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I can't see anything obvious in the logs from the failed run, but perhaps you will be able to. Here is the BWA run: --- logs/[email protected][bwa_index] Pack FASTA... 0.00 sec[bwa_index] Construct BWT for the packed sequence...[bwa_index]…
Ah, the problem was with that we had a local version of BWA 0.6.2-r126 installed, which was being used by the script. When I set my path to use the bwa 0.5.8c (r1536) that was packaged with Genome Strip, it worked fine. Thanks very much.