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

FilterMutectCalls complains about the --ob-prior file's result

Follow
Avatar
Thomas Sunghoon Huh

Hi team,

While I'm using the Mutect2, the FilterMutectCalls failed to execute with the error message descripted below.

It is strange that the f1r2 orientation bias was calculated together with the Mutect2 was launched. 

What I have tried was unzip the f1r2.tar.gz file and checked the file content. The content seems correct. 

Because I never experienced this error before, I wish you could give me kind explanation or troubleshoot guideline.

Best, Thomas.

REQUIRED for all errors and issues:

a) GATK version used: 4.2.0.0
b) Exact command used:

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 -Xmx32g -DGATK_STACKTRACE_ON_USER_EXCEPTION=true -jar /user/huh/anaconda3/envs/aldetect/share/gatk4-4.2.0.0-1/gatk-package-4.2.0.0-local.jar FilterMutectCalls -R /pipeline/reference/GRCh38/Homo_sapiens_assembly38.MaskV1.fasta -V /pipeline/180bp_pbmc/vcf/RES-096.mt2.vcf -O /pipeline/180bp_pbmc/vcf/RES-096.mt2.filtered.vcf --ob-priors /pipeline/180bp_pbmc/vcf/RES-096.f1r2.tar.gz --contamination-table /pipeline/180bp_pbmc/vcf/RES-096.calculatecontamination.table --tumor-segmentation /pipeline/180bp_pbmc/vcf/RES-096.tumor_segments.table --tmp-dir /pipeline/180bp_pbmc/vcf/RES-096/filter_mutect_call_tmp


c) Entire program log:
```

12:36:07.760 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/user/huh/anaconda3/envs/aldetect/share/gatk4-4.2.0.0-1/gatk-package-4.2.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Apr 11, 2023 12:36:07 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
12:36:07.886 INFO  FilterMutectCalls - ------------------------------------------------------------
12:36:07.887 INFO  FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.2.0.0
12:36:07.887 INFO  FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
12:36:07.887 INFO  FilterMutectCalls - Executing as huh@node09 on Linux v4.18.0-305.3.1.el8.x86_64 amd64
12:36:07.887 INFO  FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_302-b08
12:36:07.887 INFO  FilterMutectCalls - Start Date/Time: April 11, 2023 12:36:07 PM KST
12:36:07.887 INFO  FilterMutectCalls - ------------------------------------------------------------
12:36:07.887 INFO  FilterMutectCalls - ------------------------------------------------------------
12:36:07.887 INFO  FilterMutectCalls - HTSJDK Version: 2.24.0
12:36:07.888 INFO  FilterMutectCalls - Picard Version: 2.25.0
12:36:07.888 INFO  FilterMutectCalls - Built for Spark Version: 2.4.5
12:36:07.888 INFO  FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
12:36:07.888 INFO  FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
12:36:07.888 INFO  FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
12:36:07.888 INFO  FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
12:36:07.888 INFO  FilterMutectCalls - Deflater: IntelDeflater
12:36:07.888 INFO  FilterMutectCalls - Inflater: IntelInflater
12:36:07.888 INFO  FilterMutectCalls - GCS max retries/reopens: 20
12:36:07.888 INFO  FilterMutectCalls - Requester pays: disabled
12:36:07.888 INFO  FilterMutectCalls - Initializing engine
12:36:08.242 INFO  FeatureManager - Using codec VCFCodec to read file file:///pipeline/180bp_pbmc/vcf/RES-096.mt2.vcf
12:36:08.373 INFO  FilterMutectCalls - Done initializing engine
12:36:08.461 INFO  IOUtils - Extracting data from archive: file:///pipeline/180bp_pbmc/vcf/RES-096.f1r2.tar.gz
12:36:08.466 INFO  IOUtils - Extracting file: ./RES-096.ref_histogram
12:36:08.468 INFO  IOUtils - Extracting file: ./RES-096.alt_table
12:36:08.689 INFO  IOUtils - Extracting file: ./RES-096.alt_histogram
12:36:08.702 INFO  FilterMutectCalls - Shutting down engine
[April 11, 2023 12:36:08 PM KST] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2373976064
***********************************************************************

A USER ERROR has occurred: Bad input: format error in '/pipeline/180bp_pbmc/vcf/RES-096/filter_mutect_call_tmp/extract1505886170186663745/RES-096.ref_histogram' at line 6: mismatch between number of values in line (65) and number of columns (1)

***********************************************************************
org.broadinstitute.hellbender.exceptions.UserException$BadInput: Bad input: format error in '/pipeline/180bp_pbmc/vcf/RES-096/filter_mutect_call_tmp/extract1505886170186663745/RES-096.ref_histogram' at line 6: mismatch between number of values in line (65) and number of columns (1)
    at org.broadinstitute.hellbender.utils.tsv.TableReader.formatException(TableReader.java:237)
    at org.broadinstitute.hellbender.utils.tsv.TableReader.fetchNextRecord(TableReader.java:362)
    at org.broadinstitute.hellbender.utils.tsv.TableReader.access$200(TableReader.java:99)
    at org.broadinstitute.hellbender.utils.tsv.TableReader$1.hasNext(TableReader.java:472)
    at java.util.Iterator.forEachRemaining(Iterator.java:115)
    at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
    at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482)
    at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:472)
    at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708)
    at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
    at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:566)
    at org.broadinstitute.hellbender.utils.tsv.TableReader.toList(TableReader.java:532)
    at org.broadinstitute.hellbender.tools.walkers.readorientation.ArtifactPriorCollection.readArtifactPriors(ArtifactPriorCollection.java:73)
    at org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ReadOrientationFilter.lambda$new$0(ReadOrientationFilter.java:26)
    at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1384)
    at java.util.stream.ReferencePipeline$Head.forEach(ReferencePipeline.java:647)
    at org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ReadOrientationFilter.<init>(ReadOrientationFilter.java:25)
    at org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2FilteringEngine.buildFiltersList(Mutect2FilteringEngine.java:311)
    at org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2FilteringEngine.<init>(Mutect2FilteringEngine.java:60)
    at org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls.onTraversalStart(FilterMutectCalls.java:138)
    at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1056)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
    at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
    at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
    at org.broadinstitute.hellbender.Main.main(Main.java:289)

```

0

6 comments

Sort by Date Votes
  • Avatar
    David Benjamin

    What is your Mutect2 command?

    0
    Comment actions Permalink
  • Avatar
    Thomas Sunghoon Huh

    Sorry for the late reply.

    I was almost buried in the pile of documents recent days.

    Command line I used :

    gatk --java-options '-Xmx32g' Mutect2 --tmp-dir gatk_tmp -L /panel/dev/C_WES_hg38.sort.bed -I bam/RES-096.bqsr.bam --reference /pipeline/reference/GRCh38/Homo_sapiens_assembly38.MaskV1.fasta --f1r2-tar-gz vcf/RES-096.f1r2.tar.gz -O vcf/RES-096.mt2.vcf --create-output-variant-md5 true --bam-output bcf/RES-096.mt2.haplotype.bam --create-output-bam-md5 true

    Thanks.

    0
    Comment actions Permalink
  • Avatar
    David Benjamin

    Thomas Sunghoon Huh I have never seen this error before, but it seems like running different versions of the GATK for Mutect2 and FilterMutectCalls could do it.  I notice that the two tools are being run from different directories and that one is being invoked with java -jar path_to_gatk.jar while one is invoked with the gatk shell script.  Could you verify that Mutect2 is also running version 4.2.0.0?

    If that doesn't fix it, I will have to think much harder.

    0
    Comment actions Permalink
  • Avatar
    Thomas Sunghoon Huh

    David Benjamin

    Sorry for the late reply. After re-ran the Mutect2 again, those errors disappeared. As you mentioned, it might be the problem of the version.

    Thank you!

    0
    Comment actions Permalink
  • Avatar
    Daniel Gaston

    Hi Everyone,

    I am receiving this same error, but I am running back to back commands from the same gatk script between MuTect2 and FilterMutect. For context this is tumour-only and I am calling on algined RNA-Seq data.

    My MuTect2 command is: 

    gatk Mutect2 -I recalibrated.bam -R ref_genome.fa --germline-resourceaf-only-gnomad.hg38.vcf.gz --native-pair-hmm-threads 8 --f1r2-tar-gz mutect.f1r2.tar.gz -G StandardMutectAnnotation -O mutect2.vcf

    my FilterMutect command is:

    gatk FilterMutectCalls -V mutect2.vcf -R ref_genome.fa --ob-priors mutect.f1r2.tar.gz -O mutect2.filtered.vcf

    Any insight? I haven't been able to sort this out

     

    0
    Comment actions Permalink
  • Avatar
    David Benjamin

    Are you running this locally, on the cloud, or on.a batch server like SLURM or SGE?

    0
    Comment actions Permalink

Please sign in to leave a comment.

Welcome

Forum Guidelines

GATK Announcements

Become a GATK Guru

Read Before You Post

Get Email Notifications

Didn't find what you were looking for?

New post

Quick Links

GATK Latest Releases

Known Issues & Troubleshooting

Submitting a Bug Report

How to Track a Github issue

GATK on the Cloud with Terra

Recent GATK News

GATK Blog Posts

GATK Twitter Page

About the GATK community

  • 133,119 Total Users
  • 0 Comments
  • 0 Posts
  • 0 Votes
Powered by Zendesk