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cdanielmachado / carveme

CarveMe: genome-scale metabolic model reconstruction
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urllib.error.HTTPError: HTTP Error 404 executing carveme_init #96

Closed jzaabat closed 3 years ago

jzaabat commented 4 years ago

Hello, I've seen a similar issue was recently addressed. Has the path changed again to get refseq_release_92.tsv.gz? I got this error when executing carveme_init. Downloading data/input/refseq_release_92.tsv.gz Traceback (most recent call last): File "/usr/local/miniconda/python-3.6/bin/carveme_init", line 36, in urllib.request.urlretrieve(inputfile, outputfile) File "/usr/local/miniconda/python-3.6/lib/python3.6/urllib/request.py", line 248, in urlretrieve with contextlib.closing(urlopen(url, data)) as fp: File "/usr/local/miniconda/python-3.6/lib/python3.6/urllib/request.py", line 223, in urlopen return opener.open(url, data, timeout) File "/usr/local/miniconda/python-3.6/lib/python3.6/urllib/request.py", line 532, in open response = meth(req, response) File "/usr/local/miniconda/python-3.6/lib/python3.6/urllib/request.py", line 642, in http_response 'http', request, response, code, msg, hdrs) File "/usr/local/miniconda/python-3.6/lib/python3.6/urllib/request.py", line 570, in error return self._call_chain(args) File "/usr/local/miniconda/python-3.6/lib/python3.6/urllib/request.py", line 504, in _call_chain result = func(args) File "/usr/local/miniconda/python-3.6/lib/python3.6/urllib/request.py", line 650, in http_error_default raise HTTPError(req.full_url, code, msg, hdrs, fp) urllib.error.HTTPError: HTTP Error 404: Not Found

Could you please take a look?

Thanks.

jnesme commented 4 years ago

This issue is currently resolved in the master branch (https://github.com/cdanielmachado/carveme/issues/92) - but led to other issues that @cdanielmachado is working on (https://github.com/cdanielmachado/carveme/issues/95) - stay tuned

silvtal commented 4 years ago

Remove that line in the carveme/cli/carveme_init file and replace it by "data/input/refseqrelease201.tsv.gz". If you still have an error, remove the genbank line too

jzaabat commented 4 years ago

I reinstalled carveme using pip. Version 1.4.0 is now available and carveme_init has not executable path. Has this changed?

cdanielmachado commented 4 years ago

Yes, in the latest release (1.4) I removed the carveme_init file. All the internal files will now come pre-packaged in the installer. This will save a lot of trouble :)

jzaabat commented 4 years ago

Yes, in the latest release (1.4) I removed the carveme_init file. All the internal files will now come pre-packaged in the installer. This will save a lot of trouble :)

Thank you very much!

jungerm2 commented 4 years ago

Hello, I was having this issue as well but upgrading to carveme==1.4.0 did not help as now I'm getting this error:

diamond v2.0.4.142 (C) Max Planck Society for the Advancement of Science
Documentation, support and updates available at http://www.diamondsearch.org

#CPU threads: 4
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Temporary directory:
Opening the database...  [0.097s]
Error: Database was built with an older version of Diamond and is incompatible.
Failed to run diamond.

As you can see I'm running the newest diamond version (v2.0.4). Other specs include: python version: 3.7.9 OS: Windows 10 CPLEX version: 1210 Conda version: 4.8.3

Any help is appreciated. Thanks!

cdanielmachado commented 3 years ago

carveme_init is now removed. Problems with diamond will be addressed separately from this issue.