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EBI-Metagenomics / genome_uploader

Python script to upload bins and MAGs to ENA (European Nucleotide Archive)
Apache License 2.0
20 stars 3 forks source link

Connection error #9

Closed SilasK closed 1 year ago

SilasK commented 1 year ago

What can I do against connection errors.

I have only 80 genomes


urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='www.ebi.ac.uk', port=443): Max retries exceeded with url: /ena/portal/api/search (Caused by ProxyError('Cannot connect to proxy.', RemoteDisconnected('Remote end closed connection without response')))
Ge94 commented 1 year ago

Hi Silas, We have experienced intermittent downtime in querying ENA API this afternoon, but services seem to have gone back to normal now. I would suggest to retry, but please let us know whether you encounter any other issue.

SilasK commented 1 year ago

I managed to create the manifest files.

But then I got poblem with the webin java

INFO : Your application version is 5.2.0
INFO : Your application version will not be supported after 01 May 2023. The minimum supported version will be 6.0.0. Please download the latest version 6.2.0 from https://github.com/enasequence/webin-cli/releases
INFO : 
A dedicated submission API for COVID-19 genomes is available here: <a href="https://www.ebi.ac.uk/ena/submit/webin-cli">https://www.ebi.ac.uk/ena/submit/webin-cli </a> <br>
INFO : Submission has not been validated previously.
INFO : Creating report file: /scratch/rdkiesersi1/CMMG/Batches/batch0/./webin-cli.report
INFO : The submission has been validated successfully.
ERROR: Failed to upload files to webin.ebi.ac.uk using FTP. Connection timed out Failed to upload files to webin.ebi.ac.uk because of a system error.
SilasK commented 1 year ago

I tried with the latest version of the webin but no difference.


INFO : Your application version is 6.2.0
INFO : 
A dedicated submission API for COVID-19 genomes is available here: <a href="https://www.ebi.ac.uk/ena/submit/webin-cli">https://www.ebi.ac.uk/ena/submit/webin-cli </a> <br>
INFO : Submission has not been validated previously.
INFO : Creating report file: /scratch/rdkiesersi1/CMMG/Batches/batch0/./webin-cli.report
INFO : The submission has been validated successfully.
INFO : Connecting to FTP server : webin2.ebi.ac.uk
WARN : Retrying retrieving directory list from FTP server.
WARN : Retrying retrieving directory list from FTP server.
WARN : Retrying retrieving directory list from FTP server.
WARN : Retrying retrieving directory list from FTP server.
WARN : Retrying retrieving directory list from FTP server.
WARN : Retrying retrieving directory list from FTP server.
ERROR: Failed to upload files to webin.ebi.ac.uk using FTP. Connect timed out Failed to upload files to webin.ebi.ac.uk because of a system error.
ERROR: Failed to upload files to webin.ebi.ac.uk using FTP. Connect timed out Failed to upload files to webin.ebi.ac.uk because of a system error.
Ge94 commented 1 year ago

Hi Silas, I am afraid ENA's server issue is still ongoing/intermittent and connecting to webin is quite hard at the moment. Since ENA has a different infrastructure from ours, I would suggest to open a ticket with ENA support, and explain your issues. Hopefully this gets resolved soon.