Re^2: 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.

Comment on Re^2: PBS not finding file.

Replies are listed 'Best First'.
Re^3: PBS not finding file. by Jeri (Scribe) on Sep 27, 2011 at 19:11 UTC
Correction. The argument is not being passed from the qsub script, but should be.	[reply]
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` ; [download]	[reply] [d/l]