CellBender ran successfully but no HTML report generated
wendy0853 opened this issue · 9 comments
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!
cellbender:remove-background: Working on chunk (5/6)
cellbender:remove-background: Working on chunk (6/6)
cellbender:remove-background: 2024-02-26 20:42:04 Total MCKP estimation time = 94.20 sec
cellbender:remove-background: Succeeded in writing CellRanger format output to file cellbender_results.h5
cellbender:remove-background: Succeeded in writing CellRanger format output to file cellbender_results_filtered.h5
cellbender:remove-background: Saved output metrics as cellbender_results_metrics.csv
cellbender:remove-background: Unable to create report.
cellbender:remove-background: Traceback (most recent call last):
File "/Users/wendy/Documents/Programming/Programming/snRNA-Seq//CellBender/cellbender/remove_background/run.py", line 368, in compute_output_denoised_counts_reports_metrics
run_notebook_make_html(
File "/Users/wendy/Documents/Programming/Programming/snRNA-Seq//CellBender/cellbender/remove_background/report.py", line 84, in run_notebook_make_html
html_file = _to_html(file=_run_notebook(file), output=output)
File "/Users/wendy/Documents/Programming/Programming/snRNA-Seq//CellBender/cellbender/remove_background/report.py", line 54, in _to_html
os.replace(file.replace(".ipynb", ".html"), output)
FileNotFoundError: [Errno 2] No such file or directory: 'tmp.report.nbconvert.html' -> 'cellbender_results_report.html'
cellbender:remove-background: Completed remove-background.
cellbender:remove-background: 2024-02-26 20:42:16
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.