Not supporting MinKNOW 6.2.8

[HaxyMoly]

Hi, it seems the latest readfish release is not compatible with the MinKNOW 6.2.8.

This readfish version (2024.3.0) is tested for compatibility with MinKNOW v6.0.0 to v6.1.8.
This version of minknow is 6.2.8.
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 "/Users/xxx/mambaforge/envs/readfish/bin/readfish", line 8, in
sys.exit(main())
File "/Users/xxx/mambaforge/envs/readfish/lib/python3.10/site-packages/readfish/_cli_base.py", line 61, in main
raise SystemExit(args.func(parser, args, extras))
File "/Users/xxx/mambaforge/envs/readfish/lib/python3.10/site-packages/readfish/entry_points/targets.py", line 618, in run
read_until_client = RUClient(
File "/Users/xxx/mambaforge/envs/readfish/lib/python3.10/site-packages/readfish/_read_until_client.py", line 48, in init
super().init(*args, **kwargs)
File "/Users/xxx/mambaforge/envs/readfish/lib/python3.10/site-packages/readfish/read_until/base.py", line 205, in init
self.strand_classes = set(
File "/Users/xxx/mambaforge/envs/readfish/lib/python3.10/site-packages/readfish/read_until/base.py", line 206, in
self.lookup_read_class[x] for x in self.prefilter_classes
KeyError: 'short_strand'

[github-actions]

Thank you for your issue. Give us a little time to review it.

PS. You might want to check the FAQ if you haven't done so already.

This is an automated reply, generated by FAQtory

[mattloose]

Hi - we will test and get back to you asap.

Keep an eye here!

[mattloose]

Hi,

We are trying to reproduce this issue and are struggling to do so. Could you provide a the output of:

pip list

from the environment you are running readfish in?

Thanks.

[HaxyMoly]

Hi,

We are trying to reproduce this issue and are struggling to do so. Could you provide a the output of:

pip list

from the environment you are running readfish in?

Thanks.

Thanks for your prompt reply, here is my environment.

Package Version

---

about-time 4.2.1
alive-progress 3.2.0
Arpeggio 2.0.2
attrs 24.3.0
biopython 1.85
cachetools 5.5.1
cattrs 24.1.2
certifi 2024.12.14
charset-normalizer 3.4.1
cigar 0.1.3
click 8.1.8
Columnar 1.1.0
cuteSV 2.1.1
cutevariant 0.4.5
exceptiongroup 1.2.2
grapheme 0.6.0
grpcio 1.70.0
idna 3.10
iniconfig 2.0.0
Jinja2 3.1.5
joblib 1.4.2
mappy 2.28
mappy-rs 0.0.7
Markdown 3.7
MarkupSafe 3.0.2
minknow_api 6.2.1
more-itertools 10.6.0
numpy 1.26.4
ont-pybasecall-client-lib 7.6.8
packaging 24.2
pip 24.3.1
pluggy 1.5.0
progressbar2 4.5.0
protobuf 4.25.5
pyRFC3339 1.1
pysam 0.22.1
PySide6 6.8.1.1
PySide6_Addons 6.8.1.1
PySide6_Essentials 6.8.1.1
pytest 8.3.4
python-utils 3.9.1
pytz 2024.2
PyVCF3 1.0.3
PyYAML 6.0.2
read_until 2.1.0
readfish 2024.3.0
readfish_summarise 0.2.7
requests 2.32.3
rtoml 0.12.0
scikit-learn 1.6.1
scipy 1.15.1
setuptools 75.8.0
shiboken6 6.8.1.1
textX 1.8.0
threadpoolctl 3.5.0
tomli 2.2.1
toolz 1.0.0
typing_extensions 4.12.2
urllib3 2.3.0
wheel 0.45.1

[mattloose]

Could you try running a playback sequencing run on your system to check that works, and then retesting running readfish?

[Adoni5]

Readfish can connect to a position that is not sequencing, but it will not be able to run - and will crash out with the error you saw as it is impossible for MinKNOW to provide some of the information that readfish queries for without ongoing sequencing.

I have just tested the latest version of MinKNOW against readfish and am unable to create your error, unless sequencing is not running.