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metageni / SUPER-FOCUS

A tool for agile functional analysis of shotgun metagenomic data
GNU General Public License v3.0
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Error in formating databases #88

Open Felipe-Alexandre opened 5 months ago

Felipe-Alexandre commented 5 months ago

While trying to format diamond database using superfocus_downloadDB, using:

superfocus_downloadDB -i /home/.local/lib/python3.8/site-packages/superfocus_app/db/static/diamond/ -a diamond -c 90

The command returns the error

cat: '/home/.local/lib/python3.8/site-packages/superfocus_app/db/static/diamond/90_clusters/*.faa': No such file or directory

But when I check the files present in the 90_clusters.db.dmnd.zip downloaded, none of them contains a "*faa" file.

It is possible that diamond changed the files in the links? How can I find these faa files to format the databases?

metageni-twist commented 2 months ago

this has been resolved

anmolchaudhry commented 3 weeks ago

I am facing a similar issue when downloading the v1 of the 95 cluster diamond database (https://open.flinders.edu.au/ndownloader/files/44075153). Upon unzipping it in the intended directory there is no faa file to be found and the same error as mentioned is returned when running the superfocus_downloadDB command (cat: '/home/.local/lib/python3.8/site-packages/superfocus_app/db/static/diamond/90_clusters/.faa': No such file or directory). Please suggest a fix.

Macbit commented 2 weeks ago

I am facing a similar issue when downloading the v1 of the 95 cluster diamond database (https://open.flinders.edu.au/ndownloader/files/44075153). Upon unzipping it in the intended directory there is no _faa file to be found and the same error as mentioned is returned when running the superfocus_downloadDB command (cat: '/home/.local/lib/python3.8/site-packages/superfocus_app/db/static/diamond/90clusters/.faa': No such file or directory). Please suggest a fix.

You do not need to run superfocus_downloadDB if you already have a compatible DIAMOND database (.dmnd file). Simply download, unzip, and move it to the appropriate SUPER-FOCUS directory. For my setup, the database was placed in /opt/miniconda3/envs/superfocus_env/lib/python3.8/site-packages/superfocus_app/db/static/diamond. Note that I had to manually create the diamond directory. You can use the command which superfocus to determine the exact installation path of SUPER-FOCUS, ensuring that you set the correct folder to copy the .dmnd file into.

After setting up the database, I executed SUPER-FOCUS with the following command:

superfocus -q /your_fastq_input/S01_deduped.fastq -dir /your_output_directory/super -a diamond -db DB_95 -b /opt/miniconda3/envs/superfocus_env/lib/python3.8/site-packages/superfocus_app -t 4 -mi 60 -ml 15 -e 0.00001 -p 0 -f 1 -n 1 -d

Please adjust the parameters according to your specific needs.