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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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Not being able to finish the tutorial/test #337

Closed franztastic closed 4 months ago

franztastic commented 4 months ago

Hi everyone, First of all, thanks for the nice program, I'm excited to have it aaalmost working... After few days handling all the problems with the permissions, I'm trying to run the tutorial experiment and I'm facing a "RUN ERROR" just a minute after starting it.

I have a MinKNOW v. 5.8.6, Dorado 7.2.13 and running in a UBUNTU 22.04.4.

Screenshot at 2024-02-27 16-47-03

Here are the logs obtained of the experiment. control_server_log-0.txt It says something regarding a callibration set, but I'm sure I haven't changed anything about callibration...

Thank you very much for your help, best wishes and have a nice day!

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alexomics commented 4 months ago

Hi there, it looks like you are running the simulation using the original demo bulk FAST5 file that we provided. This was sequenced on a MinION flow cell, for PromethION you will need a different bulk FAST5 file which you can find under the "Configuring bulk FAST5 file Playback" header here: https://looselab.github.io/readfish/getting-started.html. Currently that bulk FAST5 file is at: https://s3.amazonaws.com/nanopore-human-wgs/bulkfile/PC24B243_20220512_1516_PAK21362_3H_sequencing_run_NA12878_sheared20kb_3d5147fc.fast5 This file is approx 35Gb in size.

franztastic commented 4 months ago

Yay! Finally I have it working!!! Thanks a million for the speed of your answer! Best wishes and thanks again!

alexomics commented 4 months ago

Fantastic! If you hit any other problems feel free to open another issue 😊

bioteksampath commented 3 months ago

Hi @franztastic and @alexomics,

I have same RUN ERROR issue on my demo run with in minutes of loading MinION data using playback option in MinKnow UI. I have a MinKnow with Dorado and running in a UBUNTU 22

Not sure where should I start? I currently struck at this step - https://github.com/LooseLab/readfish?tab=readme-ov-file#configuring-bulk-fast5-file-playback

Screenshot from 2024-04-09 10-31-19

@franztastic Wondering, what are permission error I should be checking. I do have full permission on 5555

$ ll /tmp/.guppy/
srwxrwxrwx 1 minknow minknow 0 Mar 28 09:04 5555

Thanks for your help, sam

bioteksampath commented 3 months ago

@alexomics thanks for your prompt respose: im using this file GXB02001_20230509_1250_FAW79338_X3_sequencing_run_NA12878_B1_19382aa5_ef4362cd.fast5