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.