Troubleshooting
If the DRAGEN system does not seem to be responding, do the following:
To determine if the DRAGEN system is hanging, follow the instructions in How to Determine if the System is Hanging.
Collect diagnostic information after a hang, or a crash, as described in Sending Diagnostic Information to Illumina Support.
After all information has been collected, reset your system. if needed, as described in Resetting Your System after a Crash or Hang.
How to Determine if the System is Hanging
The DRAGEN system has a watchdog to monitor the system for hangs. If a run seems to be taking longer than it should, the watchdog may not be detecting the hang. Here are some things to try:
Run the top command to find the active DRAGEN process. If your run is healthy, you should expect to see it consuming over 100% of the CPU. If it is consuming 100% or less, then your system may be hanging.
Run the du -s command in the directory of the output BAM/SAM file. During a normal run, this directory should be growing with either intermediate output data (when sort is enabled) or BAM/SAM data.
Sending Diagnostic Information to Illumina Support
Illumina would like your feedback on your DRAGEN system, including any reports of system malfunction. In the event of a crash, hang, or watchdog fault, run the sosreport command to collect diagnostic and configuration information, as follows:
sudo sosreport --batch --tmp-dir /staging/tmp
This command takes several minutes to execute and reports the location where it has saved the diagnostic information in /staging/tmp. Please include the report when you submit a support ticket for Illumina Technical Support.
Resetting Your System after a Crash or Hang
If the DRAGEN system crashes or hangs, the dragen_reset utility must be run to reinitialize the hardware and software. This utility is automatically executed by the host software any time it detects an unexpected condition. In this case, the host software shows the following message:
Running dragen_reset to reset DRAGEN Bio-IT processor and software
If the software is hanging, please collect diagnostic information as described in subsection [Sending Diagnostic Information to Illumina Support]{.underline} and then execute dragen_reset manually, as follows:
<INSTALL_PATH>/bin/dragen_reset
Any execution of dragen_reset requires the reference genome to be reloaded to the DRAGEN board. The host software automatically reloads the reference on the next execution.
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