but it fails to perform the command.

That is not much to go on.

Given that a) the command is a perl script; b) you are capturing the output including that to the scripts stderr; aren't there any error messages or other clues contained in @out?

If not, then the logical thing to do would be to add some tracing diagnostics into run_rsem.pl.

Any ideas on why this is happening?

There is no way for anyone to hazard a guess from the information supplied.

On the other hand, you have all the tools available to you to trace the symptoms of the failure, even if you need our help in interpreting them.

Help us help you.

With the rise and rise of 'Social' network sites: 'Computers are making people easier to use everyday'
Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.
"Science is about questioning the status quo. Questioning authority".
In the absence of evidence, opinion is indistinguishable from prejudice.

The start of some sanity?

In reply to Re: Command not executing by BrowserUk
in thread Command not executing by Eldan Aranye

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