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cdanielmachado / carveme

CarveMe: genome-scale metabolic model reconstruction
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init fails to dowload refseq #68

Closed lcottret closed 4 years ago

lcottret commented 4 years ago

I'm trying to install a new version of carveme. When I do carveme_init, it fails when trying to download refseq

Downloading data/input/bigg_proteins.faa Downloading data/input/equilibrator_compounds.tsv.gz Downloading data/input/refseq_release_84.tsv.gz Traceback (most recent call last): File "/usr/local/bin/carveme_init", line 36, in urllib.request.urlretrieve(inputfile, outputfile) File "/usr/local/lib/python2.7/dist-packages/future/backports/urllib/request.py", line 196, in urlretrieve with contextlib.closing(urlopen(url, data)) as fp: File "/usr/local/lib/python2.7/dist-packages/future/backports/urllib/request.py", line 171, in urlopen return opener.open(url, data, timeout) File "/usr/local/lib/python2.7/dist-packages/future/backports/urllib/request.py", line 500, in open response = meth(req, response) File "/usr/local/lib/python2.7/dist-packages/future/backports/urllib/request.py", line 612, in http_response 'http', request, response, code, msg, hdrs) File "/usr/local/lib/python2.7/dist-packages/future/backports/urllib/request.py", line 538, in error return self._call_chain(args) File "/usr/local/lib/python2.7/dist-packages/future/backports/urllib/request.py", line 466, in _call_chain result = func(args) File "/usr/local/lib/python2.7/dist-packages/future/backports/urllib/request.py", line 620, in http_error_default raise HTTPError(req.full_url, code, msg, hdrs, fp) future.backports.urllib.error.HTTPError: HTTP Error 404: Not Found

cdanielmachado commented 4 years ago

I think this might be an issue with urllib in python 2.7. Could you try running in python 3.6 ?

lcottret commented 4 years ago

Thansk, what I did: sudo pip uninstall carveme sudo pip3 install carveme sudo pip3 install future (otherwise, carveme_init does not work) sudo carveme_init

However, an error occured with diamond, even if it is the path. I had to put the absolute path line 41. This done, it works !

Now, I have another problem : my cplex installation is in python2.7 and does not work now with carveme... But, now, it's my own problem !