Segmentation fault in pcr.seqs

Commands in mothur
1

Hi,
Currently i’m trying to run mothur analysis on computhing server. I have 2.8T free disc space and 177Gb available ram memory. I’m using mothur v.1.48.0.

But when I used pcr.seqs command, to “cut” the silva database with oligo file I’m receiving “Segmentation fault (core dumped)” error.

Full command I’m using: pcr.seqs(fasta=~/silva_file/silva.nr_v138.align, oligos=~/results_carps/v3v4.oligos, keepdots=F).

The command starts running, and this happening:
Using 88 processors.
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1668
Segmentation fault (core dumped)

What can be reason for this? I think that resources I have should be enough. If not how much space/memory should I have to run this.

2

Can you try the command again with processors=8 instead of using all 88 available on your system?

pat

3

I tried, and the result is the same, only segmentation fault happen a little bit later.
pcr.seqs(fasta=~/silva_file/silva.nr_v138.align, oligos=~/results_ca rps/v3v4.oligos, keepdots=F, processors=8)

Using 8 processors.
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18350
Segmentation fault (core dumped)

4

Hi - where are you getting silva.nr_v138.align? Can you post the content of v3v4.oligos ?

5

I downloaded silva db from the link which I found in MiSeq SOP. And this is the content of oligos file

forward TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNGGCWGCAG
reverse GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGACTACHVGGGTATCTAATCC

6

Thanks - those look like they must include adapters. Could you possibly try again only using the 16S portion of the primers?

Pat

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I received info from the lab that these are olny primer sequences, but I’ll try to validate this.

8

Hi,
You were right primers seqences from the lab included adapters and primers. After removing adapter part, pcr.seqs worked. Thanks for your help!

9

Fantastic - glad it’s working now
Pat

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