Question: Kissplice: error running ks_run_modules
0
gravatar for ciom
2.7 years ago by
ciom0
ciom0 wrote:

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.

snp rna-seq software error • 845 views
ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by ciom0

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

ADD REPLYlink written 2.7 years ago by Rohit1.4k

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!!!!

ADD REPLYlink written 2.7 years ago by ciom0

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?

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by WouterDeCoster40k
0
gravatar for siricaroberto.1
2.7 years ago by
siricaroberto.10 wrote:

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

ADD COMMENTlink written 2.7 years ago by siricaroberto.10
0
gravatar for ciom
2.7 years ago by
ciom0
ciom0 wrote:

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!

ADD COMMENTlink written 2.7 years ago by ciom0

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

ADD REPLYlink written 2.7 years ago by WouterDeCoster40k
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