Re^2: PBS not finding file.

[Jeri]

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

Your guess is correct! I had a hard time explaining that, yes, the argument should be passed from the qsub script, but it's not. I tried your code. It kills the script, as expected.

[Jeri]

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

[onelesd]

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` ;