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Problem loading modules on blacklight

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Problem loading modules on blacklight
Answer
9/25/12 10:29 PM
I recently submitted a Trinity job on Blacklight, but it failed:

PBS Job Id: 200001.tg-login1.blacklight.psc.teragrid.org
Job Name: Nawrocki3_qsub.txt
Exec host: bl1.psc.teragrid.org
Aborted by PBS Server
Job cannot be executed
See Administrator for help

I checked the log file and it says the following:

module load trinity
module: Command not found
module load java
Module: Command not found
ulimit -u unlimited
ulimit: Command not found
Trinity.pl <my trinity command was here but that's not the problem.>
Trinity.pl: Command not found

I am not sure how to get it to properly load the modules. It works fine outside of my qsub script when I do it in the command line.

This is the qsub file I am using to execute the program:


#!/bin/csh
# combine stderr and stout into one stream
#PBS -N Trinity
#PBS -l ncpus=32
#PBS -l walltime=48:00:00
#PBS -j oe
#PBS -q batch
set echo
# output
#PBS cd $SCRATCH
#PBS -o trinity.log


$SCRATCH/Ectopleura_files

load module java
load module trinity/r2011-08-20cd
load module trinity
ulimit -s unlimited
Trinity.pl --seqType fq --kmer_method meryl --cpu 64 --left old_cat_Forward_all.fastq --right old_cat_Reverse_all.fastq --output $SCRATCH --min_contig_length 200 --paired_fragment_length 175 --CPU 32--bflyCPU 32 --bflyGCThreads 32 --bflyHeapspaceInit 8G



Thanks for any help

AM Nawrocki
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