bio-ontology-research-group / mrsa-sequences

Arvados sequence uploader and analyzer for MRSA project
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Giving an error while uploading sequence data #6

Open aliraza995 opened 4 years ago

aliraza995 commented 4 years ago

Hi, While trying to use the current sequence uploader when i try to upload sequence data using following command it gives me this error:

command: python uploader/main.py -sr1 data/reads1.fastq.gz -sr2 data/reads2.fastq.gz -m data/metadata.yaml Error: File "uploader/main.py", line 117, in <module> main() File "/Users/syedar/Documents/git/mrsa-sequences/venv/lib/python3.7/site-packages/click/core.py", line 829, in call return self.main(args, kwargs) File "/Users/syedar/Documents/git/mrsa-sequences/venv/lib/python3.7/site-packages/click/core.py", line 782, in main rv = self.invoke(ctx) File "/Users/syedar/Documents/git/mrsa-sequences/venv/lib/python3.7/site-packages/click/core.py", line 1066, in invoke return ctx.invoke(self.callback, ctx.params) File "/Users/syedar/Documents/git/mrsa-sequences/venv/lib/python3.7/site-packages/click/core.py", line 610, in invoke return callback(args, kwargs) File "uploader/main.py", line 111, in main properties=properties, ensure_unique_name=True) File "/Users/syedar/Documents/git/mrsa-sequences/venv/lib/python3.7/site-packages/arvados/arvfile.py", line 469, in must_be_writable_wrapper return orig_func(self, *args, kwargs) File "/Users/syedar/Documents/git/mrsa-sequences/venv/lib/python3.7/site-packages/arvados/arvfile.py", line 270, in synchronized_wrapper return orig_func(self, args, kwargs) File "/Users/syedar/Documents/git/mrsa-sequences/venv/lib/python3.7/site-packages/arvados/retry.py", line 177, in num_retries_setter return orig_func(self, *args, kwargs) File "/Users/syedar/Documents/git/mrsa-sequences/venv/lib/python3.7/site-packages/arvados/collection.py", line 1701, in save_new self._remember_api_response(self._my_api().collections().create(ensure_unique_name=ensure_unique_name, body=body).execute(num_retries=num_retries)) File "/Users/syedar/Documents/git/mrsa-sequences/venv/lib/python3.7/site-packages/googleapiclient/_helpers.py", line 130, in positional_wrapper return wrapped(args, **kwargs) File "/Users/syedar/Documents/git/mrsa-sequences/venv/lib/python3.7/site-packages/googleapiclient/http.py", line 840, in execute raise HttpError(resp, content, uri=self.uri) arvados.errors.ApiError: <HttpError 500 when requesting https://cborg.cbrc.kaust.edu.sa/arvados/v1/collections?ensure_unique_name=true&alt=json returned "invalid character '\'' looking for beginning of object key string">