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Getting error message while running seqExport for a multi-vcf file:
Error in seqExport(genofile, gdsfile_filtered) : Not implemented in 'genotype/extra.index', please contact the author.
Session info:
R version 4.3.1 (2023-06-16) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Ventura 13.2.1 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0 locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 time zone: America/New_York tzcode source: internal attached base packages: [1] stats4 stats graphics grDevices utils datasets methods base other attached packages: [1] tidyr_1.3.1 COMBAT_0.0.4 corpcor_1.6.10 [4] mvtnorm_1.3-1 BSgenome.Hsapiens.UCSC.hg19_1.4.3 BSgenome.Hsapiens.UCSC.hg38_1.4.5 [7] BSgenome_1.68.0 rtracklayer_1.60.1 TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 [10] GenomicFeatures_1.52.2 AnnotationDbi_1.62.2 SeqArray_1.40.1 [13] gdsfmt_1.36.1 snpStats_1.50.0 Matrix_1.6-5 [16] survival_3.7-0 VariantAnnotation_1.46.0 Rsamtools_2.16.0 [19] SummarizedExperiment_1.30.2 Biobase_2.60.0 GenomicRanges_1.52.1 [22] MatrixGenerics_1.12.3 matrixStats_1.4.1 msa_1.32.0 [25] Biostrings_2.68.1 GenomeInfoDb_1.36.4 XVector_0.40.0 [28] IRanges_2.34.1 S4Vectors_0.38.2 BiocGenerics_0.46.0 loaded via a namespace (and not attached): [1] RcppAnnoy_0.0.22 splines_4.3.1 later_1.3.2 BiocIO_1.10.0 [5] bitops_1.0-8 filelock_1.0.3 tibble_3.2.1 polyclip_1.10-7 [9] XML_3.99-0.17 fastDummies_1.7.4 lifecycle_1.0.4 doParallel_1.0.17 [13] globals_0.16.3 lattice_0.22-6 MASS_7.3-60.0.1 magrittr_2.0.3 [17] plotly_4.10.4 yaml_2.3.10 httpuv_1.6.15 Seurat_5.1.0 [21] sctransform_0.4.1 spam_2.10-0 spatstat.sparse_3.1-0 sp_2.1-4 [25] reticulate_1.39.0 cowplot_1.1.3 pbapply_1.7-2 DBI_1.2.3 [29] RColorBrewer_1.1-3 abind_1.4-8 zlibbioc_1.46.0 Rtsne_0.17 [33] quadprog_1.5-8 purrr_1.0.2 RCurl_1.98-1.16 rappdirs_0.3.3 [37] circlize_0.4.16 GenomeInfoDbData_1.2.10 ggrepel_0.9.6 irlba_2.3.5.1 [41] spatstat.utils_3.1-0 listenv_0.9.1 goftest_1.2-3 RSpectra_0.16-2 [45] spatstat.random_3.3-1 fitdistrplus_1.2-1 parallelly_1.38.0 DelayedMatrixStats_1.22.6 [49] leiden_0.4.3.1 colorRamp2_0.1.0 codetools_0.2-20 DelayedArray_0.26.7 [53] xml2_1.3.6 tidyselect_1.2.1 shape_1.4.6.1 spatstat.explore_3.3-2 [57] BiocFileCache_2.8.0 GenomicAlignments_1.36.0 jsonlite_1.8.8 GetoptLong_1.0.5 [61] progressr_0.14.0 ggridges_0.5.6 iterators_1.0.14 foreach_1.5.2 [65] tools_4.3.1 progress_1.2.3 ica_1.0-3 Rcpp_1.0.13 [69] glue_1.7.0 gridExtra_2.3 DESeq2_1.40.2 dplyr_1.1.4 [73] BiocManager_1.30.25 fastmap_1.2.0 fansi_1.0.6 digest_0.6.37 [77] R6_2.5.1 mime_0.12 colorspace_2.1-1 scattermore_1.2 [81] tensor_1.5 spatstat.data_3.1-2 biomaRt_2.56.1 RSQLite_2.3.7 [85] celldex_1.10.1 utf8_1.2.4 generics_0.1.3 renv_1.0.7 [89] data.table_1.16.0 prettyunits_1.2.0 httr_1.4.7 htmlwidgets_1.6.4 [93] S4Arrays_1.0.6 uwot_0.1.16 pkgconfig_2.0.3 gtable_0.3.5 [97] blob_1.2.4 ComplexHeatmap_2.16.0 lmtest_0.9-40 htmltools_0.5.8.1 [101] dotCall64_1.1-1 clue_0.3-65 SeuratObject_5.0.2 scales_1.3.0 [105] png_0.1-8 spatstat.univar_3.0-1 rstudioapi_0.16.0 reshape2_1.4.4 [109] rjson_0.2.21 nlme_3.1-166 curl_5.2.2 cachem_1.1.0 [113] zoo_1.8-12 GlobalOptions_0.1.2 stringr_1.5.1 BiocVersion_3.17.1 [117] KernSmooth_2.23-24 parallel_4.3.1 miniUI_0.1.1.1 restfulr_0.0.15 [121] pillar_1.9.0 grid_4.3.1 vctrs_0.6.5 RANN_2.6.2 [125] promises_1.3.0 dbplyr_2.5.0 xtable_1.8-4 cluster_2.1.6 [129] cli_3.6.3 locfit_1.5-9.10 compiler_4.3.1 rlang_1.1.4 [133] crayon_1.5.3 future.apply_1.11.2 plyr_1.8.9 stringi_1.8.4 [137] deldir_2.0-4 viridisLite_0.4.2 BiocParallel_1.34.2 munsell_0.5.1 [141] lazyeval_0.2.2 spatstat.geom_3.3-2 ExperimentHub_2.8.1 RcppHNSW_0.6.0 [145] hms_1.1.3 patchwork_1.2.0 sparseMatrixStats_1.12.2 bit64_4.0.5 [149] future_1.34.0 ggplot2_3.5.1 KEGGREST_1.40.1 shiny_1.9.1 [153] interactiveDisplayBase_1.38.0 AnnotationHub_3.8.0 ROCR_1.0-11 igraph_2.0.3 [157] memoise_2.0.1 phangorn_2.11.1 fastmatch_1.1-4 bit_4.0.5 [161] ape_5.8
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Getting error message while running seqExport for a multi-vcf file:
Session info:
The text was updated successfully, but these errors were encountered: