Software Errors and Corrective Actions

If a minor error occurs, follow any troubleshooting commands in the error message that displays. Refer to the following table for additional corrective actions to address the issue. If an error cannot be corrected, contact Illumina Technical Support.

Connected Insights - Local

The following table shows issues or errors that are specific to Connected Insights - Local and provides instructions on how to correct them.

Problem or Error	Corrective Actions
After installing Connected Insights launching a browser and logging into the DRAGEN server 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 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
Connected Insights 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 command: • /mnt/<ici_mount>/d53e4b2d-0428-4b3e-92bf-955f7153c360 • /mnt/<ici_mount>/ici_/ 4. Uninstall and reinstall Connected Insights. For , use the software version identified in the downloaded file (for example,illumina_connected_insights_local_3.0.0.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_.run/mnt/<ici_mount>/ reinstall & • tail -f nohup.out b. For CIFS/NFS, run the following commands: • nohup/mnt/<ici_mount>/icipackages/illumina_connected_insights_local_.run/mnt/<ici_mount>/ reinstall & • tail -f nohup.out If the installation is successful, a success message displays in the log file (nohup.out) and on theCommand Prompt. Proceed with the remaining installation steps in Installation (Connected Insights - Local), 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.
Illumina Connected Annotations installation failed or was interrupted.	Run the following commands to delete any content at /staging/ici/nirvana_data/ • cd /staging/ici/nirvana_data • rm -rf * Make sure the following message displays: Success: Illumina Connected Insights software installation is successful. Reinstall the annotations file. For instructions, refer to Install Illumina Connected Annotations
Default-CLI-Installation uploader shows as Offline.	Run the following command: kubectl rollout restart deployment/tss-cli -n ici Wait 15 minutes and make sure that the Default-CLI-Installation uploader shows as Online.
CIViC and JAX-CKB KB file installation screen does not refresh after one hour.	Do a manual refresh.Log in to Connected Insights. Navigate to Admin Console and check if the installation is complete.
Unable to format the USBdrive or create a partition.	Format a USB with the xfs or ext4 file system using the following commands. Replace <xfs/ext4> with either xfs or ext4 depending on which file system you use. Insert the USB drive into a PC with an OS that is compatible with xfs or ext4 (for example, Linux). Run the lsblk -I 8 -d command to confirm the USB drive name. Run the following command to format the drive. Replace <sd?> with the name of the USB drive (for example,sdc). sudo mkfs -t <xfs/ext4> /dev/<sd?> Run the following command to create a partition directory: fdisk /dev/<sd?#> Make the partition in the correct format by replacing <sd?> with the name of the partition directory (for example, sdc1). mkfs.<xfs/ext4> /dev/<sd?#>
Connected Insights is not accessible and a 502 BadGateway error displays in the browser.	Make sure that the DRAGEN server 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. sudo mkfs -t <xfs/ext4> /dev/<sd?> Run the following command to create a partition directory: Set up the host name and domain. For more information, refer to Host and Domain Name section in the Prerequisites
Case processing fails and the following error message displays: Additional cases cannot be ingested because of the following resource limitations: Filesystem space: <Current space> exceeds allowable threshold 95	Make sure that the /staging drive has at least 600 GB of free space. To free up space, refer to the corrective action for when a case upload fails in Connected Insights -Local and Connected Insights - Cloud
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 asCSV files. If you do not have these permissions, provide the 777 permission to the folder or update the folder ownership to ici_user with the 755 permission and try again. Run the chmod 777 <MetaDatafolderName> to update the 777 permission. Run the following commands to change the folder ownership to ici_user with the 755 permission: • chown -R ici_user:ici_user <MetaDatafolderName> • chmod -R 755 <MetaDatafolderName> Case metadata can also be updated when editing a case. To edit a case, select Edit Case in the CaseDetails pane.
Unable to view visualizations, IGV, or download reports.	Make sure that the mounted external storage drive is accessible from the DRAGEN server as follows. 1. Log in to Connected Insights. 2. On the top toolbar, select Configuration 3. Select the General tab, and then select Data Upload. 4. Under Define and Monitor Data Uploads, make sure that the mounted directory path is accessible. 5. If you have multiple directories under the mounted path, make sure that those directories are also accessible.

Connected Insights - Cloud

There are currently no Connected Insights - Cloud -specific issues or errors.

Connected Insights Local and Connected Insights Cloud

The following table shows issues or errors that are common to both Connected Insights - Local and Connected Insights - Cloud and provides instructions on how to correct them.

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.
Case upload fails and requires reprocessing.	Delete the following files from the /<monitoringlocation>/run/ (or from /<monitoring location> for DRAGEN server 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.
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.