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nanoporetech / minknow_api

Protobuf and gRPC specifications for the MinKNOW API
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Question regarding stopped unblock calls #27

Open JensUweUlrich opened 3 years ago

JensUweUlrich commented 3 years ago

Hi,

I'm currently evaluating the adaptive sampling feature by using the minknow_api to send unblock messages to the MinKNOW GRPC server when running a bulk FAST5 playback. I recognized that some reads, for which I was sending unblock calls to MinKNOW, have not been unblocked. I also see some messages in the bream log file like the following:

[bream4.toolkit.procedure_components.sequencing_features.progressive_unblock: 105] - 2021-06-22 11:26:29,531 - INFO - Stopped 32 unblock calls

Is there a log file or a possibility to have a look at specific unblock calls and why they were stopped by MinKNOW? I would like to understand this issue. Is there something like a maximum number of unblock messages accepted by the GRPC server in MinKNOW?

Thanks Jens

0x55555555 commented 3 years ago

Is there a log file or a possibility to have a look at specific unblock calls and why they were stopped by MinKNOW? I would like to understand this issue. Is there something like a maximum number of unblock messages accepted by the GRPC server in MinKNOW?

There is not a log for specific unblock actions. If you look at the sequencing summary file for the run the end reason for each read is listed though.

Are you using the read_until_api: https://git.oxfordnanolabs.local/minknow/read_until_api I would recommend using this for some useful tools + examples around read until.

alexomics commented 3 years ago

The current public read_until_api is here https://github.com/nanoporetech/read_until_api/tree/v3.0.0