Sigprofileextractor GRCh38 Exome Reference File Not Found Error After Installation

[kevlumbus]

Hi,

I am planning to use VCF files for my samples to look for gene signatures in GRCh38, and followed your code to install the GRCh38 reference:

> library(SigProfilerExtractorR)
> install("GRCh38", rsync=FALSE, bash=TRUE)
Beginning installation. This may take up to 40 minutes to complete.
The transcriptional reference data for GRCh38 has been saved.
All reference files have been created.
Verifying and benchmarking installation now...
Starting matrix generation for SNVs and DINUCs...Completed! Elapsed time: 2.12 seconds.
Matrices generated for 1 samples with 0 errors. Total of 9631 SNVs, 0 DINUCs, and 0 INDELs were successfully analyzed.
Installation was succesful.
SigProfilerMatrixGenerator took 7.2261998653411865 seconds to complete.
To proceed with matrix_generation, please provide the path to your vcf files and an appropriate output path.
Installation complete.

However when I run sigprofilerextractor I am given a file not found error message. Is there another way to get the exome.interval_list?:

> sigprofilerextractor("vcf",".","vcf",reference_genome = "GRCh38",exome = TRUE)

************** Reported Current Memory Use: 0.61 GB *****************

Starting matrix generation for SNVs and DINUCs...Error: FileNotFoundError: [Errno 2] No such file or directory: '/home/python/Python-3.10.11_install/lib/python3.10/site-packages/SigProfilerMatrixGenerator/references/chromosomes/exome/GRCh38/GRCh38_exome.interval_list'

[mdbarnesUCSD]

Hi @kevlumbus,

Thanks for reaching out. This is an issue from SigProfilerMatrixGenerator that has been resolved in the v1.2.16 update.

pip install --upgrade SigProfilerMatrixGenerator

Please reach out if you encounter any additional issues.