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Running trinucleotideMatrix generates Error in.Call2

Open Olsennnnn opened this issue 10 months ago • 10 comments

Hi, While running, I got a mistake, like`

laml.tnm = trinucleotideMatrix(maf = maf,ref_genome = "BSgenome.Hsapiens.UCSC.hg38")
-Extracting 5' and 3' adjacent bases
Error in .Call2("C_solve_user_SEW", refwidths, start, end, width, translate.negative.coord,  : 
  solving row 32714: 'allow.nonnarrowing' is FALSE and the supplied start (242366418) is > refwidth + 1`.

sessionInfo

R version 4.3.1 (2023-06-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.6 LTS

Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so;  LAPACK version 3.9.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: Asia/Shanghai
tzcode source: system (glibc)

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] BSgenome.Hsapiens.UCSC.hg19_1.4.3 BSgenome.Hsapiens.UCSC.hg38_1.4.5
 [3] BSgenome_1.70.1                   rtracklayer_1.62.0               
 [5] BiocIO_1.12.0                     Biostrings_2.70.1                
 [7] XVector_0.42.0                    GenomicRanges_1.54.1             
 [9] GenomeInfoDb_1.38.5               IRanges_2.36.0                   
[11] S4Vectors_0.40.2                  BiocGenerics_0.48.1              
[13] maftools_2.16.0                  

loaded via a namespace (and not attached):
 [1] Matrix_1.6-4                compiler_4.3.1              rjson_0.2.21               
 [4] crayon_1.5.2                SummarizedExperiment_1.32.0 Biobase_2.62.0             
 [7] Rsamtools_2.18.0            bitops_1.0-7                GenomicAlignments_1.38.0   
[10] parallel_4.3.1              splines_4.3.1               BiocParallel_1.36.0        
[13] yaml_2.3.8                  lattice_0.22-5              DNAcopy_1.76.0             
[16] S4Arrays_1.2.0              XML_3.99-0.16               DelayedArray_0.28.0        
[19] MatrixGenerics_1.14.0       GenomeInfoDbData_1.2.11     RColorBrewer_1.1-3         
[22] SparseArray_1.2.3           zlibbioc_1.48.0             grid_4.3.1                 
[25] rstudioapi_0.15.0           data.table_1.15.2           codetools_0.2-19           
[28] survival_3.5-7              abind_1.4-5                 RCurl_1.98-1.13            
[31] restfulr_0.0.15             matrixStats_1.2.0           tools_4.3.1

Because I am using Homo_sapiens. GRCh38. DNA. Primary_assembly annotations, so I think should use GRCh38 in trinucleotideMatrix function.

Do you have any suggestion how to solve it? Thanks Olsen

Olsennnnn avatar Apr 16 '24 06:04 Olsennnnn