[bwa_aln_core] calculate SA coordinate... script.sh: line 91: 183402 Killed

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2.2 years ago

qstefano ▴ 20

Hello there,

I'm aligning my reads to a reference genome with bwa aln but checking the log file can see the error:

[bwa_aln_core] calculate SA coordinate... script.sh: line 91: 183402 Killed

The alignment is still running (I'm working on HPC) with 30 threads on one node. What possible explanation could there be?

Thanks.

HPC BWA Alignment • 736 views

ADD COMMENT • link updated 11 months ago by Ram 43k • written 2.2 years ago by qstefano ▴ 20

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For HPC, what gets your processes killed is mostly RAM. Abort the job, request more RAM e.g double, and run again.

ADD REPLY • link 2.2 years ago by Michael 54k

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Agreed. If I look here Explanation of dimension differences between bam files (BWA aln and BWA mem) you're using 30 threads already in BWA which needs a lot of memory and then 30 threads in sort (which is piped so it is more than you requested on CPU). Also, samtools needs 768MB of RAM per thread so that alone is 23GB of RAM for the sorting. Just use a low number here, something like 4 CPUs for the sort, it is relatively fast.