sigProfilerExtractor for ID(INDELS) about sigprofilerextractor

[mdbarnesUCSD]

Hi @shanimalik86,

Could you please provide the JOB_METADATA.txt from the output directory?

Thanks!

[shanimalik86]

Hi, Thanks for your response.

Below I copied the JOB_METADATA.txt

THIS FILE CONTAINS THE METADATA ABOUT SYSTEM AND RUNTIME

-------System Info-------
Operating System Name: Linux
Nodename: ai-hpcgpu15
Release: 3.10.0-1160.11.1.el7.x86_64
Version: #1 SMP Mon Nov 30 13:05:31 EST 2020

-------Python and Package Versions-------
Python Version: 3.7.3
SigProfilerExtractor Version: 1.1.15
SigProfilerPlotting Version: 1.3.2
SigProfilerMatrixGenerator Version: 1.2.13
SigProfilerAssignment Version: 0.0.19
Pandas version: 1.2.4
Numpy version: 1.21.6
Scipy version: 1.7.3
Scikit-learn version: 1.0.2

--------------EXECUTION PARAMETERS--------------
INPUT DATA
input_type: matrix
output: SOMATIC_SalivaResults_Pon_IDs
input_data: /hpcdata/dir/ZEESHAN/2024-03-02-mutationalsignature/SOMATIC_Saliva_Pon/SALIVA_Extractor/SALIVA_PON.ID96.txt
reference_genome: GRCh37
context_types: SBS96
exome: False
NMF REPLICATES
minimum_signatures: 1
maximum_signatures: 10
NMF_replicates: 100
NMF ENGINE
NMF_init: random
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: 56; Maximum number of CPU is 56
gpu: False
Solution Estimation
stability: 0.8
min_stability: 0.2
combined_stability: 1.0
allow_stability_drop: False
COSMIC MATCH
opportunity_genome: GRCh37
cosmic_version: 3.3
nnls_add_penalty: 0.05
nnls_remove_penalty: 0.01
initial_remove_penalty: 0.05
export_probabilities: True
collapse_to_SBS96: True

-------Analysis Progress-------
[2024-03-11 15:37:32] Analysis started:

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

[2024-03-11 15:37:32] Analysis started for SBS96. Matrix size [96 rows x 79 columns]

[2024-03-11 15:37:32] Normalization GMM with cutoff value set at 9600

[shanimalik86]

I got SALIVA_PON.ID96.all from Matrix script and changed the extension to .txt and gave this file to Sigprofile extractor> I followed the same process which I did for SNVs but For ID(INDEL analysis) I get error

[mdbarnesUCSD]

Hi @shanimalik86,

Thanks for sending this over. It looks like your input is single base substitutions and not indels. Would it be possible for you to share your input matrix that is causing this error? If so, could you please e-mail it to me. My e-mail is on the README.

Thanks!

[mdbarnesUCSD]

If you are still encountering this issue, please first update to sigProfilerPlotting v1.3.22. If the issue persists, please re-open this issue. Thanks!