Bwa terminated with an error exit status (137) -- Execution is retried about nextneopi

[riederd]

can you post the contents of /QRISdata/Q6373/results/results_1/work/f3/15a0370e23d72ed33088db22c6a446 as tar.gz?

[amoschoomy]

work.tar.gz

Here is the files packaged into the tar.gz format

[riederd]

Thanks!

from the .command.err log file you can see that the sambamba command was killed by your system:

38 Killed | sambamba sort --sort-picard --tmpdir=/scratch/temp/5845503 -m 64G -l 6 -t 8 -o sample1_normal_DNA_aligned.bam /dev/stdin

How much memory does your system have? I it has <=64GB you might try to lower the requested memory for sambamba (and possible also other tools) in conf/params.config:

e.g.:
SB_sort_mem = "32G"

around line 146

[amoschoomy]

I am running it in my HPC and had allocated 64GB for the memory. I will try to allocate more memory to the cluster or do what you suggested. Thanks!

[amoschoomy]

Hello again, it looks like my real issue was actually in #49. It runs into the same error as #49 . I have now allocated 500GB ram on my cluster and let see how it goes.