Created
July 12, 2022 17:38
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VGP hifiasm workflow: error report
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<_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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