Comments (3)
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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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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Considering this question resolved.
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Related Issues (20)
- Confusion on how coverage is estimated HOT 4
- Low unique alignment % HOT 8
- Analyzing spike in control performance HOT 2
- How to extract methylation levels according to bam file HOT 6
- Correcting low % methylated regions HOT 4
- help combining bismark pipeline with methylated UMIs HOT 8
- Expected unique alignment % HOT 2
- Parent process: Failed to build index HOT 3
- bismark runs to an error when I try to run it using nextflow HOT 4
- Differences in bismark convertion result HOT 1
- Bismark genome preparation issue HOT 3
- Use SRR files with .rar (ziped) format HOT 1
- Dose it necessary to place reads in working directory? HOT 1
- Issue with Perl in filter_non_conversion HOT 4
- bismark for human genome HOT 3
- ambiguous results in .bam file HOT 3
- deduplicate_bismark problem HOT 4
- index of genome faulty or non-existant HOT 5
- Bismark2summary not working for output with hisat2 HOT 6
- directional and nondirectional HOT 6
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