agat_sp_manage_functional_annotation.pl "freezing"

[Jokendo-collab]

I am running agat_sp_manage_functional_annotation.pl on my data and it get stuck as shown below for days. I have canceled and restarted the running but it still remains in that state. My gff file is 650mb and it was generated by MAKER annotation pipeline. What could be the problem?

********************************************************************************
*                              - Start parsing -                               *
********************************************************************************
-------------------------- parse options and metadata --------------------------
=> Accessing the feature_levels YAML file
Using standard /vf/users/okendojo/conda/envs/interproscan/lib/perl5/site_perl/auto/share/dist/AGAT/feature_levels.yaml file
=> Attribute used to group features when no Parent/ID relationship exists (i.e common tag):
    * locus_tag
    * gene_id
=> merge_loci option deactivated
=> Machine information:
    This script is being run by perl v5.32.1
    Bioperl location being used: /vf/users/okendojo/conda/envs/interproscan/lib/perl5/site_perl/Bio/
    Operating system being used: linux 
=> Accessing Ontology
    No ontology accessible from the gff file header!
    We use the SOFA ontology distributed with AGAT:
        /vf/users/okendojo/conda/envs/interproscan/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo
    Read ontology /vf/users/okendojo/conda/envs/interproscan/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo:
        4 root terms, and 2596 total terms, and 1516 leaf terms
    Filtering ontology:
        We found 1861 terms that are sequence_feature or is_a child of it.
--------------------------------- parsing file ---------------------------------
=> Number of line in file: 9074526
=> Number of comment lines: 4962
=> Fasta included: No
=> Number of features lines: 963704
=> Number of feature type (3rd column): 11
    * Level1: 5 => protein_match expressed_sequence_match match contig gene
    * level2: 2 => mRNA match_part
    * level3: 4 => exon five_prime_UTR CDS three_prime_UTR
    * unknown: 0 => 
=> Version of the Bioperl GFF parser selected by AGAT: 3

[Juke34]

Did you solve the problem?

[Jokendo-collab]

The problem went away. Now can you help me with adding functional annotation and meta-data on my MAKER gff? I am trying their tutorial but it is not working. I want to attach the actual gene symbols in my gff file. I cannot make sense of the attached file.

[Juke34]

I copy past what I answered on biostars

Look at Practical about Functional annotation here: https://nbisweden.github.io/workshop-genome_annotation/schedule
Install AGAT and instead to use `gff3_` scripts, use `agat_sp` scripts