Error - Mutect2 PG tag
REQUIRED for all errors and issues:
a) GATK version used: 4.3.0.0
b) Exact command used: gatk Mutect2 -R Homo_sapiens.GRCh38.dna.primary_assembly.fa -I tumor.bam -I normal.bam -normal Normal --germline-resource af-only-gnomad.hg38.vcf.gz --panel-of-normals pon.vcf.gz --af-of-alleles-not-in-resource 0.000001 -O sample.vcf.gz -bamout sample_m2.bam
c) Entire program log:
[December 8, 2022 at 11:52:41 AM KST] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2147483648
htsjdk.samtools.SAMException: 4 program groups weren't processed. Do their PP ids point to existing PGs?
@PG ID:samtools.1 PN:samtools PP:tumor
@PG ID:samtools.3 PN:samtools PP:samtools.1
@PG ID:samtools.1 PN:samtools PP:normal
@PG ID:samtools.3 PN:samtools PP:samtools.1
What should I do to solve this error? Thank you in advance.
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