Opened 4 years ago

Closed 4 years ago

#6476 closed defect (fixed)

Blast error while web services down

Reported by: chimerax-bug-report@… Owned by: Zach Pearson
Priority: normal Milestone:
Component: Infrastructure Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show AlphaFold

> alphafold match
> MKEVIYRFEKAEDYKLVPVNNIYGNVTNTGEIFCDLVFESTEISEEIAYTKTKEGVLEEASKEFKSGEEGKIVLINSFIGISITKTTARNIAYWLLKKVDELEDNE

No AlphaFold model with similar sequence for 1 sequences  

Opened 0 AlphaFold model  

> alphafold search
> MKEVIYRFEKAEDYKLVPVNNIYGNVTNTGEIFCDLVFESTEISEEIAYTKTKEGVLEEASKEFKSGEEGKIVLINSFIGISITKTTARNIAYWLLKKVDELEDNE

ChimeraX REST job id:
BZ175YJ9HYY6BLAIRNHSYJ16PCDJ7W6X5OKDR9LTSP7KQ8U6TX2GD44O0EQW21TR  

> alphafold predict
> MKEVIYRFEKAEDYKLVPVNNIYGNVTNTGEIFCDLVFESTEISEEIAYTKTKEGVLEEASKEFKSGEEGKIVLINSFIGISITKTTARNIAYWLLKKVDELEDNE

Running AlphaFold prediction  
[Repeated 2 time(s)]

Downloaded prediction file not found:
/Users/andrewkrusenstjerna/Downloads/ChimeraX/AlphaFold/prediction_1/best_model.pdb  

AlphaFold prediction finished  
Results in
/Users/andrewkrusenstjerna/Downloads/ChimeraX/AlphaFold/prediction_1  

> alphafold predict
> MKEVIYRFEKAEDYKLVPVNNIYGNVTNTGEIFCDLVFESTEISEEIAYTKTKEGVLEEASKEFKSGEEGKIVLINSFIGISITKTTARNIAYWLLKKVDELEDNE

Running AlphaFold prediction  

Downloaded prediction file not found:
/Users/andrewkrusenstjerna/Downloads/ChimeraX/AlphaFold/prediction_2/best_model.pdb  

AlphaFold prediction finished  
Results in
/Users/andrewkrusenstjerna/Downloads/ChimeraX/AlphaFold/prediction_2  
2022-03-28 10:03:40,246 WARNING Retrying (Retry(total=2, connect=None,
read=None, redirect=None, status=None)) after connection broken by
'NewConnectionError('<urllib3.connection.HTTPConnection object at
0x7fe091a5b970>: Failed to establish a new connection: [Errno 8] nodename nor
servname provided, or not known')':
/cxservices/api/v1//chimerax/job/BZ175YJ9HYY6BLAIRNHSYJ16PCDJ7W6X5OKDR9LTSP7KQ8U6TX2GD44O0EQW21TR  
2022-03-28 10:03:40,259 WARNING Retrying (Retry(total=1, connect=None,
read=None, redirect=None, status=None)) after connection broken by
'NewConnectionError('<urllib3.connection.HTTPConnection object at
0x7fe091a9b370>: Failed to establish a new connection: [Errno 8] nodename nor
servname provided, or not known')':
/cxservices/api/v1//chimerax/job/BZ175YJ9HYY6BLAIRNHSYJ16PCDJ7W6X5OKDR9LTSP7KQ8U6TX2GD44O0EQW21TR  
2022-03-28 10:03:40,263 WARNING Retrying (Retry(total=0, connect=None,
read=None, redirect=None, status=None)) after connection broken by
'NewConnectionError('<urllib3.connection.HTTPConnection object at
0x7fe091a9b2b0>: Failed to establish a new connection: [Errno 8] nodename nor
servname provided, or not known')':
/cxservices/api/v1//chimerax/job/BZ175YJ9HYY6BLAIRNHSYJ16PCDJ7W6X5OKDR9LTSP7KQ8U6TX2GD44O0EQW21TR  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/urllib3/connection.py", line 174, in _new_conn  
conn = connection.create_connection(  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/urllib3/util/connection.py", line 73, in create_connection  
for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM):  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/socket.py",
line 953, in getaddrinfo  
for res in _socket.getaddrinfo(host, port, family, type, proto, flags):  
socket.gaierror: [Errno 8] nodename nor servname provided, or not known  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/urllib3/connectionpool.py", line 699, in urlopen  
httplib_response = self._make_request(  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/urllib3/connectionpool.py", line 394, in _make_request  
conn.request(method, url, **httplib_request_kw)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/urllib3/connection.py", line 239, in request  
super(HTTPConnection, self).request(method, url, body=body, headers=headers)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/http/client.py",
line 1257, in request  
self._send_request(method, url, body, headers, encode_chunked)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/http/client.py",
line 1303, in _send_request  
self.endheaders(body, encode_chunked=encode_chunked)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/http/client.py",
line 1252, in endheaders  
self._send_output(message_body, encode_chunked=encode_chunked)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/http/client.py",
line 1012, in _send_output  
self.send(msg)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/http/client.py",
line 952, in send  
self.connect()  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/urllib3/connection.py", line 205, in connect  
conn = self._new_conn()  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/urllib3/connection.py", line 186, in _new_conn  
raise NewConnectionError(  
urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPConnection
object at 0x7fe091a9b1c0>: Failed to establish a new connection: [Errno 8]
nodename nor servname provided, or not known  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/tasks.py", line 196, in _run_thread  
self.run(*args, **kw)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/tasks.py", line 289, in run  
self.monitor()  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/webservices/cxservices_job.py", line 122, in monitor  
status = self.api.status(self.job_id).status  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api/default_api.py", line 954, in status  
(data) = self.status_with_http_info(job_id, **kwargs) # noqa: E501  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api/default_api.py", line 1013, in status_with_http_info  
return self.api_client.call_api(  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api_client.py", line 316, in call_api  
return self.__call_api(resource_path, method,  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api_client.py", line 148, in __call_api  
response_data = self.request(  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api_client.py", line 338, in request  
return self.rest_client.GET(url,  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/rest.py", line 233, in GET  
return self.request("GET", url,  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/rest.py", line 206, in request  
r = self.pool_manager.request(method, url,  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/urllib3/request.py", line 74, in request  
return self.request_encode_url(  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/urllib3/request.py", line 96, in request_encode_url  
return self.urlopen(method, url, **extra_kw)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/urllib3/poolmanager.py", line 375, in urlopen  
response = conn.urlopen(method, u.request_uri, **kw)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/urllib3/connectionpool.py", line 783, in urlopen  
return self.urlopen(  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/urllib3/connectionpool.py", line 783, in urlopen  
return self.urlopen(  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/urllib3/connectionpool.py", line 783, in urlopen  
return self.urlopen(  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/urllib3/connectionpool.py", line 755, in urlopen  
retries = retries.increment(  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/urllib3/util/retry.py", line 574, in increment  
raise MaxRetryError(_pool, url, error or ResponseError(cause))  
urllib3.exceptions.MaxRetryError:
HTTPConnectionPool(host='webservices.rbvi.ucsf.edu', port=80): Max retries
exceeded with url:
/cxservices/api/v1//chimerax/job/BZ175YJ9HYY6BLAIRNHSYJ16PCDJ7W6X5OKDR9LTSP7KQ8U6TX2GD44O0EQW21TR
(Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at
0x7fe091a9b1c0>: Failed to establish a new connection: [Errno 8] nodename nor
servname provided, or not known'))  
  
Exception in thread 1:  
urllib3.exceptions.MaxRetryError:
HTTPConnectionPool(host='webservices.rbvi.ucsf.edu', port=80): Max retries
exceeded with url:
/cxservices/api/v1//chimerax/job/BZ175YJ9HYY6BLAIRNHSYJ16PCDJ7W6X5OKDR9LTSP7KQ8U6TX2GD44O0EQW21TR
(Caused by NewConnectionError(': Failed to establish a new connection: [Errno
8] nodename nor servname provided, or not known'))  
  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/urllib3/util/retry.py", line 574, in increment  
raise MaxRetryError(_pool, url, error or ResponseError(cause))  
  
See log for complete Python traceback.  
  
BlastProtein finished.  
2022-03-28 10:03:41,085 WARNING Retrying (Retry(total=2, connect=None,
read=None, redirect=None, status=None)) after connection broken by
'NewConnectionError('<urllib3.connection.HTTPConnection object at
0x7fe09070b640>: Failed to establish a new connection: [Errno 8] nodename nor
servname provided, or not known')':
/cxservices/api/v1//chimerax/files/BZ175YJ9HYY6BLAIRNHSYJ16PCDJ7W6X5OKDR9LTSP7KQ8U6TX2GD44O0EQW21TR/_stdout  
2022-03-28 10:03:41,088 WARNING Retrying (Retry(total=1, connect=None,
read=None, redirect=None, status=None)) after connection broken by
'NewConnectionError('<urllib3.connection.HTTPConnection object at
0x7fe0907dae50>: Failed to establish a new connection: [Errno 8] nodename nor
servname provided, or not known')':
/cxservices/api/v1//chimerax/files/BZ175YJ9HYY6BLAIRNHSYJ16PCDJ7W6X5OKDR9LTSP7KQ8U6TX2GD44O0EQW21TR/_stdout  
2022-03-28 10:03:41,091 WARNING Retrying (Retry(total=0, connect=None,
read=None, redirect=None, status=None)) after connection broken by
'NewConnectionError('<urllib3.connection.HTTPConnection object at
0x7fe0907da100>: Failed to establish a new connection: [Errno 8] nodename nor
servname provided, or not known')':
/cxservices/api/v1//chimerax/files/BZ175YJ9HYY6BLAIRNHSYJ16PCDJ7W6X5OKDR9LTSP7KQ8U6TX2GD44O0EQW21TR/_stdout  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/urllib3/connection.py", line 174, in _new_conn  
conn = connection.create_connection(  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/urllib3/util/connection.py", line 73, in create_connection  
for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM):  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/socket.py",
line 953, in getaddrinfo  
for res in _socket.getaddrinfo(host, port, family, type, proto, flags):  
socket.gaierror: [Errno 8] nodename nor servname provided, or not known  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/urllib3/connectionpool.py", line 699, in urlopen  
httplib_response = self._make_request(  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/urllib3/connectionpool.py", line 394, in _make_request  
conn.request(method, url, **httplib_request_kw)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/urllib3/connection.py", line 239, in request  
super(HTTPConnection, self).request(method, url, body=body, headers=headers)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/http/client.py",
line 1257, in request  
self._send_request(method, url, body, headers, encode_chunked)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/http/client.py",
line 1303, in _send_request  
self.endheaders(body, encode_chunked=encode_chunked)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/http/client.py",
line 1252, in endheaders  
self._send_output(message_body, encode_chunked=encode_chunked)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/http/client.py",
line 1012, in _send_output  
self.send(msg)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/http/client.py",
line 952, in send  
self.connect()  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/urllib3/connection.py", line 205, in connect  
conn = self._new_conn()  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/urllib3/connection.py", line 186, in _new_conn  
raise NewConnectionError(  
urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPConnection
object at 0x7fe0907da580>: Failed to establish a new connection: [Errno 8]
nodename nor servname provided, or not known  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/ui/results.py", line 466, in run  
self._check_job()  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/ui/results.py", line 482, in _check_job  
out = self.job.get_stdout()  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/webservices/cxservices_job.py", line 203, in get_stdout  
return self.get_file("_stdout")  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/webservices/cxservices_job.py", line 194, in get_file  
content = self.api.file_get(self.job_id, filename)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api/default_api.py", line 54, in file_get  
(data) = self.file_get_with_http_info(job_id, file_name, **kwargs) # noqa:
E501  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api/default_api.py", line 120, in file_get_with_http_info  
return self.api_client.call_api(  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api_client.py", line 316, in call_api  
return self.__call_api(resource_path, method,  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api_client.py", line 148, in __call_api  
response_data = self.request(  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api_client.py", line 338, in request  
return self.rest_client.GET(url,  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/rest.py", line 233, in GET  
return self.request("GET", url,  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/rest.py", line 206, in request  
r = self.pool_manager.request(method, url,  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/urllib3/request.py", line 74, in request  
return self.request_encode_url(  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/urllib3/request.py", line 96, in request_encode_url  
return self.urlopen(method, url, **extra_kw)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/urllib3/poolmanager.py", line 375, in urlopen  
response = conn.urlopen(method, u.request_uri, **kw)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/urllib3/connectionpool.py", line 783, in urlopen  
return self.urlopen(  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/urllib3/connectionpool.py", line 783, in urlopen  
return self.urlopen(  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/urllib3/connectionpool.py", line 783, in urlopen  
return self.urlopen(  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/urllib3/connectionpool.py", line 755, in urlopen  
retries = retries.increment(  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/urllib3/util/retry.py", line 574, in increment  
raise MaxRetryError(_pool, url, error or ResponseError(cause))  
urllib3.exceptions.MaxRetryError:
HTTPConnectionPool(host='webservices.rbvi.ucsf.edu', port=80): Max retries
exceeded with url:
/cxservices/api/v1//chimerax/files/BZ175YJ9HYY6BLAIRNHSYJ16PCDJ7W6X5OKDR9LTSP7KQ8U6TX2GD44O0EQW21TR/_stdout
(Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at
0x7fe0907da580>: Failed to establish a new connection: [Errno 8] nodename nor
servname provided, or not known'))  
  
urllib3.exceptions.MaxRetryError:
HTTPConnectionPool(host='webservices.rbvi.ucsf.edu', port=80): Max retries
exceeded with url:
/cxservices/api/v1//chimerax/files/BZ175YJ9HYY6BLAIRNHSYJ16PCDJ7W6X5OKDR9LTSP7KQ8U6TX2GD44O0EQW21TR/_stdout
(Caused by NewConnectionError(': Failed to establish a new connection: [Errno
8] nodename nor servname provided, or not known'))  
  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/urllib3/util/retry.py", line 574, in increment  
raise MaxRetryError(_pool, url, error or ResponseError(cause))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1
OpenGL vendor: AppleHardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: MacBookAir10,1
      Processor Name: Unknown
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache: 8 MB
      Memory: 8 GB

Software:

    System Software Overview:

      System Version: macOS 12.2.1 (21D62)
      Kernel Version: Darwin 21.3.0
      Time since boot: 14 days 19:05

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 7
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

Change History (3)

comment:1 by Eric Pettersen, 4 years ago

Cc: Tom Goddard added
Component: Unassigned → Infrastructure
Owner: set to Zach Pearson
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Blast error while web services down

comment:2 by Zach Pearson, 4 years ago

Hopefully fixed by catching NewConnectionError in ​this commit.

Redirected webservices.rbvi.ucsf.edu to 0.0.0.0 in /etc/hosts to test.

comment:3 by Zach Pearson, 4 years ago

Resolution: → fixed
Status: assigned → closed
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