yfarjoun
commented
1 year ago Having the same problem, installed yesterday, using conda for python=3.7 and then pip-install cellbender.
Open asherkhb-ktx opened 1 year ago
yfarjoun
commented
1 year ago Having the same problem, installed yesterday, using conda for python=3.7 and then pip-install cellbender.
sjfleming
commented
1 year ago Hey Yossi! Huh, I will try to replicate this myself. I probably need to pin a version of something that’s had a recent update. Very likely nbconvert
sjfleming
commented
1 year ago @asherkhb-ktx thanks for reporting this. While I figure out the fix, if you wanted to, you could try to generate the report manually. All you need to do is open the Jupyter notebook in this repository
/cellbender/remove_background/report.ipynband manually modify the names of the input and output files and run the notebook. This is how the report gets generated (and it then gets converted to html).
sjfleming
commented
1 year ago Hm, so far I am not able to reproduce this. I am on a Mac, and if I do
(base) $ conda create -n test python=3.7
(base) $ conda activate test
(test) $ pip install cellbenderand then run this on the tiny_raw_feature_bc_matrix.h5ad created by $ python generate_tiny_10x_dataset.py (where generate_tiny_10x_dataset.py is from a clone of cellbender and can be found here), like this
(test) $ cellbender remove-background --input tiny_raw_feature_bc_matrix.h5ad --output test.h5then I do get an HTML report:
cellbender:remove-background: Succeeded in writing CellRanger format output to file tiny_test.h5
cellbender:remove-background: Succeeded in writing CellRanger format output to file tiny_test_filtered.h5
cellbender:remove-background: Saved output metrics as tiny_test_metrics.csv
[NbConvertApp] Converting notebook tmp.report.ipynb to notebook
[NbConvertApp] Writing 416208 bytes to tmp.report.nbconvert.ipynb
[NbConvertApp] Converting notebook tmp.report.nbconvert.ipynb to html
[NbConvertApp] Writing 991091 bytes to tmp.report.nbconvert.html
cellbender:remove-background: Succeeded in writing report to tiny_test_report.html
cellbender:remove-background: Completed remove-background.
cellbender:remove-background: 2023-09-20 11:04:10If I run
(test) $ pip listI see
Package Version
--------------------------------- ------------
anndata 0.8.0
anyio 3.7.1
appnope 0.1.3
argon2-cffi 23.1.0
argon2-cffi-bindings 21.2.0
attrs 23.1.0
backcall 0.2.0
beautifulsoup4 4.12.2
bleach 6.0.0
cellbender 0.3.0
certifi 2022.12.7
cffi 1.15.1
click 8.1.7
comm 0.1.4
cycler 0.11.0
debugpy 1.7.0
decorator 5.1.1
defusedxml 0.7.1
entrypoints 0.4
exceptiongroup 1.1.3
fastjsonschema 2.18.0
fonttools 4.38.0
h5py 3.8.0
idna 3.4
importlib-metadata 6.7.0
importlib-resources 5.12.0
ipykernel 6.16.2
ipython 7.34.0
ipython-genutils 0.2.0
ipywidgets 8.1.1
jedi 0.19.0
Jinja2 3.1.2
jsonschema 4.17.3
jupyter 1.0.0
jupyter_client 7.4.9
jupyter-console 6.6.3
jupyter-contrib-core 0.4.2
jupyter-contrib-nbextensions 0.7.0
jupyter_core 4.12.0
jupyter-highlight-selected-word 0.2.0
jupyter-nbextensions-configurator 0.6.3
jupyter-server 1.24.0
jupyterlab-pygments 0.2.2
jupyterlab-widgets 3.0.9
kiwisolver 1.4.5
llvmlite 0.39.1
loompy 3.0.7
lxml 4.9.3
MarkupSafe 2.1.3
matplotlib 3.5.3
matplotlib-inline 0.1.6
mistune 0.8.4
natsort 8.4.0
nbclassic 1.0.0
nbclient 0.7.4
nbconvert 6.5.4
nbformat 5.8.0
nest-asyncio 1.5.8
notebook 6.5.6
notebook_shim 0.2.3
numba 0.56.4
numexpr 2.8.6
numpy 1.21.6
numpy-groupies 0.9.22
opt-einsum 3.3.0
packaging 23.1
pandas 1.3.5
pandocfilters 1.5.0
parso 0.8.3
pexpect 4.8.0
pickleshare 0.7.5
Pillow 9.5.0
pip 22.3.1
pkgutil_resolve_name 1.3.10
prometheus-client 0.17.1
prompt-toolkit 3.0.39
psutil 5.9.5
ptyprocess 0.7.0
pycparser 2.21
Pygments 2.16.1
pyparsing 3.1.1
pyro-api 0.1.2
pyro-ppl 1.8.6
pyrsistent 0.19.3
python-dateutil 2.8.2
pytz 2023.3.post1
PyYAML 6.0.1
pyzmq 24.0.1
qtconsole 5.4.4
QtPy 2.4.0
scipy 1.7.3
Send2Trash 1.8.2
setuptools 65.6.3
six 1.16.0
sniffio 1.3.0
soupsieve 2.4.1
tables 3.7.0
terminado 0.17.1
tinycss2 1.2.1
torch 1.13.1
tornado 6.2
tqdm 4.66.1
traitlets 5.9.0
typing_extensions 4.7.1
wcwidth 0.2.6
webencodings 0.5.1
websocket-client 1.6.1
wheel 0.38.4
widgetsnbextension 4.0.9
zipp 3.15.0What do you see?
sjfleming
commented
1 year ago ( Note to self: might be some unexpected non-ascii characters in the html report (possibly due to input filename? or gene names?)... and maybe consider this https://stackoverflow.com/questions/27243129/how-to-open-html-file-that-contains-unicode-characters
instead of this https://github.com/broadinstitute/CellBender/blob/4990df713f296256577c92cab3314daeeca0f3d7/cellbender/remove_background/report.py#L59-L60 )
ZhangMH2000
commented
1 year ago @asherkhb-ktx thanks for reporting this. While I figure out the fix, if you wanted to, you could try to generate the report manually. All you need to do is open the Jupyter notebook in this repository
/cellbender/remove_background/report.ipynband manually modify the names of the input and output files and run the notebook. This is how the report gets generated (and it then gets converted to html).
Hi sjfleming. I also encountered this issue, which showed a warning or an error:
cellbender:remove-background: Unable to create report.
cellbender:remove-background: Traceback (most recent call last):
File "/home/zhangminghe/project/miniconda3/envs/cellbender/lib/python3.7/site-packages/cellbender/remove_background/run.py", line 351, in compute_output_denoised_counts_reports_metrics
output=html_report_file,
File "/home/zhangminghe/project/miniconda3/envs/cellbender/lib/python3.7/site-packages/cellbender/remove_background/report.py", line 82, in run_notebook_make_html
title=('CellBender: ' + os.path.basename(output).replace('_report.html', '')),
File "/home/zhangminghe/project/miniconda3/envs/cellbender/lib/python3.7/site-packages/cellbender/remove_background/report.py", line 60, in _postprocess_html
html = f.read()
File "/home/zhangminghe/project/miniconda3/envs/cellbender/lib/python3.7/encodings/ascii.py", line 26, in decode
return codecs.ascii_decode(input, self.errors)[0]
UnicodeDecodeError: 'ascii' codec can't decode byte 0xee in position 232667: ordinal not in range(128)However, I have a file named ‘tHCC15_cellbender_output_report.html’ in the output. This HTML file also contains information about the process. So, does this warning merely indicate that some characters cannot be encoded correctly, without affecting the overall report output? Thank you!
sjfleming
commented
1 year ago Hi @ZhangMH2000 , yes, if you have tHCC15_cellbender_output_report.html as an output file, then the contents of that file are fine. The step that is failing (for you, and maybe for some other people) is a superficial sort of a step to rename the title of the HTML report so that it looks like this when you open it:
When the error you're seeing occurs, the only difference will be that you will probably see a different title when you look at the label on the tab.
I will fix this eventually though! @ZhangMH2000 do you know if you have non-ascii characters in the name of your file?
sjfleming
commented
1 year ago Hm, or maybe the non-ascii characters could be part of feature names, I suppose
ZhangMH2000
commented
1 year ago Hi @sjfleming , the title of tHCC15_cellbender_output_report.html istmp.report.nbconvert. I don't see any non-ascii characters in the name of my input file. Other reports have correct names, such as Cellbender:tHCC16_cellbender_output. Thank you!
sjfleming
commented
1 year ago Thanks @ZhangMH2000 , good to know
Running Cellbender 0.3.0 it reports "Unable to create report" with the following Traceback,
"pip install" did yield two Errors, which may be related but didn't seem to interfere elsewhere: