search

Psy-Fer / interARTIC

InterARTIC - An interactive local web application for viral whole genome sequencing utilising the artic network pipelines..
https://psy-fer.github.io/interARTIC/
MIT License
29 stars 7 forks source link

No output on web interface when custom output directory is provided #9

Closed hasindu2008 closed 3 years ago

hasindu2008 commented 3 years ago

output-nano was specified as the output directory and there was not output on the web interface. The log messages are as below.

hasindu@hasindu-xps:~/interARTIC$ cat celery.log
[2021-02-01 22:01:51,276: INFO/MainProcess] Connected to redis://localhost:6379/0
[2021-02-01 22:01:51,283: INFO/MainProcess] mingle: searching for neighbors
[2021-02-01 22:01:52,297: INFO/MainProcess] mingle: all alone
[2021-02-01 22:01:52,303: INFO/MainProcess] celery@hasindu-xps ready.
[2021-02-01 22:02:43,723: INFO/MainProcess] Received task: main.executeJob[3aa05290-258d-4b63-ae7b-c280f03b5216]
[2021-02-01 22:02:43,724: INFO/ForkPoolWorker-1] main.executeJob[3aa05290-258d-4b63-ae7b-c280f03b5216]: In celery task, executing job...
[2021-02-01 22:02:43,736: WARNING/ForkPoolWorker-1] /home/hasindu/.local/lib/python3.8/site-packages/celery/app/trace.py:622: RuntimeWarning: Exception raised outside body: KeyError('exc_type'):
Traceback (most recent call last):
  File "/home/hasindu/.local/lib/python3.8/site-packages/celery/app/trace.py", line 412, in trace_task
    R = retval = fun(*args, **kwargs)
  File "/home/hasindu/.local/lib/python3.8/site-packages/celery/app/trace.py", line 704, in __protected_call__
    return self.run(*args, **kwargs)
  File "/home/hasindu/interARTIC/main.py", line 129, in executeJob
    raise Exception("Command {} got return code {}.\nSTDOUT: {}\nSTDERR: {}".format(cmd, returnCode, stdout, stderr))
Exception: Command cd output-nano; echo '*****STARTING GATHER COMMAND*****' >> output-nano/all_cmds_log.txt 2>> output-nano/all_cmds_log.txt; artic gather --min-length 2300 --max-length 2700 --prefix FLFL031920-kirby4 --directory /mnt/d/genome/data/FLFL031920/FLFL031920/20200330_0614_X3_ACW749_4b9280d1 --fast5-directory /mnt/d/genome/data/FLFL031920/FLFL031920/20200330_0614_X3_ACW749_4b9280d1/fast5_pass >> output-nano/all_cmds_log.txt 2>> output-nano/all_cmds_log.txt got return code 2.
STDOUT: b''
STDERR: b"/bin/sh: 1: cd: can't cd to output-nano\n/bin/sh: 1: cannot create output-nano/all_cmds_log.txt: Directory nonexistent\n/bin/sh: 1: cannot create output-nano/all_cmds_log.txt: Directory nonexistent\n"

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/hasindu/.local/lib/python3.8/site-packages/celery/app/trace.py", line 429, in trace_task
    I, R, state, retval = on_error(task_request, exc, uuid)
  File "/home/hasindu/.local/lib/python3.8/site-packages/celery/app/trace.py", line 365, in on_error
    R = I.handle_error_state(
  File "/home/hasindu/.local/lib/python3.8/site-packages/celery/app/trace.py", line 168, in handle_error_state
    return {
  File "/home/hasindu/.local/lib/python3.8/site-packages/celery/app/trace.py", line 215, in handle_failure
    task.backend.mark_as_failure(
  File "/home/hasindu/.local/lib/python3.8/site-packages/celery/backends/base.py", line 168, in mark_as_failure
    self.store_result(task_id, exc, state,
  File "/home/hasindu/.local/lib/python3.8/site-packages/celery/backends/base.py", line 442, in store_result
    self._store_result(task_id, result, state, traceback,
  File "/home/hasindu/.local/lib/python3.8/site-packages/celery/backends/base.py", line 856, in _store_result
    current_meta = self._get_task_meta_for(task_id)
  File "/home/hasindu/.local/lib/python3.8/site-packages/celery/backends/base.py", line 877, in _get_task_meta_for
    return self.decode_result(meta)
  File "/home/hasindu/.local/lib/python3.8/site-packages/celery/backends/base.py", line 344, in decode_result
    return self.meta_from_decoded(self.decode(payload))
  File "/home/hasindu/.local/lib/python3.8/site-packages/celery/backends/base.py", line 340, in meta_from_decoded
    meta['result'] = self.exception_to_python(meta['result'])
  File "/home/hasindu/.local/lib/python3.8/site-packages/celery/backends/base.py", line 300, in exception_to_python
    from_utf8(exc['exc_type']), __name__)
KeyError: 'exc_type'

  warn(RuntimeWarning(
[2021-02-01 22:02:43,739: ERROR/MainProcess] Pool callback raised exception: KeyError('exc_type')
Traceback (most recent call last):
  File "/home/hasindu/.local/lib/python3.8/site-packages/billiard/pool.py", line 1796, in safe_apply_callback
    fun(*args, **kwargs)
  File "/home/hasindu/.local/lib/python3.8/site-packages/celery/worker/request.py", line 526, in on_failure
    self.task.backend.mark_as_failure(
  File "/home/hasindu/.local/lib/python3.8/site-packages/celery/backends/base.py", line 168, in mark_as_failure
    self.store_result(task_id, exc, state,
  File "/home/hasindu/.local/lib/python3.8/site-packages/celery/backends/base.py", line 442, in store_result
    self._store_result(task_id, result, state, traceback,
  File "/home/hasindu/.local/lib/python3.8/site-packages/celery/backends/base.py", line 856, in _store_result
    current_meta = self._get_task_meta_for(task_id)
  File "/home/hasindu/.local/lib/python3.8/site-packages/celery/backends/base.py", line 877, in _get_task_meta_for
    return self.decode_result(meta)
  File "/home/hasindu/.local/lib/python3.8/site-packages/celery/backends/base.py", line 344, in decode_result
    return self.meta_from_decoded(self.decode(payload))
  File "/home/hasindu/.local/lib/python3.8/site-packages/celery/backends/base.py", line 340, in meta_from_decoded
    meta['result'] = self.exception_to_python(meta['result'])
  File "/home/hasindu/.local/lib/python3.8/site-packages/celery/backends/base.py", line 300, in exception_to_python
    from_utf8(exc['exc_type']), __name__)
KeyError: 'exc_type'
hasindu2008 commented 3 years ago

@Psy-Fer has fixed this in the latest commits