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LooseLab / readfish

CLI tool for flexible and fast adaptive sampling on ONT sequencers
https://looselab.github.io/readfish/
GNU General Public License v3.0
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Problem communicating with basecaller after MinKnow update #347

Closed gc-content closed 2 months ago

gc-content commented 2 months ago

Hello!

After installing the new version of the MinKnow (Installed version: 24.02.10, MinKNOW core: 5.9.7, Dorado: 7.3.9), readfish seems to be unable to communicate with the caller. Below I attach the stdout of readfish validate.

readfish validate human_chr_selection.toml 2024-04-16 12:56:10,639 readfish command='validate' 2024-04-16 12:56:10,639 readfish log_file=None 2024-04-16 12:56:10,639 readfish log_format='%(asctime)s %(name)s %(message)s' 2024-04-16 12:56:10,639 readfish log_level='info' 2024-04-16 12:56:10,639 readfish no_check_plugins=False 2024-04-16 12:56:10,639 readfish no_describe=False 2024-04-16 12:56:10,639 readfish prom=False 2024-04-16 12:56:10,640 readfish toml='human_chr_selection.toml' 2024-04-16 12:56:10,640 readfish.validate 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 2024-04-16 12:56:10,643 readfish.validate Loaded TOML config without error 2024-04-16 12:56:10,643 readfish.validate Initialising Caller [ont/error] basecall_service::BasecallClient::worker_loop: Connection error. [bad_reply] Could not interpret message from server for request: LOAD_CONFIG. Reply: INVALID_PROTOCOL [ont/error] basecall_service::BasecallClient::worker_loop: Connection error. [bad_reply] Could not interpret message from server for request: LOAD_CONFIG. Reply: INVALID_PROTOCOL [ont/error] basecall_service::BasecallClient::worker_loop: Connection error. [bad_reply] Could not interpret message from server for request: LOAD_CONFIG. Reply: INVALID_PROTOCOL [ont/error] basecall_service::BasecallClient::worker_loop: Connection error. [bad_reply] Could not interpret message from server for request: LOAD_CONFIG. Reply: INVALID_PROTOCOL [ont/error] basecall_service::BasecallClient::worker_loop: Connection error. [bad_reply] Could not interpret message from server for request: LOAD_CONFIG. Reply: INVALID_PROTOCOL [ont/error] basecall_service::BasecallClient::worker_loop: Connection error. [bad_reply] Could not interpret message from server for request: LOAD_CONFIG. Reply: INVALID_PROTOCOL 2024-04-16 12:56:10,695 readfish.validate Caller could not be initialised, see below for details 2024-04-16 12:56:10,695 readfish.validate Server response not formatted correctly: <result.bad_reply: 14> 2024-04-16 12:56:10,696 readfish.validate Initialising Aligner 2024-04-16 12:56:16,942 readfish.validate Aligner initialised 2024-04-16 12:56:16,942 readfish.validate Skipping descriptions due to errors.

Thanks for help, Piotr

github-actions[bot] commented 2 months ago

We found the following entries in the FAQ which you may find helpful:

Feel free to close this issue if you found an answer in the FAQ. Otherwise, please give us a little time to review.

This is an automated reply, generated by FAQtory

mattloose commented 2 months ago

Adding a comment for anyone else reading this - we are aware of this issue and a fix is in progress. It results from a change in the underlying method of calling the base caller.

PolAlentorn commented 2 months ago

Thank you for looking into it. I have exactly the same error. Any progress on how to address this error? Many thanks, Pol

mattloose commented 2 months ago

Yes - we have a version that should be released in the next 24 hours or so which will resolve this.

mattloose commented 2 months ago

Just to say we have just released the version that should fix this.

Please note that you will need to update your caller settings in your TOML file - https://github.com/LooseLab/readfish/releases/tag/2024.2.0

mattloose commented 2 months ago

I shall close this for now but please reopen if this doesn't fix it.

jennieli421 commented 1 month ago

Tried the new version today. Even though the validation was fine, when I started the run I got an error saying "no module dorado found". I tried conda and pip install pydorado but then I got an error saying "dorado does not have an attribute Caller".

mattloose commented 1 month ago

Please can you post the exact error that readfish has given?

PolAlentorn commented 1 month ago

I got this error in the validation of the toml file: readfish validate human_chr_selection.toml 2024-05-14 15:38:40,537 readfish /home/admin/miniconda3/envs/readfish/bin/readfish validate human_chr_selection.toml 2024-05-14 15:38:40,537 readfish command='validate' 2024-05-14 15:38:40,537 readfish log_file=None 2024-05-14 15:38:40,537 readfish log_format='%(asctime)s %(name)s %(message)s' 2024-05-14 15:38:40,537 readfish log_level='info' 2024-05-14 15:38:40,537 readfish no_check_plugins=False 2024-05-14 15:38:40,537 readfish no_describe=False 2024-05-14 15:38:40,537 readfish prom=False 2024-05-14 15:38:40,537 readfish toml='human_chr_selection.toml' 2024-05-14 15:38:40,538 readfish.validate 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 2024-05-14 15:38:40,541 readfish.validate Loaded TOML config without error 2024-05-14 15:38:40,541 readfish.validate Initialising Caller 2024-05-14 15:38:40,761 readfish.validate Caller could not be initialised, see below for details 2024-05-14 15:38:40,761 readfish.validate module 'dorado' has no attribute 'Caller' 2024-05-14 15:38:40,761 readfish.validate Initialising Aligner 2024-05-14 15:38:46,142 readfish.validate Aligner initialised 2024-05-14 15:38:46,143 readfish.validate Skipping descriptions due to errors.

mattloose commented 1 month ago

I've tried a clean install of readfish here and I cannot recreate your issue.

Please can you try reinstalling readfish in a clean environment - in addition can you please share the toml file you are using?

Thanks