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Old 08-10-2010, 04:09 PM   #3
PeteH
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Location: Melbourne

Join Date: Jun 2010
Posts: 64
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I'm having similar problems, but with samse. The aln step works fine for me, but samse hangs for tens of hours and only writes [bwa_read_seq] 0.0% bases are trimmed. to my *.sam file.

Prior to running BWA, my pipeline includes a python script to convert the Illumina quality scores to phred33, and a perl script to trim reads that contain adapter sequence. I have also tried it without running my perl trimming script, but samse still hangs.

Any advice on what else I can try to identify the problem is much appreciated.
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