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OLC-Bioinformatics / ConFindr

Intra-species bacterial contamination detection
https://olc-bioinformatics.github.io/ConFindr/
MIT License
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E. coli db issue #44

Closed elina2410 closed 1 year ago

elina2410 commented 1 year ago

I tried to analyse Escherichia coli fastq files. (example_R1.fastq.gz and example_2.fastq.gz) I obtained .csv file but the result is not as expected. Sample: example , Genus: NA , NumContamSNVs: 0, ContamStatus: False , PercentContam: NA, PercentContamStandardDeviation: NA, BasesExamined: 0, DatabaseDownloadDate:NA

confindr.py -i example-data -o output 2022-11-14 12:22:40 Welcome to ConFindr 0.7.0! Beginning analysis of your samples... 2022-11-14 12:22:40 Did not find rMLST databases, if you want to use ConFindr on genera other than Listeria, Salmonella, and Escherichia, you'll need to download them. Instructions are available at https://olc-bioinformatics.github.io/ConFindr/install/#downloading-confindr-databases

2022-11-14 12:22:40 Beginning analysis of sample example... 2022-11-14 12:22:40 Checking for cross-species contamination... 2022-11-14 12:22:40 Did not find databases for genus NA. 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: NA"

2022-11-14 12:22:40 Contamination detection complete!

The same problem is with Listeria monocytohenes database.

Please help..

pcrxn commented 1 year ago

Hi @elina2410, could you please try installing the most recent version of ConFindr into a new Conda environment with conda create -n confindr -c olcbioinformatics confindr=0.7.4, and then processing the data again with that environment active?

pcrxn commented 1 year ago

Will close this issue in 30 days if there aren't any updates.