bulk fast5 playback with minknow 22.05.05

[nick297]

Hi,

I'm trying to get readfish working ubuntu 20.04 with: MinKNOW core: 5.1.0 Guppy: 6.1.5 Bream: 7.1.3 Script Configuration: 5.1.5

In the testing documentation in the readme it states "In the MinKNOW GUI, right click on a sequencing position and select Reload Scripts. Your version of MinKNOW will now playback the bulkfile rather than live sequencing."

But I can't seem to be able to do this. I have a Minknow plugged in with the configuration test cell

This is the start -> Start sequencing screen This is the sequencing overview screen Is it possible to test playback wih this version of MinKnow?

Thanks, Nick

[alexomics]

Hi Nick,

This is a change in the MinKNOW UI, thank you for bringing it to my attention!

In your first screenshot there is a button, towards the top right-hand corner, with three dots arranged vertically. The Reload Scripts button is there.

Can I ask, what version/branch of readfish are you planning on using? I know that they are all a little bit fragmented at the moment so it's very confusing and I am trying to write some up-to-date/better instructions.

Best, Alex

[nick297]

Hi Alex,

Thanks, I'll test that when I next have access to the machine.

I used these commands to install these branches

pip install git+https://github.com/nanoporetech/read_until_api@v3.0.0
pip install git+https://github.com/LooseLab/readfish@guppy_6_minknow_5

But the pinned ont_pyguppy_client_lib==4.0.11 had dependency issues so I just used.

pip install ont_pyguppy_client_lib

I'm not sure if this is correct. I had readfish working really well pre-pandemic but have a fresh machine to play with now and need to reinstall with the latest MinKnow version.

Thanks, Nick

[nick297]

Sorry, meant to close this last week. I got it working thank you. Another problem I had was the configuration test cell I had was duff. A different one made it work.

If its useful for anyone, I used these settings in my toml for the basecalling to work with guppy 6.

[caller_settings]
config_name = "dna_r9.4.1_450bps_hac"
host = "ipc:///home/nick/soft/adaptive_sampling_scripts"
port = 5555
align_ref = "/home/nick/adaptive_sampling/refs/ref.mmi"

[conditions]
reference = "/home/nick/adaptive_sampling/refs/ref.mmi"

With running guppy server in /home/nick/soft/adaptive_sampling_scripts like this:

guppy_basecall_server --config dna_r9.4.1_450bps_fast.cfg -p 5555 -l /tmp/guppy -x 'cuda:0'

[santiago-es]

Hi @nick297 , I'm having an issue running the playback simulation using the same setup as you. I detail it in #205 . Effectively, after reloading scripts and inserting a configuration test cell and starting a run on my Minion MK1b, the run fails after 10 min "due to an internal error" without capturing any reads or basecalls from the playback. Did you run into this issue? Thanks!

[nick297]

Hi @santiago-es, I'm not sure if I had that error. Maybe try uploading your toml file to your github issue for us to check?

[santiago-es]

I've done so over on my issue