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in reply to Re^2: PBS not finding file.
in thread PBS not finding file.

Correction. The argument is not being passed from the qsub script, but should be.

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Re^4: PBS not finding file.
by onelesd (Pilgrim) on Sep 27, 2011 at 21:16 UTC

    Let me use my crystal ball again... are you trying to run the "qsub script" from the first code sample and get it's output? If so, use backticks.

    my $PBS_ARRAYID = '123' ;
my @output = `/usr/bin/perl /chongle/jeri/timecheck/MUSCLEHMM.pl $PBS_
+ARRAYID > /chongle/jeri/timecheck/output.$PBS_ARRAYID.txt 2> /chongle
+/jeri/timecheck/error.$PBS_ARRAYID.txt` ;

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