Not able to use the NCBI gff or gff3 format for training the sample #10
Description
Hi
I am trying to use ncbi downloaded saccharomyces cerevisiae sample(.fna) and gff for training but getting issue:
Singularity> funannotate2 train -f cleaned_GCF_000146045.2_R64_genomic.fasta -s "saccharomyces cerevisiae" -o train_result2 --cpu 16 -t GCF_000146045.2_R64_genomic.gff
ERROR: No gene models found in training set: GCF_000146045.2_R64_genomic.gff3
#Failing with both gff3 and gff
Singularity> funannotate2 train -f cleaned_GCF_000146045.2_R64_genomic.fasta -s "saccharomyces cerevisiae" -o train_result2 --cpu 16 -t GCF_000146045.2_R64_genomic.gff3
[Jun 07 06:07 PM] Python v3.10.14; funannotate2 v25.5.27; gfftk v25.4.17; buscolite v25.4.24
[Jun 07 06:07 PM] Loading genome assembly and running QC checks
[Jun 07 06:07 PM] Genome stats:
{
"n_contigs": 17,
"size": 12157105,
"n50": 924431,
"n90": 439888,
"l50": 6,
"l90": 13,
"avg_length": 715124
}
[Jun 07 06:07 PM] Getting taxonomy information
{
"superkingdom": "Eukaryota",
"kingdom": "Fungi",
"phylum": "Ascomycota",
"class": "Saccharomycetes",
"order": "Saccharomycetales",
"family": "Saccharomycetaceae",
"genus": "Saccharomyces",
"species": "Saccharomyces cerevisiae"
}
[Jun 07 06:07 PM] Choosing best augustus species based on taxonomy: saccharomyces_cerevisiae_rm11-1a_1
[Jun 07 06:07 PM] Training set [GCF_000146045.2_R64_genomic.gff3] loaded with 0 gene models
[Jun 07 06:07 PM] No gene models found in training set: GCF_000146045.2_R64_genomic.gff3
Singularity>