Closed ghost closed 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.
You mean with different BAM files?
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
Yeah, that is a hardware problem. Good on you to figure it out :)
Duplicate of https://github.com/biod/sambamba/issues/335
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 ...