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ASEReadCounter generates empty output

Hi.
I'm having trouble with ASEReadCounter, the output is empty, there's only the header containing the names of the columns.
The log is this:

20:43:53.002 INFO  ASEReadCounter - Start Date/Time: 24 de outubro de 2018 20:43:45 BRST
20:43:53.002 INFO  ASEReadCounter - ------------------------------------------------------------
20:43:53.002 INFO  ASEReadCounter - ------------------------------------------------------------
20:43:53.003 INFO  ASEReadCounter - HTSJDK Version: 2.16.1
20:43:53.003 INFO  ASEReadCounter - Picard Version: 2.18.13
20:43:53.003 INFO  ASEReadCounter - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:43:53.003 INFO  ASEReadCounter - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:43:53.003 INFO  ASEReadCounter - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:43:53.003 INFO  ASEReadCounter - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:43:53.003 INFO  ASEReadCounter - Deflater: IntelDeflater
20:43:53.003 INFO  ASEReadCounter - Inflater: IntelInflater
20:43:53.004 INFO  ASEReadCounter - GCS max retries/reopens: 20
20:43:53.004 INFO  ASEReadCounter - Requester pays: disabled
20:43:53.004 INFO  ASEReadCounter - Initializing engine
20:43:53.383 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/nalu/macaco/input_varscan/variantes/vcf_E13_1
20:43:53.405 INFO  ASEReadCounter - Done initializing engine
20:43:53.406 INFO  ProgressMeter - Starting traversal
20:43:53.406 INFO  ProgressMeter -        Current Locus  Elapsed Minutes        Loci Processed      Loci/Minute
20:43:58.672 INFO  ASEReadCounter - 2328384 read(s) filtered by: (((((((ValidAlignmentStartReadFilter AND ValidAlignmentEndReadFilter) AND HasReadGroupReadFilter) AND MatchingBasesAndQualsReadFilter) AND SeqIsStoredReadFilter) AND NotDuplicateReadFilter) AND NotSecondaryAlignmentReadFilter) AND MappedReadFilter)
  2328384 read(s) filtered by: ((((((ValidAlignmentStartReadFilter AND ValidAlignmentEndReadFilter) AND HasReadGroupReadFilter) AND MatchingBasesAndQualsReadFilter) AND SeqIsStoredReadFilter) AND NotDuplicateReadFilter) AND NotSecondaryAlignmentReadFilter)
      2328384 read(s) filtered by: (((((ValidAlignmentStartReadFilter AND ValidAlignmentEndReadFilter) AND HasReadGroupReadFilter) AND MatchingBasesAndQualsReadFilter) AND SeqIsStoredReadFilter) AND NotDuplicateReadFilter)
          2328384 read(s) filtered by: ((((ValidAlignmentStartReadFilter AND ValidAlignmentEndReadFilter) AND HasReadGroupReadFilter) AND MatchingBasesAndQualsReadFilter) AND SeqIsStoredReadFilter)
              2328384 read(s) filtered by: (((ValidAlignmentStartReadFilter AND ValidAlignmentEndReadFilter) AND HasReadGroupReadFilter) AND MatchingBasesAndQualsReadFilter)
                  2328384 read(s) filtered by: ((ValidAlignmentStartReadFilter AND ValidAlignmentEndReadFilter) AND HasReadGroupReadFilter)
                      2328384 read(s) filtered by: HasReadGroupReadFilter 

20:43:58.674 INFO  ProgressMeter -             unmapped              0.1                     0              0.0
20:43:58.674 INFO  ProgressMeter - Traversal complete. Processed 0 total loci in 0.1 minutes.
20:43:58.675 INFO  ASEReadCounter - Shutting down engine
[24 de outubro de 2018 20:43:58 BRST] org.broadinstitute.hellbender.tools.walkers.rnaseq.ASEReadCounter done. Elapsed time: 0.22 minutes.
Runtime.totalMemory()=8367636480

My command line looks like this:

gatk ASEReadCounter -R /path/to/ref.fa \ -I /path/to/sample.bam \ -V /path/to/VCFfile.vcf \ -O output.csv

What could be wrong? I've tried using another vcf file but I still get the same empty output.
Thanks.

Answers

  • Steph_UCSteph_UC Member
    edited October 14

    @nalu Was this problem solved?
    I am having the same exact problem. I don't know what is wrong. I created a test where I clearly have HET variants in the region and reads that map there. My output file only contains the header and nothing else and no error message is shown. Just this message below

    10:32:52.638 INFO ASEReadCounter - ------------------------------------------------------------
    10:32:52.639 INFO ASEReadCounter - The Genome Analysis Toolkit (GATK) v4.1.3.0
    10:32:52.639 INFO ASEReadCounter - For support and documentation go to https://software.broadinstitute.org/gatk/
    10:32:52.639 INFO ASEReadCounter - Executing as XXXXX on Linux v3.10.0-514.el7.x86_64 amd64
    10:32:52.639 INFO ASEReadCounter - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_102-b14
    10:32:52.639 INFO ASEReadCounter - Start Date/Time: October 14, 2019 10:32:50 AM PDT
    10:32:52.640 INFO ASEReadCounter - ------------------------------------------------------------
    10:32:52.640 INFO ASEReadCounter - ------------------------------------------------------------
    10:32:52.640 INFO ASEReadCounter - HTSJDK Version: 2.20.1
    10:32:52.640 INFO ASEReadCounter - Picard Version: 2.20.5
    10:32:52.640 INFO ASEReadCounter - HTSJDK Defaults.COMPRESSION_LEVEL : 2
    10:32:52.640 INFO ASEReadCounter - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
    10:32:52.640 INFO ASEReadCounter - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
    10:32:52.640 INFO ASEReadCounter - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
    10:32:52.640 INFO ASEReadCounter - Deflater: IntelDeflater
    10:32:52.641 INFO ASEReadCounter - Inflater: IntelInflater
    10:32:52.641 INFO ASEReadCounter - GCS max retries/reopens: 20
    10:32:52.641 INFO ASEReadCounter - Requester pays: disabled
    10:32:52.641 INFO ASEReadCounter - Initializing engine
    10:32:53.238 INFO FeatureManager - Using codec VCFCodec to read file file:///mnt/beegfs/Steph_WKDIR/Testing/myvcf.vcf
    10:32:53.253 INFO ASEReadCounter - Done initializing engine
    10:32:53.254 INFO ProgressMeter - Starting traversal
    10:32:53.255 INFO ProgressMeter - Current Locus Elapsed Minutes Loci Processed Loci/Minute
    10:33:31.395 INFO ASEReadCounter - 35086385 read(s) filtered by: (((((((ValidAlignmentStartReadFilter AND ValidAlignmentEndReadFilter) AND HasReadGroupReadFilter) AND MatchingBasesAndQualsReadFilter) AND SeqIsStoredReadFilter) AND NotDuplicateReadFilter) AND NotSecondaryAlignmentReadFilter) AND MappedReadFilter)
    35086385 read(s) filtered by: ((((((ValidAlignmentStartReadFilter AND ValidAlignmentEndReadFilter) AND HasReadGroupReadFilter) AND MatchingBasesAndQualsReadFilter) AND SeqIsStoredReadFilter) AND NotDuplicateReadFilter) AND NotSecondaryAlignmentReadFilter)
    35086385 read(s) filtered by: (((((ValidAlignmentStartReadFilter AND ValidAlignmentEndReadFilter) AND HasReadGroupReadFilter) AND MatchingBasesAndQualsReadFilter) AND SeqIsStoredReadFilter) AND NotDuplicateReadFilter)
    35086385 read(s) filtered by: ((((ValidAlignmentStartReadFilter AND ValidAlignmentEndReadFilter) AND HasReadGroupReadFilter) AND MatchingBasesAndQualsReadFilter) AND SeqIsStoredReadFilter)
    35086385 read(s) filtered by: (((ValidAlignmentStartReadFilter AND ValidAlignmentEndReadFilter) AND HasReadGroupReadFilter) AND MatchingBasesAndQualsReadFilter)
    35086385 read(s) filtered by: ((ValidAlignmentStartReadFilter AND ValidAlignmentEndReadFilter) AND HasReadGroupReadFilter)
    35086385 read(s) filtered by: HasReadGroupReadFilter

    10:33:31.397 INFO ProgressMeter - unmapped 0.6 0 0.0
    10:33:31.397 INFO ProgressMeter - Traversal complete. Processed 0 total loci in 0.6 minutes.
    10:33:31.398 INFO ASEReadCounter - Shutting down engine
    [October 14, 2019 10:33:31 AM PDT] org.broadinstitute.hellbender.tools.walkers.rnaseq.ASEReadCounter done. Elapsed time: 0.68 minutes.
    Runtime.totalMemory()=3591372800

  • nalunalu Member
    Hi!
    Yes, I solved this problem but it was a while ago so I can't remember exactly what was the problem.
    My best guess is it's because the read groups are messed up or non-existent. So you could try using the tool AddOrReplaceReadGroups to specify the read groups for your file.
    Try following this advices here: https://gatkforums.broadinstitute.org/gatk/discussion/2909

    Good luck!
  • Steph_UCSteph_UC Member

    I forgot to update,
    Thank you @nalu
    It was a read group assignment problem.
    Picard 's AddOrReplaceReadGroups solved it.

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