I have had bowtie2 crash repeatedly on HiSeq data, both paired end and single end. Each time, no errors are reported, and the SAM file is truncated. I am including a sample data set, which has this problem reproducibly (forward and reverse reads from a large experiment chopped up by split): https://dl.dropbox.com/u/5275622/test.tar.gz
I've tried changing threading and mapping algorithms, but no luck. This is a rare and insidious error.
Any help would be appreciated!
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