[fongchun]

You can try trimming your FASTQ files and see how that goes. Sickle trims based on quality scores, so you would only lose low quality bases:
https://github.com/najoshi/sickle

We'll give that a try. Thanks!

[AlliCox]

My original BWA issue did not get resolved. I am using Mac OS X 10.7 and I have seen reports of other Mac users reporting the same problem. When I switched from BWA 0.6.2 to BWA 0.5.9, it was working fine.

As I was writing this reply, I noticed BWA 0.7.0 was released last week. I am not sure if that one solves any of the Mac issues. See changelog here:

https://github.com/lh3/bwa/blob/master/NEWS

I used BWA for 2x250bp reads and I did not encounter any problems. From BWA main page:

hi,
It looks like the last 3 versions of bwa, including the latest released last week, don't work on a Mac. I downloaded 0.5.10 and I think things are working now. It's definitely taking much longer to make the .sai file, so I see that as a good sign.
Thanks!

[wlangdon]

I just ran into this after I aligned human paired-end sequences against the tiny non-human genome included in the distribution kit.
Opps:-(
Bill