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sgsutcliffe / Wastewater_Analysis_Pipeline

A bioinformatics pipeline for analysis of SARS-CoV-2 from wastewater samples
MIT License
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missing kraken database Kraken2wViruses in working directory #4

Open EricFournier3 opened 1 year ago

EricFournier3 commented 1 year ago

https://github.com/sgsutcliffe/Wastewater_Analysis_Pipeline/blob/6e0437f43278bb270f0eec276783bbfaf3755aa1/QC_parallelization_V2.py#L34

sgsutcliffe commented 1 year ago

Thanks for reminding me about this! I had forgotten I hadn’t addressed this before making it public!

I wonder what your opinion is here. I had trouble building Kraken2 databases (due to an absence of internet on Narval-server). What I did was transferred the one from Genpipes.

I think there is two options:

1) I put the code in the readme as to how to build the database before running. I think here I should add an option for users to point to their database in case they don’t want to build a new database just for running the tool. It’s the quickest fix for me.

2) Build the database into the singularity container. I like this option less, as it does not provide the user with opportunity to customize the contaminants they are looking for and would become out of date the longer the user has gone since building the container.

Best, Steven

On Mar 16, 2023, at 8:53 AM, Eric Fournier @.***> wrote:

https://github.com/sgsutcliffe/Wastewater_Analysis_Pipeline/blob/6e0437f43278bb270f0eec276783bbfaf3755aa1/QC_parallelization_V2.py#L34

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EricFournier3 commented 1 year ago

I don't see Kraken2wViruses in Genpipe (/cvmfs/soft.mugqic/CentOS6/software/kraken2/kraken2-2.1.0/db) . Did you get it from Beluga ?

Or I can download it with ./kraken2-build --download-library viral --threads 30 --db Kraken2wViruses

I m not sure if your Kraken2wViruses contains only viral taxon or all taxons

sgsutcliffe commented 1 year ago

That is the path I used on Narval for the database

On Mar 16, 2023, at 11:34 AM, Eric Fournier @.***> wrote:

I don't see Kraken2wViruses in Genpipe (/cvmfs/soft.mugqic/CentOS6/software/kraken2/kraken2-2.1.0/db) . Did you get it from Beluga ?

Or I can download it with ./kraken2-build --download-library viral --threads 30 --db Kraken2wViruses

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EricFournier3 commented 1 year ago

I think you miss the path

EricFournier3 commented 1 year ago

I think first option is the best