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Troubleshooting guide: Uploading metadata

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Overview

If something is wrong with uploaded metadata files, the CZ GEN EPI platform will generate error (highlighted in red) and warning (highlighted in yellow) messages that need to be resolved to successfully upload samples. The following troubleshooting guide details common error and warning messages while uploading metadata files to the platform and how to resolve them.






Error: Missing data fields (headers)

MissingDataFields.png

Example error message stating that metadata upload file is missing some of the required column headers.

Resolution: Check your metadata upload file to ensure all of the following column headers are present and spelled exactly as listed below (note capitalization and spacing). Find the absent or misspelled headers and make corrections as needed (the order of headers in the file does not matter) and re-import your metadata file:

  • Sample Name (from FASTA)
  • Private ID
  • GISAID ID (Public ID) - Optional or Genbank Accession (Public ID) - Optional
  • Collection Date
  • Collection Location
  • Sequencing Date - Optional
  • Sample is Private

Error: Duplicate IDs

DuplicateIDs.png

Example error message indicating that there are duplicate IDs for some of the Private IDs and/or Public IDs in your metadata file.

Resolution: Edit your metadata file to correct the IDs for identified samples with duplicate IDs. Make sure each sample has a unique Public ID and Private ID, then re-submit the file. Alternatively, if working with less than 100 sequences, you can edit the metadata for these samples manually through the web interface (the duplicated IDs will be highlighted).Example_DuplicateIDs.png

Example metadata table highlighting duplicate Public IDs.

Error: Data formatting

DataFormatting.png

Example error message indicating that metadata upload file has invalid formatting in some data rows.

Resolution: Edit your metadata file to correct the metadata format. Make sure your metadata entries follow the required format:

  • Collection Date: YYYY-MM-DD
  • Collection Location: Continent or Region/Country/State or Province/Division (e.g., North America/USA/California/San Francisco)
  • Sequencing Date (Optional): YYYY-MM-DD

You can edit the metadata format manually through the web interface’s metadata table (if working with less than 100 sequences) or you can edit the missing data in your metadata file and re-upload it. Re-uploading a metadata file will overwrite the original file.

Warning: Missing samples

Warning_MissingSample.png

Example warning message stating that metadata upload file does not have data rows that correspond to samples uploaded in the preceding sample upload step.

Resolution: Identify which samples are missing on your metadata file. You can edit the metadata for these samples manually through the web interface or you can edit the missing data in your metadata file and re-upload it. Re-uploading a metadata file will overwrite the original file.

Warning: Extraneous sample entries

Warning_ExtraneousSamples.png

Example warning message indicating that metadata upload file contains data rows for Sample ID(s) that were not uploaded in the preceding sample upload step.

Resolution: If you did not intend to upload those samples, no action is necessary. If you do intend to upload those samples, you will need to go "Back" to the "Sample Upload" step to add a fasta file containing sequence data for the missing samples.WarningExample_ExtraneousSample.png

Example metadata table highlighting Sample ID not found in imported sequence file.

Warning: Unknown data fields

Warning_UnknownData.png

Example warning message indicating that metadata upload file contains data fields that the platform does not recognize. This can be caused by mis-spelled or extraneous metadata column headers.

Resolution: If you included extra metadata columns in your upload file, no action is necessary as the platform will simply ignore the extra columns. If there are no extra metadata columns, check your metadata upload file to ensure all of the following column headers are present and spelled exactly as listed below (note capitalization and spacing). Find the absent or misspelled headers and make corrections as needed (the order of headers in the file does not matter):

  • Sample Name (from FASTA)
  • Private ID
  • GISAID ID (Public ID) - Optional or Genbank Accession (Public ID) - Optional
  • Collection Date
  • Collection Location
  • Sequencing Date - Optional
  • Sample is Private

Warning: Missing required data for some samples

Warning_MissingRequiredData.png

Example warning message indicating that metadata upload file has a data row that is missing required information (e.g., Collection Date).

Resolution: You can edit the metadata to include the missing information manually through the web interface or you can add the missing data in your metadata file and re-upload it. Re-uploading a metadata file will overwrite the original file.

Warning: Autocorrected location

Warning_AutocorrectedLocation.png

Example warning message indicating that metadata upload file had some data rows with incorrectly formatted data and the platform corrected it automatically.

Resolution: Check the autocorrected values (same as "Updated Value") to make sure they match your sample collection location. If updated values are correct, proceed to the Review page and continue with the upload.WarningExample_AutocorrectedLocation.png

Example of metadata table highlighting updated Collection Location value.

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