search

Public-Health-Bioinformatics / cpo-pipeline

An analysis pipeline for the purpose of investigating Carbapenemase-Producing Organisms.
MIT License
1 stars 2 forks source link

Configuration error: databases/abricate_cpo_plasmid_db #47

Closed dfornika closed 5 years ago

dfornika commented 5 years ago

I'm seeing error messages in the logs when running the pipeline:

{"analysis_id": "114e1038-f7a3-4234-b7b0-acc6f1881b1d", "sample_id": "BC19A227A", "pipeline_version": "0.1.0", "timestamp": "2019-05-02T00:22:14.656615+00:00", "configuration_attribute": "databases/abricate_cpo_plasmid_db", "event": "configuration_failed", "level": "error"}
{"analysis_id": "dd5ea069-4e46-40c1-b5b9-5cc2950cd289", "sample_id": "BC19A228A", "pipeline_version": "0.1.0", "timestamp": "2019-05-02T00:25:00.525266+00:00", "configuration_attribute": "databases/abricate_cpo_plasmid_db", "event": "configuration_failed", "level": "error"}
...

Suggesting that the abricate_cpo_plasmid_db config value is not being loaded correctly.

DiDigsDNA commented 5 years ago

I'll take a look at this.

DiDigsDNA commented 5 years ago

I think the problem is happening here: https://github.com/Public-Health-Bioinformatics/cpo-pipeline/blob/a5c81ef12880c22e027d977ed2778543e8cca9e8/cpo_pipeline/resistance/pipeline.py#L98

We're checking that carbapenemases exists as a path but we should be checking inside abricate_datadir.

dfornika commented 5 years ago

Yes, I think that's right. Could you submit a pull-request?