MinKNOW (guppy) not having the permission to basecall or demultiplex from a different location

Question

[adhamzul]

Hello everyone.

I am still quite new at bioinformatics and I am sorry if this seems like a silly question.

I used Nanopore MinION to sequence a genome, and now I am trying to sequence another genome and I launched MinKNOW for the first time since March.

As a little test run and getting used to MinKNOW again, I decided to basecall some files that I had from March using the new 'super-accuracy' model, but as soon as I set everything in MinKNOW, and move to the Experiments page, nothing is there.

So for some reason I decided to reinstall MinKNOW as per the Nanopore protocol, including doing a full uninstall.

So I am currently on Ubuntu 18.04, in the Host Settings, MinKNOW is 21.06.13, MinKNOW GUI is 4.3.28.

I remember being able to see Guppy's and the API's version too when I hover over the MinKNOW version but maybe it changed in the newer version?

Anyways, even after I reinstalled, I still ran into the same problem.

I checked MinKNOW's log folder, and I took a look at mk_manager_svc_log. I get the following:

2021-11-11 09:19:36.239438    INFO: starting_up (basecall_manager)
    version: 4.3.12
    hostname: user
2021-11-11 09:19:36.244405   ERROR: failed_to_start_crashpad (config)
    message: Failed to find crashpad database
2021-11-11 09:19:36.314636    INFO: manager_notified_new_local_auth_token (util)
    expires_in: 89999862595767ns
2021-11-11 09:40:54.379202    INFO: running_client (basecall_manager)
    executable: /opt/ont/guppy/bin/guppy_basecall_client
    id: 1
    arguments: --port
               5555
               --server_file_load_timeout
               600
               --num_callers=1
               --save_path
               /home2/Genome_sequences/20210506_data/20210421/20211110_basecalling
               --config
               dna_r9.4.1_450bps_sup.cfg
               --input_path
               /home2/Genome_sequences/20210506_data/20210421
               --compress_fastq
               --barcode_kits
               SQK-RBK004
               --trim_barcodes
               --min_score
               60.000000
               --progress_stats_frequency=2
2021-11-11 09:40:54.398641 WARNING: output_unexpectedly_terminated (basecall_manager)
    error: (2:std::asio.misc): [0x0x11338d8]: End of file
    id: 1
2021-11-11 09:40:54.398904   ERROR: analysis_process_failed (basecall_manager)
    exit_code: 255
    output: boost::filesystem::status: Permission denied: "/home2/Genome_sequences/20210506_data/20210421/20211110_basecalling"

I have the suspicion that the problem is because I am directing MinKNOW to a different directory than the default directory, but I do not know how to include the current directory and the default directory (the directory where it is installed by default does not have a lot of memory, so I move old data to a different directory).

If anyone have any idea on why this happens, and if it is possible to allow MinKNOW to basecall from a different directory.

Best regards,

Adham

[cfos4698]

I don't have a direct answer for you. Anything ONT can be mysterious and difficult to set up. However, there might be something here that can assist: https://github.com/sirselim . Miles's guides have helped me a lot in the past.

[colindaven]

Remember to back up your data before playing around too much.

Check the permissions on the directory, and all directories above it. Heres a simple guide:

https://opensource.com/article/19/6/understanding-linux-permissions

eg 
cd /home2/Genome_sequences/20210506_data/20210421/20211110_basecalling

ls -l 
cd /home2/Genome_sequences/20210506_data/20210421/
ls -l

Does the user you are running Minknow / guppy as have permissions to write to the directory

sudo su YOUR_MINKNOW_USER
cd /home2/Genome_sequences/20210506_data/20210421/
#create a text file
touch test.txt

# you might then need to change the rights
cd /home2/
sudo chown -R YOUR_MINKNOW_USER *
# grant read and write access to ALL users (can obviously be dangerous, better to set up correctly with users and groups)
sudo chmod -R 777 some_directory

etc. You can change the directories back if you make a mistake.

If all that works, it might be a more sinister problem ...

[adhamzul]

Thank you cfos4698 and colindaven for the replies.

I have yet to tinker with things. I was able to successfully run a sequencing run on MinION last week, and MinKNOW was able to save the data to its default directory. But, whenever I try to basecall on MinKNOW from the default data directory, the permission problem persists.

I talked with my supervisor and we decided to try and contact Nanopore for support. Will try and update the thread with the problems and solutions (if available) for the record.

Answer 1

[Abdullah K]

Hey.

I had the same problem, contacted support, and got this!

https://community.nanoporetech.com/support/articles/191

Good luck.