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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

submg pipeline errors

When submitting reads/assemblies/bins through the submg pipeline, the run reports validation failures before it starts. Common messages:

MessageCause / Fix
has no paired-end read filesThe sample has no read with both R1 and R2. submg only accepts paired-end FASTQ.
has reads without MD5 checksumsCalculate MD5 checksums on both R1 and R2 before running submg.
has no assembly file … run the MAG pipeline firstNo assembly FASTA on disk for the sample. Run the MAG pipeline (or fix the assembly path).
Study is missing ENA accession (PRJ*)Register the study via the XML path first so it has a PRJ... accession.
ENA Test registration … is older than 24 hoursThe test study registration has expired. Re-register the study on ENA Test, then re-run submg.
submg command not found in PATHThe submg CLI isn’t available in the run’s conda environment. Install it or fix the configured environment.

Re-submission

If a submission fails:

  1. Fix the reported errors
  2. Retry the submission from the Submissions Dashboard — SeqDesk generates fresh XML each time
  3. For partial failures (some samples accepted, others rejected), the re-run reuses the existing study accession and submits only the samples that still lack one — there is no separate per-sample retry

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 record stores the generated XML in its xmlContent field. Expand the row in the Submissions Dashboard to read exactly what was sent to ENA.

ENA Receipt

There is no separate receiptXml column. ENA’s receipt and any error text are nested inside the submission’s response JSON (under receipt), which the dashboard renders in the registration-steps timeline:

  • 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