Hello ,this is what I am doing on my server. The module I am loading are those required to be able to call Mothur correcly within my working environment, it may change for you. I would use “current” in the batch file instead of the complete path + file name, it will save you errors. Hope it helps,
I am using IBM machine with LSF (just like PBS/SLURM) for resource management. I have already got all the “final.93.opti_mcc.list” type of files. The process is still running since the last 24 hours and I don’t know when is it going to finish. (Please note I don’t have vsearch executable in my folder.) Here is what I get about my job.
bjobs -l 1154
Job <1154>, User , Project , Status , Queue , Command <
#!/bin/bash;#BSUB -R “rusage[mem=800GB]”;./mothur “#cluste
r.split(file=final.file, count=final.count_table, cutoff=0
.03, processors=10)”>, Share group charged
Thu Mar 31 17:14:52: Submitted from host , CWD <$HOME/simplestat/cl
ustersplit>, Requested Resources <rusage[mem=819200.00]>;
Thu Mar 31 17:14:52: Started 1 Task(s) on Host(s) , Allocated 1 Slo
t(s) on Host(s) , Execution Home </home/ibm>,
Execution CWD </home/ibm/simplestat/clustersplit>;
Fri Apr 1 11:27:38: Resource usage collected.
The CPU time used is 148675 seconds.
MEM: 757.3 Gbytes; SWAP: 0 Mbytes; NTHREAD: 5
PGID: 148682; PIDs: 148682 148683 148687 148688
MAX MEM: 757.3 Gbytes; AVG MEM: 574 Gbytes
READ: ~0 bytes; WRITE: ~0 bytes
r15s r1m r15m ut pg io ls it tmp swp mem
loadSched - - - - - - - - - - -
loadStop - - - - - - - - - - -