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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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Gave SBS output when input is DBS #81

Closed shaoyiZ closed 3 years ago

shaoyiZ commented 3 years ago

When I run the extractor for my DBS.all outputs from MatrixGenerater, the extractor still gave me SBS outputs in the results file. Can you give some insights into what might have caused this issue?

Thanks a lot, Shaoyi

ntbeileh commented 3 years ago

Could you attach your JOB_METADATA.txt from the run so I can take a look?

shaoyiZ commented 3 years ago

Hi!

Thanks for replying! Here is the METADATA: THIS FILE CONTAINS THE METADATA ABOUT SYSTEM AND RUNTIME

-------System Info------- Operating System Name: Darwin Nodename: Shaoyis-Mini Release: 20.5.0 Version: Darwin Kernel Version 20.5.0: Sat May 8 05:10:31 PDT 2021; root:xnu-7195.121.3~9/RELEASE_ARM64_T8101

-------Python and Package Versions------- Python Version: 3.9.5 Sigproextractor Version: 1.0.15 SigprofilerPlotting Version: 1.1.15 SigprofilerMatrixGenerator Version: 1.1.28 Pandas version: 1.2.4 Numpy version: 1.20.3 Scipy version: 1.6.3 Scikit-learn version: 0.24.2

--------------EXECUTION PARAMETERS-------------- INPUT DATA input_type: matrix output: DBS1- input_data: /Users/shaoyizhang/Desktop/DNV-/output/DBS/ASD-.DBS186.all reference_genome: GRCh37 context_types: SBS186 exome: False NMF REPLICATES minimum_signatures: 1 maximum_signatures: 10 NMF_replicates: 100 NMF ENGINE NMF_init: nndsvd_min precision: single matrix_normalization: gmm resample: True seeds: random min_NMF_iterations: 10,000 max_NMF_iterations: 1,000,000 NMF_test_conv: 10,000 NMF_tolerance: 1e-15 CLUSTERING clustering_distance: cosine EXECUTION cpu: 8; Maximum number of CPU is 8 gpu: False Solution Estimation stability: 0.8 min_stability: 0.2 combined_stability: 1.0 COSMIC MATCH opportunity_genome: GRCh37 nnls_add_penalty: 0.05 nnls_remove_penalty: 0.01 initial_remove_penalty: 0.05 de_novo_fit_penalty: 0.02 refit_denovo_signatures: True

-------Analysis Progress------- [2021-06-11 18:10:51] Analysis started:

##################################

[2021-06-11 18:10:51] Analysis started for SBS186. Matrix size [186 rows x 1 columns]

[2021-06-11 18:10:51] Normalization GMM with cutoff value set at 18600

[2021-06-11 18:31:04] SBS186 de novo extraction completed for a total of 1 signatures! Execution time:0:20:12

[2021-06-11 18:31:05] Analysis ended:

-------Job Status------- Analysis of mutational signatures completed successfully! Total execution time: 0:20:13 Results can be found in: DBS1- folder

shaoyiZ commented 3 years ago

Now that I looked into this metadata, it seems like it has started analysis for SBS186, not DBS. But I am pretty sure I directly used the DBS.ALL file that was generated by the matrix generator (as you can see in the input data log).

ntbeileh commented 3 years ago

As of now SigProfilerExtractor does not support decomposition plots for DBS186. However all other outputs that you got labeled SBS186 are the correct results corresponding to DBS186. The name is just labeled SBS186 even though they are actually results for DBS186.

shaoyiZ commented 3 years ago

Thanks a lot!

Sincerely, Shaoyi