search

nextgenusfs / funannotate

Eukaryotic Genome Annotation Pipeline
http://funannotate.readthedocs.io
BSD 2-Clause "Simplified" License
301 stars 82 forks source link

Malformed GFF file for funannotate annotate #873

Closed MesYosra closed 1 year ago

MesYosra commented 1 year ago

funannotate v1.8.13

Hello, I am trying to get funannotate annotate to work on my data with the command :
funannotate annotate --gff "/shared/home/ymestiri/projects/annotation_fusarium/yosra/Funannotate/UK0001. gff3" --fasta "/shared/home/ymestiri/projects/annotation_fusarium/yosra/Funannotate/UK0001.fasta" --iprscan "/shared/home/ymestiri/projects/annotation_fusarium/yosra/Funannotate/UK0001_gene. fasta.xml" -d "/shared/home/ymestiri/projects/annotation_fusarium/yosra/Funannotate/FUNANNOTATE_DB" --species "Pseudocercospora fijiensis" --cpus 10 -o "/shared/home/ymestiri/projects/annotation_fusarium/yosra/Funannotate/annotated/". . I have an error :

"Error, can't find ID or Parent. GFF file malformed. VMNF01000004.1 BRAKER CDS 1600277 1601047 0.91 + 0 Parent=jg4615T0" some examples from the gff3 file below

MesYosra commented 1 year ago 
VMNF01000004.1  BRAKER  gene    1600277 1601863 .   +   .   ID=jg4615;Name=jg4615
VMNF01000004.1  BRAKER  mRNA    1600277 1601863 .   +   .   ID=jg4615T0;Parent=jg4615
VMNF01000004.1  BRAKER  start_codon 1600277 1600279 .   +   0   Parent=jg4615T0
VMNF01000004.1  BRAKER  CDS 1600277 1601047 0.91    +   0   Parent=jg4615T0
VMNF01000004.1  BRAKER  CDS 1601095 1601322 1   +   0   Parent=jg4615T0
VMNF01000004.1  BRAKER  CDS 1601372 1601863 1   +   0   Parent=jg4615T0
VMNF01000004.1  BRAKER  stop_codon  1601861 1601863 .   +   0   Parent=jg4615T0
VMNF01000013.1  BRAKER  gene    206335  208048  .   -   .   ID=jg9620;Name=jg9620
VMNF01000013.1  BRAKER  mRNA    206335  208048  .   -   .   ID=jg9620T0;Parent=jg9620
VMNF01000013.1  BRAKER  stop_codon  206335  206337  .   -   0   Parent=jg9620T0
VMNF01000013.1  BRAKER  CDS 206335  206466  0.83    -   0   Parent=jg9620T0
VMNF01000013.1  BRAKER  CDS 206522  208048  0.59    -   0   Parent=jg9620T0
VMNF01000013.1  BRAKER  start_codon 208046  208048  .   -   0   Parent=jg9620T0
VMNF01000009.1  BRAKER  gene    2697787 2699947 .   -   .   ID=jg9030;Name=jg9030
VMNF01000009.1  BRAKER  mRNA    2697787 2699947 .   -   .   ID=jg9030T0;Parent=jg9030
VMNF01000009.1  BRAKER  stop_codon  2697787 2697789 .   -   0   Parent=jg9030T0
VMNF01000009.1  BRAKER  CDS 2697787 2697818 1   -   2   Parent=jg9030T0
VMNF01000009.1  BRAKER  CDS 2697873 2698858 1   -   1   Parent=jg9030T0
VMNF01000009.1  BRAKER  CDS 2698907 2699601 1   -   0   Parent=jg9030T0
VMNF01000009.1  BRAKER  CDS 2699659 2699869 1   -   1   Parent=jg9030T0
VMNF01000009.1  BRAKER  CDS 2699925 2699947 1   -   0   Parent=jg9030T0
VMNF01000009.1  BRAKER  start_codon 2699945 2699947 .   -   0   Parent=jg9030T0
VMNF01000003.1  BRAKER  gene    3603034 3607860 .   -   .   ID=jg7817;Name=jg7817
VMNF01000003.1  BRAKER  mRNA    3603034 3607860 .   -   .   ID=jg7817T0;Parent=jg7817
VMNF01000003.1  BRAKER  stop_codon  3603034 3603036 .   -   0   Parent=jg7817T0
VMNF01000003.1  BRAKER  CDS 3603034 3605124 1   -   0   Parent=jg7817T0
VMNF01000003.1  BRAKER  CDS 3605186 3605259 0.84    -   2   Parent=jg7817T0
VMNF01000003.1  BRAKER  CDS 3607176 3607860 0.96    -   0   Parent=jg7817T0
VMNF01000003.1  BRAKER  start_codon 3607858 3607860 .   -   0   Parent=jg7817T0
VMNF01000007.1  BRAKER  gene    5465290 5467137 .   +   .   ID=jg1690;Name=jg1690
VMNF01000007.1  BRAKER  mRNA    5465290 5467137 .   +   .   ID=jg1690T0;Parent=jg1690
VMNF01000007.1  BRAKER  start_codon 5465290 5465292 .   +   0   Parent=jg1690T0
VMNF01000007.1  BRAKER  CDS 5465290 5465397 0.47    +   0   Parent=jg1690T0
VMNF01000007.1  BRAKER  CDS 5465449 5466010 0.99    +   0   Parent=jg1690T0
VMNF01000007.1  BRAKER  CDS 5466056 5466622 1   +   2   Parent=jg1690T0
VMNF01000007.1  BRAKER  CDS 5466674 5466849 1   +   2   Parent=jg1690T0
VMNF01000007.1  BRAKER  CDS 5466919 5467137 1   +   0   Parent=jg1690T0
VMNF01000007.1  BRAKER  stop_codon  5467135 5467137 .   +   0   Parent=jg1690T0
nextgenusfs commented 1 year ago

The error message should be obvious? The sub features (CDS) do not have ID= field in column 9.