How can I resume a failed/interrupted Mutect2 tumor-only mode run?
Answered
Hello,
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/4.1.4.1 htslib
gatk Mutect2 -R data/genome/cf4.b6.14.fa \
-I Sample0005.recal.bam \
--max-mnp-distance 0 \
-O Sample0005.vcf.gz
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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Thank you for your post, Anna Darlene van der Heiden! I want to let you know we have received your question and will be moving it to the Community Discussions -> General Discussion topic, as the Other topic is for reporting bugs and issues with GATK.
We'll get back to you if we have any updates or follow up questions. Please see our Support Policy for more details about how we prioritize responding to questions.
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Hi Anna Darlene van der Heiden,
Unfortunately there is no way to resume your Mutect2 run. If there are samples that are large and having a difficult time finishing, you can break up your analysis by intervals and then merge the output VCFs with MergeVCFs: https://gatk.broadinstitute.org/hc/en-us/articles/5358883370011-MergeVcfs-Picard-.
Let me know if you have any other questions.
Best regards,
Genevieve
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Hi Anna,
We haven't heard from you in a while so we're going to close out this ticket in our system. If you still require assistance, simply respond to this thread and we'll be happy to pick up where we left off!
Kind regards,
Genevieve
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