Thank you for developing the amazing tool. I had been using readfish for simulated adaptive sampling for a while, and it worked fine previously. However, after MinKnow was updated, my scripts are failing. At first, I used readfish installed using pip install readfish[all]. When testing unblock response, I get the following error, the same as issue #389, even when the sequencing is ongoing.
(readfish) ubuntu@ip-10-0-3-36:~$ readfish unblock-all --device MS00000 --experiment-name 'A'
2025-07-11 14:20:04,908 readfish /home/ubuntu/miniforge3/envs/readfish/bin/readfish unblock-all --device MS00000 --experiment-name A
2025-07-11 14:20:04,908 readfish chemistry=<Chemistry.SIMPLEX: 'simplex'>
2025-07-11 14:20:04,908 readfish command='unblock-all'
2025-07-11 14:20:04,908 readfish debug_log=True
2025-07-11 14:20:04,908 readfish device='MS00000'
2025-07-11 14:20:04,908 readfish dry_run=False
2025-07-11 14:20:04,908 readfish experiment_name='A'
2025-07-11 14:20:04,908 readfish host='127.0.0.1'
2025-07-11 14:20:04,908 readfish log_file=None
2025-07-11 14:20:04,908 readfish log_format='%(asctime)s %(name)s %(message)s'
2025-07-11 14:20:04,908 readfish log_level='info'
2025-07-11 14:20:04,908 readfish max_unblock_read_length_seconds=5
2025-07-11 14:20:04,908 readfish port=None
2025-07-11 14:20:04,908 readfish throttle=0.4
2025-07-11 14:20:04,908 readfish unblock_duration=0.1
2025-07-11 14:20:04,908 readfish wait_for_ready=120
2025-07-11 14:20:04,908 readfish Version=2024.3.0
2025-07-11 14:20:04,939 readfish.unblock-all This readfish version (2024.3.0) is tested for compatibility with MinKNOW v6.0.0 to v6.0.0.
This version of minknow is 6.4.9.
If readfish fails please try to upgrade readfish.
If there isn't a newer version of readfish and readfish is failing, please open an issue:
https://github.com/LooseLab/readfish/issues
Traceback (most recent call last):
File "/home/ubuntu/miniforge3/envs/readfish/bin/readfish", line 8, in <module>
sys.exit(main())
File "/home/ubuntu/miniforge3/envs/readfish/lib/python3.10/site-packages/readfish/_cli_base.py", line 61, in main
raise SystemExit(args.func(parser, args, extras))
File "/home/ubuntu/miniforge3/envs/readfish/lib/python3.10/site-packages/readfish/entry_points/unblock_all.py", line 66, in run
ret = targets.run(parser, args, extras)
File "/home/ubuntu/miniforge3/envs/readfish/lib/python3.10/site-packages/readfish/entry_points/targets.py", line 618, in run
read_until_client = RUClient(
File "/home/ubuntu/miniforge3/envs/readfish/lib/python3.10/site-packages/readfish/_read_until_client.py", line 48, in __init__
super().__init__(*args, **kwargs)
File "/home/ubuntu/miniforge3/envs/readfish/lib/python3.10/site-packages/readfish/read_until/base.py", line 205, in __init__
self.strand_classes = set(
File "/home/ubuntu/miniforge3/envs/readfish/lib/python3.10/site-packages/readfish/read_until/base.py", line 206, in <genexpr>
self.lookup_read_class[x] for x in self.prefilter_classes
KeyError: 'short_strand'
I noticed that this issue is solved by a recent pull request #391, and I tried to reinstall the newest version of readfish via
pip uninstall readfish
pip install git+https://github.com/LooseLab/readfish
It turns out that this resolves the previous bug, and readfish is able to run
(readfish) ubuntu@ip-10-0-3-36:~$ readfish unblock-all --device MS00000 --experiment-name 'A'
2025-07-11 14:20:39,328 readfish /home/ubuntu/miniforge3/envs/readfish/bin/readfish unblock-all --device MS00000 --experiment-name A
2025-07-11 14:20:39,328 readfish chemistry=<Chemistry.SIMPLEX: 'simplex'>
2025-07-11 14:20:39,328 readfish command='unblock-all'
2025-07-11 14:20:39,328 readfish debug_log=True
2025-07-11 14:20:39,328 readfish device='MS00000'
2025-07-11 14:20:39,328 readfish dry_run=False
2025-07-11 14:20:39,328 readfish experiment_name='A'
2025-07-11 14:20:39,328 readfish host='127.0.0.1'
2025-07-11 14:20:39,328 readfish log_file=None
2025-07-11 14:20:39,328 readfish log_format='%(asctime)s %(name)s %(message)s'
2025-07-11 14:20:39,328 readfish log_level='info'
2025-07-11 14:20:39,328 readfish max_unblock_read_length_seconds=5
2025-07-11 14:20:39,328 readfish port=None
2025-07-11 14:20:39,328 readfish throttle=0.4
2025-07-11 14:20:39,328 readfish unblock_duration=0.1
2025-07-11 14:20:39,328 readfish wait_for_ready=120
2025-07-11 14:20:39,328 readfish Version=2024.3.0
2025-07-11 14:20:39,361 readfish.unblock-all This readfish version (2024.3.0) is tested for compatibility with MinKNOW v6.0.0 to v6.0.0.
This version of minknow is 6.4.9.
If readfish fails please try to upgrade readfish.
If there isn't a newer version of readfish and readfish is failing, please open an issue:
https://github.com/LooseLab/readfish/issues
2025-07-11 14:20:39,403 readfish._read_until_client Protocol phase changed to PHASE_SEQUENCING
2025-07-11 14:20:39,404 readfish._read_until_client Protocol state changed to PROTOCOL_RUNNING
2025-07-11 14:20:39,405 readfish.unblock-all eJxtj1EKwjAQRP9zitADCPrvSUIIadjW0M1uzaba4xtBrAn+7b4ZhhkTPCJkJ1BKpFlOxI5Xq0zy6/qPmwxzZBJrFfkE+qqHjUbksOiaNKgUyYXbRotU6ayS34/3oorPM5T3baySGozgmH5Chi+dpganDUvsvR/YWWtVgXuP6qAG+ZEf4Jp+hzgC8tM1Ww7xBaW9au4=
2025-07-11 14:20:39,413 readfish.unblock-all Configuration description:
Region unblock all (control=False).
Region applies to section of flow cell (# = applied, . = not applied):
################################
################################
################################
################################
################################
################################
################################
################################
2025-07-11 14:20:39,416 readfish.unblock-all Fetching Run Configuration
2025-07-11 14:20:39,418 readfish.unblock-all Run Configuration Received
2025-07-11 14:20:39,418 readfish.unblock-all run_id=05db6c4e-34f5-45b2-9c15-a22eb5439760
2025-07-11 14:20:39,418 readfish.unblock-all break_reads_after_seconds=1.0
2025-07-11 14:20:39,418 readfish.unblock-all sample_rate=4000
2025-07-11 14:20:39,418 readfish.unblock-all Initialising Caller
2025-07-11 14:20:39,419 readfish.unblock-all Caller initialised
2025-07-11 14:20:39,419 readfish.unblock-all Using the `no_op` Caller. No base-calling will be performed, and minimum viable results will be yielded back for each read provided.
2025-07-11 14:20:39,419 readfish.unblock-all Initialising Aligner
2025-07-11 14:20:39,420 readfish.unblock-all Aligner initialised
2025-07-11 14:20:39,420 readfish.unblock-all Starting main loop
2025-07-11 14:20:39,420 readfish.unblock-all Generating aligner description, if possible...
2025-07-11 14:20:39,420 readfish.unblock-all Using the `no_op` Aligner. No alignments will be performed, and all Results will be passed through.
2025-07-11 14:20:39,424 readfish.unblock-all readfish started in PHASE_SEQUENCING. Fully sequencing first read from each channel.
However, the output simply stops here and no more log is printed as the sequencing is running. The read distribution is also different from the one shown in README, and I don't quite see the unblocking response - a lot of the sequenced reads are still long.
Currently, I'm using Minknow version 25.03.9 (MinKNOW core: 6.4.9, Dorado: 7.8.3, Bream: 8.4.4, Script Configuration: 6.4.11). I'm using python3.10 in a Miniforge 3 virtual environment, and everything was run on an Ubuntu 22.04 machine. and here's my pip list:
(readfish) ubuntu@ip-10-0-3-36:~$ pip list
Package Version
------------------------- --------
about-time 4.2.1
alive-progress 3.2.0
attrs 25.3.0
cattrs 25.1.1
click 8.2.1
exceptiongroup 1.3.0
grapheme 0.6.0
grpcio 1.73.0
iniconfig 2.1.0
mappy 2.30
mappy-rs 0.0.7
minknow_api 6.4.3
more-itertools 10.7.0
numpy 1.26.4
ont-pybasecall-client-lib 7.8.3
ont-pyguppy-client-lib 7.2.15
packaging 25.0
pip 25.1.1
pluggy 1.6.0
protobuf 4.25.8
Pygments 2.19.1
pyRFC3339 1.1
pytest 8.4.0
pytz 2025.2
readfish 2024.3.0
readfish_summarise 0.2.7
rtoml 0.12.0
setuptools 80.9.0
tomli 2.2.1
typing_extensions 4.14.0
wheel 0.45.1
I'm wondering if this is the issue related to the versions of Minknow or readfish. I would really appreciate your help. Thank you in advance!
Thank you for developing the amazing tool. I had been using readfish for simulated adaptive sampling for a while, and it worked fine previously. However, after MinKnow was updated, my scripts are failing. At first, I used readfish installed using
pip install readfish[all]. When testing unblock response, I get the following error, the same as issue #389, even when the sequencing is ongoing.I noticed that this issue is solved by a recent pull request #391, and I tried to reinstall the newest version of readfish via
It turns out that this resolves the previous bug, and readfish is able to run
However, the output simply stops here and no more log is printed as the sequencing is running. The read distribution is also different from the one shown in README, and I don't quite see the unblocking response - a lot of the sequenced reads are still long.
Currently, I'm using Minknow version 25.03.9 (MinKNOW core: 6.4.9, Dorado: 7.8.3, Bream: 8.4.4, Script Configuration: 6.4.11). I'm using python3.10 in a Miniforge 3 virtual environment, and everything was run on an Ubuntu 22.04 machine. and here's my pip list:
I'm wondering if this is the issue related to the versions of Minknow or readfish. I would really appreciate your help. Thank you in advance!