Hi. I used RNA-seq and protein data to annotate the genes and I want to assign the gene ontology terms to the genes. To minimize duplications, I obtained the longest isoform with agat and then detected orthogroups/orthologs with Orthofinder. InterproScan, eggnog-mapper, and deepGoplus failed in my HPC; but, there are related species in NCBI with gene_ontology files. I used the related species. I want to transfer the go-terms, either pairwisely, but I thought it would be more interesting to see - as confidence, how many go-terms are supported by multiple-species. The orthogroups file looks like this:

head Orthogroups.tsv
Orthogroup      Canlup  Hydlep  LW1     Lepwed  Mirang  Mirleo  Neosch  Ursarc

where each column is separated by tab, and each gene within a column by ", ".

The GOA files look like this:

head GCF_002201575.2_ASM220157v2_gene_ontology.gaf -n 12
!gaf-version: 2.2
!generated-by: NCBI
!date-generated: 2023-11-10
!
!interProScan version: 5.64-96.0
!PANTHER version: 17.0
!GO version: 2023-07-27
!
!#DB    GeneID  Symbol  Qualifier       GO_ID   Reference       Evidence_Code   With,From       Aspect  Gene_Name       Gene_Synonym    Type    Taxon   Date    Assigned_By    Annot_Ext       Gene_Product_Form_ID
NCBIGene        110569606       SHROOM2 located_in      GO:0005912      PMID:30032202   IEA     PANTHER:PTN001805876|UniProtKB:A0A5F4BXY6       C       NA            protein  taxon:29088     20231110        RefSeq
NCBIGene        110569606       SHROOM2 involved_in     GO:0007015      PMID:30032202   IEA     PANTHER:PTN001805876|UniProtKB:A0A5F4BXY6       P       NA            protein  taxon:29088     20231110        RefSeq
NCBIGene        110569606       SHROOM2 located_in      GO:0016324      PMID:30032202   IEA     PANTHER:PTN001805876|UniProtKB:A0A5F4BXY6       C       NA            protein  taxon:29088     20231110        RefSeq

I extracted the gene ontology terms with:

awk '!/^!/ {print $2 "\t" $5}' species.gaf > species.gene2go.tsv

and now I have the gene_id<TAB>GO:XXXXXXX table

head Neosch.gene2go.tsv
110569606       GO:0005912
110569606       GO:0007015
110569606       GO:0016324
110569606       GO:0030864
110569606       GO:0043296
110569606       GO:0051015

How can I map/transfer the go-terms to the genes?

Thanks;