exon start coordinate > end coordinate after collapse

[YIGUIz]

Copy and paste the exact command you tried to run
singularity exec /flair\:2.0.0--pyhdfd78af_1 flair collapse -g GCF_002263795.3_ARS-UCD2.0_genomic.fna -s 10 -t 50 --quality 10 --gtf ${i}.gtf -q ${i}.bed -r ${i}.fq --output blood_4_${i} --stringent --check_splice --generate_map --no_gtf_end_adjustment --trust_ends

How did you install Flair?
singularity

What happened?
exon start coordinate > end coordinate after collapse

The same problem is here. I used lastest version, But it still have this problem. #84

No report error message

[cafelton]

Can you please post the input bed file for running this command so we can reproduce your error?