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OLC-Bioinformatics / ConFindr

Intra-species bacterial contamination detection
https://olc-bioinformatics.github.io/ConFindr/
MIT License
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Didn't save genus-specific databases to temporary directory #57

Open chen1i6c04 opened 7 months ago

chen1i6c04 commented 7 months ago

I set option --tmp in confindr, the full command is

confindr -i input_dir -d database --rmlst -tmp tmpdir -o output_dir

But it seem not to save genus-specific databases to temporary directory.

  2023-11-20 15:43:28  Welcome to ConFindr 0.8.1! Beginning analysis of your samples... 
  2023-11-20 15:43:28  Beginning analysis of sample reads... 
  2023-11-20 15:43:28  Checking for cross-species contamination... 
  2023-11-20 15:43:39  Did not find databases for genus Campylobacter. You can download the rMLST database to get access to all genera (see https://olc-bioinformatics.github.io/ConFindr/install/). Alternatively, if you have a high-quality core-genome derived database for your genome of interest, we would be happy to add it - open an issue at https://github.com/OLC-Bioinformatics/ConFindr/issues with the title "Add genus-specific database: Campylobacter"

  2023-11-20 15:43:39  Contamination detection complete!

When I remove option -tmp, it can finish.