bismark_methylation_extractor multicore option about bismark

[FelixKrueger]

Hi Albert, the multi-core option works on extracting the methylation information from the BAM file. The subsequent bedGraph sorting and cytosine report step do in fact run on a single core. It would appear that your status report is generated at the cytosine report stage, and 13% might be just about 1 core at 100% on an 8 core machine, would that make sense? This step iterates through the genomic sequence, identifies every C and looks up whether or not the C was found in the coverage file. I theory this could be made more parallel, e.g. by doing it for each chromosome separately, but we did't find it very pressing to work on the efficiency of this step.

[avilella]

Gotcha. So I expect 100% usage in the bam reading step, then after that, 1
CPU.

Definitely going to create a new feature request for this ;-)

On Fri, Jul 1, 2016 at 9:31 AM, FelixKrueger [email protected]
wrote:

Hi Albert, the multi-core option works on extracting the methylation
information from the BAM file. The subsequent bedGraph sorting and cytosine
report step do in fact run on a single core. It would appear that your
status report is generated at the cytosine report stage, and 13% might be
just about 1 core at 100% on an 8 core machine, would that make sense? This
step iterates through the genomic sequence, identifies every C and looks up
whether or not the C was found in the coverage file. I theory this could be
made more parallel, e.g. by doing it for each chromosome separately, but we
did't find it very pressing to work on the efficiency of this step.

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[FelixKrueger]

Considering this question resolved.