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We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
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If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
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Attention:
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!
DepthOfCoverage memory usage
igor
New YorkMember ✭✭
Is there a way to manage DepthOfCoverage memory usage? I am having problems when I give it a large intervals file. I can successfully run other tools like RealignerTargetCreator, IndelRealigner, and BaseRecalibrator, which seem like they would be more memory-intensive. I can also run DepthOfCoverage with --omitIntervalStatistics --omitLocusTable --omitDepthOutputAtEachBase. However, running it with just --omitDepthOutputAtEachBase gives me a memory error:##### ERROR MESSAGE: There was a failure because you did not provide enough memory to run this program. See the -Xmx JVM argument to adjust the maximum heap size provided to Java
Is there any way to optimize that?
Tagged:
Answers
You can give GATK 4GB of memory like this:
I already assign certain amounts of memory for all of the tools, which is much larger than the BAM sizes. I can do that. My question is why DepthOfCoverage is only one that has any problems and only with certain parameters.
@igor
Hi,
I suspect you have some regions of very high coverage. DepthOfCoverage performs badly on those regions because it does not apply any downsampling, but other tools do not perform badly on those regions because they do apply downsampling.
-Sheila
I explicitly turn off downsampling on all tools. Also, DepthOfCoverage works, but only with certain parameters. That is the troubling part for me.
So what you're really saying is that asking DoC to calculate Interval Statistics and/or Locus Tables is taking too much memory? This seems reasonable to me. The help for --omitLocusTable says that you're deciding whether to calculate "per-sample per-depth counts of loci". You've not described your data at all, but it's not hard to imagine that computing a depth histogram for every sample simultaneously might require some memory.
I am only using one sample at a time.