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AlexandrovLab / SigProfilerExtractor

SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.
BSD 2-Clause "Simplified" License
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Generating plots for COSMIC_v3.3_DBS_GRCh37 now... #182

Closed JLiandbear closed 1 year ago

JLiandbear commented 1 year ago

Hello, Really appreciate your support towards the analysis of SigProfiler. I have noticed something a bit strange during my analysis. Would be grateful to confirm with you whether this is a real concern. Here's my command:

data="/mnt/research-data/SigProfiler/vcf" sig.sigProfilerExtractor("vcf", "Extractor_test", data, reference_genome="GRCh38", opportunity_genome = "GRCh38", exome = True, minimum_signatures=1, maximum_signatures=2)

I notice on screen message, it used COSMIC_v3.3_DBS_GRCh37 and COSMIC_v3.3_SBS_GRCh37 to generate plots. " Decomposing De Novo Signatures ..... Generating plots for COSMIC_v3.3_DBS_GRCh37 now... Plots for COSMIC_v3.3_DBS_GRCh37 have been successfully installed. Decompositon Plot:DBS78A |▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉| 1/1 [100%]

Assigning decomposed signature |████████████████████████████████████████| 74/74 [100%] in 0.5s (163.88/s)

Your Job Is Successfully Completed! Thank You For Using SigProfilerAssignment."

My data was based on GRCh38 and I installed GRCh38 reference genome using command:

from SigProfilerMatrixGenerator import install as genInstall genInstall.install('GRCh38', bash=True)

I looked into COSMIC Mutational Signatures Data Files and there're GRCh38 SBS and DBS versions.

I am wondering whether I am using wrong settings? Please advise where I am possibly wrong. Here's the version info of installations: Successfully installed PyMuPDF-1.21.0 PyPDF2-2.11.2 SigProfilerAssignment-0.0.20 SigProfilerExtractor-1.1.16 SigProfilerMatrixGenerator-1.2.13 about-time-3.1.1 alive-progress-2.4.1 cycler-0.11.0 grapheme-0.6.0 joblib-1.2.0 kiwisolver-1.4.4 matplotlib-3.4.3 nimfa-1.4.0 numpy-1.23.5 nvidia-cublas-cu11-11.10.3.66 nvidia-cuda-nvrtc-cu11-11.7.99 nvidia-cuda-runtime-cu11-11.7.99 nvidia-cudnn-cu11-8.5.0.96 packaging-21.3 pandas-1.5.2 patsy-0.5.3 pdf2image-1.16.0 pillow-9.3.0 psutil-5.9.4 pyparsing-3.0.9 python-dateutil-2.8.2 pytz-2022.6 reportlab-3.6.12 scikit-learn-1.1.3 scipy-1.9.3 sigProfilerPlotting-1.3.6 statsmodels-0.13.5 threadpoolctl-3.1.0 torch-1.13.0 typing_extensions-4.4.0

Thank you very much

mdbarnesUCSD commented 1 year ago

Hi @JLiandbear,

Thank you for reaching out with this issue. This issue is specific to the decomposition plots and was introduced with the v0.0.20 SigProfilerAssignment update and should be resolved in SigProfilerAssignment's v0.0.21 update (pull request #60). Please reach out if you continue to receive this issue after updating SigProfilerAssignment to v0.0.21.

Thanks, Mark