Error - unused argument (sample_reconstruction_plots = sample_reconstruction_plots)

[eltonjrv]

Dear SigProfilerAssignmentR developers,

Thanks for the tool!

I've successfully (I believe) gone through all your installation steps. When attempting to run cosmic_fit I'm getting stuck with the following error:

cosmic_fit(samples="./", output="./", input_type='vcf', context_type="96", collapse_to_SBS96=TRUE, cosmic_version=3.3, exome=FALSE, genome_build="GRCh38") Error in Analyze$cosmic_fit(samples = samples, output = output, signatures = signatures, : unused argument (sample_reconstruction_plots = sample_reconstruction_plots)

Below is my python config:

library(reticulate) py_config() python: /nobackup/fbsev/bioinformatics-tools/miniconda3/envs/SigProfAssignR/bin/python3 libpython: /nobackup/fbsev/bioinformatics-tools/miniconda3/envs/SigProfAssignR/lib/libpython3.7m.so pythonhome: /nobackup/fbsev/bioinformatics-tools/miniconda3/envs/SigProfAssignR:/nobackup/fbsev/bioinformatics-tools/miniconda3/envs/SigProfAssignR version: 3.7.12 | packaged by conda-forge | (default, Oct 26 2021, 06:08:21) [GCC 9.4.0] numpy: /nobackup/fbsev/bioinformatics-tools/miniconda3/envs/SigProfAssignR/lib/python3.7/site-packages/numpy numpy_version: 1.21.6 sys: [builtin module]

Any clue on that? I'm not even typing the "sample_reconstruction_plots" parameter from cosmic_fit function.

Thanks

[marcos-diazg]

Dear @eltonjrv,

Thanks so much for your interest in our tool. Could you please check which version of the Python package for SigProfilerAssignment you are using? You can do that by typing pip list from your terminal.

Thanks! Best,

Marcos

[eltonjrv]

Thanks for your prompt reply, Marcos. Here it goes: $ pip list Package Version

---

about-time 4.2.1 alive-progress 3.1.5 argcomplete 1.12.3 biopython 1.76 chardet 5.2.0 charset-normalizer 2.0.12 cryptography 36.0.2 cycler 0.11.0 dnaio 0.5.0 dxpy 0.337.0 eggnog-mapper 2.1.12 grapheme 0.6.0 joblib 1.3.2 kiwisolver 1.4.5 matplotlib 3.4.3 numpy 1.21.6 packaging 23.2 pandas 1.3.5 patsy 0.5.6 Pillow 9.5.0 pip 24.0 psutil 5.9.4 pyparsing 3.1.1 PyPDF2 3.0.1 python-dateutil 2.8.2 pytz 2024.1 reportlab 4.1.0 requests 2.27.1 scikit-learn 1.0.2 scipy 1.7.3 seaborn 0.12.2 setuptools 69.0.3 SigProfilerAssignment 0.0.19 SigProfilerMatrixGenerator 1.2.13 sigProfilerPlotting 1.3.2 six 1.16.0 sklearn 0.0.post12 statsmodels 0.13.5 threadpoolctl 3.1.0 typing_extensions 4.7.1 websocket-client 0.54.0 wheel 0.42.0 XlsxWriter 1.4.3 xopen 1.0.1

Thanks again

[marcos-diazg]

Thanks for sending this! Could you please upgrade your SigProfilerAssignment Python package? You can do that by running pip install SigProfilerAssignment --upgrade. You are currently using a pretty old version (v0.0.19, from November 2022). Updating to the most recent v0.1.3 should solve your issue, but please let us know if that's not the case.

[eltonjrv]

Hi Marcus,

I've run the upgrade command you told me, but it maintains v0.0.19. Attached is a log file from that upgrade command. Any other tip to get it upgraded?

Thanks upgrade.log

[marcos-diazg]

Hi again Elton,

Unfortunately, I think the version of Python/Matplotlib installed in your SigProfAssignR conda environment is too old for the newest SigProfilerAssignment to be installed. That's why Pip is maintaining v0.0.19. I suggest creating a new conda environment with Python 3.10 and installing the newest SigProfilerAssignment. You can do that by running the following:

conda create --name new_SigProfAssignR -y
conda activate new_SigProfAssignR
conda install python=3.10 -y
pip install SigProfilerAssignment

After this, you just need to connect the new Python installation with R and Reticulate by using the commands explained in the README. I hope this helps, and please let me know if you still have any issues or have further questions.

Thanks again for your interest! Best,

Marcos

[eltonjrv]

Thanks a lot Marcos! Issue solved under python 3.10. I've now got the following versions in my new conda environment: SigProfilerAssignment 0.1.3 SigProfilerMatrixGenerator 1.2.25 sigProfilerPlotting 1.3.20

I'm now experiencing an issue of cosmic_fit not recognizing my MAF format. I'll try to work around this for a while, and will then open a new issue herein in case I can't circumvent.

Thanks again, Best, Elton

[marcos-diazg]

Hi Elton!

I'm glad the issue was solved. Regarding any formatting issues, the input handling for all SigProfiler tools is done by SigProfilerMatrixGenerator (or its R counterpart, SigProfilerMatrixGeneratorR). I recommend checking the README of the tools, as well as their wiki page. Example files are usually very useful to troubleshoot any formatting issues with your input files.

I hope this helps, and please feel free to reopen the GitHub ticket if needed.

Best wishes,

Marcos