SigProfilerSimulator gives "UnboundLocalError: local variable 'dinuc_mat' referenced before assignment"

[burcakotlu]

Dear all,

I'm running SigProfilerTopography while simulating mutations with a bed file (chrom_based=True, seqInfo=True, exome=None, cushion=0).

You can reach the python here: /tscc/nfs/home/burcak/developer/SigProfilerTopographyRuns/Mutographs_ESCC_552/pbs_py_files/all_escc_552_samples_ENCFF169EST_H3K4me1_simulations.py

As you can find in the SPT call python file, bed file is here and has no Y chromosome :
bed_file = "/tscc/lustre/restricted/alexandrov-ddn/users/burcak/data/bed_for_SPS/ENCFF169EST_H3K4me1_regions_for_simulator.bed"

Again as you can see from the SPT call python file, input files are under
inputDir= '/tscc/lustre/restricted/alexandrov-ddn/users/burcak/SigProfilerTopographyRuns/Mutographs_ESCC_552/all_escc_552_samples_ENCFF169EST_H3K4me1_simulations'

However, SPMG gives the following error:

Traceback (most recent call last):
File "/tscc/nfs/home/burcak/developer/SigProfilerTopographyRuns/Mutographs_ESCC_552/pbs_py_files/all_escc_552_samples_ENCFF169EST_H3K4me1_simulations.py", line 51, in
topography.runAnalyses(genome,
File "/tscc/nfs/home/burcak/.local/lib/python3.9/site-packages/SigProfilerTopography/Topography.py", line 2138, in runAnalyses
simulator.SigProfilerSimulator(jobname,
File "/tscc/nfs/home/burcak/.local/lib/python3.9/site-packages/SigProfilerSimulator/SigProfilerSimulator.py", line 291, in SigProfilerSimulator
matGen.SigProfilerMatrixGeneratorFunc(project, genome, project_path ,plot=False, exome=exome, bed_file=bed_file, chrom_based=True, cushion=cushion)
File "/tscc/nfs/home/burcak/.local/lib/python3.9/site-packages/SigProfilerMatrixGenerator/scripts/SigProfilerMatrixGeneratorFunc.py", line 2078, in SigProfilerMatrixGeneratorFunc
matrices["DINUC"] = dinuc_mat
UnboundLocalError: local variable 'dinuc_mat' referenced before assignment

SPMG log files are under:
/tscc/lustre/restricted/alexandrov-ddn/users/burcak/SigProfilerTopographyRuns/Mutographs_ESCC_552/all_escc_552_samples_ENCFF169EST_H3K4me1_simulations/logs

I hope you can help me to resolve this issue asap.

Best wishes,
Burcak

[burcakotlu]

My concern is the bed file.

This bed file contains the H3K4me1 regions and their left (100KB) and right (100KB) flanking regions.
bed_file = "/tscc/lustre/restricted/alexandrov-ddn/users/burcak/data/bed_for_SPS/ENCFF169EST_H3K4me1_regions_for_simulator.bed"

Due to the flanking regions, it might have overlapping regions. Might this create a problem?