R2D - liftover and metatranscript data points

[gsukrit]

Hello team,

Thank you so much for making the R2Dtool. I am using it on CHEUI solo output to map it back to genomic coordinates. However, after I run the r2d liftover command, I am getting the following warnings:
image
What could be the possible reason for this as these genes are showing modified at multiple sites (with >0.9 modified_probability) in the site_level_m5C_predictions.txt. All of these occurrences got covered in the .bed file created using cheui_to_bed.sh but during liftover I got these warnings.

Also, for plotting the metatranscript plot, there is an option to print the data points in a tab seperated file. Is it possible to get a descriptor for the headers of the file. This is how my file is looking:

Also, is it possible to get the CDS/5'UTR/3'UTR ditribution for each entry on my CHEUItoBED output (basically mapping for the contigs that are actually used for plotting on the metaTranscript plot).

Any help in this regard would be greatly appreciated.