[torqueusers] Script problem (can't find executable)
Kevin Van Workum
vanw at sabalcore.com
Thu Nov 11 06:50:46 MST 2010
On Thu, Nov 11, 2010 at 6:42 AM, Guille <guillermo.marco at gmail.com> wrote:
> 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/
> #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
> 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 :)
Perhaps 'tophat' is on your submitting machine only, and not on your
> torqueusers mailing list
> torqueusers at supercluster.org
Kevin Van Workum, PhD
Sabalcore Computing Inc.
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