Error in preparedb when using chembl and -np

[asaltala]

Hi,

When I use the following line:
vsflow preparedb -d chembl -o chembl_ecfp4 -f ecfp -np 6

it crashes right away with this error:
Start: 04/12/2023, 11:48:13
Running in parallel mode on 6 threads
Downloading database chembl ...
Traceback (most recent call last):
File "/home/andrea/anaconda3/envs/vsflow/bin/vsflow", line 6, in
run.main()
File "/home/andrea/anaconda3/envs/vsflow/lib/python3.9/site-packages/vslib/run.py", line 1560, in main
args.func(args)
File "/home/andrea/anaconda3/envs/vsflow/lib/python3.9/site-packages/vslib/run.py", line 1167, in prep_db
mols = read.req_chembl(args.nproc, pool)
File "/home/andrea/anaconda3/envs/vsflow/lib/python3.9/site-packages/vslib/read.py", line 18, in req_chembl
r = urlopen("https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_28/chembl_28_chemreps.txt.gz",
File "/home/andrea/anaconda3/envs/vsflow/lib/python3.9/urllib/request.py", line 214, in urlopen
return opener.open(url, data, timeout)
File "/home/andrea/anaconda3/envs/vsflow/lib/python3.9/urllib/request.py", line 523, in open
response = meth(req, response)
File "/home/andrea/anaconda3/envs/vsflow/lib/python3.9/urllib/request.py", line 632, in http_response
response = self.parent.error(
File "/home/andrea/anaconda3/envs/vsflow/lib/python3.9/urllib/request.py", line 561, in error
return self._call_chain(*args)
File "/home/andrea/anaconda3/envs/vsflow/lib/python3.9/urllib/request.py", line 494, in _call_chain
result = func(*args)
File "/home/andrea/anaconda3/envs/vsflow/lib/python3.9/urllib/request.py", line 641, in http_error_default
raise HTTPError(req.full_url, code, msg, hdrs, fp)
urllib.error.HTTPError: HTTP Error 404: Not Found

Instead if i remove the -np flag it seems to go through with no errors.

I've also tested it with the pdb database instead of chemble with and without -np and it works fine. So could it be an issue with the chemble database servers?

Thanks a lot,
Andrea

[zhaohongyi2023]

Hello Andrea,

I have installed vsflow, but when I run vsflow in the miniconda, it shows: 'vsflow' is not an internal or external command, nor is it a executable program or batch file. Could you please tell me how to address this issue?
Thank you!

Hongyi