Badly placed ()'s

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# 8  
Originally Posted by rdrtx1
Does the directive file have to have a pbs extension? i.e. sleep.pbs
No - I was working with .sh. Edit: I'm working with SGE not PBS.

---------- Post updated at 04:30 AM ---------- Previous update was at 04:25 AM ----------

Originally Posted by MadeInGermany
It looks like you run your script by tcsh.
Is /bin/bash really a bash?
I believe so:

ls -l /bin/bash
-rwxr-xr-x 1 root root 768952 Sep 26  2014 /bin/bash

/bin/bash --version
GNU bash, version 3.2.25(1)-release (x86_64-redhat-linux-gnu)
Copyright (C) 2005 Free Software Foundation, Inc.

Originally Posted by MadeInGermany
I see you run it with qsub. Don't know what qsub is but maybe you should force a bash with
qsub -o fastqc.log /bin/bash ~/bin/

Unable to run job: Script length does not match declared length.

Last edited by una1992; 10-26-2017 at 07:54 AM..
# 9  

Just a guess, change from:
fastqc -f fastq -o /data4/user/test/fastqc/ $i

to (by adding quotes):
fastqc -f fastq -o /data4/user/test/fastqc/ "$i"

Good luck ... cheers, drl
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