LSTM_extract.py predict 0 reads in bamfile

[MaestSi]

Dear developers, I'm running dena on a dataset, and I am not able to get any results. In particular, I noticed that this command: python3 /DENA/step4_predict/LSTM_extract.py predict --fast5 FAST5_dir --corr_grp RawGenomeCorrected_000 --bam transcriptome.bam --sites candidate_predict_pos.txt --label "dena_label" --windows 2 2 --processes 1 --debug is producing only *_tmp empty files. I noticed from the standard error that the tool is able to find reads in fast5 but not in bam file, e.g.:

transcript1	pos1-pos2found x reads in fast5
transcript1	pos1-pos2found 0 reads in bamfile

Do you know what may have caused the issue? Thanks in advance, Simone