Calling mothur in bsub/LSF queue for a computational cluster

Commands in mothur
1

Hi - Trying to run mothur on our computational cluster with LSF queueing commands.
Mothur runs fine from the command line, but for numerous applications would like to submit it into our queue to run on multiple cores.

We use the bsub command to submit jobs to the queue. I consistently get “TERM environment variable not set.” when submitting mothur jobs (example error below). This happens regardless of submitting an interactive process, or creating a shell script with export TERM=xterm prior to calling mothur (seems the user’s local environmental variables are not preserved or recognized in the session). I can run various other applications through bsub without this error. Our cluster runs on CentOS Linux.

batchfile –

Use to test submission of analysis to queue via LSF

summary.seqs(fasta="/home/CCTM/ScholssSOP/GQY1XT001.shhh.fasta")

jobfile –
mothur batchfile

command that’s run to execute –
bsub < jobfile

Here’s the output showing the error.

Thanks for any help.

LSBATCH: User input

/opt/mothur/bin/mothur /home/CCTM/SchlossSOP/batchfile

Successfully completed.
Resource usage summary:
CPU time : 0.02 sec.
Max Memory : 2 MB
Max Swap : 34 MB
Max Processes : 1
Max Threads : 1

The output (if any) follows:
TERM environment variable not set.

2

TERM errors generally have to do with how you have your computer setup.