tophat errors

Greg · 01-12-2010, 08:55 AM

Does anyone know where there is a list of what all the tophat errors mean?

For example, I have been getting:
...
[Tue Jan 12 09:04:36 2010] Searching for junctions via segment mapping
[FAILED]
Error: segment-based junction search failed with err = -6
when trying to align some 32bp illumina reads. What does error -6 mean? (or 1-5 for that matter) If I run truncated versions of the same data set (up to under a million reads or so) it will run without error but the junction file will be empty.

much appreciated.

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01-12-2010, 08:55 AM	#1
Greg Member Location: British Columbia Join Date: Oct 2009 Posts: 31	tophat errors Does anyone know where there is a list of what all the tophat errors mean? For example, I have been getting: ... [Tue Jan 12 09:04:36 2010] Searching for junctions via segment mapping [FAILED] Error: segment-based junction search failed with err = -6 when trying to align some 32bp illumina reads. What does error -6 mean? (or 1-5 for that matter) If I run truncated versions of the same data set (up to under a million reads or so) it will run without error but the junction file will be empty. much appreciated.