Hello, I am running BAMBU with my datasets. It looks like the error is saying the reference annotation isn't correct, but I used these three files in other long read packages and worked well. Is there anything I missed in the command line? I tried moving the files into the directory too, but it fails with the same reasons. I converted fastq file to sam file using minimap2, sam file into bam file using samtools. I am using cDNA!
I used these command lines to convert fastq file to bam file.
./minimap2 -t 8 -ax splice /home/seong/R/x86_64-pc-linux-gnu-library/4.1/bambu/extdata/hg38.fa /data/long_read/ENCBS944CBA/ENCFF263YFG.fastq -o /data/long_read/ENCBS944CBA/ENCFF263YFG.sam
samtools view -@ 8 -Sb -o /data/long_read/ENCBS944CBA/ENCFF563QZR.bam /data/long_read/ENCBS944CBA/ENCFF563QZR.sam