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ParkinsonLab / MetaPro

GNU General Public License v3.0
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Kaiju database: unable to retrieve all genome files #22

Closed DGleason-680 closed 7 months ago

DGleason-680 commented 7 months ago

When preparing the Kaiju database via "/pipeline_tools/kaiju/makeDB.sh" (as outlined on the tutorial page), the full list of genome files should be 40,251 but I am only receiving 38,976. Several files return "wget: unable to resolve host address ‘na’". I assuming this is an issue with either the makeDB.sh or the host.

I'm wondering if this will pose a problem when running the pipeline on samples. Are all genome files necessary to successfully run MetaPro?

billytaj commented 7 months ago

This sounds like a kaiju issue. not quite a MetaPro issue. MetaPro does not check for database robustness. It has no concept of whether or not a database is complete. It will only check if certain databases have been indexed, all for the purpose of making it run. <running well is subjective, and user + input data + database - dependent>