core dump sambamba depth

[ghost]

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]

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]

You mean with different BAM files?

[ghost]

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]

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

Duplicate of #335