nanoporetech/pod5-file-format

MantaControl': Unable to read fast5 file at /path/: HDF5 exception",

franztastic opened this issue · 2 comments

franztastic commented

Hi everyone
I am trying to use a .fast5 file for an adaptive sampling simulation from a .pod5 obtained in a sunylationbefore.
I've converted from .pod5 to .fast5. as in the Simulated Playback in the MinKnow (v.23.11.7) asks for a file with .fast5 extension.

After 40seconds, it appears a "run error", stopping the simulation.

image

Checking the minknow.service status, it says the following:

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I've given the file total permits, I've changed the directory where it is placed...

(Also, I am not sure if that's the correct place to put the error or should I do it in minknow_api, so apologies if I am doing it wrong)

  • Pod5 Version: 0.3.6
  • Python Version: 3.10.12
  • Platform: Ubuntu 22.04

Thank you very much for your attention, best wishes!

minknowbot commented

Hi @franztastic ,

The read-based pod5 files minknow writes cannot be used to simulate data playback in minknow.

You need to record a bulk-fast5 file with raw data to simulate data playback.

If you need suppot doing this please contact Nanopore Support who can assist you with this.

Thanks,

  • George
  • 😄1
franztastic commented

understood! Thanks!