Tophat Error "segment-based junction search failed"

Question

[AyehSadr]

Dear All

I have an error when run the tophat in some of samples, "segment-based junction search failed with err =-9". I would appreciate to guide me to solve it.

[2015-06-14 03:30:56] Searching for junctions via segment mapping
    [FAILED]
Error: segment-based junction search failed with err =-9
    found 0 potential small insertions

Answer 1

[Sukhi Singh]

Check segment_juncs.log in your tophat output dir that you gave with the current command. This will give you some hints.

Also, try running each command from run.log, to see where the halt is exactly coming from and why.

[AyehSadr]

Unfortunately I couldn't find the problem, however I checked the segment-juncs run-log and tophat-log

[tiago211287]

I got a similar error, in the segment_juncs.log, the error was on the end:

Loading left segment hits.
open: Too many open files

And found that, as in the: http://yagays.github.io/blog/2013/06/23/tophat-too-many-open-files/

This usually happens when using "-p" option with a large value (many threads). TopHat may produce many intermediate files, the number of which is proportional to this value; sometimes the number of the files may go over the maximum number of files a process is allowed to open. The solution is to raise the limit to a higher number (e.g. 10000). For Mac, you can change this using a command, "sudo sysctl -w kern.maxfiles=10240".