NCBI SRA Submission - BioProject Creation
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If the “validate metadata file only” box is checked, nothing will be submitted to the SRA. The metadata you entered will be validated, and if it passes iPlant quality CyVerse quality checks, the submission.xml file will be created in the Analysis output folder. If the metadata fails validation, no submission.xml file will be created and the error will be logged in the Analysis output folder in the logs/condor-stderr-0 folder.
Output File(s)
Just like other iPlant jobsCyVerse jobs, output will be generated in an analysis folder Output contains 2 folders:
- logs folder with information on job execution that includes a ‘.manifest.txt’. file with a log of the files transferred to the SRA servers.
- folder named with your iPlant username CyVerse username and the top-level BioProject folder ID that contains the submission.xml (metadata file formatted for ingestion by the SRA) and a submit.ready file used to signal SRA systems that submission is complete and to process the submission package.
What happens after submission?
What happens at SRA? iPlant CyVerse systems connect to SRA systems and create the submission folder on the SRA side. Files are transferred and a submit.ready file is sent to the SRA to signal that the submission package is complete and they can begin processing. The SRA system validates the submission package and generates a report.xml file containing any errors detected. The SRA system sends notification email(s) to the contact email provided in the BioProject metadata template, and to the iPlant team CyVerse team to notify of either a successful or failed submission. If there are errors, you can retrieve the submission report.xml file from SRA servers with the 'NCBI SRA Submission Report Retrieval' App in the DE, make corrections, and resubmit (see below).
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