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Error in .Call2("C_solve_user_SEW", refwidths, start, end, width, translate.negative.coord

Dear guys,

Any solutions for the error when trying to construct the trinucleotideMatrix?

test_maf.tnm = trinucleotideMatrix(maf = test_maf,  ref_genome = "BSgenome.Hsapiens.UCSC.hg38" ) ## some site/region cause the error
-Extracting 5' and 3' adjacent bases
-Extracting +/- 20bp around mutated bases for background C>T estimation
Error in .Call2("C_solve_user_SEW", refwidths, start, end, width, translate.negative.coord,  : 
  solving row 999368: 'allow.nonnarrowing' is FALSE and the supplied end (38055) is > refwidth

Though changing the C_solve_user_SEW function to set the allow.nonnarrowing to TRUE by copying the whole IRanges-constructor.R script, it does not affect, and still shows the allow.nonnarrowing is FALSE.

Thanks a lot for any guidance!

maftools
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updated by garcesj • garcesj • written by alwayshope • alwayshope

Dear all, I encounter the exact same issue, did you manage to find a solution for this error? Thanks a lot!

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written by Charles.G • Charles.G

1 answer

I had the same error running a similar tool. It came from using a different genome reference between the tool and the MAF: the error says the length of one of your chromosomes is bigger than the reference the tool is using.

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written by garcesj • garcesj

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