velveth segmentation fault

Question

[emma.berdan]

Hi everyone,

I am trying to run velveth on some paired end data I have but as soon as I submit the command I get an automatic segmentation fault from slurm. I have tried velveth with the test data and it runs fine, help! Here is my command:

srun velveth allsix 31 -shortPaired -fastq -separate /datana2/berdan/reads/allbig_1.fastq /datana2/berdan/reads/allbig_2.fastq -strand_specific

I have tried it both with and without the -strand_specific command just in case that was causing the problem.

Thanks!

Emma

Answer 1

[Ram]

This might be because of memory problems. velvet is a memory hog IIRC and you'll need to give it a lot of RAM. What are the specs you're giving it?

[emma.berdan]

I am specifying a lot of memory for SLURM (--mem=200000) and the segmentation fault comes immediately (like less than 1 second after the command is issued). This makes me think that memory may not be the problem. I have tried running it as both srun and as an sbatch file but both fail immediately.