Read Until on a Promethion

[axgraf]

Hi Matt,
thank you for this nice peace of software. I have used your code and extened it to enable targeted enrichment from a BED file. Not perfect yet but it works! So I didn't use the generator script.

Up to now, we have managed to run Read Until on a Minion with great results. Now we tried it on a Promethion. I have set the first channel to 1 and the last channel to 3000. I'm using the fast basecalling model. Running it with a single worker it seems not to catch up with the guppy basecaller, so we increased the workers (to 6), which seems to be able to handle the number of reads:

`2020-05-12 15:42:38,611 [read_until_lafuga] Thread:6 21 reads/0.28550s Unblocked: 1565 Target: 398 Total reads: 4682 Guppy queue: 11
2020-05-12 15:42:38,612 [read_until_lafuga] Thread:3 1 reads/0.09670s Unblocked: 1667 Target: 460 Total reads: 4889 Guppy queue: 11
Throttle: 0.0032995089422911406
2020-05-12 15:42:38,647 [read_until_lafuga] Thread:2 5 reads/0.13400s Unblocked: 1591 Target: 426 Total reads: 4845 Guppy queue: 0
Throttle: 0.09994410490617156
2020-05-12 15:42:38,669 [read_until_lafuga] Thread:1 2 reads/0.13900s Unblocked: 1529 Target: 431 Total reads: 4708 Guppy queue: 4
2020-05-12 15:42:38,722 [read_until_lafuga] Thread:4 1 reads/0.10409s Unblocked: 1688 Target: 469 Total reads: 5077 Guppy queue: 6
Throttle: 0.09996974118985236
2020-05-12 15:42:38,866 [read_until_lafuga] Thread:3 5 reads/0.14211s Unblocked: 1668 Target: 460 Total reads: 4894 Guppy queue: 1

But Minknow only partially shows some unblocking or some kind of unblocking waves over the flowcell.
My assumption is that the basecalling and unblocking decisions are fast enough but that the Minkow RPC port can't handle the unblocking actions in time!? Do you have any experience/advices?

Have you ever tried to run RU on a promethION or do you have any advices what we could do? Or is it currently not possible to run it on a promethION?

Thank you for your help
Best Alex

[mattloose]

HI Alex,

Currently it's not possible to run on PromethION. We do mention this in our preprint I think. We don't advise that you run on PromethION at present until such a time as ONT provide some deeper fixes about this.

Cheers

Matt

[mattloose]

I've just checked the preprint and we do say it should "in principle" scale to the promethION - and that does hold true - but I'd wait for further news before trying this out on that platform.

[axgraf]

Hi Matt,
thank you for the quick reply. So we will not further try to get that running and wait for further updates!
Best Alex

[hasindu2008]

Is readfish going to support the PromethION soon? Currently, is it limited by the compute-power of the GPUs on the PromethION or is it a limitation of the read until API?

[mattloose]

Hi - the limitation is neither of these. Its more fundamental to the platform and is being worked on by ont. I’d keep an eye on announcements from ONT about this.