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PierreBSC / Viral-Track

MIT License
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Recommended R version? #11

Open sfortma2 opened 3 years ago

sfortma2 commented 3 years ago

Hey,

Thank you for creating and sharing such an important program. I am running into issues with dependencies on my R environment using my university cluster. I see that you specify BiocManager 3.10 on this github which would imply R version 3.6. On the actual publication, R version 3.5 is listed. Which R version do you recommend for Viral-Track?

Thanks, Seth

PierreBSC commented 3 years ago

Hi Seth,

Thank you for this heartwarming message :) So we tested Viral-Track on various computer configurations, inlcuding R 3.5 and R 3.6 so I don't think it would really affect how Viral-Track works. What kinds of problems are you facing ?

Best

Pierre

sfortma2 commented 3 years ago

Hey Pierre,

Thanks for the quick response. So I was able to solve my R problem by using conda to download the r-XML package, which otherwise I couldn't update for some reason. After that I was able to install the R packages and ran Viral-Tracker on several PBMC samples, revealing mostly bacteriophages and retroviruses. However, I'm getting an error on the last step, demultiplexing. It's unclear to me exactly what's supposed to be in the target and parameters files for this step. Are they the identical files used in the viral scanning step? I'm getting the following error when I run the demultiplexing step using the same 2 files as before: Error in file(file, "rt") : cannot open the connection Calls: read.table -> file In addition: Warning message: In file(file, "rt") : cannot open file '~output_dir//~sample///QC_filtered.txt': No such file or directory Execution halted The multiple backslashes seem to be throwing off the path to the filtered virus file. Looking at the Viral_Track_cell_demultiplexing.R file, it appears this path is created by joining strings from the Output_directory, the path from the target.txt file, and the characters "/QC_filtered.txt". I'm not sure why the extra slashes are being added when they're joined. Any idea what's going on here?

Thanks again for the help! Seth

harris-yh-wong commented 3 years ago

I think R 4.0 breaks the code at line 343 of Viral-track-scanning.R, now matrix objects inherit the "array" class as well.