[bwa_aln_core] calculate SA coordinate... script.sh: line 91: 183402 Killed
0
0
Entering edit mode
3 months 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.

Error BWA HPC Alignment • 251 views
ADD COMMENT
2
Entering edit mode

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

ADD REPLY
1
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

Great, thank you both for the great explanation!

ADD REPLY

Login before adding your answer.

Traffic: 2259 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6