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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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Could not concatenate clusters at level 90 #83

Closed wittney-m closed 1 year ago

wittney-m commented 1 year ago

I am attempting to format the diamond databases that I have already downloaded. Currently the databases are uncompressed in folders with the following paths

The example of the file listed in each folder is 98_clusters.db.dmnd, which is downloaded directly from the github instructions. When I run the following command superfocus_downloadDB -a diamond -c 90,95,98,100 -i /home/wdmays/miniconda3/envs/super-focus/lib/python3.11/site-packages/superfocus_app/db/static/diamond/

I receive this error: Concatenating /home/wdmays/miniconda3/envs/super-focus/lib/python3.11/site-packages/superfocus_app/db/static/diamond/90_clusters/.faa > 90_clusters.fasta cat: /home/wdmays/miniconda3/envs/super-focus/lib/python3.11/site-packages/superfocus_app/db/static/diamond/90_clusters/.faa: No such file or directory [2023-10-08 20:07:53,087 - ERROR] Could not concatenate clusters at level 90

How do I format the databases with download_DB?

metageni-twist commented 1 year ago

hi - i tested and worked fine on my side. Could you please list the files you have here /home/wdmays/miniconda3/envs/super-focus/lib/python3.11/site-packages/superfocus_app/db/static/diamond/90_clusters/.

wittney-m commented 1 year ago

Hi,

When I unzipped the file from here, which was the diamond version 3 90 cluster, the only file that is present is 90_clusters.db.dmnd. Is this incorrect?

metageni-twist commented 1 year ago

I see. So you downloaded the databases formatted already.

Please see https://github.com/metageni/SUPER-FOCUS#downloading-prebuilt-databases in the DIAMOND section. Pretty much now you need to move the database files into the correct database directory.