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NCBI Prokaryotic Genome Annotation Pipeline
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[BUG] pgap.py --update #271

Closed nptgiang0211 closed 5 months ago

nptgiang0211 commented 10 months ago

After downloading the file pgap.py from https://github.com/ncbi/pgap/raw/prod/scripts/pgap.py, I attempted to run ./pgap.py --update, but I encountered an issue. Here is the report:

./pgap.py --update Traceback (most recent call last): File "/home/molbiolab320/biotools/pgap/scripts/./pgap.py", line 994, in main params = Setup(args) ^^^^^^^^^^^ File "/home/molbiolab320/biotools/pgap/scripts/./pgap.py", line 532, in init self.remote_versions = self.get_remote_versions() ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/molbiolab320/biotools/pgap/scripts/./pgap.py", line 606, in get_remote_versions response = urlopen('https://api.github.com/repos/ncbi/pgap/releases/latest') ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.11/urllib/request.py", line 216, in urlopen return opener.open(url, data, timeout) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.11/urllib/request.py", line 519, in open response = self._open(req, data) ^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.11/urllib/request.py", line 541, in _open return self._call_chain(self.handle_open, 'unknown', ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.11/urllib/request.py", line 496, in _call_chain result = func(*args) ^^^^^^^^^^^ File "/usr/local/lib/python3.11/urllib/request.py", line 1419, in unknown_open raise URLError('unknown url type: %s' % type) urllib.error.URLError:

Please help me, I cannot fix it :"(((

azat-badretdin commented 10 months ago

Thank you for your report, @nptgiang0211!

It looks like you had some kind of Internet connectivity issue. To eliminate this possibility, can you try to download https://api.github.com/repos/ncbi/pgap/releases/latest from command line? curl -nOL https://api.github.com/repos/ncbi/pgap/releases/latest or using your favorite command line downloader?

nptgiang0211 commented 10 months ago

Thank you for your report, @nptgiang0211!

It looks like you had some kind of Internet connectivity issue. To eliminate this possibility, can you try to download https://api.github.com/repos/ncbi/pgap/releases/latest from command line? curl -nOL https://api.github.com/repos/ncbi/pgap/releases/latest or using your favorite command line downloader?

Thank you for your reply, but I tried to use the command curl -nOL https://api.github.com/repos/ncbi/pgap/releases/latest, and then ran ./pgap.py --update again. However, I'm still encountering the same error lines.

azat-badretdin commented 10 months ago

It looks like your report is truncated: 

File "/usr/local/lib/python3.11/urllib/request.py", line 1419, in unknown_open
raise URLError('unknown url type: %s' % type)
urllib.error.URLError:

This should be followed by a line:

unknown url type: <....>

could you please post the complete output formatted as "code"?

Thanks!