# Segmentation fault in pcr.seqs **URL:** \ **Category:** Commands in mothur\ **Created:** [September 11, 2023, 8:38am UTC](https://forum.mothur.org/t/segmentation-fault-in-pcr-seqs/21942 "2023-09-11T08:38:43Z")\ **Posts on this page:** 10\ **Page:** 1
**Author:** ![jakim](https://avatars.discourse-cdn.com/v4/letter/j/ec9cab/32.png) [@jakim](https://forum.mothur.org/u/jakim)\ **Post date:** [September 11, 2023, 8:38am UTC](https://forum.mothur.org/t/segmentation-fault-in-pcr-seqs/21942/1 "2023-09-11T08:38:43Z")
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. 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 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. ---
**Author:** ![pschloss](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/pschloss/32/4_2.png) [@pschloss](https://forum.mothur.org/u/pschloss)\ **Post date:** [September 11, 2023, 3:39pm UTC](https://forum.mothur.org/t/segmentation-fault-in-pcr-seqs/21942/2 "2023-09-11T15:39:09Z")
Can you try the command again with `processors=8` instead of using all 88 available on your system? pat ---
**Author:** ![jakim](https://avatars.discourse-cdn.com/v4/letter/j/ec9cab/32.png) [@jakim](https://forum.mothur.org/u/jakim)\ **Post date:** [September 11, 2023, 4:13pm UTC](https://forum.mothur.org/t/segmentation-fault-in-pcr-seqs/21942/3 "2023-09-11T16:13:36Z")
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. > 1000 > 1000 > 1000 > 1000 > 1000 > 1000 > 1000 > 1000 > 2000 > 2000 > 2000 > 2000 > 2000 > 2000 > 2000 > 2000 > 3000 > 3000 > 3000 > 3000 > 3000 > 3000 > 3000 > 3000 > 4000 > 4000 > 4000 > 4000 > 4000 > 4000 > 4000 > 4000 > 5000 > 5000 > 5000 > 5000 > 5000 > 5000 > 5000 > 5000 > 6000 > 6000 > 6000 > 6000 > 6000 > 6000 > 6000 > 6000 > 7000 > 7000 > 7000 > 7000 > 7000 > 7000 > 7000 > 7000 > 8000 > 8000 > 8000 > 8000 > 8000 > 8000 > 8000 > 8000 > 9000 > 9000 > 9000 > 9000 > 9000 > 10000 > 9000 > 10000 > 9000 > 9000 > 10000 > 10000 > 11000 > 10000 > 11000 > 10000 > 11000 > 11000 > 10000 > 10000 > 12000 > 11000 > 12000 > 11000 > 12000 > 12000 > 11000 > 11000 > 13000 > 12000 > 13000 > 12000 > 13000 > 13000 > 12000 > 12000 > 14000 > 13000 > 14000 > 13000 > 14000 > 14000 > 13000 > 13000 > 15000 > 14000 > 15000 > 14000 > 15000 > 15000 > 14000 > 14000 > 16000 > 15000 > 16000 > 15000 > 16000 > 15000 > 16000 > 15000 > 17000 > 16000 > 17000 > 17000 > 16000 > 17000 > 16000 > 18000 > 16000 > 18000 > 18000 > 18350 > Segmentation fault (core dumped) ---
**Author:** ![pschloss](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/pschloss/32/4_2.png) [@pschloss](https://forum.mothur.org/u/pschloss)\ **Post date:** [September 11, 2023, 4:42pm UTC](https://forum.mothur.org/t/segmentation-fault-in-pcr-seqs/21942/4 "2023-09-11T16:42:27Z")
Hi - where are you getting `silva.nr_v138.align`? Can you post the content of `v3v4.oligos` ? ---
**Author:** ![jakim](https://avatars.discourse-cdn.com/v4/letter/j/ec9cab/32.png) [@jakim](https://forum.mothur.org/u/jakim)\ **Post date:** [September 12, 2023, 6:59am UTC](https://forum.mothur.org/t/segmentation-fault-in-pcr-seqs/21942/5 "2023-09-12T06:59:01Z")
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 ---
**Author:** ![pschloss](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/pschloss/32/4_2.png) [@pschloss](https://forum.mothur.org/u/pschloss)\ **Post date:** [September 12, 2023, 1:19pm UTC](https://forum.mothur.org/t/segmentation-fault-in-pcr-seqs/21942/6 "2023-09-12T13:19:10Z")
Thanks - those look like they must include adapters. Could you possibly try again only using the 16S portion of the primers? Pat ---
**Author:** ![jakim](https://avatars.discourse-cdn.com/v4/letter/j/ec9cab/32.png) [@jakim](https://forum.mothur.org/u/jakim)\ **Post date:** [September 12, 2023, 1:32pm UTC](https://forum.mothur.org/t/segmentation-fault-in-pcr-seqs/21942/7 "2023-09-12T13:32:47Z")
I received info from the lab that these are olny primer sequences, but I’ll try to validate this. ---
**Author:** ![jakim](https://avatars.discourse-cdn.com/v4/letter/j/ec9cab/32.png) [@jakim](https://forum.mothur.org/u/jakim)\ **Post date:** [September 13, 2023, 6:46am UTC](https://forum.mothur.org/t/segmentation-fault-in-pcr-seqs/21942/8 "2023-09-13T06:46:22Z")
Hi, You were right primers seqences from the lab included adapters and primers. After removing adapter part, pcr.seqs worked. Thanks for your help! ---
**Author:** ![pschloss](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/pschloss/32/4_2.png) [@pschloss](https://forum.mothur.org/u/pschloss)\ **Post date:** [September 13, 2023, 12:38pm UTC](https://forum.mothur.org/t/segmentation-fault-in-pcr-seqs/21942/9 "2023-09-13T12:38:57Z")
Fantastic - glad it’s working now Pat ---
**Author:** ![system](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/system/32/2_2.png) [@system](https://forum.mothur.org/u/system)\ **Post date:** [September 23, 2023, 12:39pm UTC](https://forum.mothur.org/t/segmentation-fault-in-pcr-seqs/21942/10 "2023-09-23T12:39:19Z")
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