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May 14, 2021 06:24
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ssl error run 2
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| Output: | |
| ``` | |
| run at 2021-05-13 17:32:33.076136 | |
| run at 2021-05-13 17:32:35.094340 | |
| run at 2021-05-13 17:32:36.977748 | |
| run at 2021-05-13 17:32:38.854865 | |
| run at 2021-05-13 17:32:40.755098 | |
| wait at 2021-05-13 17:32:41.120666 | |
| wait at 2021-05-13 17:32:42.447928 | |
| run at 2021-05-13 17:32:42.576260 | |
| wait at 2021-05-13 17:32:43.476152 | |
| wait at 2021-05-13 17:32:44.552502 | |
| run at 2021-05-13 17:32:44.557964 | |
| ``` | |
| Error: | |
| ``` | |
| Exception in thread Thread-1: | |
| Traceback (most recent call last): | |
| File "/home/mwatson9/miniconda3/envs/snakemake_pure/lib/python3.9/threading.py", line 954, in _bootstrap_inner | |
| self.run() | |
| File "/home/mwatson9/miniconda3/envs/snakemake_pure/lib/python3.9/threading.py", line 892, in run | |
| self._target(*self._args, **self._kwargs) | |
| File "/home/mwatson9/miniconda3/envs/snakemake_pure/lib/python3.9/site-packages/snakemake/executors/google_lifesciences.py", line 926, in _wait_for_jobs | |
| status = self._retry_request(request) | |
| File "/home/mwatson9/miniconda3/envs/snakemake_pure/lib/python3.9/site-packages/snakemake/executors/google_lifesciences.py", line 889, in _retry_request | |
| raise ex | |
| File "/home/mwatson9/miniconda3/envs/snakemake_pure/lib/python3.9/site-packages/snakemake/executors/google_lifesciences.py", line 878, in _retry_request | |
| Traceback (most recent call last): | |
| File "/home/mwatson9/miniconda3/envs/snakemake_pure/lib/python3.9/http/client.py", line 552, in _get_chunk_left | |
| chunk_left = self._read_next_chunk_size() | |
| return request.execute() | |
| File "/home/mwatson9/miniconda3/envs/snakemake_pure/lib/python3.9/http/client.py", line 519, in _read_next_chunk_size | |
| return int(line, 16) | |
| File "/home/mwatson9/miniconda3/envs/snakemake_pure/lib/python3.9/site-packages/googleapiclient/_helpers.py", line 134, in positional_wrapper | |
| ValueError: invalid literal for int() with base 16: b'\n' | |
| During handling of the above exception, another exception occurred: | |
| Traceback (most recent call last): | |
| File "/home/mwatson9/miniconda3/envs/snakemake_pure/lib/python3.9/http/client.py", line 569, in _readall_chunked | |
| chunk_left = self._get_chunk_left() | |
| return wrapped(*args, **kwargs) | |
| File "/home/mwatson9/miniconda3/envs/snakemake_pure/lib/python3.9/http/client.py", line 554, in _get_chunk_left | |
| raise IncompleteRead(b'') | |
| File "/home/mwatson9/miniconda3/envs/snakemake_pure/lib/python3.9/site-packages/googleapiclient/http.py", line 920, in execute | |
| http.client.IncompleteRead: IncompleteRead(0 bytes read) | |
| During handling of the above exception, another exception occurred: | |
| Traceback (most recent call last): | |
| resp, content = _retry_request( | |
| File "/home/mwatson9/miniconda3/envs/snakemake_pure/lib/python3.9/site-packages/snakemake/__init__.py", line 695, in snakemake | |
| success = workflow.execute( | |
| File "/home/mwatson9/miniconda3/envs/snakemake_pure/lib/python3.9/site-packages/snakemake/workflow.py", line 1017, in execute | |
| success = scheduler.schedule() | |
| File "/home/mwatson9/miniconda3/envs/snakemake_pure/lib/python3.9/site-packages/googleapiclient/http.py", line 222, in _retry_request | |
| File "/home/mwatson9/miniconda3/envs/snakemake_pure/lib/python3.9/site-packages/snakemake/scheduler.py", line 489, in schedule | |
| self.run(runjobs) | |
| File "/home/mwatson9/miniconda3/envs/snakemake_pure/lib/python3.9/site-packages/snakemake/scheduler.py", line 500, in run | |
| executor.run_jobs( | |
| File "/home/mwatson9/miniconda3/envs/snakemake_pure/lib/python3.9/site-packages/snakemake/executors/__init__.py", line 136, in run_jobs | |
| self.run( | |
| File "/home/mwatson9/miniconda3/envs/snakemake_pure/lib/python3.9/site-packages/snakemake/executors/google_lifesciences.py", line 806, in run | |
| result = self._retry_request(operation) | |
| File "/home/mwatson9/miniconda3/envs/snakemake_pure/lib/python3.9/site-packages/snakemake/executors/google_lifesciences.py", line 889, in _retry_request | |
| raise ex | |
| File "/home/mwatson9/miniconda3/envs/snakemake_pure/lib/python3.9/site-packages/snakemake/executors/google_lifesciences.py", line 878, in _retry_request | |
| return request.execute() | |
| File "/home/mwatson9/miniconda3/envs/snakemake_pure/lib/python3.9/site-packages/googleapiclient/_helpers.py", line 134, in positional_wrapper | |
| return wrapped(*args, **kwargs) | |
| File "/home/mwatson9/miniconda3/envs/snakemake_pure/lib/python3.9/site-packages/googleapiclient/http.py", line 920, in execute | |
| resp, content = _retry_request( | |
| File "/home/mwatson9/miniconda3/envs/snakemake_pure/lib/python3.9/site-packages/googleapiclient/http.py", line 191, in _retry_request | |
| resp, content = http.request(uri, method, *args, **kwargs) | |
| File "/home/mwatson9/miniconda3/envs/snakemake_pure/lib/python3.9/site-packages/oauth2client/transport.py", line 173, in new_request | |
| resp, content = request(orig_request_method, uri, method, body, | |
| raise exception | |
| File "/home/mwatson9/miniconda3/envs/snakemake_pure/lib/python3.9/site-packages/oauth2client/transport.py", line 280, in request | |
| return http_callable(uri, method=method, body=body, headers=headers, | |
| File "/home/mwatson9/miniconda3/envs/snakemake_pure/lib/python3.9/site-packages/googleapiclient/http.py", line 191, in _retry_request | |
| File "/home/mwatson9/miniconda3/envs/snakemake_pure/lib/python3.9/site-packages/httplib2/__init__.py", line 1708, in request | |
| (response, content) = self._request( | |
| File "/home/mwatson9/miniconda3/envs/snakemake_pure/lib/python3.9/site-packages/httplib2/__init__.py", line 1424, in _request | |
| (response, content) = self._conn_request(conn, request_uri, method, body, headers) | |
| File "/home/mwatson9/miniconda3/envs/snakemake_pure/lib/python3.9/site-packages/httplib2/__init__.py", line 1405, in _conn_request | |
| content = response.read() | |
| File "/home/mwatson9/miniconda3/envs/snakemake_pure/lib/python3.9/http/client.py", line 462, in read | |
| return self._readall_chunked() | |
| File "/home/mwatson9/miniconda3/envs/snakemake_pure/lib/python3.9/http/client.py", line 576, in _readall_chunked | |
| raise IncompleteRead(b''.join(value)) | |
| http.client.IncompleteRead: IncompleteRead(1266 bytes read) | |
| resp, content = http.request(uri, method, *args, **kwargs) | |
| File "/home/mwatson9/miniconda3/envs/snakemake_pure/lib/python3.9/site-packages/oauth2client/transport.py", line 173, in new_request | |
| resp, content = request(orig_request_method, uri, method, body, | |
| File "/home/mwatson9/miniconda3/envs/snakemake_pure/lib/python3.9/site-packages/oauth2client/transport.py", line 280, in request | |
| return http_callable(uri, method=method, body=body, headers=headers, | |
| File "/home/mwatson9/miniconda3/envs/snakemake_pure/lib/python3.9/site-packages/httplib2/__init__.py", line 1708, in request | |
| ``` |
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