Open wendy0853 opened 7 months ago
I got same errors.
Same, with latest version set up in Conda on Linux
Hi, Thanks for developing CellBender! I also got the same error today using python 3.7.16 and cellbender 0.3.0 in conda. Thank you
Edit: I just figured out why it was not working for me: I needed to install manually lxml_html_clean in my conda environment. It then worked!
Same, with latest version set up in Conda on Linux
With latest/master version (19 April), the issue no longer arises in my setup.
I am having a similar issue with the official 0.3.0 docker image
cellbender:remove-background: Unable to create report.
cellbender:remove-background: Traceback (most recent call last):
File "/opt/conda/lib/python3.7/site-packages/cellbender/remove_background/run.py", line 351, in compute_output_denoised_counts_reports_metrics
output=html_report_file,
File "/opt/conda/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 "/opt/conda/lib/python3.7/site-packages/cellbender/remove_background/report.py", line 59, in _postprocess_html
with open(file, mode='r') as f:
FileNotFoundError: [Errno 2] No such file or directory: 'cellbender_report.html'
cellbender:remove-background: Completed remove-background.
cellbender:remove-background: 2024-05-03 19:42:01
I got the same error message using python 3.7.16 and cellbender 0.3.0 in linux-x64
I got the same error message using python 3.7.16 and cellbender 0.3.0 in linux-x64
fixed after pip install lxml_html_clean
The solution provided by @zofieLin worked for me (virtual environment on both my macOS and my Linux server).
pip install lxml_html_clean
Thanks so much!
I didn't encounter this problem when I was using v0.3.1. But now as the software has been temporarily downgraded to v0.3.0 (due to a bug announced on the main page), this error message showed up after running the program for almost a whole day. Strongly suggest the developer team should add this to the installation instructions.
I'm also using an old version for GPU compatibility, but I fail to generate the html file even after installing via pip install lxml_html_clean in my environment. Any other thoughts on this?
Hello!
This is my first time running CellBender and I'm so happy I got it to work! However, when looking over the output files, it seems like I'm missing an output_report.html file. Below is the log for the failure. I used python3.8 and CellBender v0.3.1. Please let me know if there's anything I can do to obtain the html summary. Thanks!