Running mothur in hpc

Commands in mothur
1

Hi,

I’m using mothur in hpc, but is totally noob about it. How do I monitor my mothur run in hpc?

2

Hi,

I’d encourage you to reach out to your HPC staff to see if they can help you with how to monitor your jobs. Often they will offer classes to help new users.

Pat

3

Hi Pat,

They did actually give me some commands to monitor the run, but unfortunately it does not work with mothur, it just gives blank. It works well with Trinity though. So I was wondering if there would be anyone in the forum that could help.

4

Hi,

I used to run mothur command in a batch mode. And run it on our server but in the background. Here are how I run it:

  1. Create a mothur.batch file, like below (set up the directory correctly):
make.contigs(inputdir=/staton/projects/soybean_rhizosphere/2018_fungicide/seed_treatment/16S/00_raw_fastq,outputdir=/staton/projects/soybean_rhizosphere/2018_fungicide/seed_treatment/16S/02_mothur,file=Seed.file,oligos=Seed.oligo,processors=30)

summary.seqs(inputdir=/staton/projects/soybean_rhizosphere/2018_fungicide/seed_treatment/16S/02_mothur,fasta=Seed.trim.contigs.fasta,processors=30)

screen.seqs(fasta=Seed.trim.contigs.fasta,group=Seed.contigs.groups,maxambig=0,maxlength=428,processors=30)
  1. Create a screen and run the mothur.batch command:
screen -S screen_mothur 
mothur mothur.batch

  1. Now, you can see the running process on your screen. In order to let it run in the background, you will need to press Control+A+D to send the command in the background (detach it).

  2. Whenever you got time and want to check the running process, attach the screen by running

screen -r screen_mothur
5. After checking the status, press Control+A+D again to detach the screen.

Alternatively, if you want to run it as a job file, you can write a job script as you did for trinity and run sh job_file. In this way, you won’t be able to monitor what is going on, but you can always go to mothur log file to see what is done. Below it an example of my job file:

#PBS -S /bin/bash
#PBS -A UT-TNEDU0031
#PBS -l nodes=1,walltime=72:00:00
#PBS -N Cultivar

module load mothur #(this is to load mothur into the environment)
cd $PBS_O_WORKDIR
mothur cultivar.batch

Hope this will be helpful.

5

you can also use less or tail to monitor the logfile

6

This topic was automatically closed 10 days after the last reply. New replies are no longer allowed.