Rainbow assembly- segmentation fault?

Question

[phair.nikki]

Hello, I am reletively new to bioinformatics and I'm hoping someone will be able to answer my question.

I am trying to use Rainbow to assemble RADseq (short paired-end) reads and eventually call for SNPs. However, I get exit status 139 and the error file says: "/var/spool/PBS/mom_priv/jobs/13307.launch.hpc.SC: line 15: 5705 Segmentation fault rainbow merge -a -i cat.rbdiv.out -o cat.rbasm.out -N 500"

This appears to be a problem with the merging step of rainbow. I get this error with both trimmed and raw reads, but other people are using rainbow on our HPC without any problems so I'm assuming it has something to do with my data...

My script:

module load app/rainbow
rainbow cluster -1 forward -2 reverse > cat.rbcluster.out 2> log
rainbow div -i cat.rbcluster.out -o cat.rbdiv.out
rainbow merge -a -i cat.rbdiv.out -o cat.rbasm.out -N 500

Has anyone seen this error or have any suggestions on how to fix this?

Thanks in advance

[GenoMax]

Looks like you are using PBS scheduler. Are you assigning adequate memory for this job (assuming the command you are using for rainbow are correct)?

[h.mon]

My experience is Torque / PBS would explicit say if memory was insufficient. But why are you looking at /var/spool/PBS/mom_priv? What are the messages from stdout and stderr (which, if memory servers me right, you set with #PBS -o and #PBS -e)?

[bioinfo]

Today, when I was running the Rainbow on the cluster I noticed the similar issue. I have assigned 600 GB memory still it fails ("segmentation fault"). Now I am suspecting whether Rainbow requires few TBs of RAM at "merge" step.

Answer 1

[chris.bird]

This happened to me because my input file was formatted incorrectly.