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Old 05-14-2014, 02:07 AM   #29
Location: Sweden

Join Date: Mar 2014
Posts: 12

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.

Last edited by N00bSeq; 05-15-2014 at 01:02 AM.
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