Login Troubleshooting and Support
If you encounter login issues, try the following:
Verify your password is entered correctly (case-sensitive).
Ensure your internet connection is stable.
Reset your password by clicking Forgot your password? on the login page if needed.
For persistent issues, contact the Franklin Support team via:
• The chat icon in the bottom-right corner of the screen
File Upload Troubleshooting
If your file appears to be stuck during the upload or annotation process for an extended period, this usually indicates an issue with the file upload system. Please follow the steps below to troubleshoot and resolve the issue:
Quick Steps to Resolve the Issue:
Check Your Internet Connection:
Ensure your connection is stable and continuous throughout the upload process.Switch Browsers:
Try using an alternative browser (e.g., Chrome, Firefox, Safari) to rule out browser-related issues.Refresh the Page:
Sometimes the upload is progressing normally in the background, but the browser doesn’t update the status in real time. Press F5 (or Ctrl/Command + R) or click the refresh icon next to the URL bar.Clear Your Browser Cache:
Cached data may interfere with uploads. Clear your cache by pressing Cmd + Shift + R on a Mac, or Ctrl + F5 on a PC.Verify File Format:
Make sure the file is in a supported format such as VCF, FASTQ, BAM, etc.Cancel and Re-Upload the File:
If the file is still stuck, cancel the current upload and try again from the beginning.
To cancel a case:From Franklin’s main page, click on “My Cases” at the top of the screen.
Locate the relevant case. On the right-hand side of the file upload status bar, click the three dots and select “Edit Case Details.”
In the pop-up window, click “Delete Case” at the bottom-left corner to remove the stuck upload.
Inspect File Integrity:
Make sure the file is not corrupted or partially exported. Try opening the file locally before re-uploading.Check Metadata Requirements:
Ensure all required fields (e.g., sample name, genome build) are correctly filled in during the upload process.
Tertiary Analysis Troubleshooting
Tertiary analysis takes place once the relevant VCF files have been linked to the sample and once it is done, the case is available to the user.
If a sample is marked as ‘Error’, perform the following verifications to identify and resolve the issue:
Ensure that the reference genome version indicated in the VCF header (default: hg19) matches the reference version assigned to the sample.
Confirm that the VCF file contains variants.
Note: By default, VCF files with no variants trigger an annotation error unless otherwise configured during the implementation process.If a ‘name in VCF’ parameter was specified in the sample sheet, verify that it matches the sample column name within the VCF file.
Ensure that at least one sample column exists in the VCF file.
Verify that the VCF file adheres to the VCF v4.2 specification, including but not limited to:
All fields in the sample column are populated in every variant line.
Required fields for the specific variant caller (GT field for GATK) are present and complete.
No extraneous or malformed characters have been introduced (e.g. parentheses added by spreadsheet editors like Excel when saving the file).
The VCF file does not exceed 10 million variants. Files of this size are not supported unless explicitly enabled by Franklin Professional Services.
In rare cases, a sample may be shown as ‘Processing – Annotation’ while effectively being in an error state. Treat these cases with the same troubleshooting steps and urgency as a sample marked ‘Error’.
If all validations have been exhausted and the issue persists, contact Franklin Support for further assistance.
QC Troubleshooting
Coverage-based and analysis-based parameters are displayed in the QC part of the workbench screen and are used to assess the quality of the sample and sequencing.
If some of the parameters are marked as N/A, and are expected to be shown in the analysis QC, first verify that the sample has coverage available by entering the Coverage Report screen. If it does and the QC data is not available, contact Franklin Support. If coverage is not available, verify that the sample contains a BAM file by checking the Case Details widget. If a BAM file exists, contact Franklin Support, otherwise inspect if it exists in the source location from which the samples files were uploaded. If the BAM exists in this location and was not uploaded, this means the assay is not configured to require the BAM file to be present in the sample upload, and you will need to contact Franklin Support to configure this.
If some parameters are marked as Failed in the QC screen, this may indicate that there has been an issue with upstream processes - sequencing/secondary analysis etc. If upon inspection, you have found no internal issues, contact Franklin Support in this regard.
Analysis Workbench and Variants Screen Troubleshooting
If the analysis workbench / variants screen does not load and an error message appears on the screen, please wait several seconds and then try loading the screen again by refreshing or hard-refreshing. If that does not solve the issue, contact Franklin Support.
Browser Freezing Troubleshooting
If the browser fails to load or the screen becomes unresponsive, wait a few seconds and then attempt to reload the page using a standard or hard refresh. If the issue persists, please contact Franklin Support.
Still Stuck? Contact Genoox Support
If the issues persists after trying the steps above, please contact Franklin’s clinical experts via chat or email. Include the following details in your message:
Full name.
Organization name.
Email used to access Franklin.
File name.
Time of upload attempt.
Any relevant information that might help.
Attach a screenshot of the error message (either from the browser screen or browser console).
Attach the name of the stuck file.