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...
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