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ENA SubmissionTroubleshooting ENA

Troubleshooting ENA

This page covers common issues when submitting to the European Nucleotide Archive and how to resolve them.

Common Errors

Invalid Taxonomy ID

Error: “Taxon is not submittable” or “Invalid TAXON_ID”

Cause: The taxId does not exist in NCBI taxonomy or is not a valid submittable taxon.

Fix:

  1. Verify the taxId at NCBI Taxonomy 
  2. Use the organism autocomplete in SeqDesk to search for the correct entry
  3. For metagenomic samples, use the correct metagenome identifier (e.g., 408170 for human gut metagenome)

Missing Required Fields

Error: “Missing mandatory attribute” or “Required field not provided”

Cause: A MIxS checklist field that ENA requires is empty.

Fix:

  1. Check which checklist type is selected for the study
  2. Review the sample metadata table for empty required fields
  3. Fill in all mandatory fields for the selected checklist

Duplicate Alias

Error: “Alias already exists in the submission account”

Cause: The study or sample alias has already been used in a previous submission to ENA (including test submissions that haven’t expired).

Fix:

  1. Change the alias to a unique value
  2. Wait 24 hours if this was a test submission (test data expires)
  3. Check your ENA Webin portal for existing submissions with the same alias

Authentication Failed

Error: “401 Unauthorized” or “Invalid credentials”

Cause: ENA Webin credentials are incorrect or expired.

Fix:

  1. Go to Admin → ENA Configuration
  2. Verify the username (format: Webin-XXXXX)
  3. Re-enter the password
  4. Use the Test Connection button to verify credentials work

Connection Timeout

Error: “Connection refused” or “Request timeout”

Cause: Cannot reach ENA servers.

Fix:

  1. Check your server’s internet connectivity
  2. Verify firewall rules allow outbound HTTPS to ebi.ac.uk
  3. Check if ENA is experiencing downtime at ENA Status 
  4. Retry the submission after a few minutes

Description Too Short

Error: “Study description must be at least 50 characters”

Cause: ENA requires meaningful descriptions, not placeholder text.

Fix: Write a detailed description of the research project, methodology, and goals. This description becomes part of the public record.

Re-submission

If a submission fails:

  1. Fix the reported errors
  2. Retry the submission — SeqDesk will generate fresh XML
  3. For partial failures (some samples accepted, others rejected), retry only the failed samples

Updating Submitted Records

After successful submission:

  • Study accessions are permanent and cannot be changed
  • Sample metadata can be updated through ENA’s Webin portal
  • Additional samples can be submitted to an existing study
  • Contact ENA support for corrections to accession records

Debugging

Viewing Generated XML

The Submission table stores the generated XML for each submission attempt. Check the xmlContent and requestPayload fields to see exactly what was sent to ENA.

ENA Receipt

The receiptXml field contains ENA’s full response, including:

  • Success/failure status
  • Assigned accession numbers
  • Detailed error messages

Test Mode Workflow

A recommended workflow for debugging:

  1. Enable test mode in ENA settings
  2. Submit to the test server
  3. Check the receipt for any errors
  4. Fix issues and resubmit
  5. Once all validations pass, disable test mode
  6. Submit to production