can't download database

[ncanaless]

Hi i've been trying to download the SUPER-FOCUS database and getting this error:

$wget edwards.sdsu.edu/superfocus/downloads/db.zip ... HTTP request sent, awaiting response... 503 Service Temporarily Unavailable 2022-03-15 12:26:16 ERROR 503: Service Temporarily Unavailable.

is there any solution to this problem? thanks in advance

[metageni]

@linsalrob: Any idea what happened to the server?

[metageni]

@ncanaless: I'm checking with @linsalrob what's up. Depending what happened, i will move the db somewhere else. thanks

[ncanaless]

that would be amazing, thank you so much

[metageni]

I'm moving it to another server. stay tuned.

[metageni]

@ncanaless: I'm sorry; we are still working on it. For now, it lives here --- https://drive.google.com/file/d/1jTo2e5UQLkEItRrgTJhOhXZAAUV-ACd7/view?usp=sharing

I will be moving it to a more appropriate location soon.

[ncanaless]

Hi @metageni , i was able to download the database, thanks for the quick response, but now i'm getting another issue trying to format it. (i downloaded and unziped following the manual instructions) superfocus_downloadDB -i clusters/ -a diamond -c 90,95 Traceback (most recent call last): File "/home/metagroup/anaconda3/envs/metaphlan/bin/superfocus_downloadDB", line 10, in sys.exit(main()) File "/home/metagroup/anaconda3/envs/metaphlan/lib/python3.7/site-packages/superfocus_app/superfocus_downloadDB.py", line 158, in main db_dir_exists = Path(args.db_dir).exists() and Path(args.db_dir).is_dir() File "/home/metagroup/anaconda3/envs/metaphlan/lib/python3.7/pathlib.py", line 1027, in new self = cls._from_parts(args, init=False) File "/home/metagroup/anaconda3/envs/metaphlan/lib/python3.7/pathlib.py", line 674, in _from_parts drv, root, parts = self._parse_args(args) File "/home/metagroup/anaconda3/envs/metaphlan/lib/python3.7/pathlib.py", line 658, in _parse_args a = os.fspath(a) TypeError: expected str, bytes or os.PathLike object, not NoneType

I'm using superfocus in a conda enviroment, with python 3.7 as extra information

[metageni]

I see. Sorry about it. it was a bug introduced when there was a PR to introduce an alternative directory for the db.

The slowest path to fix this, for now, is to pass a path when formating the database to where it is going to live

superfocus_downloadDB -i clusters/ -a diamond -c 90,95 -db_dir PATH_DB

and when running superfocus, passing the db at --alternate_directory.

I will fix the bug now, and it should be live on bioconda the change tomorrow. Sorry about that.

[metageni]

here is the fix for the bug for reference https://github.com/metageni/SUPER-FOCUS/pull/79

[ncanaless]

thanks a lot for your help, i think now i'm able to run the program, again thank you so much