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Old 01-06-2015, 03:45 AM   #32
Location: Dresden

Join Date: Jul 2012
Posts: 49
Default same in v2.0.13

Originally Posted by N00bSeq View Post
I am getting the same error (fail when reporting output tracks) on tophat 2.0.11. I have made three mapping runs for each of 12 samples. Of these, only the ones using both --no-discordant and --no-mixed together fail (I have not tried these two parameters individually), and runs with these options fail for all 12 samples.

My reads have been trimmed, and pairs may not be of equal size. But as far as I understand, tophat should be able to handle that. At least, it certainly seems to when not using these particular parameters. Number of paired reads are around 30-40 M.

Increasing RAM did not help in my case.

I had the same experience with v2.0.13. Tophat stopped reporting the error when the 2 options, --no-discordant and --no-mixed, where removed.
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