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biod / sambamba

Tools for working with SAM/BAM data
http://thebird.nl/blog/D_Dragon.html
GNU General Public License v2.0
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core dump sambamba depth #408

Closed ghost closed 4 years ago

ghost commented 4 years ago

Hello, I am using sambamba 0.7.0 and get the following error:

./mapping.sh: line 32: 8447 Segmentation fault (core dumped) ./sambamba-0.7.0-linux-static depth window -w 20000 -T 0 -t $threads -F 'mapping_quality >= 0' $out.sorted.bam > $out.cov

It only happens with one of my bam file. I don't understand what this file has that is peculiar. It's 22 Gb long, I could try to send it through wetransfer. I have tried several versions of sambamba. Any suggestion? thank you EDIT: I solved the problem by using 20 threads instead of 48 ...

ghost commented 4 years ago

Hello again, actually this issue shows up quite regularly and when it happens I have to try different values of threads until there is no more core dumps.

pjotrp commented 4 years ago

You mean with different BAM files?

ghost commented 4 years ago

yes with different bam files. Note that I am not able to reproduce the problem on different computers, so it might be related to the CPU. The core dump happens regularly with a Intel(R) Xeon(R) CPU E5-2650 v4 @ 2.20GHz While so far I haven't experienced it on my laptop running with a Intel(R) Xeon(R) CPU E3-1505M v5 @ 2.80GHz

pjotrp commented 4 years ago

Yeah, that is a hardware problem. Good on you to figure it out :)

Duplicate of https://github.com/biod/sambamba/issues/335