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Tophat2 Error during 'Searching for junctions via segment mapping'

I am trying to use the CIRCexplorer2 pipeline to process some paired-end RNAseq data. I have having difficulty with the tophat-fusion step.

The error message reads:

[2016-11-04 13:01:43] Searching for junctions via segment mapping [FAILED]

Error: segment-based junction search failed with err =-6 Reason: image not found

I am not sure what this means. Any help would be greatly appreciated!

Thanks.

rna-seq
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written by christ.li • christ.li

I am on OS X and I have the most recent version 2.1.1. It is the pre-compiled binary.

I also thought the same thing, so I reduced the # of threads. I think it shouldn't be a memory issue because I've frequently used STAR and the workstation handles STAR quite well.

Thoughts?

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written by christ.li • christ.li

Hi，Have you solved this problem as I ran into the same trouble? Thanks！

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written by wgmzky • wgmzky

Hi, I am on OS X 10.12.1 and firstly I had the pre-complied binary version 2.1.1 which met the same trouble, but after I changed to version 2.0.14, the problem fixed. Hope useful to you.

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written by wgmzky • wgmzky

Thank you! Switching to the previous release solved the problem!

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written by christ.li • christ.li

1 answer

Resolved: Use tophat v2.0.14

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written by christ.li • christ.li

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