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Old 06-22-2011, 06:16 AM   #6
Location: Brock University

Join Date: Dec 2010
Posts: 66

In my experience BWA won't really ever error out unless there's a problem with your data or your command (or lack of memory). As long as your data/commands are correct you can just use a shell script - command n in a shell script will wait until command (n - 1) is complete before running so you're guaranteed to start in the correct order.

As far as you yourself knowing if the .sai stage is complete, just check your stderr output - if it says "n sequences have been processed", where n = the number of sequences in your FASTQ file, then it's complete. But the shell will check this for you if it's running a script.
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