looselab / minotour-docker Goto Github PK

When I try to run minFQ / minotour on Docker, I get RPC error.
minFQ -k 2645d7e2ebalablabla -ip 145.xxx.xxx.xxx -hn localhost -p 8100 -nf
->
<_InactiveRpcError of RPC that terminated with:
status = StatusCode.UNAVAILABLE
details = "failed to connect to all addresses"
debug_error_string = "{"created":"@1653160488.112296657","description":"Failed to pick subchannel",

Debugging -> tail -f -n 100 /var/lib/minotour/logs/celery.log
16624:[2022-05-20 23:02:08,011: ERROR/ForkPoolWorker-1] artic.utils.update_pangolin[06bde82d-5482-4173-87ed-5103c3a353c6]: b'pangolin updated to v4.0.6\npangolearn updated to 2022-04-22\nconstellations updated to v0.1.10\nscorpio updated to v0.3.17\npango-designation updated to v1.9\n'

I think we've had this issue before....

Running ARTIC:

    return func(*args, **kwargs)
  File "/home/rory/Projects/minotourapp/artic/views.py", line 462, in get_artic_summary_table_data
    amplicon_stats = get_amplicon_stats(
  File "/home/rory/Projects/minotourapp/artic/utils.py", line 544, in get_amplicon_stats
    raise e
  File "/home/rory/Projects/minotourapp/artic/utils.py", line 541, in get_amplicon_stats
    with open(coverage_path, "rb") as fh:
FileNotFoundError: [Errno 2] No such file or directory: '/home/rory/Projects/data/Artic/artic/Temp_results/86_470_artic/unclassified/unclassified.coverage.dat'
"GET /api/v1/artic/visualisation/summary-table-data/?flowcellId=86&_=1624443820418 HTTP/1.1" 500 24337
(base) root@db42b19e2189:/var/lib/minotour/apps/minotourapp# tail -f 200 minotour.log
tail: cannot open '200' for reading: No such file or directory
==> minotour.log <==
  File "/home/rory/envs/minotour/lib/python3.8/site-packages/rest_framework/decorators.py", line 50, in handler
    return func(*args, **kwargs)
  File "/home/rory/Projects/minotourapp/artic/views.py", line 462, in get_artic_summary_table_data
    amplicon_stats = get_amplicon_stats(
  File "/home/rory/Projects/minotourapp/artic/utils.py", line 544, in get_amplicon_stats
    raise e
  File "/home/rory/Projects/minotourapp/artic/utils.py", line 541, in get_amplicon_stats
    with open(coverage_path, "rb") as fh:
FileNotFoundError: [Errno 2] No such file or directory: '/home/rory/Projects/data/Artic/artic/Temp_results/86_470_artic/unclassified/unclassified.coverage.dat'
"GET /api/v1/artic/visualisation/summary-table-data/?flowcellId=86&_=1624443820418 HTTP/1.1" 500 24337
^C```

I have an issues regarding operating tasks in the GUI of minoTour. If I am starting any tasks, e.g. Minimap2, there will be an infinite loop and it won´t produce any output.

minotour (docker) is running on localhost, 8100

When I try to run minFQ with key and port, I get an error - "failed to connect to all addresses". Any tips or suggestions?

minFQ -k 201d23868f2e9722066a15459889f1d80c894b0c -p 8100
<_InactiveRpcError of RPC that terminated with:
status = StatusCode.UNAVAILABLE
details = "failed to connect to all addresses"
debug_error_string = "{"created":"@1654699347.250973082","description":"Failed to pick subchannel","file":"src/core/ext/filters/client_channel/client_channel.cc","file_line":3217,"referenced_errors":[{"created":"@1654699347.250971952","description":"failed to connect to all addresses","file":"src/core/lib/transport/error_utils.cc","file_line":165,"grpc_status":14}]}"

best regards
R

[2022-06-08T15:02:40] INFO [minFQ.minknow_connection.init:402] Installed minknow API Version 5.0.0.1
[2022-06-08T15:02:40] DEBUG [minknow_api.load_grpc_credentials:341] Reading ssl certificate
[2022-06-08T15:02:40] DEBUG [minknow_api.load_grpc_credentials:361] Getting local token
[2022-06-08T15:02:40] DEBUG [root.get_local_authentication_token_file:53] Unable to connect to manager on port '9502' to retrieve local auth token path
Traceback (most recent call last):
File "/home/brug.r/Documents/virtualPythonEnv/minotour/lib/python3.8/site-packages/minknow_api/manager.py", line 51, in get_local_authentication_token_file
return service.local_authentication_token_path().path
File "/home/brug.r/Documents/virtualPythonEnv/minotour/lib/python3.8/site-packages/minknow_api/manager_service.py", line 1095, in local_authentication_token_path
return run_with_retry(self._stub.local_authentication_token_path,
File "/home/brug.r/Documents/virtualPythonEnv/minotour/lib/python3.8/site-packages/minknow_api/manager_service.py", line 85, in run_with_retry
result = MessageWrapper(method(message, timeout=timeout), unwraps=unwraps)
File "/home/brug.r/Documents/virtualPythonEnv/minotour/lib/python3.8/site-packages/grpc/_channel.py", line 946, in call
return _end_unary_response_blocking(state, call, False, None)
File "/home/brug.r/Documents/virtualPythonEnv/minotour/lib/python3.8/site-packages/grpc/_channel.py", line 849, in _end_unary_response_blocking
raise _InactiveRpcError(state)
grpc._channel._InactiveRpcError: <_InactiveRpcError of RPC that terminated with:
status = StatusCode.UNAVAILABLE
details = "failed to connect to all addresses"
debug_error_string = "{"created":"@1654714960.599588044","description":"Failed to pick subchannel","file":"src/core/ext/filters/client_channel/client_channel.cc","file_line":3217,"referenced_errors":[{"created":"@1654714960.599587075","description":"failed to connect to all addresses","file":"src/core/lib/transport/error_utils.cc","file_line":165,"grpc_status":14}]}"

I have a problem with the graphical user interface. I used the Docker solution to install minoTour. I´ve also created an account - a normal user as well as an admin - but it is just possible for me to login in minoTour from the computer where I´ve installed the normal user and the admin. I cannot login in minoTour from another computer although the installation of the other computer was succesful.

The web container - keeps having the status restarting
8b3abe0ee643 adoni5/minotourapp_web "/var/lib/minotour/a…" 12 days ago Restarting (255) 6 seconds ago web

docker logs web
->
Error: please install pangolin_data with
pip install git+https://github.com/cov-lineages/pangolin-data.git

best regards
Rudolf