Bug Report - Error Encountered in readfish Command Execution

[IguodalaYan]

Dear readfish Team,

I am writing to report a bug that I encountered while using the readfish tool. When I executed the following command during the scanning of active pores in miniknow:

readfish targets --experiment-name "dongtaoreadfish" --device X3 --toml gemome_selection.toml --log-file RU_log.log

I received the following error message:

Exception in thread read_until-1:
Traceback (most recent call last):
File "/home/grid/anaconda3/lib/python3.9/threading.py", line 980, in _bootstrap_inner
self.run()
File "/home/grid/anaconda3/lib/python3.9/threading.py", line 917, in run
self._target(*self._args, **self._kwargs)
File "/data/conda/readfish/lib/python3.9/site-packages/read_until/base.py", line 384, in _run
reads = self.connection.data.get_live_reads(self._runner(**kwargs))
TypeError: _runner() got an unexpected keyword argument 'max_unblock_read_length_seconds'

I am reaching out to seek your support and assistance in resolving this problem.

Please let me know if you need any additional information to investigate and address this issue. Thank you for your help!

Best regards,
Yuxi Yan
Southern university of science and technology
zzuyanyuxi@163.com

[alexomics]

This looks like an issue with either the read until API or MinKNOW API. Please could you share your conda environment configuration or run: pip list and paste the output here?

[IguodalaYan]

wow, ultra-fast reply！
Package Version

---

alabaster 0.7.12
anaconda-client 1.11.0
anaconda-navigator 2.3.1
anaconda-project 0.11.1
anyio 3.5.0
appdirs 1.4.4
argon2-cffi 21.3.0
argon2-cffi-bindings 21.2.0
arrow 1.2.2
astroid 2.11.7
astropy 5.1
atomicwrites 1.4.0
attrs 21.4.0
Automat 20.2.0
autopep8 1.6.0
Babel 2.9.1
backcall 0.2.0
backports.functools-lru-cache 1.6.4
backports.tempfile 1.0
backports.weakref 1.0.post1
bcrypt 3.2.0
beautifulsoup4 4.11.1
binaryornot 0.4.4
bitarray 2.5.1
bkcharts 0.2
black 22.6.0
bleach 4.1.0
bokeh 2.4.3
boto3 1.24.28
botocore 1.27.28
Bottleneck 1.3.5
brotlipy 0.7.0
certifi 2022.9.14
cffi 1.15.1
chardet 4.0.0
charset-normalizer 2.0.4
click 8.0.4
cloudpickle 2.0.0
clyent 1.2.2
colorama 0.4.5
colorcet 3.0.0
conda 22.9.0
conda-build 3.22.0
conda-content-trust 0.1.3
conda-pack 0.6.0
conda-package-handling 1.9.0
conda-repo-cli 1.0.20
conda-token 0.4.0
conda-verify 3.4.2
constantly 15.1.0
cookiecutter 1.7.3
cryptography 37.0.1
cssselect 1.1.0
cycler 0.11.0
Cython 0.29.32
cytoolz 0.11.0
daal4py 2021.6.0
dask 2022.7.0
datashader 0.14.1
datashape 0.5.4
debugpy 1.5.1
decorator 5.1.1
defusedxml 0.7.1
diff-match-patch 20200713
dill 0.3.4
distributed 2022.7.0
docutils 0.18.1
entrypoints 0.4
et-xmlfile 1.1.0
fastjsonschema 2.16.2
filelock 3.6.0
flake8 4.0.1
Flask 1.1.2
fonttools 4.25.0
fsspec 2022.7.1
future 0.18.2
gensim 4.1.2
glob2 0.7
gmpy2 2.1.2
greenlet 1.1.1
h5py 3.7.0
HeapDict 1.0.1
holoviews 1.15.0
hvplot 0.8.0
hyperlink 21.0.0
idna 3.3
imagecodecs 2021.8.26
imageio 2.19.3
imagesize 1.4.1
importlib-metadata 4.11.3
incremental 21.3.0
inflection 0.5.1
iniconfig 1.1.1
intake 0.6.5
intervaltree 3.1.0
ipykernel 6.15.2
ipython 7.31.1
ipython-genutils 0.2.0
ipywidgets 7.6.5
isort 5.9.3
itemadapter 0.3.0
itemloaders 1.0.4
itsdangerous 2.0.1
jdcal 1.4.1
jedi 0.18.1
jeepney 0.7.1
jellyfish 0.9.0
Jinja2 2.11.3
jinja2-time 0.2.0
jmespath 0.10.0
joblib 1.1.0
json5 0.9.6
jsonschema 4.16.0
jupyter 1.0.0
jupyter_client 7.3.4
jupyter-console 6.4.3
jupyter_core 4.11.1
jupyter-server 1.18.1
jupyterlab 3.4.4
jupyterlab-pygments 0.1.2
jupyterlab-server 2.10.3
jupyterlab-widgets 1.0.0
keyring 23.4.0
kiwisolver 1.4.2
lazy-object-proxy 1.6.0
libarchive-c 2.9
llvmlite 0.38.0
locket 1.0.0
lxml 4.9.1
lz4 3.1.3
mappy 2.26
Markdown 3.3.4
MarkupSafe 2.0.1
matplotlib 3.5.2
matplotlib-inline 0.1.6
mccabe 0.7.0
mistune 0.8.4
mkl-fft 1.3.1
mkl-random 1.2.2
mkl-service 2.4.0
mock 4.0.3
mpmath 1.2.1
msgpack 1.0.3
multipledispatch 0.6.0
munkres 1.1.4
mypy-extensions 0.4.3
navigator-updater 0.3.0
nbclassic 0.3.5
nbclient 0.5.13
nbconvert 6.4.4
nbformat 5.5.0
nest-asyncio 1.5.5
networkx 2.8.4
nltk 3.7
nose 1.3.7
notebook 6.4.12
numba 0.55.1
numexpr 2.8.3
numpy 1.21.5
numpydoc 1.4.0
olefile 0.46
openpyxl 3.0.10
packaging 21.3
pandas 1.4.4
pandocfilters 1.5.0
panel 0.13.1
param 1.12.0
parsel 1.6.0
parso 0.8.3
partd 1.2.0
pathlib 1.0.1
pathspec 0.9.0
patsy 0.5.2
pep8 1.7.1
pexpect 4.8.0
pickleshare 0.7.5
Pillow 9.2.0
pip 22.2.2
pkginfo 1.8.2
platformdirs 2.5.2
plotly 5.9.0
pluggy 1.0.0
ply 3.11
poyo 0.5.0
prometheus-client 0.14.1
prompt-toolkit 3.0.20
Protego 0.1.16
psutil 5.9.0
ptyprocess 0.7.0
py 1.11.0
pyasn1 0.4.8
pyasn1-modules 0.2.8
pycodestyle 2.8.0
pycosat 0.6.3
pycparser 2.21
pyct 0.4.8
pycurl 7.45.1
PyDispatcher 2.0.5
pydocstyle 6.1.1
pyerfa 2.0.0
pyflakes 2.4.0
Pygments 2.11.2
PyHamcrest 2.0.2
PyJWT 2.4.0
pylint 2.14.5
pyls-spyder 0.4.0
pyodbc 4.0.34
pyOpenSSL 22.0.0
pyparsing 3.0.9
PyQt5-sip 12.11.0
pyrsistent 0.18.0
PySocks 1.7.1
pytest 7.1.2
python-dateutil 2.8.2
python-lsp-black 1.2.1
python-lsp-jsonrpc 1.0.0
python-lsp-server 1.5.0
python-slugify 5.0.2
python-snappy 0.6.0
pytz 2022.1
pyviz-comms 2.0.2
PyWavelets 1.3.0
pyxdg 0.27
PyYAML 6.0
pyzmq 23.2.0
QDarkStyle 3.0.2
qstylizer 0.1.10
QtAwesome 1.0.3
qtconsole 5.3.2
QtPy 2.2.0
queuelib 1.5.0
regex 2022.7.9
requests 2.28.1
requests-file 1.5.1
rope 0.22.0
Rtree 0.9.7
ruamel-yaml-conda 0.15.100
s3transfer 0.6.0
scikit-image 0.19.2
scikit-learn 1.0.2
scikit-learn-intelex 2021.20221004.171807
scipy 1.9.1
Scrapy 2.6.2
seaborn 0.11.2
SecretStorage 3.3.1
Send2Trash 1.8.0
service-identity 18.1.0
setuptools 63.4.1
sip 6.6.2
six 1.16.0
smart-open 5.2.1
sniffio 1.2.0
snowballstemmer 2.2.0
sortedcollections 2.1.0
sortedcontainers 2.4.0
soupsieve 2.3.1
Sphinx 5.0.2
sphinxcontrib-applehelp 1.0.2
sphinxcontrib-devhelp 1.0.2
sphinxcontrib-htmlhelp 2.0.0
sphinxcontrib-jsmath 1.0.1
sphinxcontrib-qthelp 1.0.3
sphinxcontrib-serializinghtml 1.1.5
spyder 5.3.3
spyder-kernels 2.3.3
SQLAlchemy 1.4.39
statsmodels 0.13.2
sympy 1.10.1
tables 3.6.1
tabulate 0.8.10
TBB 0.2
tblib 1.7.0
tenacity 8.0.1
terminado 0.13.1
testpath 0.6.0
text-unidecode 1.3
textdistance 4.2.1
threadpoolctl 2.2.0
three-merge 0.1.1
tifffile 2021.7.2
tinycss 0.4
tldextract 3.2.0
toml 0.10.2
tomli 2.0.1
tomlkit 0.11.1
toolz 0.11.2
tornado 6.1
tqdm 4.64.1
traitlets 5.1.1
Twisted 22.2.0
typing_extensions 4.3.0
ujson 5.4.0
Unidecode 1.2.0
urllib3 1.26.11
w3lib 1.21.0
watchdog 2.1.6
wcwidth 0.2.5
webencodings 0.5.1
websocket-client 0.58.0
Werkzeug 2.0.3
whatthepatch 1.0.2
wheel 0.37.1
widgetsnbextension 3.5.2
wrapt 1.14.1
wurlitzer 3.0.2
xarray 0.20.1
xlrd 2.0.1
XlsxWriter 3.0.3
yapf 0.31.0
zict 2.1.0
zipp 3.8.0
zope.interface 5.4.0

[alexomics]

I can't see either minknow api or the read until api in that output. Is this for the conda/python environment that you are running readfish from?

[IguodalaYan]

Sorry, the above information is listed in the conda environment.
This is the readfish environment

readfish --version
readfish 0.0.11a4
Miniknow 22.12.5(foca) Minikonw prompted me to update, but I didn't.

[alexomics]

Okay, it looks like nothing is getting installed. Can you try creating a new conda environment:

name: readfish_test
channels:
  - bioconda
  - conda-forge
  - defaults
dependencies:
  - python=3.8
  - pip
  - pip:
    - git+https://github.com/nanoporetech/read_until_api@v3.4.1
    - ont-pyguppy-client-lib==6.4.2
    - git+https://github.com/LooseLab/readfish@dev_staging

You should change the version for ont-pyguppy-client-lib to match the current version on your system.

Copy that code block into a file, for example readfish_test.yml, and then:

create a new environment

conda env create -f readfish_test.yml

activate the environment

conda activate readfish_test

Then try the readfish command again.

[IguodalaYan]

I updated the reply, please see it. Thanks~

[alexomics]

It looks like it’s the read until api that’s outdated. Updating it to v3.4.1 should resolve the issue

[IguodalaYan]

I used the python3 to install the readfish.
It seems not works.

[Adoni5]

Hi @IguodalaYan - try updating the read-until-api with the following command -
pip install git+https://github.com/nanoporetech/read_until_api@v3.4.1 - this will install version 3.4.1