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hall-lab / speedseq

A flexible framework for rapid genome analysis and interpretation
MIT License
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segmentation fault with realign #99

Open shukwong opened 7 years ago

shukwong commented 7 years ago

Hi

I was able to run speedseq realign without issues on one node but when I submitted it as an array job it gave me seg fault towards the end. The error messages are as follows: 291167 Segmentation fault | /itmi/speedseq/0.1.2//bin/sambamba view -S -f bam -l 0 /dev/stdin 291168 Segmentation fault | /itmi/speedseq/0.1.2//bin/sambamba sort -t 16 -m 18G --tmpdir=/data/tmp/sample1//full -o /data/tmp/sample1//sample1.bam.1.bam /dev/stdin

Thanks for your help! Wendy

cc2qe commented 7 years ago

This seems like you may be running out of RAM. Try reducing the memory usage with the -M flag.