Segmentation fault classify.seqs

mothur bugs
1

Dear all,

I have a 'Segmentation fault" problem when running mothur v.1.36.1. I’ve been using this version without a problem and done most of my analysis with it but suddenly it keeps on crashing during the “classify.seqs” step in batch mode in which I get the following error:

mothur > classify.seqs(fasta=current, count=current, reference=/home/vimac/Databases/Silva/SILVA_128/SSURef_NR99_v128/silva.nr_v128/silva.nr_v128.align, taxonomy=/home/vimac/Databases/Silva/SILVA_128/SSURef_NR99_v128/silva.nr_v128/silva.nr_v128.tax, cutoff=80)
Using G1_cDNAs.stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.uchime.pick.count_table as input file for the count parameter.
Using G1_cDNAs.stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.fasta as input file for the fasta parameter.

Using 4 processors.
Reading template taxonomy… DONE.
Reading template probabilities… Segmentation fault

When checking at the log file there is not much more info:
Using 4 processors.
Reading template taxonomy… DONE.

I tried re-running old data which worked fine before and it crashes at the same step.

I’m running mothur on a Biolinux 8 with 32GB RAM and 1TB of disk so memory should not be a problem.

Any ideas on how to solve this?

Thank you.

2

Could you try it with 2 or even 1 processor?

Pat

3

Hi Pat,

I tried running it again with 1, 2 and 8 processors and I always get the same segmentation fault error. I even tried with the mothur example data and it also crashes.

Any idea of how to proceed?

Thanks

4

Sorry, I missed that you are using v.1.36. You really should update hte version to 1.39.5 and try again.

Pat