agat_sp_extract_sequences.pl Could not open index file but it exists

[hans-vg]

Describe the bug
When running the command, it gets towards the bottom of the process but then errors saying the it could not open the index file. This is a resulting GFF file from MAKER output.

General (please complete the following information):

• AGAT version v1.4.0
• AGAT installation/use miniforge mamba install
• OS: Ubuntu

To Reproduce
agat_sp_extract_sequences.pl --gff highquality_set_aed03.gff --fasta JG_Nov2021_contig.fa -t cds -o highquality_set_aed03.CDS.fasta

Additional context
Log file:

agat_sp_extract_sequences.pl --gff highquality_set_aed03.gff --fasta JG_Nov2021_contig.fa -t cds -o highquality_set_aed03.CDS.fasta

 ------------------------------------------------------------------------------
|   Another GFF Analysis Toolkit (AGAT) - Version: v1.4.0                      |
|   https://github.com/NBISweden/AGAT                                          |
|   National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se         |
 ------------------------------------------------------------------------------
=> Using standard /home/hvasquezgross/miniforge3/envs/agat/lib/perl5/site_perl/auto/share/dist/AGAT/agat_config.yaml config file
We will extract the cds sequences.
Reading file highquality_set_aed03.gff
                                        
                                       
                          ------ Start parsing ------                           
-------------------------- parse options and metadata --------------------------
=> Accessing the feature_levels YAML file
Using standard /home/hvasquezgross/miniforge3/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/hvasquezgross/miniforge3/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/hvasquezgross/miniforge3/envs/agat/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo
	Read ontology /home/hvasquezgross/miniforge3/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: 1615817
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 1615817
=> Number of feature type (3rd column): 6
	* Level1: 1 => gene
	* level2: 1 => mRNA
	* level3: 4 => exon three_prime_UTR five_prime_UTR CDS
	* unknown: 0 => 
=> Version of the Bioperl GFF parser selected by AGAT: 3
Parsing: 100% [======================================================]D 0h03m05s
                 ------ End parsing (done in 188 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 1 seconds -------------------------------

--------------------------- Check5: l1 linked to l2 ----------------------------
No problem found
------------------------------ done in 1 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 24 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 18 seconds ------------------------------

----------------------------- Check10: check utrs ------------------------------
No UTRs created
No UTRs locations modified
No supernumerary UTRs removed
------------------------------ done in 11 seconds ------------------------------

------------------------ Check11: all level2 locations -------------------------
No problem found
------------------------------ done in 16 seconds ------------------------------

------------------------ Check12: all level1 locations -------------------------
No problem found
------------------------------ done in 2 seconds -------------------------------

---------------------- Check13: remove identical isoforms ----------------------
None found
------------------------------ done in 0 seconds -------------------------------
                  ------ End checks (done in 73 second) ------                  


Parsing Finished

------------- EXCEPTION -------------
MSG: Could not open index file JG_Nov2021_contig.fa.index: No such file or directory
STACK Bio::DB::IndexedBase::_open_index /home/hvasquezgross/miniforge3/envs/agat/lib/perl5/site_perl/Bio/DB/IndexedBase.pm:678
STACK Bio::DB::IndexedBase::_index_files /home/hvasquezgross/miniforge3/envs/agat/lib/perl5/site_perl/Bio/DB/IndexedBase.pm:655
STACK Bio::DB::IndexedBase::index_file /home/hvasquezgross/miniforge3/envs/agat/lib/perl5/site_perl/Bio/DB/IndexedBase.pm:488
STACK Bio::DB::IndexedBase::new /home/hvasquezgross/miniforge3/envs/agat/lib/perl5/site_perl/Bio/DB/IndexedBase.pm:365
STACK toplevel /home/hvasquezgross/miniforge3/envs/agat/bin/agat_sp_extract_sequences.pl:158

File listing after run:
ls -alh

drwxrwxr-x 2 hvasquezgross hvasquezgross   14 Aug 29 16:51 .
drwxrwxr-x 3 hvasquezgross hvasquezgross   18 Aug 29 15:23 ..
-rw-rw-r-- 1 hvasquezgross hvasquezgross 5.4K Aug 29 17:03 highquality_set_aed03.agat.log
-rw-rw-r-- 1 hvasquezgross hvasquezgross    0 Aug 29 16:58 highquality_set_aed03.CDS.fasta
-rw-r--r-- 1 hvasquezgross hvasquezgross 279M Aug 29 15:53 highquality_set_aed03.gff
-rw-rw-r-- 1 hvasquezgross hvasquezgross 3.1G Aug 29 16:00 JG_Nov2021_contig.fa
-rw-r--r-- 1 hvasquezgross hvasquezgross 336K Aug 29 16:05 JG_Nov2021_contig.fa.index

[Juke34]

No idea, this is strange. Did you try by removing the index and re-run ?