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Old 11-16-2010, 01:27 PM   #5
SongLi
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Location: Durham

Join Date: Oct 2010
Posts: 19
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Hi James,

Since you have solved the problem, would you mind post what the messages you get when the read RTF file passed?

On my side the error is:
[Tue Nov 16 17:02:17 2010] Reading known junctions from GTF file
[FAILED]
Error: could not execute prep_reads

That may help me to figure out what's wrong in my case.
Thanks,



Quote:
Originally Posted by James View Post
I fixed this problem. It may have been two things:

It may have been calling an older prep_reads I had lurking in my path.

It said I was calling tophat v1.1.0 even though I downloaded v1.1.3. I just re-downloaded the binaries and replaced them. Now it tells me I'm running v1.1.3.

I'm running Mac OSX 10.5.8. by the way.
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