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loqus-related subprocess error

See original GitHub issue

We’ve been seeing this error since quite some time, so I’ll just drop it here:

2020-03-19 12:42:36,105 - scout.server.app - ERROR: Exception on /cust003/20045/4d9e1dc578dcd0f97c193206f1f23e72 [GET] [in /home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/site-packages/flask/app.py:1891]
Traceback (most recent call last):
  File "/home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/site-packages/flask/app.py", line 2446, in wsgi_app
    response = self.full_dispatch_request()
  File "/home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/site-packages/flask/app.py", line 1951, in full_dispatch_request
    rv = self.handle_user_exception(e)
  File "/home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/site-packages/flask/app.py", line 1820, in handle_user_exception
    reraise(exc_type, exc_value, tb)
  File "/home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/site-packages/flask/_compat.py", line 39, in reraise
    raise value
  File "/home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/site-packages/flask/app.py", line 1949, in full_dispatch_request
    rv = self.dispatch_request()
  File "/home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/site-packages/flask/app.py", line 1935, in dispatch_request
    return self.view_functions[rule.endpoint](**req.view_args)
  File "/home/hiseq.clinical/SERVER/apps/scout/git/scout/scout/server/utils.py", line 23, in decorated_function
    context = f(*args, **kwargs)
  File "/home/hiseq.clinical/SERVER/apps/scout/git/scout/scout/server/blueprints/variant/views.py", line 56, in variant
    store, loqusdb, data["case"], data["variant"]
  File "/home/hiseq.clinical/SERVER/apps/scout/git/scout/scout/server/blueprints/variant/controllers.py", line 263, in observations
    obs_data = loqusdb.get_variant(variant_query) or {}
  File "/home/hiseq.clinical/SERVER/apps/scout/git/scout/scout/server/extensions/loqus_extension.py", line 142, in get_variant
    raise err
  File "/home/hiseq.clinical/SERVER/apps/scout/git/scout/scout/server/extensions/loqus_extension.py", line 139, in get_variant
    output = execute_command(variant_call)
  File "/home/hiseq.clinical/SERVER/apps/scout/git/scout/scout/server/extensions/loqus_extension.py", line 28, in execute_command
    raise err
  File "/home/hiseq.clinical/SERVER/apps/scout/git/scout/scout/server/extensions/loqus_extension.py", line 25, in execute_command
    output = subprocess.check_output(cmd, shell=False)
  File "/home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/subprocess.py", line 336, in check_output
    **kwargs).stdout
  File "/home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/subprocess.py", line 418, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['/home/hiseq.clinical/miniconda/envs/P_loqusdb/bin/loqusdb', '--config', '/home/hiseq.clinical/servers/config/clinical-db.scilifelab.se/loqusdb.yaml', 'variants', '--to-json', '--variant-id', '2_109381037_G_C', '--case-count']' returned non-zero exit status 1

Issue Analytics

State:
Created 4 years ago
Comments:6 (3 by maintainers)

Top GitHub Comments

1reaction

dnilcommented, Sep 1, 2020

Possible, connection setup is different from continuous query I guess, but it may also have to do with other other system resources like socket reuse? I’m very tempted to try making a simple wsgi json interface for loqus and try it. Ideally there should be a simple complete click-to-gRPC-interface-cast: Erik S mentioned he saw a student announcing work on that, but nothing official out yet…

0reactions

moonsocommented, Sep 1, 2020

I’m convinced that this has to do with our sub optimal setup with heavy workload on the only one running mongod process