GitLab

Hi,

I'm trying to assign taxonomy to my sequences like so:

obi ecotag -m 0.60 --taxonomy Coll01_r140_stripped/taxonomy/my_tax -R Coll01_r140_stripped/Coll01_r140_refs_clean Coll01_r140_stripped/otu85_sequences Coll01_r140_stripped/assigned_sequences

But I get the following error message:

Traceback (most recent call last):
  File "/kyukon/home/gent/462/vsc46214/obitools3/obi3-env/bin/obi", line 4, in <module>
    __import__('pkg_resources').run_script('OBITools3==3.0.1b24', 'obi')
  File "/kyukon/home/gent/462/vsc46214/obitools3/obi3-env/lib/python3.10/site-packages/pkg_resources/__init__.py", line 722, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/kyukon/home/gent/462/vsc46214/obitools3/obi3-env/lib/python3.10/site-packages/pkg_resources/__init__.py", line 1561, in run_script
    exec(code, namespace, namespace)
  File "/kyukon/home/gent/462/vsc46214/obitools3/obi3-env/lib/python3.10/site-packages/OBITools3-3.0.1b24-py3.10-linux-x86_64.egg/EGG-INFO/scripts/obi", line 62, in <module>
    config[root_config_name]['module'].run(config)
  File "python/obitools3/commands/ecotag.pyx", line 80, in obitools3.commands.ecotag.run
  File "python/obitools3/dms/view/view.pyx", line 704, in obitools3.dms.view.view.View_comments.__getitem__
KeyError: b'ref_db_threshold'

In trying to figure out what might be causing the ref_db_treshold error, the only thing that comes to mind is that I didn't run obi build_ref_db, because that didn't work and gave an error. Is obi build_ref_db needed to be able to run obi ecotag?

For reference, I used the following commands to build the db:

obi import --fasta-input ./otus85_stripped.fasta Coll01_r140_stripped/otu85_sequences

obi import --taxdump taxdump.tar.gz Coll01_r140_stripped/taxonomy/my_tax

obi import --fasta-input ./Coll01_r140_cleaned.fasta Coll01_r140_stripped/Coll01_r140_refs

obi grep --require-rank=species --require-rank=genus --require-rank=family --taxonomy Coll01_r140_stripped/taxonomy/my_tax Coll01_r140_stripped/Coll01_r140_refs Coll01_r140_stripped/Coll01_r140_refs_clean

obi ecotag -m 0.60 --taxonomy Coll01_r140_stripped/taxonomy/my_tax -R Coll01_r140_stripped/Coll01_r140_refs_clean Coll01_r140_stripped/otu85_sequences Coll01_r140_stripped/assigned_sequences

Kind regards, Sam