I used bwa to align a short read file to a reference sequence. I ran it several 
times, and I got different results for the runs on the same input dataset.
The fist run, it generated a ~280,000 lines "gzipped file". I checked the file 
on the server, and it was actually a sam file, not gzipped.
The second run, it generated ~90,000 lines sam file.
The third run, it generated ~130,000 lines sam file.
The fourth run, it generated ~220,000 lines "gzipped file"

Does anyone meet the similar problem?
Thank you very much.


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