ENA validate and test work, but submission ends prematurely #124

iwilkie · 2024-06-11T06:42:45Z

Hi,

I've noticed this a few times when submitting to ENA via the webin-cli, but haven't been able to figure out what the issue is. The validate and test submission steps work, but the actual submission ends prematurely and doesn't report any errors/messages.

This is what I ran (username and password redacted):

$ java -jar webin-cli-7.2.1.jar -context genome -userName 🟥  -password 🟥 -manifest chordibacter_forsetii/manifest.txt -inputDir chordibacter_forsetii/ -outputDir chordibacter_forsetii/ -validate
INFO : Your application version is 7.2.1
INFO : Please upgrade to Webin-CLI version 7.0.1 or later if you see the following error: Failed to initialise validator. Could not retrieve BioSample.
INFO : Submission(s) validated successfully.
INFO : Creating report file: /Users/iwilkie/Desktop/PhD/ENA_submit/chordibacter_forsetii/./webin-cli.report

$ java -jar webin-cli-7.2.1.jar -context genome -userName 🟥  -password 🟥 -manifest chordibacter_forsetii/manifest.txt -inputDir chordibacter_forsetii/ -outputDir chordibacter_forsetii/ -submit -test
INFO : Your application version is 7.2.1
INFO : Please upgrade to Webin-CLI version 7.0.1 or later if you see the following error: Failed to initialise validator. Could not retrieve BioSample.
INFO : Connecting to FTP server : webin2.ebi.ac.uk
INFO : Creating report file: /Users/iwilkie/Desktop/PhD/ENA_submit/chordibacter_forsetii/./webin-cli.report
INFO : Uploading file: /Users/iwilkie/Desktop/PhD/ENA_submit/chordibacter_forsetii/20110523_Bin_36_1.fa.gz
INFO : Files have been uploaded to webin2.ebi.ac.uk. 
INFO : The submission has been completed successfully. The following analysis accession was assigned to the submission: ERZ24776052
INFO : This was a TEST submission(s).

$ java -jar webin-cli-7.2.1.jar -context genome -userName 🟥  -password 🟥  -manifest chordibacter_forsetii/manifest.txt -inputDir chordibacter_forsetii/ -outputDir chordibacter_forsetii/ -submit
INFO : Your application version is 7.2.1
INFO : Please upgrade to Webin-CLI version 7.0.1 or later if you see the following error: Failed to initialise validator. Could not retrieve BioSample.

manifest.txt.report is empty (in the second step it just said "This was a TEST submission(s).", but it was overwritten)

webin-cli.report:

2024-06-10T18:54:08 INFO : Connecting to FTP server : webin2.ebi.ac.uk
2024-06-10T18:54:09 INFO : Uploading file: /Users/iwilkie/Desktop/PhD/ENA_submit/chordibacter_forsetii/20110523_Bin_36_1.fa.gz
2024-06-10T18:54:16 INFO : Files have been uploaded to webin2.ebi.ac.uk. 
2024-06-10T18:54:16 INFO : The submission has been completed successfully. The following analysis accession was assigned to the submission: ERZ24776052
2024-06-10T18:54:16 INFO : This was a TEST submission(s).

It seems like the submit step doesn't actually work, has anybody encountered this before? As I mentioned, I've encountered this before, but last time I just waited some hours, then re-ran the submit step, and then it worked. Is it something I'm missing/doing incorrectly, or a server-side issue?

Thanks! :)

The text was updated successfully, but these errors were encountered:

iwilkie · 2024-06-11T16:09:54Z

In case anybody should run into this issue, I've managed to stumble into the solution:

Delete all files generated by the validation and test submission
Rerun the submission

I guess the tool runs into an issue trying to rewrite the files that it previously generated...

Hope that helps you!

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ENA validate and test work, but submission ends prematurely #124

ENA validate and test work, but submission ends prematurely #124

ENA validate and test work, but submission ends prematurely #124

ENA validate and test work, but submission ends prematurely #124

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