[torqueusers] Script problem (can't find executable)

Guille guillermo.marco at gmail.com
Thu Nov 11 04:42:34 MST 2010


Hi guys i've made a PBS script to launch another program called "tophat"

tophat is located at /usr/local/bin/tophat

Here's my pbs script located in /home/PBS_scripts/

#!/bin/sh
#PBS -l walltime=00:05:00
#PBS -N tophat_script
#PBS -o tophat_script.out
#PBS -e tophat_scriptb.err

echo Script starts..
cd /usr/local/bin/
./tophat -r 150 /data/results/Sl65/reference_genome/GRch37.58/hg19 1_1.fa
1_2.fa
echo Script ends..

This job script never uses any node or procesor, (1 node and 1 procesor by
default) and apears in queue as "C" state.

The tophat_scriptb.err looks like this:

/opt/torque/mom_priv/jobs/22825.sistemas-genom8.sistemas.local.SC: line 9:
./tophat: No such file or directory

How the hell i can specify the path to my script location because i've tried
doing cd like the script above and using PBS_O_PATH but nothing seems to
work..

Thanks for help :)
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