How to restore an interrupted execution while running HaplotypeCaller
Hi, everyone
Recently I was running a process with HaplotypeCaller that was taking couple of days but the process stopped running at region chr6:114178160. I wonder if it is possible to restore the HaplotypeCaller running session from this specific region. Do I have to run the entire process again?
Additional available information:
a) GATK version used: v4.1.9.0
b) Exact command used:
command="$gatk HaplotypeCaller -R $ref -ERC GVCF -O $gvcf" #-L $intervals"
for i in "${bams[@]}"; do
command="$command -I $i"
done
# run GVCF
eval "$command"
Thank you
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Thank you for your post, David Medina ! I want to let you know we have received your question. 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, everyone
I have the same question about restarting or recovering HaplotypeCaller process
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HaplotypeCaller cannot be resumed or recovered therefore you need to re-run HaplotypeCaller on problematic intervals again but we need more details as to understand why it stops or stalls after a certain amount of time. Can you provide us more specifics about your running environment, samples, reference genome, command line etc.?
Regards.
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I was running around two days:
gatk --java-options "-Xmx54g" HaplotypeCaller --native-pair-hmm-threads 12 --reference GCF_000260255.1_OctDeg1.0_genomic.fna -ERC GVCF --input UACH8217.bam --output ./snp_reducido/UACH8217.gvcf
But after a strong storm, the electricity went out, and the HaplotypeCaller process could not finish; I got an incomplete UACH8217.gvcf file and not the UACH8217.gvcf.idx file. Is there a way to resume the process? -
Our recommendation would be to split your genome into non overlapping intervals and call each interval separately and gather all files once complete. This way you may be able to resume and complete missing parts when there are interruptions.
Regards.
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