UGENE Forum - NCBI Taxonomy not accessible

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NCBI Taxonomy not accessible - NGS Data Analysis (Read 3695 times)

Jan 20^th, 2021 at 11:14am

zachary33 Offline
YaBB Newbies

Posts: 3

Hi,

I am creating an NGS SE workflow and using the "Filter by Classification" and "Classification Report" elements. However, when I validate the workflow, both elements report the error "Taxonomy classification data from NCBI are not available."

What should I do to make the taxonomy data from NCBI available?

I have downloaded the UGENE Taxonomy from the Reference Data listed on the UGENE downloads and components page. But I still have the same problem. Thank you for your help!

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Reply #1 - Jan 20^th, 2021 at 2:44pm

Dmitrii Sukhomlinov Offline
YaBB Administrator
Russia

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Posts: 82

Hello,
First of all, pay attention that metagenomic classification is available on Linux and macOS only and isn't available for Windows.

The second thing is that the best way to install all required configurations for metagenomic classification workflows is to use the UGENE online-installer, which you can download from the following page: http://ugene.net/download.html (see the attached picture 1).

If you want to set up it manually you have to do the following: go to the UGENE folder and open the "data" folder. Here you need to create the folder called "ngs_classification". In this folder create folders "clark", "diamond", "kraken" and "metaphlan2", download the corresponding databases from the "Download all" page ( http://ugene.net/download-all_html ) and put them into corresponding folders (the "clark" example on picture 2). The taxonomy should be located in the "ngs_classification" folder (picture 3). Also, you need to download the full pack of External tools.

As far as I am concerned, the best way is to install the "metagenomics" package with the online-installer.