Collapse step didn't output a gtf file without a reference annotation

[dudududu12138]

Hi, I recently ran flair in the unguided mode, that is, I didn't offer a reference annotation. There are no error message. But there are only 2 outputs: 1)isoforms.bed,2)isoforms.fa. The isoforms.gtf was missing. Do you know the reason? Below are my codes:

bam2Bed12 -i ../minimap2/$sample.sorted.bam >$out/$sample.bed

flair collapse -t 10 \
        -q $input/${sample}.bed \
        -r ../reads/$sample/$sample.fastq \
        -g $ref \
        -o $output/$sample/$sample

By the way, I also ran flair collapse with a reference annotation. I followed your pipeline. But there are many other outputs. Could you explain the outputs except of stringent.isoforms.bed,stringent.isoforms.fa and stringent.isoforms.gtf? Below are the outputs and my codes :

stringent.annotated_transcripts.alignment.counts
stringent.annotated_transcripts.bed
stringent.annotated_transcripts.fa
stringent.annotated_transcripts.isoform.read.map.txt
stringent.annotated_transcripts.supported.bed
stringent.combined.isoform.read.map.txt
stringent.isoform.read.map.txt
stringent.isoforms.bed
stringent.isoforms.fa
stringent.isoforms.gtf

flair collapse -g genome.fa --gtf gene_annotations.gtf -q reads.flair_all_corrected.bed -r reads.fastq
--stringent --check_splice --generate_map --annotation_reliant generate

Waiting for your reply. Thanks!