Troubleshooting guide: Updating metadata

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 update metadata. The following troubleshooting guide details common error and warning messages while uploading files to edit sample metadata on the platform and how to resolve them. 

Common error messages

Error: Missing fields (headers)

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. 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:

• Current Private ID
• New Private ID - Optional
• GISAID ID (Public ID) or Genbank Accession (Public ID) - Optional
• Collection Date
• Collection Location
• Sequencing Date - Optional
• Sample is Private

Error: Duplicate IDs

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 upload file to correct the IDs for those samples so each sample has a unique Public ID and Private ID, then re-submit the file. Alternatively, you can manually correct those metadata in the interface table below the warning if you are editing 100 or fewer samples.

Example of metadata table highlighting duplicate Public IDs.

Error: Data formatting

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

Resolution: Edit your metadata upload file to correct the metadata formatting for those samples, then re-submit the file. Alternatively, you can manually correct those metadata in the interface table below the warning (the cells requiring correction will be highlighted).

Example of metadata table highlighting duplicate cells requiring correction.

Common warning messages

Warning: Absent metadata entries

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

Resolution: Edit your metadata upload file to include the missing metadata for those samples, then re-submit the file. Alternatively, you can manually enter those metadata in the interface table below the warning if you are editing 100 or fewer samples.

Warning: Extraneous sample entries

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 through the preceding sample selection step to first select those samples prior to updating metadata for them.

Warning: Unknown data fields

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 did not intend to include extra metadata columns, no action is necessary. 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. Find the absent or misspelled headers and make corrections as needed (the order of headers in the file does not matter):

• Current Private ID
• New Private ID - Optional
• GISAID ID (Public ID) or Genbank Accession (Public ID) - Optional
• Collection Date
• Collection Location
• Sequencing Date - Optional
• Sample is Private