I am working on creating a Panel of Normals starting by calling all my normal samples using the tumor-only mode.
This is the code and GATK version that I am using:
module load bioinfo-tools GATK/18.104.22.168 htslib
gatk Mutect2 -R data/genome/cf4.b6.14.fa \
-I Sample0005.recal.bam \
--max-mnp-distance 0 \
I am running this in my university's computer cluster where I am required to assign an approximate running time for each job. Most of my samples finished without issue in the 3-days running time I assigned them, but one of them came back with the following error:
slurmstepd: error: *** JOB 6574710 ON s24 CANCELLED AT 2022-07-20T13:41:53 DUE TO TIME LIMIT ***
My question is: Does Mutect2 have any kind of feature that would allow me to resume this job without having to restart from the very beginning?
Thank you in advance
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