Running multiple qiimes concurrently before refreshing the cache causes fireworks

[BenKaehler]

Bug Description
I tried to run 10 qiimes concurrently before I had refreshed the cache.

My log follows. Manually refreshing the cache before starting fixed the problem.

Screenshots

Click to expand!

2018-04-26 22:34:40,847:compute-5-2.local:34110:INFO:{'bash_command': ('qiime', 'feature-classifier', 'fit-classifier-naive-bayes', '--i-reference-reads', '../ref/99_otus_v4.qza', '--i-reference-taxonomy', '../ref/99_otu_taxonomy.qza', '--o-classifier', 'classifiers/99_otus_v4-{}.qza', '--i-class-weight', 'weights/{}.qza'), 'log_level': 'INFO', 'log_path': 'log'}
2018-04-26 22:34:40,865:compute-5-2.local:34110:INFO:{'mpi_logging': '0.1.1-dev', 'dispatcher': '0.1.1-dev', 'mpimap': '0.1.1-dev'}
2018-04-26 22:34:47,648:compute-5-4.local:6665:WARNING:Got return code 1 for
qiime feature-classifier fit-classifier-naive-bayes --i-reference-reads ../ref/99_otus_v4.qza --i-reference-taxonomy ../ref/99_otu_taxonomy.qza --o-classifier classifiers/99_otus_v4-weights-normalise-False-unobserved-weight-1e-06-fold-4.qza --i-class-weight weights/weights-normalise-False-unobserved-weight-1e-06-fold-4.qza:
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
Traceback (most recent call last):
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/cache.py", line 118, in _get_cached_state
    return json.load(fh)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/__init__.py", line 268, in load
    parse_constant=parse_constant, object_pairs_hook=object_pairs_hook, **kw)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/__init__.py", line 319, in loads
    return _default_decoder.decode(s)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/decoder.py", line 339, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/decoder.py", line 355, in raw_decode
    obj, end = self.scan_once(s, idx)
json.decoder.JSONDecodeError: Expecting ',' delimiter: line 1 column 24585 (char 24584)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/bin/qiime", line 11, in <module>
    sys.exit(qiime())
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/click/core.py", line 722, in __call__
    return self.main(*args, **kwargs)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/click/core.py", line 697, in main
    rv = self.invoke(ctx)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/click/core.py", line 1061, in invoke
    cmd_name, cmd, args = self.resolve_command(ctx, args)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/click/core.py", line 1100, in resolve_command
    cmd = self.get_command(ctx, cmd_name)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/commands.py", line 99, in get_command
    plugin = self._plugin_lookup[name]
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/commands.py", line 75, in _plugin_lookup
    import q2cli.cache
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/cache.py", line 302, in <module>
    CACHE = DeploymentCache()
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/cache.py", line 61, in __init__
    self._state = self._get_cached_state(refresh=refresh)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/cache.py", line 123, in _get_cached_state
    return json.load(fh)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/__init__.py", line 268, in load
    parse_constant=parse_constant, object_pairs_hook=object_pairs_hook, **kw)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/__init__.py", line 319, in loads
    return _default_decoder.decode(s)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/decoder.py", line 339, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/decoder.py", line 355, in raw_decode
    obj, end = self.scan_once(s, idx)
json.decoder.JSONDecodeError: Expecting ',' delimiter: line 1 column 24585 (char 24584)

2018-04-26 22:34:47,724:compute-5-4.local:6664:WARNING:Got return code 1 for
qiime feature-classifier fit-classifier-naive-bayes --i-reference-reads ../ref/99_otus_v4.qza --i-reference-taxonomy ../ref/99_otu_taxonomy.qza --o-classifier classifiers/99_otus_v4-weights-normalise-False-unobserved-weight-1e-06-fold-2.qza --i-class-weight weights/weights-normalise-False-unobserved-weight-1e-06-fold-2.qza:
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
Traceback (most recent call last):
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/cache.py", line 118, in _get_cached_state
    return json.load(fh)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/__init__.py", line 268, in load
    parse_constant=parse_constant, object_pairs_hook=object_pairs_hook, **kw)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/__init__.py", line 319, in loads
    return _default_decoder.decode(s)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/decoder.py", line 339, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/decoder.py", line 355, in raw_decode
    obj, end = self.scan_once(s, idx)
json.decoder.JSONDecodeError: Expecting ',' delimiter: line 1 column 24585 (char 24584)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/bin/qiime", line 11, in <module>
    sys.exit(qiime())
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/click/core.py", line 722, in __call__
    return self.main(*args, **kwargs)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/click/core.py", line 697, in main
    rv = self.invoke(ctx)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/click/core.py", line 1061, in invoke
    cmd_name, cmd, args = self.resolve_command(ctx, args)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/click/core.py", line 1100, in resolve_command
    cmd = self.get_command(ctx, cmd_name)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/commands.py", line 99, in get_command
    plugin = self._plugin_lookup[name]
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/commands.py", line 75, in _plugin_lookup
    import q2cli.cache
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/cache.py", line 302, in <module>
    CACHE = DeploymentCache()
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/cache.py", line 61, in __init__
    self._state = self._get_cached_state(refresh=refresh)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/cache.py", line 123, in _get_cached_state
    return json.load(fh)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/__init__.py", line 268, in load
    parse_constant=parse_constant, object_pairs_hook=object_pairs_hook, **kw)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/__init__.py", line 319, in loads
    return _default_decoder.decode(s)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/decoder.py", line 339, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/decoder.py", line 355, in raw_decode
    obj, end = self.scan_once(s, idx)
json.decoder.JSONDecodeError: Expecting ',' delimiter: line 1 column 24585 (char 24584)

2018-04-26 22:34:47,755:compute-5-4.local:6663:WARNING:Got return code 1 for
qiime feature-classifier fit-classifier-naive-bayes --i-reference-reads ../ref/99_otus_v4.qza --i-reference-taxonomy ../ref/99_otu_taxonomy.qza --o-classifier classifiers/99_otus_v4-weights-normalise-False-unobserved-weight-1e-06-fold-7.qza --i-class-weight weights/weights-normalise-False-unobserved-weight-1e-06-fold-7.qza:
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
Traceback (most recent call last):
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/cache.py", line 118, in _get_cached_state
    return json.load(fh)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/__init__.py", line 268, in load
    parse_constant=parse_constant, object_pairs_hook=object_pairs_hook, **kw)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/__init__.py", line 319, in loads
    return _default_decoder.decode(s)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/decoder.py", line 339, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/decoder.py", line 355, in raw_decode
    obj, end = self.scan_once(s, idx)
json.decoder.JSONDecodeError: Expecting ',' delimiter: line 1 column 24585 (char 24584)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/bin/qiime", line 11, in <module>
    sys.exit(qiime())
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/click/core.py", line 722, in __call__
    return self.main(*args, **kwargs)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/click/core.py", line 697, in main
    rv = self.invoke(ctx)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/click/core.py", line 1061, in invoke
    cmd_name, cmd, args = self.resolve_command(ctx, args)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/click/core.py", line 1100, in resolve_command
    cmd = self.get_command(ctx, cmd_name)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/commands.py", line 99, in get_command
    plugin = self._plugin_lookup[name]
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/commands.py", line 75, in _plugin_lookup
    import q2cli.cache
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/cache.py", line 302, in <module>
    CACHE = DeploymentCache()
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/cache.py", line 61, in __init__
    self._state = self._get_cached_state(refresh=refresh)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/cache.py", line 123, in _get_cached_state
    return json.load(fh)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/__init__.py", line 268, in load
    parse_constant=parse_constant, object_pairs_hook=object_pairs_hook, **kw)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/__init__.py", line 319, in loads
    return _default_decoder.decode(s)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/decoder.py", line 339, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/decoder.py", line 355, in raw_decode
    obj, end = self.scan_once(s, idx)
json.decoder.JSONDecodeError: Expecting ',' delimiter: line 1 column 24585 (char 24584)

2018-04-26 22:34:49,521:compute-5-0.local:39148:WARNING:Got return code 1 for
qiime feature-classifier fit-classifier-naive-bayes --i-reference-reads ../ref/99_otus_v4.qza --i-reference-taxonomy ../ref/99_otu_taxonomy.qza --o-classifier classifiers/99_otus_v4-uniform.qza --i-class-weight weights/uniform.qza:
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
Traceback (most recent call last):
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/cache.py", line 118, in _get_cached_state
    return json.load(fh)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/__init__.py", line 268, in load
    parse_constant=parse_constant, object_pairs_hook=object_pairs_hook, **kw)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/__init__.py", line 319, in loads
    return _default_decoder.decode(s)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/decoder.py", line 339, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/decoder.py", line 357, in raw_decode
    raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 49229 (char 49228)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/bin/qiime", line 11, in <module>
    sys.exit(qiime())
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/click/core.py", line 722, in __call__
    return self.main(*args, **kwargs)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/click/core.py", line 697, in main
    rv = self.invoke(ctx)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/click/core.py", line 1061, in invoke
    cmd_name, cmd, args = self.resolve_command(ctx, args)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/click/core.py", line 1100, in resolve_command
    cmd = self.get_command(ctx, cmd_name)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/commands.py", line 99, in get_command
    plugin = self._plugin_lookup[name]
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/commands.py", line 75, in _plugin_lookup
    import q2cli.cache
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/cache.py", line 302, in <module>
    CACHE = DeploymentCache()
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/cache.py", line 61, in __init__
    self._state = self._get_cached_state(refresh=refresh)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/cache.py", line 123, in _get_cached_state
    return json.load(fh)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/__init__.py", line 268, in load
    parse_constant=parse_constant, object_pairs_hook=object_pairs_hook, **kw)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/__init__.py", line 319, in loads
    return _default_decoder.decode(s)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/decoder.py", line 339, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/decoder.py", line 355, in raw_decode
    obj, end = self.scan_once(s, idx)
json.decoder.JSONDecodeError: Expecting ':' delimiter: line 1 column 223221 (char 223220)

2018-04-26 22:34:49,675:compute-5-0.local:39147:WARNING:Got return code 1 for
qiime feature-classifier fit-classifier-naive-bayes --i-reference-reads ../ref/99_otus_v4.qza --i-reference-taxonomy ../ref/99_otu_taxonomy.qza --o-classifier classifiers/99_otus_v4-weights-normalise-False-unobserved-weight-1e-06-fold-3.qza --i-class-weight weights/weights-normalise-False-unobserved-weight-1e-06-fold-3.qza:
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
Traceback (most recent call last):
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/cache.py", line 118, in _get_cached_state
    return json.load(fh)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/__init__.py", line 268, in load
    parse_constant=parse_constant, object_pairs_hook=object_pairs_hook, **kw)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/__init__.py", line 319, in loads
    return _default_decoder.decode(s)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/decoder.py", line 339, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/decoder.py", line 355, in raw_decode
    obj, end = self.scan_once(s, idx)
json.decoder.JSONDecodeError: Expecting ':' delimiter: line 1 column 49415 (char 49414)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/bin/qiime", line 11, in <module>
    sys.exit(qiime())
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/click/core.py", line 722, in __call__
    return self.main(*args, **kwargs)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/click/core.py", line 697, in main
    rv = self.invoke(ctx)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/click/core.py", line 1061, in invoke
    cmd_name, cmd, args = self.resolve_command(ctx, args)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/click/core.py", line 1100, in resolve_command
    cmd = self.get_command(ctx, cmd_name)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/commands.py", line 99, in get_command
    plugin = self._plugin_lookup[name]
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/commands.py", line 75, in _plugin_lookup
    import q2cli.cache
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/cache.py", line 302, in <module>
    CACHE = DeploymentCache()
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/cache.py", line 61, in __init__
    self._state = self._get_cached_state(refresh=refresh)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/cache.py", line 123, in _get_cached_state
    return json.load(fh)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/__init__.py", line 268, in load
    parse_constant=parse_constant, object_pairs_hook=object_pairs_hook, **kw)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/__init__.py", line 319, in loads
    return _default_decoder.decode(s)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/decoder.py", line 339, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/decoder.py", line 355, in raw_decode
    obj, end = self.scan_once(s, idx)
json.decoder.JSONDecodeError: Expecting property name enclosed in double quotes: line 1 column 99399 (char 99398)

2018-04-26 22:35:26,448:compute-5-2.local:34111:WARNING:Got return code 1 for
qiime feature-classifier fit-classifier-naive-bayes --i-reference-reads ../ref/99_otus_v4.qza --i-reference-taxonomy ../ref/99_otu_taxonomy.qza --o-classifier classifiers/99_otus_v4-weights-normalise-False-unobserved-weight-1e-06-fold-5.qza --i-class-weight weights/weights-normalise-False-unobserved-weight-1e-06-fold-5.qza:
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
Traceback (most recent call last):
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/cache.py", line 118, in _get_cached_state
    return json.load(fh)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/__init__.py", line 268, in load
    parse_constant=parse_constant, object_pairs_hook=object_pairs_hook, **kw)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/__init__.py", line 319, in loads
    return _default_decoder.decode(s)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/decoder.py", line 339, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/decoder.py", line 355, in raw_decode
    obj, end = self.scan_once(s, idx)
json.decoder.JSONDecodeError: Expecting ',' delimiter: line 1 column 24577 (char 24576)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/bin/qiime", line 11, in <module>
    sys.exit(qiime())
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/click/core.py", line 722, in __call__
    return self.main(*args, **kwargs)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/click/core.py", line 697, in main
    rv = self.invoke(ctx)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/click/core.py", line 1061, in invoke
    cmd_name, cmd, args = self.resolve_command(ctx, args)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/click/core.py", line 1100, in resolve_command
    cmd = self.get_command(ctx, cmd_name)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/commands.py", line 99, in get_command
    plugin = self._plugin_lookup[name]
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/commands.py", line 75, in _plugin_lookup
    import q2cli.cache
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/cache.py", line 302, in <module>
    CACHE = DeploymentCache()
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/cache.py", line 61, in __init__
    self._state = self._get_cached_state(refresh=refresh)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/cache.py", line 123, in _get_cached_state
    return json.load(fh)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/__init__.py", line 268, in load
    parse_constant=parse_constant, object_pairs_hook=object_pairs_hook, **kw)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/__init__.py", line 319, in loads
    return _default_decoder.decode(s)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/decoder.py", line 339, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/decoder.py", line 355, in raw_decode
    obj, end = self.scan_once(s, idx)
json.decoder.JSONDecodeError: Expecting ',' delimiter: line 1 column 73866 (char 73865)

2018-04-26 22:35:26,623:compute-5-2.local:34112:WARNING:Got return code 1 for
qiime feature-classifier fit-classifier-naive-bayes --i-reference-reads ../ref/99_otus_v4.qza --i-reference-taxonomy ../ref/99_otu_taxonomy.qza --o-classifier classifiers/99_otus_v4-weights-normalise-False-unobserved-weight-1e-06-fold-9.qza --i-class-weight weights/weights-normalise-False-unobserved-weight-1e-06-fold-9.qza:
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
Traceback (most recent call last):
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/cache.py", line 118, in _get_cached_state
    return json.load(fh)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/__init__.py", line 268, in load
    parse_constant=parse_constant, object_pairs_hook=object_pairs_hook, **kw)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/__init__.py", line 319, in loads
    return _default_decoder.decode(s)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/decoder.py", line 339, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/decoder.py", line 355, in raw_decode
    obj, end = self.scan_once(s, idx)
json.decoder.JSONDecodeError: Expecting ',' delimiter: line 1 column 24577 (char 24576)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/bin/qiime", line 11, in <module>
    sys.exit(qiime())
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/click/core.py", line 722, in __call__
    return self.main(*args, **kwargs)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/click/core.py", line 697, in main
    rv = self.invoke(ctx)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/click/core.py", line 1061, in invoke
    cmd_name, cmd, args = self.resolve_command(ctx, args)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/click/core.py", line 1100, in resolve_command
    cmd = self.get_command(ctx, cmd_name)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/commands.py", line 99, in get_command
    plugin = self._plugin_lookup[name]
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/commands.py", line 75, in _plugin_lookup
    import q2cli.cache
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/cache.py", line 302, in <module>
    CACHE = DeploymentCache()
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/cache.py", line 61, in __init__
    self._state = self._get_cached_state(refresh=refresh)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/cache.py", line 123, in _get_cached_state
    return json.load(fh)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/__init__.py", line 268, in load
    parse_constant=parse_constant, object_pairs_hook=object_pairs_hook, **kw)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/__init__.py", line 319, in loads
    return _default_decoder.decode(s)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/decoder.py", line 339, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/decoder.py", line 355, in raw_decode
    obj, end = self.scan_once(s, idx)
json.decoder.JSONDecodeError: Expecting ',' delimiter: line 1 column 73866 (char 73865)

2018-04-26 22:35:26,825:compute-5-1.local:42065:WARNING:Got return code 1 for
qiime feature-classifier fit-classifier-naive-bayes --i-reference-reads ../ref/99_otus_v4.qza --i-reference-taxonomy ../ref/99_otu_taxonomy.qza --o-classifier classifiers/99_otus_v4-weights-normalise-False-unobserved-weight-1e-06-fold-6.qza --i-class-weight weights/weights-normalise-False-unobserved-weight-1e-06-fold-6.qza:
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
Traceback (most recent call last):
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/cache.py", line 118, in _get_cached_state
    return json.load(fh)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/__init__.py", line 268, in load
    parse_constant=parse_constant, object_pairs_hook=object_pairs_hook, **kw)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/__init__.py", line 319, in loads
    return _default_decoder.decode(s)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/decoder.py", line 339, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/decoder.py", line 355, in raw_decode
    obj, end = self.scan_once(s, idx)
json.decoder.JSONDecodeError: Expecting ',' delimiter: line 1 column 24577 (char 24576)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/bin/qiime", line 11, in <module>
    sys.exit(qiime())
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/click/core.py", line 722, in __call__
    return self.main(*args, **kwargs)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/click/core.py", line 697, in main
    rv = self.invoke(ctx)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/click/core.py", line 1061, in invoke
    cmd_name, cmd, args = self.resolve_command(ctx, args)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/click/core.py", line 1100, in resolve_command
    cmd = self.get_command(ctx, cmd_name)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/commands.py", line 99, in get_command
    plugin = self._plugin_lookup[name]
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/commands.py", line 75, in _plugin_lookup
    import q2cli.cache
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/cache.py", line 302, in <module>
    CACHE = DeploymentCache()
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/cache.py", line 61, in __init__
    self._state = self._get_cached_state(refresh=refresh)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/cache.py", line 123, in _get_cached_state
    return json.load(fh)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/__init__.py", line 268, in load
    parse_constant=parse_constant, object_pairs_hook=object_pairs_hook, **kw)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/__init__.py", line 319, in loads
    return _default_decoder.decode(s)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/decoder.py", line 339, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/decoder.py", line 355, in raw_decode
    obj, end = self.scan_once(s, idx)
json.decoder.JSONDecodeError: Expecting ',' delimiter: line 1 column 73866 (char 73865)

2018-04-26 22:35:27,012:compute-5-1.local:42064:WARNING:Got return code 1 for
qiime feature-classifier fit-classifier-naive-bayes --i-reference-reads ../ref/99_otus_v4.qza --i-reference-taxonomy ../ref/99_otu_taxonomy.qza --o-classifier classifiers/99_otus_v4-weights-normalise-False-unobserved-weight-1e-06-fold-1.qza --i-class-weight weights/weights-normalise-False-unobserved-weight-1e-06-fold-1.qza:
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
Traceback (most recent call last):
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/cache.py", line 118, in _get_cached_state
    return json.load(fh)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/__init__.py", line 268, in load
    parse_constant=parse_constant, object_pairs_hook=object_pairs_hook, **kw)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/__init__.py", line 319, in loads
    return _default_decoder.decode(s)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/decoder.py", line 339, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/decoder.py", line 355, in raw_decode
    obj, end = self.scan_once(s, idx)
json.decoder.JSONDecodeError: Expecting ',' delimiter: line 1 column 24577 (char 24576)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/bin/qiime", line 11, in <module>
    sys.exit(qiime())
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/click/core.py", line 722, in __call__
    return self.main(*args, **kwargs)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/click/core.py", line 697, in main
    rv = self.invoke(ctx)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/click/core.py", line 1061, in invoke
    cmd_name, cmd, args = self.resolve_command(ctx, args)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/click/core.py", line 1100, in resolve_command
    cmd = self.get_command(ctx, cmd_name)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/commands.py", line 99, in get_command
    plugin = self._plugin_lookup[name]
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/commands.py", line 75, in _plugin_lookup
    import q2cli.cache
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/cache.py", line 302, in <module>
    CACHE = DeploymentCache()
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/cache.py", line 61, in __init__
    self._state = self._get_cached_state(refresh=refresh)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/cache.py", line 123, in _get_cached_state
    return json.load(fh)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/__init__.py", line 268, in load
    parse_constant=parse_constant, object_pairs_hook=object_pairs_hook, **kw)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/__init__.py", line 319, in loads
    return _default_decoder.decode(s)
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/decoder.py", line 339, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/home/kaehler/miniconda2/envs/qiime2-2018.2/lib/python3.5/json/decoder.py", line 355, in raw_decode
    obj, end = self.scan_once(s, idx)
json.decoder.JSONDecodeError: Expecting ',' delimiter: line 1 column 73866 (char 73865)

[ebolyen]

We should probably write the config to a temp location and move it after it is fully written, then we won't have to mess with locking or other things like that.

[danteese]

It would be nice if you can provide some code to reproduce the error above. I tried the command qiime dev refresh-cache & qiime dev refresh-cache & qiime dev refresh-cache and I didn't detect something different from the normal execution...

[ebolyen]

Wow this is an older issue!
I'm still able to reproduce with something like this:

for i in `seq 1 20`; do qiime dev refresh-cache &  done

[1]   Done                    qiime dev refresh-cache
[2]   Done                    qiime dev refresh-cache
[3]   Done                    qiime dev refresh-cache
[4]   Done                    qiime dev refresh-cache
[5]   Done                    qiime dev refresh-cache
[6]   Done                    qiime dev refresh-cache
[7]   Done                    qiime dev refresh-cache
[8]   Exit 1                  qiime dev refresh-cache
[9]   Done                    qiime dev refresh-cache
[10]   Done                    qiime dev refresh-cache
[11]   Done                    qiime dev refresh-cache
[12]   Done                    qiime dev refresh-cache
[13]   Done                    qiime dev refresh-cache
[14]   Exit 1                  qiime dev refresh-cache
[15]   Done                    qiime dev refresh-cache
[16]   Done                    qiime dev refresh-cache
[17]   Done                    qiime dev refresh-cache
[18]   Done                    qiime dev refresh-cache
[19]-  Exit 1                  qiime dev refresh-cache
[20]+  Done                    qiime dev refresh-cache

Same JSONDecodeError as it tramples over itself.

Is this something you'd be interested in helping with @danteese?

[danteese]

For sure, old issue!
And it's quite interesting because this is your execution on my computer:

(qiime2-dev) > $ for i in `seq 1 20`; do qiime dev refresh-cache &  done
[2] 79152
[3] 79153
[4] 79154
[5] 79155
[6] 79156
[7] 79157
[8] 79158
[9] 79159
[10] 79160
[11] 79161
[12] 79162
[13] 79163
[14] 79164
[15] 79165
[16] 79166
[17] 79167
[18] 79168
[19] 79169
[20] 79170
[21] 79171

dantebazaldua@x86_64-apple-darwin13 ~                                        [17:45:17]
(qiime2-dev) > $ QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.

[17]    79167 done       qiime dev refresh-cache
[4]    79154 done       qiime dev refresh-cache
(qiime2-dev) > $
[19]    79169 done       qiime dev refresh-cache
(qiime2-dev) > $
[15]    79165 done       qiime dev refresh-cache
(qiime2-dev) > $
[12]    79162 done       qiime dev refresh-cache
(qiime2-dev) > $
[11]    79161 done       qiime dev refresh-cache
(qiime2-dev) > $
[10]    79160 done       qiime dev refresh-cache
(qiime2-dev) > $
[9]    79159 done       qiime dev refresh-cache
(qiime2-dev) > $
[7]    79157 done       qiime dev refresh-cache
(qiime2-dev) > $
[6]    79156 done       qiime dev refresh-cache
(qiime2-dev) > $
[5]    79155 done       qiime dev refresh-cache
(qiime2-dev) > $
[3]    79153 done       qiime dev refresh-cache
(qiime2-dev) > $
[21]  + 79171 done       qiime dev refresh-cache
(qiime2-dev) > $
[20]  + 79170 done       qiime dev refresh-cache
(qiime2-dev) > $
[18]  + 79168 done       qiime dev refresh-cache
(qiime2-dev) > $
[16]  + 79166 done       qiime dev refresh-cache
(qiime2-dev) > $
[14]  + 79164 done       qiime dev refresh-cache
(qiime2-dev) > $
[13]  + 79163 done       qiime dev refresh-cache
(qiime2-dev) > $
[8]  + 79158 done       qiime dev refresh-cache
(qiime2-dev) > $
[2]  + 79152 done       qiime dev refresh-cache

As you can see I'm not able to reproduce the exit 1 with the JSONDecodeError. My first thought would be the version of qiime2-dev but I'm not sure ...

[ElDeveloper]

Running the same command in a linux machine I wasn't able to replicate the problem. All jobs finished without any problem.

…

On (Sep-17-19|15:53), Dante Bazaldua wrote: For sure, old issue! And it's quite interesting because this is your execution in my computer: ``` (qiime2-dev) > $ for i in `seq 1 20`; do qiime dev refresh-cache & done [2] 79152 [3] 79153 [4] 79154 [5] 79155 [6] 79156 [7] 79157 [8] 79158 [9] 79159 [10] 79160 [11] 79161 [12] 79162 [13] 79163 [14] 79164 [15] 79165 [16] 79166 [17] 79167 [18] 79168 [19] 79169 [20] 79170 [21] 79171 ***@***.***_64-apple-darwin13 ~ [17:45:17] (qiime2-dev) > $ QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment. QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment. QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment. QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment. QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment. QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment. QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment. QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment. QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment. QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment. QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment. QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment. QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment. QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment. QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment. QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment. QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment. QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment. QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment. QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment. [17] 79167 done qiime dev refresh-cache [4] 79154 done qiime dev refresh-cache (qiime2-dev) > $ [19] 79169 done qiime dev refresh-cache (qiime2-dev) > $ [15] 79165 done qiime dev refresh-cache (qiime2-dev) > $ [12] 79162 done qiime dev refresh-cache (qiime2-dev) > $ [11] 79161 done qiime dev refresh-cache (qiime2-dev) > $ [10] 79160 done qiime dev refresh-cache (qiime2-dev) > $ [9] 79159 done qiime dev refresh-cache (qiime2-dev) > $ [7] 79157 done qiime dev refresh-cache (qiime2-dev) > $ [6] 79156 done qiime dev refresh-cache (qiime2-dev) > $ [5] 79155 done qiime dev refresh-cache (qiime2-dev) > $ [3] 79153 done qiime dev refresh-cache (qiime2-dev) > $ [21] + 79171 done qiime dev refresh-cache (qiime2-dev) > $ [20] + 79170 done qiime dev refresh-cache (qiime2-dev) > $ [18] + 79168 done qiime dev refresh-cache (qiime2-dev) > $ [16] + 79166 done qiime dev refresh-cache (qiime2-dev) > $ [14] + 79164 done qiime dev refresh-cache (qiime2-dev) > $ [13] + 79163 done qiime dev refresh-cache (qiime2-dev) > $ [8] + 79158 done qiime dev refresh-cache (qiime2-dev) > $ [2] + 79152 done qiime dev refresh-cache ``` As you can see I'm not able to reproduce the exit 1 with the JSONDecodeError. My first thought would be the version of qiime2-dev but I'm not sure ... -- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: #186 (comment)

[ebolyen]

You both must have nicer computers than me. What about 100 iterations? Really we just need it to read as the file is being written.