Unicycler and GNU parallel
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8 months ago
emmanouil.a ▴ 100

Hi,

unfortunately Unicycler forum is inactive and I would like to ask some info.

I'm using a workstation of 56 CPUs with GNU parallel.

When I'm running Unicycler with the "--threads 25" option is going "fast".

When I use GNU parallel, 2 jobs in parallel, is going slower even if I use the "--treads 25" option for all jobs.

I just made a copy of a fastq file (pair-end) to create the samples for the jobs.

Do you have any experience with this and any advice?

Thank you!

Unicycler parallel • 458 views
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Entering edit mode
8 months ago
ole.tange ★ 4.2k

I have no experience with Unicycler, but what you describe sounds very similar to the problem with multi-threaded tesseract: https://github.com/tesseract-ocr/tesseract/issues/3109

Maybe Unicycler uses the same threading technique?

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Hi, thank you very much for your feedback! I will check what threading technique Unicycler use.

Best

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