Please help run_dbcan

IFB Core Cluster
1

Hello,

I'm writing again to ask for your help, because it's been already more than one month since I requested this and I did not have any answer:

I'm trying to use run_dbcan in the cluster, but when I do it I get this error:
ERROR: No CAZy DIAMOND database found. Please make sure that your CAZy DIAMOND databased is named 'CAZy.dmnd' and is located in your database directory

Is the database already in the cluster? if so, can you please provide the path. If not, Can you download it or please tell me how to do it, I've tried to but I couldn't manage.
Also, it would be better to have the last version of run_dbcan. If possible I would like better to request its installation, along with the latest database.

Thank you so much for any help you can provide.

I look forward to your response.

2

Hello @jramirez, is this run_dbcan command something installed as part of a module on the cluster ? Or is it something you installed yourself ?

3

Hell, run_dbcan it's already in the cluster, the version instralled is the v2 and the latest it's v3, in fact could be cooler to have the latest version (available here Installation — dbcan).
Anyway, the issue is that when you run it, regardless of the version, you need to specify the database folder (db), and I haven't figure out quite well how to find these folders, or their bath, in the cluster. I mean, for example when you use AUGUSTUS you also need to provide a folder path, but I didn't know how to find it, so I asked you guys and you provided it, this case is similñar to that one.

Thanks

Julie

4

As far as I understand, we need to install new version of run_dbcan (bioconda package:dbcan) and build a database with dbcan_build as described here: https://dbcan.readthedocs.io/en/latest/installation.html

Github run_dbcan repository: https://github.com/linnabrown/run_dbcan

5

Yes, it could be good to have the lastest version available there.

6

Hi @jramirez, run-dbcan is now updated to version 4.1.4 (module load run-dbcan/4.1.4) and the dbcan databases are available in /shared/bank/dbcan/2024-03-29 :wink:

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