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I have re-run some analysis to build a reference database, and have successfully imported the embl database and the tax dump with obi -import, and run ecoPCR.

I have followed the the tutorial from step 7.1 onward, keeping the exact same code (replacing wolf by my_project in the code below:

Now I wanted to filter sequences that have taxonomic annotation but run into an error:

The command I use is:

obi grep --require-rank=species --require-rank=genus --require-rank=family --taxonomy my_project/taxonomy/my_tax my_project/Chiar16S_refs my_project/Chiar16S_refs_clean

The command runs but then fails with No local taxa (now it also fails with view already exists if I run it again).

Indexing taxon names...
DEBUG /tmp/pip-install-36kc02g6/OBITools3/src/obiview.c:1643:obi_new_view, obi_errno = 35, errno = 25 : 
Name of new view ('Chiar16S_refs_clean') already exists

Reading 2321738 taxa...
No local taxa

My folder structure is the following: The parent folder from which I call the command:

ls .

my_project.obidms
EMBL
taxdump
taxdump.tar.gz


ls my_project.obidms

my_project_infos
COUNT.obicol
DEFINITION.obicol
family_name.obicol
family.obicol
forward_error.obicol
forward_match.obicol
forward_tm.obicol
genus_name.obicol
genus.obicol
ID.obicol
LINES.obicol
NUC_SEQ.obicol
OBIBLOB_INDEXERS
organism.obicol
rank.obicol
reverse_error.obicol
reverse_match.obicol
reverse_tm.obicol
scientific_name.obicol
seq_length.obicol
seq_length_ori.obicol
species_name.obicol
species.obicol
strand.obicol
superkingdom_name.obicol
superkingdom.obicol
TAXID.obicol
TAXONOMY
VIEWS

Apologies for requesting your help again!