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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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"MinKNOW not found on this computer" #211

Closed merfre closed 2 years ago

merfre commented 2 years ago

Hello,

I just reinstalled ReadFish on my machine (Ubuntu 20.04) using the instructions on the README and when I tried to test it on a playback run (which had already begun sequencing) got this output:

sudo /home/merfre/readfish/bin/readfish targets --device MN17166 --experiment-name "RU Test basecall and map" --toml /home/merfre/human_chr_selection.toml --log-file ru_adap_gpu_test.log

2022-09-06 14:33:37,252 Manager /home/merfre/readfish/bin/readfish targets --device MN17166 --experiment-name RU Test basecall and map --toml /home/merfre/human_chr_selection.toml --log-file ru_adap_gpu_test.log 2022-09-06 14:33:37,252 Manager batch_size=512 2022-09-06 14:33:37,252 Manager cache_size=512 2022-09-06 14:33:37,252 Manager channels=[1, 512] 2022-09-06 14:33:37,252 Manager chunk_log=chunk_log.log 2022-09-06 14:33:37,252 Manager command=targets 2022-09-06 14:33:37,252 Manager device=MN17166 2022-09-06 14:33:37,252 Manager dry_run=False 2022-09-06 14:33:37,252 Manager experiment_name=RU Test basecall and map 2022-09-06 14:33:37,252 Manager func=<function run at 0x7fad54089a60> 2022-09-06 14:33:37,252 Manager host=127.0.0.1 2022-09-06 14:33:37,253 Manager log_file=ru_adap_gpu_test.log 2022-09-06 14:33:37,253 Manager log_format=%(asctime)s %(name)s %(message)s 2022-09-06 14:33:37,253 Manager log_level=info 2022-09-06 14:33:37,253 Manager paf_log=paflog.log 2022-09-06 14:33:37,253 Manager port=9501 2022-09-06 14:33:37,253 Manager read_cache=AccumulatingCache 2022-09-06 14:33:37,253 Manager run_time=172800 2022-09-06 14:33:37,253 Manager throttle=0.1 2022-09-06 14:33:37,253 Manager toml=/home/merfre/human_chr_selection.toml 2022-09-06 14:33:37,253 Manager unblock_duration=0.1 2022-09-06 14:33:37,253 Manager workers=1 2022-09-06 14:33:37,256 Manager Initialising minimap2 mapper 2022-09-06 14:33:41,644 Manager Mapper initialised 2022-09-06 14:33:41,644 read_until_api_v2.main Client type: many chunk 2022-09-06 14:33:41,644 read_until_api_v2.main Cache type: AccumulatingCache 2022-09-06 14:33:41,644 read_until_api_v2.main Filter for classes: adapter and strand 2022-09-06 14:33:41,644 read_until_api_v2.main Creating rpc connection for device MN17166. Traceback (most recent call last): File "/home/merfre/readfish/bin/readfish", line 11, in load_entry_point('readfish==0.0.4', 'console_scripts', 'readfish')() File "/home/merfre/readfish/lib/python3.8/site-packages/ru/cli.py", line 33, in main args.func(parser, args) File "/home/merfre/readfish/lib/python3.8/site-packages/ru/ru_gen.py", line 493, in run read_until_client = read_until.ReadUntilClient( File "/home/merfre/readfish/lib/python3.8/site-packages/read_until_api_v2/main.py", line 240, in init self.connection, self.message_port = get_rpc_connection( File "/home/merfre/readfish/lib/python3.8/site-packages/read_until_api_v2/load_minknow_rpc.py", line 163, in get_rpc_connection load_rpc(reload) File "/home/merfre/readfish/lib/python3.8/site-packages/read_until_api_v2/load_minknow_rpc.py", line 139, in load_rpc raise ValueError("MinKNOW not found on this computer") ValueError: MinKNOW not found on this computer

This is my config file:

[caller_settings]
config_name = "dna_r9.4.1_450bps_fast.cfg"
host = "ipc:///tmp/.guppy"
port = 5557

[conditions]
reference = "/home/merfre/human_reference.mmi"

[conditions.0]
name = "select_chr_21_22"
control = false
min_chunks = 0
max_chunks = inf
targets = ["CM000683.2", "CM000684.2"]
single_on = "stop_receiving"
multi_on = "stop_receiving"
single_off = "unblock"
multi_off = "unblock"
no_seq = "proceed"
no_map = "proceed"

This is how I started my basecalling server:

sudo guppy_basecall_server --log_path guppy.log --config dna_r9.4.1_450bps_fast.cfg --port /tmp/.guppy/5557 --device cuda:0 --gpu_runners_per_device 8 --num_callers 4 --chunks_per_runner 1024 --chunk_size 1000

ONT Guppy basecall server software version 6.1.1+1f6bfa7f8, client-server API version 11.0.0, minimap2 version 2.22-r1101 log path: guppy.log chunk size: 1000 chunks per runner: 1024 max queued reads: 2000 num basecallers: 4 num socket threads: 2 max returned events: 50000 gpu device: cuda:0 kernel path:
runners per device: 8 Use of this software is permitted solely under the terms of the end user license agreement (EULA).By running, copying or accessing this software, you are demonstrating your acceptance of the EULA. The EULA may be found in /opt/ont/guppy/bin

Config loaded: config file: /opt/ont/guppy/data/dna_r9.4.1_450bps_fast.cfg model file: /opt/ont/guppy/data/template_r9.4.1_450bps_fast.jsn model version id 2021-05-17_dna_r9.4.1_minion_96_29d8704b adapter scaler model file: None Starting server on port: ipc:///tmp/.guppy/5557

The readfish conda environment was active and I also tried to run it without sudo ('readfish targets --device MN17166 --experiment-name "RU Test basecall and map" --toml /home/merfre/human_chr_selection.toml --log-file ru_adap_gpu_test.log`), but that resulted in the same error. I am using minknow 5 and guppy 6.1.1

merfre commented 2 years ago

Duplicate issue and will write new one related to the installation of the new readfish updates.