ConnectionError

[nukaemon]

Dear developers,

When I tried the following, it seemed to return some results into purities_and_logs without any error message.

$ python3
>>> from puree import *
>>> test_data_path = 'test.tsv'
>>> gene_id_nomenclature = 'HGNC'
>>> p = PUREE()
>>> purities_and_logs = p.get_output(test_data_path, gene_id_nomenclature)
Sample names were not encrypted... Encryption is completed.

However, I could find only tmp_dir directory and the modified input file with the first column encrypted but no column informing estimated purity. When I checked purities_and_logs, it contained the following error message at the second index.

>>> purities_and_logs
(False, ConnectionError(ProtocolError('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer'))))

Do you think this is due to some network problems in my environment? If so, is there any workaround , for example, to run whole process in local?

[erevkov]

Hi, and thank you for trying our method! Sorry for the late reply. We have recently attempted to make the connection to the web service more stable, could you please try the method again and see if it works for you? Additionally, something like that might be happening if your input file size is too big to consistently go through. To make sure the connection can handle the transfer we have limited the input file size limit to around 400 MB, but just to be safe perhaps you could also try subsetting your input to below 200 MB per submission to start with? You might need to split your input matrix into several parts by samples (rows). Let us know if it helps.

Finally, if you would prefer to run the method locally, you could obtain the internal source code of the method for academic use - please contact the corresponding author of the original paper for that.