Question: Tophat2 Error during 'Searching for junctions via segment mapping'
0
gravatar for christ.li
4.3 years ago by
christ.li10
christ.li10 wrote:

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 • 1.8k views
ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by christ.li10

Which operating system do you use, how did you install the software and which version do you have?

Based on other discussions: https://biostar.usegalaxy.org/p/17880/ & http://seqanswers.com/forums/showthread.php?t=12856 the error could also be related to memory issues (but then the error message would be fairly aspecific!)

ADD REPLYlink modified 4.3 years ago • written 4.3 years ago by WouterDeCoster45k

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?

ADD REPLYlink written 4.3 years ago by christ.li10

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

ADD REPLYlink written 4.3 years ago by wgmzky10
1

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.

ADD REPLYlink written 4.3 years ago by wgmzky10

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

ADD REPLYlink written 4.3 years ago by christ.li10
1
gravatar for christ.li
4.3 years ago by
christ.li10
christ.li10 wrote:

Resolved: Use tophat v2.0.14

ADD COMMENTlink written 4.3 years ago by christ.li10
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