Problem communicating with basecaller after MinKnow update #347
Comments
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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 |
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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. |
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Thank you for looking into it. I have exactly the same error. Any progress on how to address this error? |
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Yes - we have a version that should be released in the next 24 hours or so which will resolve this. |
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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 |
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I shall close this for now but please reopen if this doesn't fix it. |
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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". |
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Please can you post the exact error that readfish has given? |
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I got this error in the validation of the toml file: |
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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 |
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
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