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NCBI Taxonomy not accessible - NGS Data Analysis (Read 1026 times)
Jan 20th, 2021 at 11:14am

zachary33   Offline
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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 20th, 2021 at 2:44pm

Dmitrii Sukhomlinov   Offline
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Russia

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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.
 

picture_1.png (173 KB | 60 )
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picture_2.png (74 KB | 62 )
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picture_3.png (93 KB | 57 )
picture_3.png

Best regards,
Dmitrii Sukhomlinov,
UGENE team.
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Reply #2 - Jan 21st, 2021 at 10:19am

zachary33   Offline
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Thank you so much. I will try this.

Yes, my system is currently running Linux.
 
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Reply #3 - Apr 2nd, 2021 at 10:57am

Bobby Rencher   Offline
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It didn't create quite my data analysis on it.
 
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