No output when running hmm_frag_fit.py

[hvbakel]

I've been trying to get the hmm script to run on a set of bigwig files from a total RNA-Seq experiment. The reads were mapped with STAR, converted to bedGraph with 'bedtools genomecov', and then converted to bigwig using the kent ucsc utils. When running the hmm, it seems to be skipping all genes with the error message "Skipping - the coding region is not expressed". A few others give a "wrong isoform" error.

The fact that the script doesn't seem to register any read coverage suggests that something may be wrong with the way the bigwig files are formatted. Do you have any idea what the issue may be?