search

gagneurlab / FRASER

FRASER - Find RAre Splicing Events in RNA-seq
MIT License
39 stars 22 forks source link

Getting error when counting splice sites #79

Open fburdet opened 2 years ago

fburdet commented 2 years ago

Hello,

I installed the package on an Ubuntu 22 server.

When running fds <- countRNAData(settings) with my own data (ONT bam files), the first steps work ok, but then I get

Mon Aug 29 17:58:49 2022: In total 239257 splice sites (acceptor/donor) will be counted ... Error in reducer$value.cache[[as.character(idx)]] <- values : wrong args for environment subassignment In addition: Warning message: In parallel::mccollect(wait = FALSE, timeout = 1) : 1 parallel job did not deliver a result

What could be the issue?

Thanks

moe1619 commented 1 year ago

I get the same error running FRASER via DROP. Happens only intermittently. I think its inadequate memory?

vyepez88 commented 7 months ago

Hi, yes, we have seen this happening, most likely due to the program running out of memory. Can you please try rerunning it? If using DROP, use the -k parameter on the snakemake run, and be sure to have recount: FALSE in the config file.

OlgaVT commented 1 month ago

Hi,

I am having the same error while counting split reads. My input is ~100 bam files with >100M reads each. I tried to run with and without parallelization, and also to allocate more memory. It did not help. Could you advise what I could try or any work arounds?

Thank you!