Error about demux_isoseq_with_genome.py

[Yuzhang0102]

Hi, I used the same pipeline with the @kmattioli to process the isoseq data, but i met an error when running demux_isoseq_with_genome.py. The closed issue is in the link #167 (comment)

WARNING: Could not find PB.9996.2|3:104721362-104790835(-)|transcript/114028 in clustered.hq.fasta.collapsed.read_stat.txt. No demux output for this sequence! WARNING: Could not find PB.9996.3|3:104780666-104790835(-)|transcript/83742 in clustered.hq.fasta.collapsed.read_stat.txt. No demux output for this sequence!

It warns that every transcript is not in the read_stat.txt. And the transcript ID in the read_stat.txt and the ID int the filtered.rep.fa are different indeedly. But i used the files are the output from the pipeline. What's the problem with my code?

demux_isoseq_with_genome.py --mapped_fafq clustered.hq.fasta.collapsed.filtered.rep.fa --read_stat clustered.hq.fasta.collapsed.read_stat.txt --classify_csv all_classify.report.csv -o clustered.hq.fasta.collapsed.filtered.mapped_fl_count.txt

clustered.hq.fasta.collapsed.filtered.rep.fa from the get_abundance_post_collapse.py after collapse_isoforms_by_sam.py,
clustered.hq.fasta.collapsed.read_stat.txt from the collapse_isoforms_by_sam.py,
all_classify.report.csv is from merging the each sample .flnc.report.csv from the isoseq3 refine step

Thanks!