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colomemaria / epiAneufinder

R package to detect breakpoints and assign somies to scATAC-seq data
GNU General Public License v3.0
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Error: node stack overflow #14

Closed Urja25 closed 1 year ago

Urja25 commented 1 year ago

Hi,

I ran epiAneufinder and it crashed right after generating the tsv file for copy number changes: [1] "Successfully assigned gain-loss" A .tsv file with the results has been written to disk. It contains the copy number states for each cell per bin. 0 denotes 'Loss', 1 denotes 'Normal', 2 denotes 'Gain'. The error message was: Error: node stack overflow In addition: Warning message: In fread(input) : Detected 1 column names but the data has 5 columns (i.e. invalid file). Added 4 extra default column names at the end. Execution halted

How do I fix this problem?

Are there any plotting functions that I can use readily to obtain a heatmap or copy number plots?

Thanks a lot!

Best, Urja

Urja25 commented 1 year ago

So it turns out that the bug was with ggdendro and has been resolved: https://github.com/andrie/ggdendro/issues/27#issuecomment-1743261773

You can install the developer's version of the ggdendro package from github and then try running epiAneufinder and it should work.