# Running Mothur commands through a HPC

**URL:** <https://forum.mothur.org/t/running-mothur-commands-through-a-hpc/3320>\
**Category:** Commands in mothur\
**Created:** [July 10, 2017, 2:04pm UTC](https://forum.mothur.org/t/running-mothur-commands-through-a-hpc/3320 "2017-07-10T14:04:01Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![NicoleDames14](https://avatars.discourse-cdn.com/v4/letter/n/ecccb3/32.png) [@NicoleDames14](https://forum.mothur.org/u/NicoleDames14)\
**Post date:** [July 10, 2017, 2:04pm UTC](https://forum.mothur.org/t/running-mothur-commands-through-a-hpc/3320/1 "2017-07-10T14:04:01Z")

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Hi,

I would like to start running my analysis in batch mode using our universities HPC, but before I begin I’m testing out how to write a basic script with a simple summary.seqs command.

Below is what I’ve run:  
[b]#!/bin/bash  
#PBS -N sumseqNic  
#PBS -l nodes=1:ppn=2:series600   
#PBS -l walltime=00:01:00  
#PBS -m e

module add software/mothur-1.36.1  
cd mothur  
mothur

#summary.seqs(fasta=18S.unique.filter.fasta, name=18S.names)[/b]

  
My logfile only has these errors repeated:

mothur \>  
[ERROR]: You are missing (  
Invalid.

Any help on how I should be formatting my script to get a valid output would be much appreciated.

  
Thanks,

Nicole

---

<div class="post-metadata">

**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:** [July 13, 2017, 11:24am UTC](https://forum.mothur.org/t/running-mothur-commands-through-a-hpc/3320/2 "2017-07-13T11:24:30Z")

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You need to run…

```nohighlight
mothur

mothur "#summary.seqs(fasta=18S.unique.filter.fasta, name=18S.names)"

```

Also, you really don’t want to run 1.36.1. The best version to use is the current - 1.39.5

Pat