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abyzovlab / CNVpytor

a python extension of CNVnator -- a tool for CNV analysis from depth-of-coverage by mapped reads
MIT License
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I have Filtration error #146

Open hayeon-pak opened 1 year ago

hayeon-pak commented 1 year ago

Hi :)

When I tried this process cnvpytor -root $out_root -view $bin_size <<ENDL set Q0_range -1 0.5 set p_range 0 0.0001 set p_N 0 0.5 print calls set print_filename dir/to/sample.vcf set annotate print calls quit ENDL

I got this error.

Traceback (most recent call last): File "/dir/to/.local/lib/python3.8/site-packages/urllib3/connection.py", line 158, in _new_conn conn = connection.create_connection( File "/dir/to/.local/lib/python3.8/site-packages/urllib3/util/connection.py", line 80, in create_connection raise err File "/dir/to/.local/lib/python3.8/site-packages/urllib3/util/connection.py", line 70, 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 "/dir/to/.local/lib/python3.8/site-packages/urllib3/connectionpool.py", line 597, in urlopen httplib_response = self._make_request(conn, method, url, File "/dir/to/.local/lib/python3.8/site-packages/urllib3/connectionpool.py", line 343, in _make_request self._validate_conn(conn) File "/dir/to/.local/lib/python3.8/site-packages/urllib3/connectionpool.py", line 839, in _validate_conn conn.connect() File "/dir/to/.local/lib/python3.8/site-packages/urllib3/connection.py", line 301, in connect conn = self._new_conn() File "/dir/to/.local/lib/python3.8/site-packages/urllib3/connection.py", line 167, in _new_conn raise NewConnectionError( urllib3.exceptions.NewConnectionError: <urllib3.connection.VerifiedHTTPSConnection object at 0x7fb6aa3b8730>: Failed to establish a new connection: [Errno 110] Connection timed out

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/dir/to/miniconda3/lib/python3.8/site-packages/requests/adapters.py", line 440, in send resp = conn.urlopen( File "/dir/to/.local/lib/python3.8/site-packages/urllib3/connectionpool.py", line 637, in urlopen retries = retries.increment(method, url, error=e, _pool=self, File "/dir/to/.local/lib/python3.8/site-packages/urllib3/util/retry.py", line 399, in increment raise MaxRetryError(_pool, url, error or ResponseError(cause)) urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='grch37.rest.ensembl.org', port=443): Max retries exceeded with url: /overlap/region/human/chrX:117457601-117457900?content-type=application/json;feature=gene; (Caused by NewConnectionError('<urllib3.connection.VerifiedHTTPSConnection object at 0x7fb6aa3b8730>: Failed to establish a new connection: [Errno 110] Connection timed out'))

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/dir/to/miniconda3/bin/cnvpytor", line 8, in sys.exit(main()) File "/dir/to/miniconda3/lib/python3.8/site-packages/cnvpytor/main.py", line 303, in main view.prompt() File "/dir/to/miniconda3/lib/python3.8/site-packages/cnvpytor/viewer.py", line 501, in prompt self.print_calls_file() File "/dir/to/miniconda3/lib/python3.8/site-packages/cnvpytor/viewer.py", line 997, in print_calls_file calls = self.get_calls() File "/dir/to/miniconda3/lib/python3.8/site-packages/cnvpytor/viewer.py", line 954, in get_calls row.append(annotator.get_info("%s:%d-%d" % (c, call["start"], call["end"]))) File "/dir/to/miniconda3/lib/python3.8/site-packages/cnvpytor/annotator.py", line 50, in get_info response = requests.get(self.url_template.format(region=region)) File "/dir/to/miniconda3/lib/python3.8/site-packages/requests/api.py", line 75, in get return request('get', url, params=params, kwargs) File "/dir/to/miniconda3/lib/python3.8/site-packages/requests/api.py", line 61, in request return session.request(method=method, url=url, kwargs) File "/dir/to/miniconda3/lib/python3.8/site-packages/requests/sessions.py", line 529, in request resp = self.send(prep, send_kwargs) File "/dir/to/miniconda3/lib/python3.8/site-packages/requests/sessions.py", line 645, in send r = adapter.send(request, kwargs) File "/dir/to/miniconda3/lib/python3.8/site-packages/requests/adapters.py", line 519, in send raise ConnectionError(e, request=request) requests.exceptions.ConnectionError: HTTPSConnectionPool(host='grch37.rest.ensembl.org', port=443): Max retries exceeded with url: /overlap/region/human/chrX:117457601-117457900?content-type=application/json;feature=gene; (Caused by NewConnectionError('<urllib3.connection.VerifiedHTTPSConnection object at 0x7fb6aa3b8730>: Failed to establish a new connection: [Errno 110] Connection timed out'))

Thanks your help :)