Tools and Utilities

The following tools and utilities are available with the DRAGEN installation:

• Hardware Accelerated BCL Conversion

• Illumina Connected Annotations (Nirvana)

• System Health Monitoring

• Hardware-Accelerated Compression and Decompression

• Licensing and Usage

The following tools are released concurrently with DRAGEN, but available separately:

• DRAGEN Reports

Monitoring System Health

When DRAGEN runs, a daemon dragend is started that communicates with the FPGA card. This daemon will monitor FPGA temperature while DRAGEN is running and abort DRAGEN when the temperature exceeds a configured threshold.

To display the current temperature of the DRAGEN server FPGA, use the dragen_info -t command.

% dragen_info -t
FPGA Temperature: 42C  (Max Temp: 49C, Min Temp: 39C)

Logging

All hardware events are logged to /var/log/messages and /var/log/dragen_mond.log. The following shows an example in /var/log/messages of a temperature alarm:

  Jul 16 12:02:34 komodo dragen_mond[26956]: WARNING: FPGA software over temperature alarm has been triggered -- temp threshold: 85 (Chip status: 0x80000001)
  Jul 16 12:02:34 komodo dragen_mond[26956]: Current FPGA temp: 86, Max temp: 88, Min temp: 48
  Jul 16 12:02:34 komodo dragen_mond[26956]: All dragen processes will be stopped until alarm clears
  Jul 16 12:02:34 komodo dragen_mond[26956]: Terminating dragen in process 1510 with SIGUSR2 signal

By default, temperature is logged to /var/log/dragen_mond.log every hour:

  Aug 01 09:16:50 Setting FPGA hardware max temperature threshold to 100
  Aug 01 09:16:50 Setting FPGA software max temperature threshold to 85
  Aug 01 09:16:50 Setting FPGA software min temperature threshold to 75
  Aug 01 09:16:50 FPGA temperatures will be logged every 3600 seconds
  Aug 01 09:16:50 Current FPGA temperature is 52 (Max temp = 52, Min temp = 52)
  Aug 01 10:16:50 Current FPGA temperature is 53 (Max temp = 56, Min temp = 49)
  Aug 01 11:16:50 Current FPGA temperature is 54 (Max temp = 56, Min temp = 49)

If DRAGEN is executing when a thermal alarm is detected, the following is displayed in the terminal window of the DRAGEN process:

  **********************************************************
  **  Received external signal -- aborting dragen.        **
  **  An issue has been detected with the dragen card.    **
  **  Check /var/log/messages for details.                **
  **                                                      **
  **  It may take up to a minute to complete shutdown.    **
  **********************************************************

If you see this message, stop running the DRAGEN software. Do the following to alleviate the overheating condition on the card:

• Be sure that there is ample air flow over the card. Consider moving the card to a slot where there is more air flow, adding another fan or increasing the fan speed.

• Give the card more space in the box. If there are available PCIe slots, move the card so that it has empty slots on either side.

Contact Illumina Technical Support if you are having trouble resolving the thermal alarm on your system.

Hardware Alarms

The following table lists the hardware events logged by the monitor when an alarm is triggered:

ID	Description	Monitor Action
0	Software overheating	Terminate usage until DRAGEN server FPGA cools to software minimum temperature.
1	Hardware overheating	Fatal. Aborts dragen software; system reboot required
2	Board SPD overheating	Logged as nonfatal
3	SODIMM overheating	Logged as nonfatal
4	Power 0	Fatal. Aborts dragen software; system reboot required
5	Power 1	Fatal. Aborts dragen software; system reboot required
6	DRAGEN server FPGA power	Logged as nonfatal
7	Fan 0	Logged as nonfatal
8	Fan 1	Logged as nonfatal
9	SE5338	Fatal. Aborts dragen software; system reboot required
10--30	Undefined (Reserved)	Fatal. Aborts dragen software; system reboot required

Fatal alarms prevent the DRAGEN host software from running and require a system reboot. When a software overheating alarm is triggered, the monitor looks for and aborts any running DRAGEN processes. The monitor continues to abort any new DRAGEN processes until the temperature decreases to the minimum threshold and the hardware clears the chip status alarm. When the software overheating alarm clears, DRAGEN jobs can resume executing.

Contact Illumina Technical Support with details from the log files if any of these alarms are triggered on your system.

Hardware-Accelerated Compression and Decompression

Gzip compression is ubiquitous in bioinformatics. FASTQ files are often gzipped, and the BAM format itself is a specialized version of gzip. For that reason, DRAGEN provides hardware support for accelerating compression and decompression of gzipped data. If your input files are gzipped, DRAGEN detects that and decompresses the files automatically. If your output is BAM files, then the files are automatically compressed.

DRAGEN provides standalone command-line utilities to enable you to compress or decompress arbitrary files. These utilities are analogous to the Linux gzip and gunzip commands, but are named dzip and dunzip (dragen zip and dragen unzip). Both utilities are able to accept as input a single file, and produce a single output file with the .gz file extension removed or added, as appropriate. For example:

  dzip file1      \# produces output file file1.gz\
  dunzip file2.gz \# produces output file file2

Currently, dzip and dunzip have the following limitations and differences from gzip/gunzip:

• Each invocation of these tools can handle only a single file. Additional file names (including those produced by a wildcard * character) are ignored.

• They cannot be run at the same time as the DRAGEN host software.

• They do not support the command line options found in gzip and gunzip (eg, --recursive, --fast, ‑‑best, ‑‑stdout).

Licensing and Usage

DRAGEN includes tools to assist with licensing, more information can be found in the Licensing Reference Section.