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  • How to Determine if the System is Hanging
  • Sending Diagnostic Information to Illumina Support
  • Resetting Your System after a Crash or Hang

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  1. Reference

Troubleshooting

PreviousSupplementary InformationNextCiting DRAGEN software

Last updated 1 year ago

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If the DRAGEN system does not seem to be responding, do the following:

  1. To determine if the DRAGEN system is hanging, follow the instructions in .

  2. Collect diagnostic information after a hang, or a crash, as described in .

  3. After all information has been collected, reset your system. if needed, as described in .

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.

How to Determine if the System is Hanging
Sending Diagnostic Information to Illumina Support
Resetting Your System after a Crash or Hang