error in de_novo_fit_penalty
Closed this issue · 6 comments
Hi, I'm trying to use sigprofiler to extract mutations from mm10 catalogues.
I'm getting an error when I run the code:
Line:
sigprofilerextractor("vcf",
"sigprofiler",
"/Volumes/archive/cancergeneticslab/ConorM/MouseAnalysis/totalVCFhets/",
"mm10")
Error:
TypeError: sigProfilerExtractor() got an unexpected keyword argument 'de_novo_fit_penalty'
Other info:
sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux
py_config()
python: /usr/bin/python3.6
libpython: /usr/lib64/libpython3.6m.so
pythonhome: //usr://usr
version: 3.6.8 (default, Aug 13 2020, 07:46:32) [GCC 4.8.5 20150623 (Red Hat 4.8.5-39)]
numpy: /usr/local/lib64/python3.6/site-packages/numpy
numpy_version: 1.17.4
sys: [builtin module]
NOTE: Python version was forced by use_python function
Trying to set de_novo_fit_penalty manually did not help. Any suggestions?
Thanks
Conor
Dear Conor,
Thanks so much for your question. Could you please check that you are using the latest SigProfilerExtractor version? You can do that by running pip install SigProfilerExtractor --upgrade. Also, you can try to install the tool on a specific conda environment by using the following commands:
conda create --name sigprofilerextractorR -y
conda activate sigprofilerextractorR
conda install -c conda-forge r-base r-devtools r-reticulate python=3.9 -y
echo 'devtools::install_github("AlexandrovLab/SigProfilerExtractorR")' | Rscript -
Please let me know if this helps. Best,
Marcos
Please reopen the ticket if you are still experiencing any issues. Thanks for your interest!
Hi, I'm experiencing the same issue after having updated SigProfilerExtractor to v1.1.13
As indicated in #10, this has now been fixed in the most recent v1.1.13 of SigProfilerExtractorR. Thanks for letting us know, and sorry for the inconvenience.
Hi! sorry If I'm taking back this issue, but I had a similar error with the version 1.1.16. I installed it with pip (pip install SigProfilerExtractor) and found a similar error, that is
TypeError: sigProfilerExtractor() got an unexpected keyword argument 'refit_denovo_signatures'
Then, thanks to your comments, I tried to solve the problem by dowloading the v1.1.13 (pip install SigProfilerExtractor==1.1.13) and everything worked fine. I don't know if is a bug or something else but I just wanted to report this.
Thank you for your tool,
Giuseppe.
Dear @Giuseppe1995,
Thanks for reaching out. This issue has now been solved in the newest version of SigProfilerExtractorR v1.1.16. Please proceed to update the package and let us know if you have any further problems.