Killed process dedup

[denise0593]

Dear author,
I'm trying to run umi dedup on a bam file, but the process is always killed. I've used the same command on many other bams and the process ends, only with two samples, the process is killed. I cannot understand why.

umi_error.txt

[IanSudbery]

Process killed comes from your operating system (linux in your case). The most common cause is the system running out of memory.

[denise0593]

Thanks @IanSudbery is there any option to parallelize the process?
I can't see anything in the help...

[IanSudbery]

Unfortunately there is no parallelization at the moment. There is a long standing open issue to implement this, but so far everything we have tried as made the processing slower, rather than quicker. If you want to parallelize, I suggest that you divide your bam file into contigs, and run each contig separately, and then combine the outputs. However, be aware that if you are having trouble with running out of memory for a running everything on a single processor, parallelelized processes tend to use more memory than single threaded ones. Ian Sudbery (He/Him) Senior Lecturer in Bioinformatics, Sheffield Institute for Nucleic Acids, School of Biosciences, The University of Sheffield. web: www.sudlab.co.uk Tel: 0114 222 2738 Twitter: IanSudbery Show Calendar Availability <https://calendar.google.com/calendar/u/0?cid=aS5zdWRiZXJ5QHNoZWZmaWVsZC5hYy51aw>

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