xxx found in FL count file but not in input fasta

[pgupta3005]

Hi. I used SQANTI3 after running the FLAIR correct --> collapse --> quantify steps. As an input, give the collapsed isoforms gtf and the isoform counts, along with genome gtf and genome fasta files. It runs smoothly with no errors. However, in the log file, I can see several 'xxx found in FL count file but not in input fasta.' warning messages. Please find the screenshot attached. However, the isoforms mentioned in these lines do appear in the classification.txt file with their corresponding counts in the FL column.

I wish to understand which input fasta are we talking about and can something be done to prevent this warning message.