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AlexandrovLab / SigProfilerMatrixGenerator

SigProfilerMatrixGenerator creates mutational matrices for all types of somatic mutations. It allows downsizing the generated mutations only to parts for the genome (e.g., exome or a custom BED file). The tool seamlessly integrates with other SigProfiler tools.
BSD 2-Clause "Simplified" License
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An IndexError with generating the mutational matrix #185

Closed Xinwen1206 closed 4 months ago

Xinwen1206 commented 5 months ago

I got this error when I run this function in R. Do you know why it comes from and how I can address it?

Running SigProfilerMatrixGeneratorR... Starting matrix generation for SNVs and DINUCs... Error in py_call_impl(callable, call_args$unnamed, call_args$named) : IndexError: index out of range

It seems come from this code: catalogue_generator_single at MutationMatrixGenerator.py#451 for l in range(start1 + 1, start2, 1): if l - 1 < len(chrom_string):

Thanks!

mdbarnesUCSD commented 4 months ago

Hi @Xinwen1206,

Could you please provide the full list of commands that you used to run the code? Also, what input are you using?

Thanks!

Xinwen1206 commented 4 months ago

Hi @mdbarnesUCSD,

Thanks so much for your reply! I found that the error was caused by using the wrong genome. Once I corrected it, the error was resolved.