Software Errors and Corrective Actions

Problem or Error

Corrective Actions

Connected Insights - Local software installation failed.

Perform the following steps: 1. Identify and end existing processes using the following command: ps aux|grep ici_installer 2. If no results return, proceed to step 3. If a process ID returns, replace <pid> in the following command and run it to end the process kill -9 <pid> 3. If the following directories are present under the mounting drive, run the rm -rf <folderName> command: • /mnt/<ici_mount>/d53e4b2d-0428-4b3e-92bf-955f7153c360 • /mnt/<ici_mount>/ici_<ServerHostname>/ 4. Uninstall and reinstall Connected Insights - Local software. For , use the software version identified in the downloaded file (for example,illumina_connected_insights_local_5.0.0.run). The installation process can take approximately one hour to 100 minutes based on network speed. a. For USB, run the following commands: • nohup /media/usbinstall/illumina_connected_insights_local_<version>.run reinstall & • tail -f nohup.out b. For CIFS/NFS, run the following commands: • nohup /mnt/<ici_mount>/icipackages/illumina_connected_insights_local_<version>.run reinstall & • tail -f nohup.out If the installation is successful, a success message displays in the log file (nohup.out) and on the Command Prompt. Proceed with the remaining installation steps in Installation (Connected Insights - Local software), starting with the installation of Illumina Connected Annotations. If a message indicating that the installation is successful does not display, run the kubectl get pods-n ici command. Identify the services that are not running or do not have the 1/1 status and contact Illumina Technical Support.

After installing Connected Insights - Local software launching a browser and logging into the DRAGEN server v4 does not work.

Make sure that the host and domain name prerequisites are met. For more information, refer to Prerequisites. If there is no DNS, then make sure that the IP address and fully qualified domain name of the DRAGEN server v4 is added to hosts file of your remote PC. This file is in the following locations: • Windows: C:\Windows\System32\Drivers\etc\hosts • Linux/Mac: /etc/hosts. Ensure you are accessing the application URL with the link provided at the end of the Software installtion success message in nohup.out file. If trying to launch the application in browser after a reboot, ensure you allow 15 mins for the Connected Insights - Local software application to come up before accessing the application on browser.

Software update from Administration Console failed when choosing Install All action.

Make sure all the below conditions are met when you choose Install All action. 1. Package files are not partially downloaded. 2. No Case is in processing status and 3. The /staging (on DRAGEN server v4) has minimum of 200 GB free space.

Default-CLI-Installation Data uploader on Configuration -> Data Upload page shows as Offline.

Make sure the external storage drive is accessible. Run the following command to retry: kubectl rollout restart deployment/tss-cli -n ici Wait 15 minutes and make sure that the Default-CLI-Installation uploader shows as Online.

CIViC, JAX-CKB or OncoKB knowledge base installation screen does not refresh to login screen or previously accessed page after one hour.

Do a manual refresh. Log in to Connected Insights - Local software. Navigate to Admin Console and check if the current installed version is updated .

Connected Insights - Local software is not accessible and a 502 BadGateway error displays in the browser.

Make sure that the DRAGEN server v4 IP address is not in the range of 10.42.. or 10.43.. and that your internal IP Table routing rules do not block these ranges. If the IP address is in one of these ranges, change the IP address. Set up the host name and domain. For more information, refer to Host and Domain Name section in the Prerequisites

Data upload fails and Case not created from a secondary analysis folder.

Make sure following conditions are not true: 1) /staging drive has less than 150 GB of free space. Minimum requirement is 150 GB or more. 2) Configured external storage drive is accessible on the DRAGEN server v4. 3) Mount permissions of the configured external storage drive is not altered from its configured values on the Admin Console -> Storage drives page. 4) UID/GID permissions of user used to configure external storage drive has read and write access to the secondary analysis input run folders or the secondary analysis input folder has "755" permission on all the sub-folders and files. 5) Genome Equivalent Samples (GEs) balance is greater than 0. 6) Sample Sheet is correctly configured. To re upload the data to create case after correcting above conditions, Click on Requeue action against the Data upload configuration on Configuration page.

Case processing fails with "Has issues".

Make sure following conditions are not true: 1) /staging drive has less than 150 GB of free space. Minimum requirement is 150 GB or more. 2) Configured external storage drive is accessible on the DRAGEN server v4. 3) Mount permissions of the configured external storage drive is not altered from its configured values on the Admin Console -> Storage drives page. To reanalyze after correcting above conditions, Click on Reanalyze action on Case Overview page to re-analyze the case if the Case has all the required molecular data.

Case processing fails with "Has issues" after Reanalysis

Follow below steps to re-upload the case from the secondary analysis run folder. Using "Delete" action, delete the Case from Case list. Ensure the secondary analysis is still available one of the configured Data Upload location. Click Requeue against the Data upload Configuration and wait for the software to upload the run folder with delete Case again. Attempt to process the case with the disease information.

Errors occurred while mounting CIFS or the CIFS mounted directory in /etc/fstab failed to persist after rebooting.

Confirm that the file paths and characters used are correct. Run the man mount.cifs command to view options and arguments, including alternates to the user and password options.

Errors occurred while mounting NFS or the NFS-mounted directory in /etc/fstab failed to persist after rebooting.

Confirm that the file paths and characters used are correct. Run the man mount.nfs command to view options and arguments.

Case metadata does not upload.

Make sure that you have read/write permissions for the folder where the metadata files are stored as CSV files. If you do not have these permissions, provide full permissions (777) to the folder or update the folder ownership to UID/GID of the external storage Connected Insights - Local software is configured and with the 755 permission. Run following command to provide full permission: chmod 777 <MetaDatafolderName>. Run the following commands to change the folder ownership to Connected Insights - Local software UID/GID user with the 755 permission: • chown -R <UID>:<GID> <MetaDatafolderName> • chmod -R 755 <MetaDatafolderName> Case metadata can also be updated by 1) Editing a case from the user interface. To edit a case, select Edit Case in the Case Details pane. or 2) uploading the csv file from the "New Case" -> "Import from csv" action from Case list page.

Unable to view visualizations, IGV, or download reports from Case overview page.

Make sure following conditions are not true: 1) Mounted external storage drive is accessible from the DRAGEN server v4. 2) Mount permissions of the mounted external storage drive is not altered from its configured values on the Admin Console -> Storage drives page. 3) Make sure all the configured secondary analysis data monitoring path and the run folders locations are accessible as follows: Log in to Connected Insights - Local software. b. On the top toolbar, select Configuration c. Select the General tab, and then select Data Upload. d. Under Define and Monitor Data Uploads, make sure that the mounted directory path is accessible. e. If you have multiple directories under the mounted path, make sure that those directories are also accessible. Application also throws Notification banner messages on Case list page if the mounted external storage is not accessible or if the permission is altered.

License Installation fails with "Encryption Error".

When this error appears, it means the license is not intended for this server. Ensure to upload the correct license file for the current DRAGEN server v4.

Connected Insights - Local software displays below notification on Case list page and new case Creation is Blocked. "Unable to reach to License Manager. Please refer troubleshooting section in the User guide for instructions to ensure License manager is active. Case ingestion is blocked until the License manager is active."

1) Make sure the Illumina License Manager service is in active status by running below command: systemctl status illumina-license-manager.service. If the service is not in "active" status, run below commands to stop/start the service. systemctl stop illumina-license-manager.service systemctl start illumina-license-manager.service 2) Make sure the DRAGEN server v4 hostname or the IP address is registered in your network's DNS (Domain Name Server)

Cases are not created from a secondary analysis run folder work after deleting a case from Case listing page.

To re-upload a case from a given run folder after deleting a case from the UI, 1) Go to Configuration page -> Data Upload page 2) Delete the Workflow configuration where the run folder was stored 3) Re-Add the workflow configuration. Allow few minutes for Data Uploader to ingest the deleted cases from the run folder. Note: If there are other run folders in the monitoring location, application will update the existing case only if they are in 'Missing Rquired Data', 'Awaiting molecular data' and 'Has issues' status.

Case processing hangs in "Processing" status indefintely after DRAGEN server v4 reboot.

Contact Illumina Support team.

My Knowledge Base bulk upload fails with validation errors when uploas was initiated along with multiple Case processing in parallel

Re-Upload the same csv file and application shall all the failed re-upload assertions.

Problem or Error

Corrective Actions

Case upload fails and requires reprocessing.

Delete the following files from the /<monitoringlocation>/run/ (or from /<monitoring location> for DRAGEN server v4 standalone results) folders added by Connected Insights: • UploadSuccess.txt • UploadFailed.txt • AnalysisUploading.txt After performing this action, the application resumes the case upload or recreates the case from the run folder after the upload criteria is met.

Problem or Error

Corrective Actions

Login or display issues.

Chrome, Firefox, and Safari are the currently supported browsers. Make sure you are using the latest version of the browser.

A PDF report does not generate when the JSON used is larger than 1 MB. This problem can occur when reporting structural variants that overlap many transcripts or genes.

Remove all assertions for some of the variants in the report. For more information, refer to Edit, Remove, and Archive Assertions

Cannot delete an entry from My Knowledge Base.

Archive the assertion. For more information, refer to Edit, Remove,and Archive Assertions

A report is approved with a variant that must be removed.

Edit the report and remove assertions for the applicable variant.For more information, refer to Reports.

Cannot filter for the variants with findings in the Overview section.

Genes with findings are sorted so that they appear at the top of the page.

Unable to view the list of genes associated with a disease.

View the genes in the disease configuration. For more information, refer to Disease Configuration.

Cannot change the test definition for a case after it is assigned.

Create a case with the correct test definition.