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I have recently obtained the MinION USB genome (DNA) sequencer, which to my disappointment doesn't seem to be working in Ubuntu properly.

I'm using the 12.04 release of Ubuntu. The sequencer is properly detected by the script/driver that comes with it, but seems to be unable to detect the sample.

I'm attaching the screenshot of the process. Any help would be greatly appreciated!

enter image description here

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Try running the script/sample collecting program as root with gksu –  hexafraction Jun 11 '12 at 17:52
    
Does the device throw some useful messages on /var/log/syslog or something? –  Christian Jun 15 '12 at 20:18
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3 Answers

Seeing as the device is properly detected by the script, it seems more likely that your problem is on the gene sequencer side of things, rather than being an Ubuntu issue. Are there any other utilities which will allow you to communicate with your sequencer for any other features, perhaps a calibration routine? If Ubuntu can communicate with the machine and get it to do other things, I would expect the problem is with the gene sequencer rather than with the computer. Another possible test is to try using another operating system, if there is software available. Finally, make sure you sequencer has the latest firmware, and that the software you are using to connect is up to date.

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There is another thing I am going to speculate about, that is, running it from shell might not give the most out of the priority. This is Oxford nanopore sequencer that needs full authentication before one can be allowed on their grid. He's not having sufficient information to run and access the sample - that's what I think. –  all4naija Jun 15 '12 at 0:14
    
This is a self-contained DNA sequencer. It's interface is most likely a normal USB serial port adapter which the provided script is talking to - which seems to be working properly. I agree that the problem is probably with the sequencer end of things, and not the interface with the computer. GridION is not a "cloud computing" platform, it's a parallel array of gene sequencers for larger jobs. –  Adrian Jun 15 '12 at 22:10
    
For more information: nanoporetech.com/technology/the-gridion-system/… –  all4naija Jun 15 '12 at 22:55
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A wild guess: Could it be a permissions issue? Some devices work OK for some operations when run as an ordinary user, but require root privileges to perform other operations. Thus, you might try sudo ./gseq and see if that helps. If that helps but you don't want to run as root all the time, you can track down the device file(s) and change their permissions to give yourself access to the device using your normal account. This would probably involve creating udev rules. I won't go into that here since this solution is a bit of a long shot.

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Is it possible that the 6 hour life of the device has been exceeded? It's seems likely that it's more of a device error or a process problem. MinION technical support should possibly be your main contact to resolve this issue since it does appear that the program is communicating with the device.

Chris

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