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Stop in Mutect2 running on an early phase
Hello, GATK team
I have some problems with running Mutect2
I have some sample aligned hg19 (including chrM, 1-22, X, Y) reference genome
and I did run mutect2 with these samples (normal and tumor, also)
but when I checked output vcf files, only I could see variants on chrM and chr1
so, I did re-run mutect2 and stopping situation in mutect2 running on chromosome 1 early phase and that look like just end of analysis procedure (no error message, no warning message)
I attached captured image about this situation
How can i solve this?