gff3 to gtf

Question

[bestone]

Hello everyone, I am trying to convert gff3 file to gtf file for that I used the command below:
agat_convert_sp_gff2gtf.pl -i input.gff3 -o genes.gtf

But it did not work. Can anyone help me with this issue?

[Juke34]

Could you elaborate? What is not working? Do you have any error message?

[bestone]

Using standard /Users/uguremre/opt/anaconda3/lib/perl5/site_perl/auto/share/dist/AGAT/config.yaml file
Update config
Reading input file

 ------------------------------------------------------------------------------
|   Another GFF Analysis Toolkit (AGAT) - Version: v1.0.0                      |
|   https://github.com/NBISweden/AGAT                                          |
|   National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se         |
 ------------------------------------------------------------------------------


                          ------ Start parsing ------                           
-------------------------- parse options and metadata --------------------------
=> Accessing the feature_levels YAML file
Using standard /Users/uguremre/opt/anaconda3/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: /Users/uguremre/opt/anaconda3/lib/perl5/site_perl/Bio/
    Operating system being used: darwin 
=> Accessing Ontology
    No ontology accessible from the gff file header!
    We use the SOFA ontology distributed with AGAT:
        /Users/uguremre/opt/anaconda3/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo
    Read ontology /Users/uguremre/opt/anaconda3/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 ---------------------------------
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!      input.gff3 does not exist. Please verify the input file name/path       !
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

Answer 1

[Juke34]

Reading the error message, it sounds quite obvious, you didn't provide an existing file. If you look into your current directory there is no file called input.gff3.

[bestone]

It worked thank you so much Juke have a good day