Download databases issue

[imanyass]

Hello, I hope you're well. I followed the recommended procedure to install ggcaller from the source. However, upon attempting to run ggcaller, I encountered the following error. I've already downloaded the model database into the models directory as advised in previous issues, but the error persists. Could you please assist me with resolving this? Thank you in advance.

Building coloured compacted DBG... Generating graph stop codon index... Mapping contigs to graph... Downloading databases... Traceback (most recent call last): File "conda/envs/ggcaller/lib/python3.9/urllib/request.py", line 1346, in do_open h.request(req.get_method(), req.selector, req.data, headers, File "conda/envs/ggcaller/lib/python3.9/http/client.py", line 1285, in request self._send_request(method, url, body, headers, encode_chunked) File "conda/envs/ggcaller/lib/python3.9/http/client.py", line 1331, in _send_request self.endheaders(body, encode_chunked=encode_chunked) File "conda/envs/ggcaller/lib/python3.9/http/client.py", line 1280, in endheaders self._send_output(message_body, encode_chunked=encode_chunked) File "conda/envs/ggcaller/lib/python3.9/http/client.py", line 1040, in _send_output self.send(msg) File "conda/envs/ggcaller/lib/python3.9/http/client.py", line 980, in send self.connect() File "conda/envs/ggcaller/lib/python3.9/http/client.py", line 1447, in connect super().connect() File "conda/envs/ggcaller/lib/python3.9/http/client.py", line 946, in connect self.sock = self._create_connection( File "conda/envs/ggcaller/lib/python3.9/socket.py", line 844, in create_connection raise err File "conda/envs/ggcaller/lib/python3.9/socket.py", line 832, in create_connection sock.connect(sa) TimeoutError: [Errno 110] Connection timed out

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "conda/envs/ggcaller/bin/ggcaller", line 33, in sys.exit(load_entry_point('ggCaller==1.3.4', 'console_scripts', 'ggcaller')()) File "conda/envs/ggcaller/lib/python3.9/site-packages/ggCaller-1.3.4-py3.9-linux-x86_64.egg/ggCaller/main.py", line 436, in main db_dir = download_db() File "conda/envs/ggcaller/lib/python3.9/site-packages/ggCaller-1.3.4-py3.9-linux-x86_64.egg/models/main.py", line 15, in download_db filename = wget.download(url, out=module_dir) File "conda/envs/ggcaller/lib/python3.9/site-packages/wget.py", line 526, in download (tmpfile, headers) = ulib.urlretrieve(binurl, tmpfile, callback) File "conda/envs/ggcaller/lib/python3.9/urllib/request.py", line 239, in urlretrieve with contextlib.closing(urlopen(url, data)) as fp: File "conda/envs/ggcaller/lib/python3.9/urllib/request.py", line 214, in urlopen return opener.open(url, data, timeout) File "conda/envs/ggcaller/lib/python3.9/urllib/request.py", line 517, in open response = self._open(req, data) File "conda/envs/ggcaller/lib/python3.9/urllib/request.py", line 534, in _open result = self._call_chain(self.handle_open, protocol, protocol + File "conda/envs/ggcaller/lib/python3.9/urllib/request.py", line 494, in _call_chain result = func(*args) File "conda/envs/ggcaller/lib/python3.9/urllib/request.py", line 1389, in https_open return self.do_open(http.client.HTTPSConnection, req, File "conda/envs/ggcaller/lib/python3.9/urllib/request.py", line 1349, in do_open raise URLError(err) urllib.error.URLError: <urlopen error [Errno 110] Connection timed out> srun: error: compf008: task 0: Exited with exit code 1

[samhorsfield96]

Hi, sorry to hear you ran into this issue. This has been encountered before, please see here: https://github.com/bacpop/ggCaller/issues/16#issuecomment-1828314000

[samhorsfield96]

Closed as repeated issue.

[imanyass]

Hi, thanks for your message. Although I downloaded the database as recommended I'm still encountering the same problem. Any advice?

[samhorsfield96]

Hi, what was the error message? Also, which directory did you place the database file in?

[imanyass]

Hi, thanks for your message. I placed the database file in the models directory but when I run ggcaller I'm still having the same error Building coloured compacted DBG... Generating graph stop codon index... Mapping contigs to graph... Downloading databases... Traceback (most recent call last): File "conda/envs/ggcaller/lib/python3.9/urllib/request.py", line 1346, in do_open h.request(req.get_method(), req.selector, req.data, headers, File "conda/envs/ggcaller/lib/python3.9/http/client.py", line 1285, in request self._send_request(method, url, body, headers, encode_chunked) File "conda/envs/ggcaller/lib/python3.9/http/client.py", line 1331, in _send_request self.endheaders(body, encode_chunked=encode_chunked) File "conda/envs/ggcaller/lib/python3.9/http/client.py", line 1280, in endheaders self._send_output(message_body, encode_chunked=encode_chunked) File "conda/envs/ggcaller/lib/python3.9/http/client.py", line 1040, in _send_output self.send(msg) File "conda/envs/ggcaller/lib/python3.9/http/client.py", line 980, in send self.connect() File "conda/envs/ggcaller/lib/python3.9/http/client.py", line 1447, in connect super().connect() File "conda/envs/ggcaller/lib/python3.9/http/client.py", line 946, in connect self.sock = self._create_connection( File "conda/envs/ggcaller/lib/python3.9/socket.py", line 844, in create_connection raise err File "conda/envs/ggcaller/lib/python3.9/socket.py", line 832, in create_connection sock.connect(sa) TimeoutError: [Errno 110] Connection timed out

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "conda/envs/ggcaller/bin/ggcaller", line 33, in sys.exit(load_entry_point('ggCaller==1.3.4', 'console_scripts', 'ggcaller')()) File "conda/envs/ggcaller/lib/python3.9/site-packages/ggCaller-1.3.4-py3.9-linux-x86_64.egg/ggCaller/main.py", line 436, in main db_dir = download_db() File "conda/envs/ggcaller/lib/python3.9/site-packages/ggCaller-1.3.4-py3.9-linux-x86_64.egg/models/main.py", line 15, in download_db filename = wget.download(url, out=module_dir) File "conda/envs/ggcaller/lib/python3.9/site-packages/wget.py", line 526, in download (tmpfile, headers) = ulib.urlretrieve(binurl, tmpfile, callback) File "conda/envs/ggcaller/lib/python3.9/urllib/request.py", line 239, in urlretrieve with contextlib.closing(urlopen(url, data)) as fp: File "conda/envs/ggcaller/lib/python3.9/urllib/request.py", line 214, in urlopen return opener.open(url, data, timeout) File "conda/envs/ggcaller/lib/python3.9/urllib/request.py", line 517, in open response = self._open(req, data) File "conda/envs/ggcaller/lib/python3.9/urllib/request.py", line 534, in _open result = self._call_chain(self.handle_open, protocol, protocol + File "conda/envs/ggcaller/lib/python3.9/urllib/request.py", line 494, in _call_chain result = func(*args) File "conda/envs/ggcaller/lib/python3.9/urllib/request.py", line 1389, in https_open return self.do_open(http.client.HTTPSConnection, req, File "conda/envs/ggcaller/lib/python3.9/urllib/request.py", line 1349, in do_open raise URLError(err) urllib.error.URLError: <urlopen error [Errno 110] Connection timed out> srun: error: compa016: task 0: Exited with exit code 1

my command-line is srun ggcaller --refs FastaFiles.ls The models directory includes init.py
main.py
ggCallerdb.tar.bz2

Is there any option that I should specify to use the downloaded database?

[samhorsfield96]

Hi, I believe the issue is that the databases file is not being copied to the ggcaller conda lib directory. Please navigate to the source ggCaller directory and try running with python ggcaller-runner.py --refs /path/to/FastaFiles.ls

[imanyass]

Hello, it is working! Thanks for your help.

[samhorsfield96]

Closed as completed.