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@gallardoalba
Created July 12, 2022 17:38
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VGP hifiasm workflow: error report
<_io.TextIOWrapper name='/tmp/tmp6i6m2z63/Estimated Genome size' mode='r' encoding='UTF-8'>
Failed to execute Galaxy activity, throwing ErrorRunResponse
Traceback (most recent call last):
File "/home/laptop/.local/lib/python3.8/site-packages/urllib3/response.py", line 700, in _update_chunk_length
self.chunk_left = int(line, 16)
ValueError: invalid literal for int() with base 16: b''
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/laptop/.local/lib/python3.8/site-packages/urllib3/response.py", line 441, in _error_catcher
yield
File "/home/laptop/.local/lib/python3.8/site-packages/urllib3/response.py", line 767, in read_chunked
self._update_chunk_length()
File "/home/laptop/.local/lib/python3.8/site-packages/urllib3/response.py", line 704, in _update_chunk_length
raise InvalidChunkLength(self, line)
urllib3.exceptions.InvalidChunkLength: InvalidChunkLength(got length b'', 0 bytes read)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/laptop/.local/lib/python3.8/site-packages/requests/models.py", line 816, in generate
yield from self.raw.stream(chunk_size, decode_content=True)
File "/home/laptop/.local/lib/python3.8/site-packages/urllib3/response.py", line 575, in stream
for line in self.read_chunked(amt, decode_content=decode_content):
File "/home/laptop/.local/lib/python3.8/site-packages/urllib3/response.py", line 796, in read_chunked
self._original_response.close()
File "/usr/lib/python3.8/contextlib.py", line 131, in __exit__
self.gen.throw(type, value, traceback)
File "/home/laptop/.local/lib/python3.8/site-packages/urllib3/response.py", line 458, in _error_catcher
raise ProtocolError("Connection broken: %r" % e, e)
urllib3.exceptions.ProtocolError: ("Connection broken: InvalidChunkLength(got length b'', 0 bytes read)", InvalidChunkLength(got length b'', 0 bytes read))
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/laptop/.local/lib/python3.8/site-packages/planemo/galaxy/activity.py", line 53, in execute
return _execute(ctx, config, runnable, job_path, **kwds)
File "/home/laptop/.local/lib/python3.8/site-packages/planemo/galaxy/activity.py", line 227, in _execute
run_response.collect_outputs(ctx, output_directory)
File "/home/laptop/.local/lib/python3.8/site-packages/planemo/galaxy/activity.py", line 424, in collect_outputs
cwl_output = output_to_cwl_json(
File "/home/laptop/.local/lib/python3.8/site-packages/galaxy/tool_util/cwl/util.py", line 456, in output_to_cwl_json
dataset_dict = get_dataset(output_metadata)
File "/home/laptop/.local/lib/python3.8/site-packages/planemo/galaxy/activity.py", line 403, in get_dataset
destination = self.download_output_to(ctx, dataset_details, output_directory, filename=filename)
File "/home/laptop/.local/lib/python3.8/site-packages/planemo/galaxy/activity.py", line 486, in download_output_to
self._history_content_download(
File "/home/laptop/.local/lib/python3.8/site-packages/planemo/galaxy/activity.py", line 515, in _history_content_download
for chunk in r.iter_content(chunk_size=bioblend.CHUNK_SIZE):
File "/home/laptop/.local/lib/python3.8/site-packages/requests/models.py", line 818, in generate
raise ChunkedEncodingError(e)
requests.exceptions.ChunkedEncodingError: ("Connection broken: InvalidChunkLength(got length b'', 0 bytes read)", InvalidChunkLength(got length b'', 0 bytes read))
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