GATK BQSR is taking too long to be run (running since last 6 days)

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Niharika

• November 07, 2023 05:10

REQUIRED for all errors and issues:
a) GATK version used: 4.0.5.1
b) Exact command used:gatk BaseRecalibrator -I Alignment/SRR******_aln_pe_withRG.bam -R GATKBQSR/genome.fna --known-sites GATKBQSR/GRCh38_latest_dbSNP_all.vcf --sequence-dictionary GATKBQSR/genome.dict -O GATKBQSR/Build_model/recal_data.table  
c) Entire program log: Not generated yet

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  Gökalp Çelik

  • November 07, 2023 06:56

  Hi Niharika

  How many reads do you have in that bam file? Also can you share the specs of the compute environment that you are running this tool? 

  It is possible that the java VM is actually hung and the tool itself is not doing anything at all.

  Can you provide us more information about these matters?

  Regards. 

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  Niharika

  • December 01, 2023 12:08

  Hello,

  Using sorted bam solved my problem

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