Closed JLiandbear closed 1 year ago
Please update sigProfilerPlotting to v1.3.5 or newer. The issue should be resolved in that release. Please reach out if the issue persists.
Please update sigProfilerPlotting to v1.3.5 or newer. The issue should be resolved in that release. Please reach out if the issue persists.
Thanks for the quick reply. I have upgrade my python and sigProfilerPlotting to the latest version and get the test run done without any error.
Here's my command:
data="/mnt/research-data/PRJ-CRC/JunLi/IMAP/WES/SigProfiler/vcf" sig.sigProfilerExtractor("vcf", "Extractor_test", data, reference_genome="GRCh38", opportunity_genome = "GRCh38", exome = True, minimum_signatures=1, maximum_signatures=2)
However, I notice in 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 in advance
Hi SigProfiler team I had the following error while running:
There may be an issue with the formatting of your matrix file. Traceback (most recent call last): File "/home/julie/envs/SigProfiler/lib/python3.7/site-packages/sigProfilerPlotting/sigProfilerPlotting.py", line 4743, in plotDBS fig_orig=pickle.load(open(spplt.path[0]+'/templates/DBS78.pkl','rb')) FileNotFoundError: [Errno 2] No such file or directory: '/home/julie/envs/SigProfiler/lib/python3.7/site-packages/sigProfilerPlotting/templates/DBS78.pkl'
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "", line 1, in
File "/home/julie/envs/SigProfiler/lib/python3.7/site-packages/SigProfilerExtractor/sigpro.py", line 789, in sigProfilerExtractor
sub.export_information(loopResults, m, layer_directory, index, colnames, wall=wall, sequence=sequence)
File "/home/julie/envs/SigProfiler/lib/python3.7/site-packages/SigProfilerExtractor/subroutines.py", line 1110, in export_information
plot.plotDBS(signature_subdirectory+"/"+mutation_type+"_S"+str(i)+"_Signatures"+".txt", signature_subdirectory+"/Signature_plot" , "S"+str(i), "78", True, custom_text_upper=stability_list, custom_text_middle=total_mutation_list)
File "/home/julie/envs/SigProfiler/lib/python3.7/site-packages/sigProfilerPlotting/sigProfilerPlotting.py", line 4883, in plotDBS
os.remove(output_path + 'DBS_78plots' + project + '.pdf')
FileNotFoundError: [Errno 2] No such file or directory: 'Extractor_test/DBS78/All_Solutions/DBS78_1_Signatures/Signatures/Signature_plotDBS_78_plots_S1.pdf'
I have read issue #170, removed previous SigProfilerPlotting and re-install SigProfilerPlotting-1.3.2. I am using: python 3.7.15 SigProfilerAssignment-0.0.19 SigProfilerExtractor-1.1.15 SigProfilerMatrixGenerator-1.2.13 sigProfilerPlotting-1.3.2 matplotlib 3.4.3
Thank you in advance for any advice. Regards