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BaseRecalibrator Error

bruce01bruce01 Posts: 20Member
edited September 2012 in Ask the GATK team

Hi, I am getting an error (no info given about causes unfortunately) following running BaseRecalibrator:

java -Xmx4g -jar $tool/GenomeAnalysisTK.jar \ 
    -T BaseRecalibrator \ 
    -I $bwa/BAM/s_1.rmdup_readgps.bam \
        -R $bin/Bos_taurus.UMD3.1.66.fa \
        -knownSites $bin/Bos_taurus_UMD_3.1.DBSNP.zero.ordered.bed \
        -o $gatk/recal_rea/recal_data1.grp

I get output to screen of all chromosomes, positions etc followed by the error

chrX_dna:chromosome_chromosome:UMD3.1:X:1:148823899:1, chr1_dna:chromosome_chromosome:UMD3.1:1:1:158337067:1 #####ERROR------------------------------

Can you suggest any reasons for BaseRecalibrator giving up here? I understand the BED file is 0-based but it has been used successfully in the previous incarnation of BaseRecalibrator. I have tried the knownSites:mask,BED and it has no effect. I have all necessary readgroup info and index for BAM, and indexed BED.

Your help is much appreciated.

Post edited by Geraldine_VdAuwera on

Best Answer

  • ebanksebanks Broad InstitutePosts: 684Member, Administrator, GATK Dev, Broadie, Moderator, DSDE Member, GP Member admin
    Answer ✓

    Hi Bruce,

    What happens when you run with the test files from our bundle? Basically, I think you are encountering a UserError but somehow the error messages are not being printed correctly on your machine. I'm not sure how/why this could be (), but it's almost certainly an issue on your end that we won't be able to help you through unfortunately.

    Eric Banks, PhD -- Senior Group Leader, MPG Analysis, Broad Institute of Harvard and MIT

Answers

  • Mark_DePristoMark_DePristo Posts: 153Administrator, GATK Dev admin

    What's the full error message?

    --
    Mark A. DePristo, Ph.D.
    Co-Director, Medical and Population Genetics
    Broad Institute of MIT and Harvard

  • bruce01bruce01 Posts: 20Member
    edited September 2012

    Hi Mark,

    it is literally as I have it above:
    .#####ERROR------------------------------


    and then it quits to cmd line.

    Bruce.

    Post edited by bruce01 on
  • ebanksebanks Broad InstitutePosts: 684Member, Administrator, GATK Dev, Broadie, Moderator, DSDE Member, GP Member admin

    Hey Bruce,

    Can you please post the entire output (not just the error) of running this command (including the startup logging)?

    Eric Banks, PhD -- Senior Group Leader, MPG Analysis, Broad Institute of Harvard and MIT

  • bruce01bruce01 Posts: 20Member
    edited September 2012

    Hi Eric,

    the start log:

    INFO 07:49:19,854 HelpFormatter - --------------------------------------------------------------------------------

    INFO 07:49:19,857 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.1-8-g5efb575, Compiled 2012/08/30 14:22:17

    INFO 07:49:19,857 HelpFormatter - Copyright (c) 2010 The Broad Institute

    INFO 07:49:19,858 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk

    INFO 07:49:19,859 HelpFormatter - Program Args: -T BaseRecalibrator -I /home/bmoran/data/endo/BWA/BAM/s_1.rmdup_readgps.bam -R /home/bmoran/bin/Bos_taurus.UMD3.1.66.fa -knownSites /home/bmoran/bin/Bos_taurus_UMD_3.1.DBSNP.zero.ordered.bed -o /home/bmoran/data/endo/GATK/recal_rea/recal_data1.grp

    INFO 07:49:19,859 HelpFormatter - Date/Time: 2012/09/07 07:49:19

    INFO 07:49:19,859 HelpFormatter - --------------------------------------------------------------------------------

    INFO 07:49:19,859 HelpFormatter - --------------------------------------------------------------------------------

    INFO 07:49:19,885 ArgumentTypeDescriptor - Dynamically determined type of /home/bmoran/bin/Bos_taurus_UMD_3.1.DBSNP.zero.ordered.bed to be BED

    INFO 07:49:19,898 GenomeAnalysisEngine - Strictness is SILENT

    INFO 07:49:20,563 SAMDataSource$SAMReaders - Initializing SAMRecords in serial

    INFO 07:49:20,708 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.14

    INFO 07:49:20,738 RMDTrackBuilder - Loading Tribble index from disk for file /home/bmoran/bin/Bos_taurus_UMD_3.1.DBSNP.zero.ordered.bed



    Then its spits out a lot of positions from the BED file I have (this is a very small sample):

    chrGJ060140.1_dna:scaffold_scaffold:UMD3.1:GJ060140.1:1:10738:1, chrGJ059471.1_dna:scaffold_scaffold:UMD3.1:GJ059471.1:1:10900:1, chrGJ059939.1_dna:scaffold_scaffold:UMD3.1:GJ059939.1:1:10915:1, chrGJ059912.1_dna:scaffold_scaffold:UMD3.1:GJ059912.1:1:10974:1, chrGJ059893.1_dna:scaffold_scaffold:UMD3.1:GJ059893.1:1:11012:1, chrGJ059957.1_dna:scaffold_scaffold:UMD3.1:GJ059957.1:1:11037:1



    then:
    .##### ERROR --------------------------------------------------

    I have run other commands in GATK and errors are usually quite helpful but this has me stumped. I am trying to use a homemade VCF converted from flat files from Ensembl so fingers crossed I get it working.

    Thanks for your help,

    Bruce.

    Post edited by bruce01 on
  • bruce01bruce01 Posts: 20Member
    edited September 2012

    It is now doing the same thing from my homemade VCF (parsed from ds_flat files). I used vcf-concat to concatenate sorted per-chromosome VCFs. I index with IGVtools but I then get the output

    INFO 13:45:33,064 HelpFormatter - --------------------------------------------------------------------------------

    INFO 13:45:33,067 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.1-8-g5efb575, Compiled 2012/08/30 14:22:17

    INFO 13:45:33,067 HelpFormatter - Copyright (c) 2010 The Broad Institute

    INFO 13:45:33,067 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk

    INFO 13:45:33,068 HelpFormatter - Program Args: -I /home/bmoran/data/endo/BWA/BAM/s_1.rmdup_readgps.bam -R /home/bmoran/bin/Bos_taurus.UMD3.1.66.fa -T RealignerTargetCreator -o /home/bmoran/data/endo/GATK/rea_recal/s_1.forIndelRealigner.intervals --known /home/bmoran/bin/snps/flat.all.sorted.vcf

    INFO 13:45:33,068 HelpFormatter - Date/Time: 2012/09/07 13:45:33

    INFO 13:45:33,069 HelpFormatter - --------------------------------------------------------------------------------

    INFO 13:45:33,069 HelpFormatter - --------------------------------------------------------------------------------

    INFO 13:45:33,081 ArgumentTypeDescriptor - Dynamically determined type of /home/bmoran/bin/snps/flat.all.sorted.vcf to be VCF

    INFO 13:45:33,085 GenomeAnalysisEngine - Strictness is SILENT
    INFO 13:45:33,524 SAMDataSource$SAMReaders - Initializing SAMRecords in serial

    INFO 13:45:33,657 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.13

    INFO 13:45:33,683 RMDTrackBuilder - Loading Tribble index from disk for file /home/bmoran/bin/snps/flat.all.sorted.vcf
    WARN 13:45:33,750 RMDTrackBuilder - Index file /home/bmoran/bin/snps/flat.all.sorted.vcf.idx is out of date (old version), deleting and updating the index file

    INFO 13:45:33,751 RMDTrackBuilder - Creating Tribble index in memory for file /home/bmoran/bin/snps/flat.all.sorted.vcf



    following which it spits out positions and ends with the error as above.

    Bruce.

    Post edited by bruce01 on
  • ebanksebanks Broad InstitutePosts: 684Member, Administrator, GATK Dev, Broadie, Moderator, DSDE Member, GP Member admin
    Answer ✓

    Hi Bruce,

    What happens when you run with the test files from our bundle? Basically, I think you are encountering a UserError but somehow the error messages are not being printed correctly on your machine. I'm not sure how/why this could be (), but it's almost certainly an issue on your end that we won't be able to help you through unfortunately.

    Eric Banks, PhD -- Senior Group Leader, MPG Analysis, Broad Institute of Harvard and MIT

  • bruce01bruce01 Posts: 20Member

    Hi Eric,

    undoubtedly it is an error on my end having had to make my own VCF file following the failure of a BED file previously used successfully on another version of your softwares. I will look at your bundles VCFs and determine what might be my issue.

    Many thanks for the support already,

    Bruce.

  • bruce01bruce01 Posts: 20Member

    Just as a follow-up I had an errant contig in my reference fasta not in my VCF, so the error was telling me that.

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