I am using iReckon for isoform quantification. Since I am only interested in annotated isoforms, I set -novel 0 in the program so that isoform discovery is skipped. However, I saw this message "No isoforms reconstructed. Check the content of your bam file and annotation file", and no output is given.

Anyone having experience with iReckon can help?

Here's my command:

java -Xmx15000M  -jar IReckon-1.0.8.jar ~/JSLIDE/liver_BAM/liver1sorted.bam GRCh38.p5.genome.fa hg38.nano.bed  -1 ~/JSLIDE/liver_BAM/liver1_R1.fastq  -2 ~/JSLIDE/liver_BAM/liver1_R2.fastq  -o liver1/ -d -novel 0 -n 4 -b 2

Thanks!