BaseRecalibrator on GATK 4.5 Takes multiple days for a sample

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Ryan Welch

• June 25, 2024 20:43

REQUIRED for all errors and issues:
a) GATK version used: 4.5
b) Exact command used: gatk BaseRecalibrator -I /data/BI_data/nbs/aligned_reads/SRR062634_sorted_dedup_reads.bam -R /data/BI_data/nbs/hg38/hg38.fa --known-sites /data/BI_data/nbs/hg38/Homo_sapiens_assembly38.dbsnp138.vcf -O /data/BI_data/nbs/final_data/recal_data.table

I tried the thread "https://gatk.broadinstitute.org/hc/en-us/community/posts/360056396392-BaseRecalibrator-takes-forever-to-run-Any-suggestions?input_string=BaseRecalibrator%20on%20GATK%204.5%20Takes%20multiple%20days%20for%20a%20sample" with no success. 

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  Gökalp Çelik

  • June 26, 2024 04:37
  • Edited

  Have you tried running BaseRecalibrator on separate chromosomes in parallel? If so which ones are taking too long?

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  Ryan Welch

  • June 26, 2024 12:44

  Hello! I will try that and post on here once it is finished. 

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  Ryan Welch

  • June 27, 2024 15:46

  That helped a lot. It takes about 12 hours now. 

  Thank you, 

  Ryan 

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