HiSeq needs to be initialised with the Illumina software

[kasbah]

In our experience at least we currently need to:

• Run the Illumina software (we run this on Windows 7)
• Shut down the Illumina software
• Run pyseq2server (on Windows 10)

If we don't do that we get these errors:

[15:24:53]  INFO     pyseq2.imager Imager initialization [2/5] completed.                                  imager.py:112
            CRITICAL pyseq2.com.async_com fpga      InvalidResponse: b'^EX2HM ERROR:Sensor problem      async_com.py:212
                     detected during EX Homing\r\n'
            INFO     pyseq2.imager Imager initialization [3/5] completed.                                  imager.py:112
[15:24:54]  CRITICAL pyseq2.com.async_com y         InvalidResponse: b'!DF1\r\n'                        async_com.py:212
            CRITICAL pyseq2.com.async_com y         InvalidResponse: b'!DF20 Vel\r\n'                   async_com.py:212
[15:24:57]  ERROR    pyseq2.com.async_com fpga       timeout after 5 s from EX2HM.                      async_com.py:269

Is this how you initialise your machines as well @chaichontat @krpandit ?

[chaichontat]

Thanks for trying! I didn't need to initialize with Illumina's software before use. You could send in your Illumina log files so I could find the differences.

Also, you only need to initialize once for each machine's power cycle. So after the first initialization, you can use pyseq2server --donotinitialize (which I have to add) to save time.

[krpandit]

I also don't need to initialize the illumina software, all the instruments/COM ports populate themselves when the HiSeq is turned on.

I think it might be an issue of the checked commands being too strict. For some of the instruments we should catch command responses that don't match and appropriately handle them.

I get these errors sometimes too, and I usually just ignore them. Especially with the filter wheels, as far as I know, there's no way to read the actual position of the wheel.