Encountering an error when I use the mt_tally() function

[shruthi-kon]

My WES files were aligned using hg38 reference genome so I did this:

if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")

BiocManager::install("BSgenome.Hsapiens.UCSC.hg38")

mt_tally <- sig_tally(
laml,
ref_genome = "BSgenome.Hsapiens.UCSC.hg38",
useSyn = TRUE
)

When I run the mt_tally() bit, I keep getting the following error:
ℹ [2023-10-21 17:22:39.280206]: Started.
ℹ [2023-10-21 17:22:39.296688]: We would assume you marked all variants' position in + strand.
✔ [2023-10-21 17:22:39.307778]: Reference genome loaded.
✔ [2023-10-21 17:22:39.325717]: Variants from MAF object queried.
✔ [2023-10-21 17:22:39.338438]: Chromosome names checked.
✔ [2023-10-21 17:22:39.351011]: Sex chromosomes properly handled.
✔ [2023-10-21 17:22:39.364481]: Only variants located in standard chromosomes (1:22, X, Y, M/MT) are kept.
✔ [2023-10-21 17:22:39.379309]: Variant start and end position checked.
✔ [2023-10-21 17:22:39.40431]: Variant data for matrix generation preprocessed.
ℹ [2023-10-21 17:22:39.415875]: SBS matrix generation - start.
ℹ [2023-10-21 17:22:39.429239]: Extracting 5' and 3' adjacent bases.
Error in .Call2("C_solve_user_SEW", refwidths, start, end, width, translate.negative.coord, :
solving row 1277: the supplied start/end lead to a negative width
ℹ [2023-10-21 17:22:39.445001]: 0.165 secs elapsed.

I tried excluding the variant at the row number and re-ran it but it gives me the same issue at another row.

I would appreciate your help in fixing this. Thank you.

[ShixiangWang]

Hi, @shruthi-kon Could you share your data to shixiang1994wang@gmail.com for debugging purposes?

[ShixiangWang]

Or at a minimal data set (subset of your data) for reproducing your error