Multicore support issues

FelixKrueger / TrimGalore

A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data

GNU General Public License v3.0

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Multicore support issues #101

Closed dahun73 closed 4 years ago

dahun73 commented 4 years ago

Hello,

I'm using Trim_galore ususally when I'm pre-processing my all raw data. However, today I found something wrong running trim_galore. Multicore support is not enabled now.

As you can see, cutadapt version is 2.10. Trim_galore version is 0.6.5dev now. Is there any solution about that?

FelixKrueger commented 4 years ago

I think enabling multicore usage requires you to specify -j 2 or more (ideally not more than 4 as it doesn't bring much extra beyond 4). In order to work fully you will need pigz and Python 3 running on your system.

dahun73 commented 4 years ago

Thank you for reply!

So, I checked my packages. I'm using 'pigz' and Python3 now. Also, our server could use 40 multi-cores now. Actually, It didn't come out multicore support issue the day before. Yesterday, it came out suddenly... Also, it came out multicore issue but it is working well(I don't know it work with multicore).

FelixKrueger commented 4 years ago

Excellent, so I think we can assume this is now all working?