Running Mothur commands through a HPC

Commands in mothur
1

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

2

You need to run…

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