GffObj::getSpliced() error: improper

Question

GffObj::getSpliced() error: improper

abcdefghijklmn97 opened this issue 2 years ago · comments

Hi
Gffread gave me this error when I ran gffread /home/longjh/20220414ticds/basicdata/jy.v2.gff3 -g YGL1.fasta -x ygl1.fa

FASTA index file YGL1.fasta.fai created.
GffObj::getSpliced() error: improper genomic coordinate 57282209 on Chr09 for evm.model.Chr09.1612

Please help me out I am stuck.

Ryann Leung · Answer 1 · Sat Mar 30 2024 22:34:42 GMT+0800 (China Standard Time)

Hi,
I've also encountered this problem.

GffObj::getSpliced() error: improper genomic coordinate 70338 on Chr1A for TraesCS1A03G0000200.1

What is more serious is that this problem will wipe out my entire 14Gb of .fasta genome file (to 0 byte) which made me so so mad! Hoping some explanations will come out.

Yanyang,
Best.

Ryann Leung · Answer 2 · Thu Apr 18 2024 10:10:10 GMT+0800 (China Standard Time)

Hi,

I've noticed that this error shows because the coordinate within the input .gff3 file is out of range, which means this coordinate does not exist in your input .fasta file. Use Shell grep command to extract the specific coordinates you want or clear out the wrong coordinate information in the annotation file may help with this problem.

Best,
Yanyang.