Re: PBS not finding file.

There is nothing inherently wrong with your first code sample.

That said, you haven't made it clear how your "qsub script" ties into your example at all, and your error messages don't help us because they are not generated by your example code.

My (wild) guess is that you call your "simple script" but don't pass it an argument, or are not passing the correct argument, which I am guessing should be your "qsub script".

Try this:

my $infile = $ARGV[0];
die "can't read infile\n" if (! -r $infile);
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Comment on Re: PBS not finding file. Download Code

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Re^2: PBS not finding file. by Jeri (Scribe) on Sep 27, 2011 at 19:09 UTC
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.	[reply]
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]