issues when running the tool

[Overcraft90]

Hi there,

I was running the following on some lupin genomes with their respective GFF annotation:

get_pangenes.pl -d 5.get_pangenes/ -n 24 -t 0 -c

However, not even after processing the first sample INLUP00165_hap1.fa.gz the tools returns the following:

# /hpc/home/ngrmtt1/.conda/envs/get_pangenes/bin/get_pangenes.pl -d 5.get_pangenes -p 0 -o 0 -r 0 -t 0 -c 1 -z 0 -I 0 -m local -w 0 -g 0 -O 0.5 -Q 50 -P 95 -N 2 -s '' -f 0 -H 0 -W '' -G '' -B '' -S '' -n 24 -R 0

# version 27052025
# results_directory=/hpc/groups/users-genetica-pop-1/ngrmtt1/sequencing/5.get_pangenes_pangenes
# parameters: MINGFFLEN=100 GFFACCEPTEDFEATS=gene,mRNA,transcript,exon,CDS GFFVALIDGENEFEAT=gene,mRNA,transcript

# checking input files...
# uncompressing 5.get_pangenes/INLUP00165_hap1.fa.gz
ERROR: no valid genes in GFF file 5.get_pangenes/INLUP00165_hap1.gff3.gz with > 1 gene,mRNA,transcript features

Is this because the annotations are in GFF3 format? If useful, I can share the files structure; let me know, thanks!

[brunocontrerasmoreira]

Sorry @Overcraft90 , only saw this today.
Please check section 'Input file format'.

For each genome you need a FASTA file and a GFF file; the GFF file must contain gene,mRNA,transcript features, otherwise you get that error message. Other accepted features are CDS and exon. Can you please share the first non-# lines in your GFF files?

[Overcraft90]

@brunocontrerasmoreira absolutely no worries! I managed to reformat my corrupted GFF3 to GFF with agat_convert_sp_gxf2gxf.pl. However, as I'm a nweby with gene annotation, I'll also share the first non-# of one of my original annotation before the fix was applied so that you can better understand the issue:

INLUP00165_hap1

scaffold_1      AUGUSTUS        transcript      9469    13971   .       +       .       ID=g1.t1;geneID=g1

[brunocontrerasmoreira]

OK, at least the first object in your data lacks a gene line, that would explain the error message.