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HaplotypeCaller successfully generated my g.vcf.gz, no error message but exit status!=0

lindenblindenb FranceMember ✭✭

Hi the gatk team,
I used HaplotypeCaller to generate a vcf file. Everything went fine : I got no error message, the vcf.gz and the vcf.gz.tbi were generated , however, the exit status was not '0' but 141

Dec 11, 2019 1:03:37 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
13:03:37.743 INFO  HaplotypeCaller - ------------------------------------------------------------
13:03:37.744 INFO  HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.1.4.1
13:03:37.744 INFO  HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/
13:03:37.745 INFO  HaplotypeCaller - Executing as [email protected] on Linux v3.10.0-957.21.3.el7.x86_64 amd64
13:03:37.745 INFO  HaplotypeCaller - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_131-b11
13:03:37.746 INFO  HaplotypeCaller - Start Date/Time: December 11, 2019 1:03:36 PM CET
13:03:37.746 INFO  HaplotypeCaller - ------------------------------------------------------------
13:03:37.746 INFO  HaplotypeCaller - ------------------------------------------------------------
13:03:37.749 INFO  HaplotypeCaller - HTSJDK Version: 2.21.0
13:03:37.750 INFO  HaplotypeCaller - Picard Version: 2.21.2
13:03:37.750 INFO  HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:03:37.750 INFO  HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:03:37.750 INFO  HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:03:37.750 INFO  HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:03:37.751 INFO  HaplotypeCaller - Deflater: IntelDeflater
13:03:37.751 INFO  HaplotypeCaller - Inflater: IntelInflater
13:03:37.751 INFO  HaplotypeCaller - GCS max retries/reopens: 20
13:03:37.751 INFO  HaplotypeCaller - Requester pays: disabled
13:03:37.751 INFO  HaplotypeCaller - Initializing engine
13:28:24.643 INFO  HaplotypeCaller - Shutting down engine
[December 11, 2019 1:28:24 PM CET] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 24.81 minutes.
Using GATK jar /sandbox/apps/bioinfo/binaries/gatk/0.0.0/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 -Djava.
io.tmpdir=. -Xmx5g -jar /path/to/gatk-package- HaplotypeCaller --tmp-dir . --reference /path/to/ref.fasta -I /path/to/input.bam -L <my-interval>  -O out.g.vcf.gz --dbsnp path/to/dbsnp_135.b3
7.vcf.gz --do-not-run-physical-phasing --emit-ref-confidence GVCF

the vcf is ok

$ bcftools view out.g.vcf.gz > /dev/null && echo ok

$ bcftools view out.g.vcf.gz 22 > /dev/null && echo ok

is there anything I can do to know about this error ? My FS is quite slow those days, is there any timeout to unlock some files ?


  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin
    edited December 2019

    Hi @lindenb

    This looks like a I/O issue. It's probably not a HaplotypeCaller issue and instead maybe happening due to the command and the way it is piped or I/O redirection

    Can you please post
    1. the entire error log
    2. the exact command as typed in the shell including any piping and I/O redirection

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