Error: no valid ID found for GFF record

[zuodabin]

Hello, I don't know what went wrong, could you tell me? thank you

[kennyworkman]

see https://github.com/gpertea/gffread/issues/84 you are likely using a gtf2.2 reference, of which the omission of transcript_id is allowed causing legacy gtf readers to complain

try using an older assembly / annotation pair alternatively try using a gff file from that assembly and converting it to gtf format

[gpertea]

If it is that GTF2.2 issue indeed, as I wrote in gpertea/gffread#84, I do not want to encourage such terrible ideas (empty string identifiers in a file format), so I recommended one of the following solutions instead:

• use the GFF3 version of that same annotation, if available ..or if that's not an option:
• use a grep filter to weed out the badly formatted lines from that GTF2.2 file, e.g. something like this:

grep -P '\btranscript_id\s+"[^"]+"'  ann_gtf22.gtf >  ann_fixed.gtf