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problem when downloading references for bacillus_anthracis.db #37

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rjsorr opened this issue Nov 16, 2023 · 0 comments
Open

problem when downloading references for bacillus_anthracis.db #37

rjsorr opened this issue Nov 16, 2023 · 0 comments

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@rjsorr
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rjsorr commented Nov 16, 2023

I am getting an error when running the "CanSNPer2-download --database bacillus_anthracis.db" command on the downloaded databases. I see the execution is making a log and a reference directory, but both are empty. I get the following error (mamba installation).

regards

(cansnper2) ubuntu@workstation:/media/ubuntu/Pandora/CanSNPer2-data/database$ Process Process-1:
Traceback (most recent call last):
File "/media/ubuntu/4TB-2/mambaforge/envs/cansnper2/lib/python3.12/urllib/request.py", line 1573, in ftp_open
fp, retrlen = fw.retrfile(file, type)
^^^^^^^^^^^^^^^^^^^^^^^
File "/media/ubuntu/4TB-2/mambaforge/envs/cansnper2/lib/python3.12/urllib/request.py", line 2448, in retrfile
conn, retrlen = self.ftp.ntransfercmd(cmd)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/media/ubuntu/4TB-2/mambaforge/envs/cansnper2/lib/python3.12/ftplib.py", line 354, in ntransfercmd
conn = socket.create_connection((host, port), self.timeout,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/media/ubuntu/4TB-2/mambaforge/envs/cansnper2/lib/python3.12/socket.py", line 852, in create_connection
raise exceptions[0]
File "/media/ubuntu/4TB-2/mambaforge/envs/cansnper2/lib/python3.12/socket.py", line 837, in create_connection
sock.connect(sa)
TimeoutError: [Errno 110] Connection timed out

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/media/ubuntu/4TB-2/mambaforge/envs/cansnper2/lib/python3.12/multiprocessing/process.py", line 314, in _bootstrap
self.run()
File "/media/ubuntu/4TB-2/mambaforge/envs/cansnper2/lib/python3.12/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/media/ubuntu/4TB-2/mambaforge/envs/cansnper2/lib/python3.12/site-packages/CanSNPer2/DownloadGenomes.py", line 65, in download
urlretrieve(link, retrieved_file)
File "/media/ubuntu/4TB-2/mambaforge/envs/cansnper2/lib/python3.12/urllib/request.py", line 240, in urlretrieve
with contextlib.closing(urlopen(url, data)) as fp:
^^^^^^^^^^^^^^^^^^
File "/media/ubuntu/4TB-2/mambaforge/envs/cansnper2/lib/python3.12/urllib/request.py", line 215, in urlopen
return opener.open(url, data, timeout)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/media/ubuntu/4TB-2/mambaforge/envs/cansnper2/lib/python3.12/urllib/request.py", line 515, in open
response = self._open(req, data)
^^^^^^^^^^^^^^^^^^^^^
File "/media/ubuntu/4TB-2/mambaforge/envs/cansnper2/lib/python3.12/urllib/request.py", line 532, in _open
result = self._call_chain(self.handle_open, protocol, protocol +
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/media/ubuntu/4TB-2/mambaforge/envs/cansnper2/lib/python3.12/urllib/request.py", line 492, in _call_chain
result = func(*args)
^^^^^^^^^^^
File "/media/ubuntu/4TB-2/mambaforge/envs/cansnper2/lib/python3.12/urllib/request.py", line 1583, in ftp_open
raise URLError(exp) from exp
urllib.error.URLError: <urlopen error [Errno 110] Connection timed out>
ls -lh

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