Thank you for the replies. I forgot to check the output in @out. Turns out the program rsem cannot find the trans.fa that I'm using as input (even though it's there). Oddly enough, when I run the code again using the konsole and not via Galaxy, it works fine.

In reply to Re^2: Command not executing by Eldan Aranye
in thread Command not executing by Eldan Aranye

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