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Question: ATACseqQC needs too much memory
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gravatar for mdurante14
7 days ago by
mdurante140
mdurante140 wrote:

I am trying to run this package on a BAM file containing 90 million paired-end reads. I am running this on a linux node with 16 cores and 256 GB of RAM. This pipeline keeps failing because it needs too much memory (267 GB on the most recent failure). Is there anything I can do to allow the package the run with enough memory (possibly splitting analysis up by chromosome and combining the output)? It is failing at the step where it is creating the shifted bam file. Any other recommendations to shift the bam files and split the NFR, and mono-/di-/tri- nucleosome reads. Thanks!

Best regards,

Michael

 

 

ADD COMMENTlink modified 6 days ago by Julie Zhu3.8k • written 7 days ago by mdurante140
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gravatar for Ou, Jianhong
7 days ago by
Ou, Jianhong1000
United States
Ou, Jianhong1000 wrote:

Hi Michael,

Thank you for trying ATACseqQC. Could you let me know the sessionInfo()? Thank you.

ADD COMMENTlink written 7 days ago by Ou, Jianhong1000
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gravatar for Julie Zhu
6 days ago by
Julie Zhu3.8k
United States
Julie Zhu3.8k wrote:

Michael,

The most recent version of ATACseqQC at http://bioconductor.org/packages/devel/bioc/html/ATACseqQC.html should run faster.

Best regards,

Julie

ADD COMMENTlink written 6 days ago by Julie Zhu3.8k
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