attachcontext/error #24
Description
We are trying mutSignatures with samonella. We have to create BSgenome for Samonellla with following code:
BSgenomeForge::forgeBSgenomeDataPkgFromNCBI(
assembly_accession = "GCA_000006945.2",
pkg_maintainer = "Jane Doe [email protected]",
organism = "Typhimurium str. LT2",
circ_seqs = ("AE006468.2"),
destdir = tempdir()
)
Stuck at this step:
vcfData_01 <- attachContext(mutData = vcfData_01,
chr_colName = "CHROM",
start_colName = "POS",
end_colName = "POS",
nucl_contextN = 3,
BSGenomeDb = Lt2)
Lt2 <- BSgenome.Tlt2.NCBI.ASM694v2::BSgenome.Tlt2.NCBI.ASM694v2
The problem is we got error message:
6956 rows were excluded from analysis
An error has occurred!
This is our input
Session Info:
R version 4.3.0 (2023-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /scrfs/apps/intel/oneapi/mkl/2021.2.0/lib/intel64/libmkl_intel_lp64.so.1; LAPACK version 3.9.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF-8 LC_COLLATE=C
[5] LC_MONETARY=C LC_MESSAGES=C LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=C LC_IDENTIFICATION=C
time zone: America/Chicago
tzcode source: system (glibc)
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] BSgenome.Tlt2.NCBI.ASM694v2_1.0.0 BiocManager_1.30.25
[3] devtools_2.4.5 usethis_3.1.0
[5] vcfR_1.15.0 mutSignatures_2.1.5
[7] foreach_1.5.2 BSgenome.Hsapiens.UCSC.hg19_1.4.3
[9] BSgenome_1.70.2 rtracklayer_1.62.0
[11] BiocIO_1.12.0 Biostrings_2.70.3
[13] XVector_0.42.0 GenomicRanges_1.54.1
[15] GenomeInfoDb_1.38.8 IRanges_2.36.0
[17] S4Vectors_0.40.2 BiocGenerics_0.48.1
[19] gridExtra_2.3 ggplot2_3.5.2
[21] kableExtra_1.4.0 reshape2_1.4.4
[23] dplyr_1.1.4
loaded via a namespace (and not attached):
[1] RColorBrewer_1.1-3 rstudioapi_0.17.1
[3] jsonlite_1.8.9 magrittr_2.0.3
[5] farver_2.1.2 rmarkdown_2.29
[7] fs_1.6.5 zlibbioc_1.48.2
[9] vctrs_0.6.5 memoise_2.0.1
[11] Rsamtools_2.18.0 RCurl_1.98-1.16
[13] htmltools_0.5.8.1 S4Arrays_1.2.0
[15] curl_5.2.1 SparseArray_1.2.2
[17] sass_0.4.9 pracma_2.4.4
[19] bslib_0.8.0 htmlwidgets_1.6.4
[21] desc_1.4.3 plyr_1.8.9
[23] cachem_1.1.0 GenomicAlignments_1.38.0
[25] mime_0.12 lifecycle_1.0.4
[27] iterators_1.0.14 pkgconfig_2.0.3
[29] Matrix_1.5-4 R6_2.6.1
[31] fastmap_1.2.0 rcmdcheck_1.4.0
[33] GenomeInfoDbData_1.2.11 MatrixGenerics_1.14.0
[35] shiny_1.10.0 digest_0.6.37
[37] ps_1.8.1 rprojroot_2.0.4
[39] pkgload_1.4.0 vegan_2.6-8
[41] abind_1.4-8 mgcv_1.9-1
[43] compiler_4.3.0 proxy_0.4-27
[45] remotes_2.5.0 withr_3.0.2
[47] doParallel_1.0.17 BiocParallel_1.36.0
[49] pkgbuild_1.4.6 MASS_7.3-58.2
[51] DelayedArray_0.28.0 sessioninfo_1.2.2
[53] rjson_0.2.23 permute_0.9-7
[55] tools_4.3.0 ape_5.8-1
[57] httpuv_1.6.15 glue_1.8.0
[59] restfulr_0.0.15 callr_3.7.6
[61] nlme_3.1-166 promises_1.3.2
[63] grid_4.3.0 cluster_2.1.6
[65] generics_0.1.3 memuse_4.2-3
[67] gtable_0.3.6 pinfsc50_1.3.0
[69] xml2_1.3.6 pillar_1.10.2
[71] stringr_1.5.1 later_1.4.1
[73] splines_4.3.0 BSgenome.Ggallus.UCSC.galGal6_1.4.2
[75] lattice_0.22-6 tidyselect_1.2.1
[77] miniUI_0.1.1.1 knitr_1.49
[79] SummarizedExperiment_1.32.0 svglite_2.1.3
[81] xfun_0.50 Biobase_2.66.0
[83] matrixStats_1.5.0 stringi_1.7.12
[85] xopen_1.0.1 yaml_2.3.10
[87] evaluate_1.0.3 codetools_0.2-20
[89] BSgenome.Mmusculus.UCSC.mm10_1.4.3 tibble_3.3.0
[91] cli_3.6.5 xtable_1.8-4
[93] systemfonts_1.2.1 processx_3.8.5
[95] jquerylib_0.1.4 dichromat_2.0-0.1
[97] Rcpp_1.0.14 XML_3.99-0.18
[99] parallel_4.3.0 ellipsis_0.3.2
[101] prettyunits_1.2.0 BSgenomeForge_1.2.3
[103] profvis_0.4.0 urlchecker_1.0.1
[105] bitops_1.0-9 viridisLite_0.4.2
[107] scales_1.4.0 purrr_1.0.2
[109] crayon_1.5.3 rlang_1.1.6
Your help will be very appreciated!