HaplotypeCaller.

    I'm running this command on a lab server using a SSH from my local machine. If this is different to NFS please let me know.


  • jreevejreeve Member

    Hi @bhanuGandham,

    ValidateSamFile picked up the problem I was missing some read group information. I fixed it up with picard tools' AddOrReplaceReadGroups and it works now. Thanks for your help.


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