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FelixKrueger / Bismark

A tool to map bisulfite converted sequence reads and determine cytosine methylation states
http://felixkrueger.github.io/Bismark/
GNU General Public License v3.0
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Methylation extractor stuck #644

Open xbarvazx opened 6 months ago

xbarvazx commented 6 months ago

Hi,

I am running methylation_extractor and the process gets stuck. I have run this successfully in the past. the output error last lines are:

Processed lines: 554500000
Finished processing child process. Exiting..

I tried it a few times and its always stuck at this part while the job seems to continue running for days.

bismark_methylation_extractor --multicore 25 --no_overlap --gzip --bedGraph --comprehensive --no_header --buffer_size 100G -o bismark_result2 raw.deduplicated.bam > bismark_extract.log 2> bismark_extract.err &

Thanks, Raz

FelixKrueger commented 6 months ago

hmm, is it sill doing something? Can you run top to see? Has it progressed to the bedGraph conversion step yet, or is it stuck at the extraction stage? You should be able to see a single splitting report and M-bias file in the folder if the extraction is complete. Is there anything informative in the STDOUT log?

The only thing that looks a little dodgy to me is the high number of --multicore ....

xbarvazx commented 6 months ago

Hi Felix,

No its stuck at the extraction stage. The log file is empty. --multicore is the available cores right? I have a whole node allocated with 80 cores. I could actually increase it if it might help?

FelixKrueger commented 6 months ago

If anything I would probably try to bring it down to point where you are happy that it is alll still working as expected... maybe --parallel 8?

xbarvazx commented 6 months ago

Hi Felix,

it worked with --parallel 8 instead or --multicore 25 Interesting that it failed now and not with other similar runs I did.

Thanks anyway! Raz