Error: segfault from C stack overflow about leafcutter HOT 7 CLOSED

Hi there, thanks for using LeafCutter! :)

Can you verify that you have cloned the most recent version of the repository?

I remember this error message coming up sometimes with an older version of prepare_results.R that came from BedTools but we've since switched to doing the joins in dplyr.

from leafcutter.

Hi,
thanks for your prompt reply.
Yes, I've been using the last version of the repository.

from leafcutter.

ok, would you mind adding this line to the top of prepare_results.R:

options(echo=TRUE)

Then could you run the script again and copy and paste what is printed out please? I'm not sure which part of the script is causing your problem.

from leafcutter.

Hi,
I included the run report in the attached file.
Thanks..
Run.log.txt

from leafcutter.

Interesting, so it appears to run all the way to end and then fail when you get to saving all the data into an R data object. So it's having trouble writing all that data to a file.

Can you tell me what kind of computer you're running the script on? How much RAM and how many CPU cores do you have? I wrote and tested that script on a 2012 MacBook Pro with 8GB of RAM. That may be the reason.

from leafcutter.

Thanks a lot for your help.
I figured out the problem.
It was about the open file and max locked memory limit. When I increased the limits, did not get the error any more.

from leafcutter.

Glad to help. I hope you enjoy using the Shiny app! 😃

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