Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

GATK process banner

Need Help?

Search our documentation

Community Forum

Hi, How can we help?

Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

Haplotype caller error file not found

Answered
0

6 comments

  • Avatar
    Genevieve Brandt (she/her)

    Hi Quentin Chartreux,

    Could you give the specific filenames in your HaplotypeCaller command that are associated with this error message?

    Best,

    Genevieve

    0
    Comment actions Permalink
  • Avatar
    Quentin Chartreux

    Hi Genevieve Brandt (she/her)

    In the log it's written : 

     -I /shared/projects/gentaumix/processed_data_set5/03_Alignment/D_recal/G632_DA_C002A5Q_1_H5N3JDSX2.DUAL2.trimmed.align.filtered.dedup.fixed.recal.bam -O /shared/projects/gentaumix/processed_data_set5/05_VCF/A_gVCF/G632_DA_C002A5Q_1_H5N3JDSX2.DUAL2.trimmed.align.filtered.dedup.fixed.recal.bam/temp_gVCF/0018.G632_DA_C002A5Q_1_H5N3JDSX2.DUAL2.trimmed.align.filtered.dedup.fixed.recal.g.vcf.gz 
    0
    Comment actions Permalink
  • Avatar
    Quentin Chartreux

    It's not an important error as at the end it work, but it's a bit annoying to have the job running for 2 hours to ultimately fail without really knowing why and only being able to restart it, hoping that this time it passes ...

    0
    Comment actions Permalink
  • Avatar
    Genevieve Brandt (she/her)

    Hi Quentin Chartreux,

    Oh yeah, you're right! It looks like the problem is from the output file. There is also another error message at the bottom:

    Caused by: java.nio.file.FileSystemException: 
    /shared/projects/gentaumix/processed_data_set5/05_VCF/A_gVCF/G632_DA_C002A5Q_1_H5N3JDSX2.DUAL2.trimmed.align.filtered.dedup.fixed.recal.bam/temp_gVCF/0018.G632_DA_C002A5Q_1_H5N3JDSX2.DUAL2.trimmed.align.filtered.dedup.fixed.recal.g.vcf.gz:
    Erreur de protocole

    srun: error: cpu-node-61: task 0: Exited with exit code 3

    This looks to me like an I/O problem which is most likely being caused by your cluster or filesystem. You can look into the exit code 3 more closely to figure out why your job is not able to create the output file.

    Best,

    Genevieve

    0
    Comment actions Permalink
  • Avatar
    Quentin Chartreux

    Hi Genevieve Brandt (she/her)

     

    I asked the administrators of our cluster, we can not find out where the problem comes from, especially since the file in question is indeed created by haplotypecaller even if it is completely empty so I do not understand well why it says it can't find it.

    0
    Comment actions Permalink
  • Avatar
    Genevieve Brandt (she/her)

    The error message that HaplotypeCaller cannot find the file doesn't usually mean it doesn't exist, usually there's another problem. There could be too many jobs writing to files in that directory, or potentially permissions issue.

    This part of the stack trace is most likely much more descriptive to what is going on in your file system:

    Caused by: java.nio.file.FileSystemException: /shared/projects/gentaumix/processed_data_set5/05_VCF/A_gVCF/G632_DA_C002A5Q_1_H5N3JDSX2.DUAL2.trimmed.align.filtered.dedup.fixed.recal.bam/temp_gVCF/0018.G632_DA_C002A5Q_1_H5N3JDSX2.DUAL2.trimmed.align.filtered.dedup.fixed.recal.g.vcf.gz: Erreur de protocole
    at sun.nio.fs.UnixException.translateToIOException(UnixException.java:91)
    at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:102)
    at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:107)
    at sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:214)
    at java.nio.file.spi.FileSystemProvider.newOutputStream(FileSystemProvider.java:434)
    at java.nio.file.Files.newOutputStream(Files.java:216)
    at htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder.build(VariantContextWriterBuilder.java:447)
    ... 11 more
    srun: error: cpu-node-61: task 0: Exited with exit code 3
    0
    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk