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Old 04-11-2012, 06:56 AM   #1
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Location: Boston

Join Date: Nov 2010
Posts: 2
Default tophat2 segment_juncs error: Error: segment-based junction search failed with err =-6


I am trying out the latest tophat2 on a small read file. My reference is the rabbit genome which has 3243 sequences (chromosomes + scaffolds).

segment_juncs.log has the following lines at the end:

>> Performing segment-search:
Loading left segment hits...
Error: invalid 'B' array subtype (^)!

Has anyone had the same issue? How to fix it? Thanks a lot.

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Old 04-16-2012, 06:37 AM   #2
Compendia Bio
Location: Ann Arbor

Join Date: Oct 2010
Posts: 35

Re-download the tophat-2.0.0 package as it was updated and try again... (Same Version. Same file name)

Originally Posted by gpertea View Post
There are quite a few different problems reported in this thread - I apologize for them. We are aware of a couple of these problems and we are trying to fix them, though we are encountering some difficulties reproducing some of these errors.
We just updated the packages on the website with a couple of last minute fixes so please re-download the tophat-2.0.0 package of your choice (yes, it's the same version, same file names) from and try running the new version again on your test data. If tophat 2 still fails at any stage in the process please report the failure at - it would also help if you attach a tarball or zip file with the content of the "logs" directory when you post a bug report there.

Thank you,
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