Kissplice: error running ks_run_modules

Question

[ciom]

Hi!

I'm trying to run kissplice in my RNAseq data but, I'm getting an error finding the BCCs:

"Problem with /usr/lib//kissplice/ks_run_modules"

Can anyone help me whit this problem?

I'll really appreciate any suggestion.

Thank you very much.

[Rohit]

It would help to know what command was run exactly and the version of the software, check if there is some hard-coded paths in the tool

[ciom]

The version is: kissplice 2.3.1

I'm running: /usr/bin/kissplice -s -k 41 -r R1.fa -r R2.fa -r singletons.fa

Thank you!!!!

[WouterDeCoster]

Please use ADD REPLY to answer to an earlier comment, as such this thread remains logically structured and easy to follow. I moved your answer now but as you can see it's not optimal.

Did the test data of the tool run successfully?

Answer 1

[siricaroberto.1]

Were you able to solve the problem? Because it happens the same to me, I use kissplice 2.2.1 and it completes the run for test data but not for my data. Thank you

Answer 2

[ciom]

Try increasing the memory of your stack before running Kissplice by:

in Linux OS: "ulimit -s unlimited" or in Mac OS: "ulimit -s <new_limit>"

That should work!

[WouterDeCoster]

Please use ADD REPLY to answer to an earlier comment, as such this thread remains logically structured and easy to follow.