Hi, while I was using the test sample data to try vgm, here comes the error message:
14:45:18.674699
Loading in data
14:45:18.753675 Loaded VDJ data
Setting GEX directory to provided path/filtered_feature_bc_matrix
14:45:19.738898 Loaded GEX data
Getting VDJ GEX stats
Starting with 1 of 2
Starting with 2 of 2
Getting 10x stats
14:45:19.78335 Got VDJ GEX stats
For sample 1: 303 cell assigned barcodes in GEX, 78 cell assigned high confidence barcodes in VDJ. Overlap: 74
For sample 2: 261 cell assigned barcodes in GEX, 160 cell assigned high confidence barcodes in VDJ. Overlap: 129
Removed a total of 0 cells with non unique barcodes in GEX
Removed a total of 0 cells with non unique barcodes in VDJ
14:45:19.828618 Starting VDJ barcode iteration 1 of 2...
Error in VDJ.proc$Nr_of_VJ_chains == 0 && VDJ.proc$Nr_of_VDJ_chains == :
'length = 78' in coercion to 'logical(1)'
Also came up with the same error when trying my own data. Not sure how to solve this.
my session info is:
R version 4.3.0 (2023-04-21)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.4.1
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
Hi, while I was using the test sample data to try vgm, here comes the error message:
14:45:18.674699 Loading in data 14:45:18.753675 Loaded VDJ data
Setting GEX directory to provided path/filtered_feature_bc_matrix 14:45:19.738898 Loaded GEX data
Getting VDJ GEX stats Starting with 1 of 2 Starting with 2 of 2 Getting 10x stats 14:45:19.78335 Got VDJ GEX stats
For sample 1: 303 cell assigned barcodes in GEX, 78 cell assigned high confidence barcodes in VDJ. Overlap: 74
For sample 2: 261 cell assigned barcodes in GEX, 160 cell assigned high confidence barcodes in VDJ. Overlap: 129
Removed a total of 0 cells with non unique barcodes in GEX
Removed a total of 0 cells with non unique barcodes in VDJ 14:45:19.828618 Starting VDJ barcode iteration 1 of 2... Error in VDJ.proc$Nr_of_VJ_chains == 0 && VDJ.proc$Nr_of_VDJ_chains == : 'length = 78' in coercion to 'logical(1)'
Also came up with the same error when trying my own data. Not sure how to solve this.
my session info is: R version 4.3.0 (2023-04-21) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Ventura 13.4.1
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: Asia/Shanghai tzcode source: internal
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] Platypus_3.4.1
loaded via a namespace (and not attached): [1] RColorBrewer_1.1-3 rstudioapi_0.15.0 jsonlite_1.8.7 shape_1.4.6
[5] magrittr_2.0.3 spatstat.utils_3.0-3 GlobalOptions_0.1.2 vctrs_0.6.3
[9] ROCR_1.0-11 memoise_2.0.1 spatstat.explore_3.2-1 ggtree_3.8.2
[13] htmltools_0.5.6 gridGraphics_0.5-1 sctransform_0.3.5 parallelly_1.36.0
[17] KernSmooth_2.23-22 htmlwidgets_1.6.2 ica_1.0-3 plyr_1.8.8
[21] plotly_4.10.2 zoo_1.8-12 cachem_1.0.8 igraph_1.5.1
[25] mime_0.12 lifecycle_1.0.3 iterators_1.0.14 pkgconfig_2.0.3
[29] Matrix_1.6-1 R6_2.5.1 fastmap_1.1.1 fitdistrplus_1.1-11
[33] future_1.33.0 shiny_1.7.5 digest_0.6.33 aplot_0.2.0
[37] colorspace_2.1-0 patchwork_1.1.3 Seurat_4.3.0.1 tensor_1.5
[41] irlba_2.3.5.1 progressr_0.14.0 fansi_1.0.4 spatstat.sparse_3.0-2
[45] httr_1.4.7 polyclip_1.10-4 abind_1.4-5 compiler_4.3.0
[49] remotes_2.4.2.1 withr_2.5.0 R.utils_2.12.2 MASS_7.3-60
[53] tools_4.3.0 lmtest_0.9-40 ape_5.7-1 httpuv_1.6.11
[57] future.apply_1.11.0 goftest_1.2-3 R.oo_1.25.0 glue_1.6.2
[61] nlme_3.1-163 promises_1.2.1 grid_4.3.0 Rtsne_0.16
[65] ade4_1.7-22 cluster_2.1.4 reshape2_1.4.4 generics_0.1.3
[69] seqinr_4.2-30 gtable_0.3.4 spatstat.data_3.0-1 R.methodsS3_1.8.2
[73] tidyr_1.3.0 data.table_1.14.8 sp_2.0-0 utf8_1.2.3
[77] spatstat.geom_3.2-4 RcppAnnoy_0.0.21 ggrepel_0.9.3 RANN_2.6.1
[81] foreach_1.5.2 pillar_1.9.0 stringr_1.5.0 yulab.utils_0.0.9
[85] spam_2.9-1 later_1.3.1 circlize_0.4.15 splines_4.3.0
[89] dplyr_1.1.3 treeio_1.24.3 lattice_0.21-8 survival_3.5-7
[93] deldir_1.0-9 tidyselect_1.2.0 miniUI_0.1.1.1 pbapply_1.7-2
[97] gridExtra_2.3 scattermore_1.2 matrixStats_1.0.0 stringi_1.7.12
[101] lazyeval_0.2.2 ggfun_0.1.2 codetools_0.2-19 tibble_3.2.1
[105] BiocManager_1.30.22 ggplotify_0.1.2 cli_3.6.1 uwot_0.1.16
[109] xtable_1.8-4 reticulate_1.31 munsell_0.5.0 Rcpp_1.0.11
[113] globals_0.16.2 spatstat.random_3.1-5 png_0.1-8 parallel_4.3.0
[117] ellipsis_0.3.2 ggplot2_3.4.3 dotCall64_1.0-2 listenv_0.9.0
[121] viridisLite_0.4.2 tidytree_0.4.5 scales_1.2.1 ggridges_0.5.4
[125] SeuratObject_4.9.9.9091 leiden_0.4.3 purrr_1.0.2 rlang_1.1.1
[129] cowplot_1.1.1
Any help would be nice, thank you!