Error in seqExport(genofile, gdsfile_filtered) : Not implemented in 'genotype/extra.index', please contact the author.

[maitree-patel]

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  

[maitree-patel]

Hi @zhengxwen! I am getting this error while running seqExport() while trying to export a .gds file that I got by converting a vcf file.

I need some help in navigating this error.
Thank you!

Best,
Maitree

[zhengxwen]

It is fixed in dce8538

You could use devtools to install this version:

library("devtools")
install_github("zhengxwen/SeqArray")

[maitree-patel]

Thank you @zhengxwen!