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NBISweden / AGAT

Another Gtf/Gff Analysis Toolkit
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Can't "continue" outside a when block at /home/lege/anaconda3/envs/agat/bin/agat_convert_sp_gff2bed.pl line 189. #383

Closed alexvasilikop closed 11 months ago

alexvasilikop commented 1 year ago

Describe the bug Hello running the function to convert the gff2bed gives me the following error:

Using standard /home/lege/anaconda3/envs/agat/lib/perl5/site_perl/auto/share/dist/AGAT/config.yaml 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 /home/lege/anaconda3/envs/agat/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: /home/lege/anaconda3/envs/agat/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:
        /home/lege/anaconda3/envs/agat/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo
    Read ontology /home/lege/anaconda3/envs/agat/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: 443934
=> Number of comment lines: 1
=> Fasta included: No
=> Number of features lines: 443933
=> Number of feature type (3rd column): 7
    * Level1: 1 => gene
    * level2: 2 => mRNA tRNA
    * level3: 4 => exon five_prime_UTR three_prime_UTR CDS
    * unknown: 0 => 
=> Version of the Bioperl GFF parser selected by AGAT: 3
                  ------ End parsing (done in 64 second) ------                 

                           ------ Start checks ------                           
---------------------------- Check1: feature types -----------------------------
----------------------------------- ontology -----------------------------------
All feature types in agreement with the Ontology.
------------------------------------- agat -------------------------------------
AGAT can deal with all the encountered feature types (3rd column)
------------------------------ done in 0 seconds -------------------------------

------------------------------ Check2: duplicates ------------------------------
None found
------------------------------ done in 0 seconds -------------------------------

-------------------------- Check3: sequential bucket ---------------------------
Nothing to check as sequential bucket!
------------------------------ done in 0 seconds -------------------------------

--------------------------- Check4: l2 linked to l3 ----------------------------
No problem found
------------------------------ done in 0 seconds -------------------------------

--------------------------- Check5: l1 linked to l2 ----------------------------
No problem found
------------------------------ done in 0 seconds -------------------------------

--------------------------- Check6: remove orphan l1 ---------------------------
We remove only those not supposed to be orphan
None found
------------------------------ done in 0 seconds -------------------------------

------------------------- Check7: all level3 locations -------------------------
------------------------------ done in 10 seconds ------------------------------

------------------------------ Check8: check cds -------------------------------
No problem found
------------------------------ done in 0 seconds -------------------------------

----------------------------- Check9: check exons ------------------------------
No exons created
No exons locations modified
No supernumerary exons removed
No level2 locations modified
------------------------------ done in 7 seconds -------------------------------

----------------------------- Check10: check utrs ------------------------------
No UTRs created
No UTRs locations modified
No supernumerary UTRs removed
------------------------------ done in 5 seconds -------------------------------

------------------------ Check11: all level2 locations -------------------------
No problem found
------------------------------ done in 8 seconds -------------------------------

------------------------ Check12: all level1 locations -------------------------
No problem found
------------------------------ done in 1 seconds -------------------------------

---------------------- Check13: remove identical isoforms ----------------------
None found
------------------------------ done in 0 seconds -------------------------------
                  ------ End checks (done in 31 second) ------                  

Can't "continue" outside a when block at /home/lege/anaconda3/envs/agat/bin/agat_convert_sp_gff2bed.pl line 189.

General (please complete the following information):

To Reproduce

agat_convert_sp_gff2bed.pl --gff Adineta_ricciae.chrom.longest.gff3 --nc filter --sub cds --outfile Adineta_ricciae.chrom.longest.bed

Best Alex

alexvasilikop commented 1 year ago

Short update, the error most likely comes from the option: --nc filter because removing this flag gives no error.

cheers Alex

Juke34 commented 11 months ago

Thank you for reporting this bug.