Multiome Processing: Cannot add Combined Clusters #2068
Replies: 4 comments
-
|
Update to this. Looks like when adding combined dims using : projMulti2 <- addCombinedDims(projMulti2, reducedDims = c("LSI_ATAC", "LSI_RNA"), name = "LSI_Combined") The column names of the combined LSI concatenate the col names from each ATAC and RNA LSI. Leading to col names to be LSI 1:30 repeated twice. The problem here is that the Seurat cannot handle disordered col names. A workaround is to manually rename the columns ex(1-30) however the problem is there is no indication of hierarchy of dimensions between ATAC and RNA |
Beta Was this translation helpful? Give feedback.
-
|
@jgranja24 @rcorces @jeffmgranja I too have encountered the sample problem:
2023-12-01 11:04:28.290088 : ERROR Found in FindNeighbors for <simpleError in validObject(.Object): invalid class “DimReduc” object: dimensions for ‘cell.embeddings’ must be in order> 2023-12-01 11:04:28.294065 : ERROR Found in runClusters for <simpleError in .logError(e, fn = "FindNeighbors", info = "", errorList = errorList, logFile = logFile): Exiting See Error Above> Error in .logError(e, fn = "runClusters", info = "", errorList = errorList, : ArchR-addClusters-81652f37adc-Date-2023-12-01_Time-11-04-28.031922.log |
Beta Was this translation helpful? Give feedback.
-
|
I'm another that has encountered this problem with the identical errors as the other users above:
2024-01-12 13:09:35.197036 : ERROR Found in FindNeighbors for <simpleError in validObject(.Object): invalid class “DimReduc” object: dimensions for ‘cell.embeddings’ must be in order> 2024-01-12 13:09:35.204622 : ERROR Found in runClusters for <simpleError in .logError(e, fn = "FindNeighbors", info = "", errorList = errorList, logFile = logFile): Exiting See Error Above> Error in .logError(e, fn = "runClusters", info = "", errorList = errorList, : |
Beta Was this translation helpful? Give feedback.
-
|
Was anyone here able to solve this problem? |
Beta Was this translation helpful? Give feedback.
Uh oh!
There was an error while loading. Please reload this page.
-
I am following the Multiome vignette and When trying to add combined clusters I am getting an error stating that the cell.embeddings must be in order. I am not sure exactly how to get around this. Anyone else run into this ?
see Logging below:
Start Time : 2023-11-30 15:21:26
------- ArchR Info
ArchRThreads = 14
ArchRGenome = Hg38
------- System Info
Computer OS = unix
Total Cores = 28
------- Session Info
R version 4.2.1 (2022-06-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.6 LTS
Matrix products: default
BLAS: /usr/local/lib/R/lib/libRblas.so
LAPACK: /usr/local/lib/R/lib/libRlapack.so
Random number generation:
RNG: L'Ecuyer-CMRG
Normal: Inversion
Sample: Rejection
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=C
[4] LC_COLLATE=C LC_MONETARY=C LC_MESSAGES=C
[7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 grid stats graphics grDevices
[7] utils datasets methods base
other attached packages:
[1] nabor_0.5.0 Seurat_5.0.0
[3] SeuratObject_5.0.0 sp_2.1-2
[5] dsassembly_1.8.4 MultiAssayExperiment_1.24.0
[7] rhdf5_2.42.1 SummarizedExperiment_1.28.0
[9] Biobase_2.58.0 RcppArmadillo_0.12.6.6.0
[11] Rcpp_1.0.11 Matrix_1.6-1.1
[13] GenomicRanges_1.50.2 GenomeInfoDb_1.34.9
[15] IRanges_2.32.0 S4Vectors_0.36.2
[17] BiocGenerics_0.44.0 sparseMatrixStats_1.10.0
[19] MatrixGenerics_1.10.0 matrixStats_1.1.0
[21] data.table_1.14.8 stringr_1.5.1
[23] plyr_1.8.9 magrittr_2.0.3
[25] ggplot2_3.4.4 gtable_0.3.4
[27] gtools_3.9.5 gridExtra_2.3
[29] devtools_2.4.5 usethis_2.2.2
[31] ArchR_1.0.3
loaded via a namespace (and not attached):
[1] rtracklayer_1.58.0
[2] scattermore_1.2
[3] tidyr_1.3.0
[4] bit64_4.0.5
[5] knitr_1.45
[6] irlba_2.3.5.1
[7] DelayedArray_0.24.0
[8] RCurl_1.98-1.13
[9] doParallel_1.0.17
[10] generics_0.1.3
[11] callr_3.7.3
[12] cowplot_1.1.1
[13] RSQLite_2.3.3
[14] RANN_2.6.1
[15] future_1.33.0
[16] artificer.mae_1.4.1
[17] bit_4.0.5
[18] base64url_1.4
[19] gp.cache_1.8.0
[20] spatstat.data_3.0-3
[21] httpuv_1.6.12
[22] genomitory_2.2.2
[23] xfun_0.41
[24] evaluate_0.23
[25] promises_1.2.1
[26] fansi_1.0.5
[27] restfulr_0.0.15
[28] igraph_1.5.1
[29] DBI_1.1.3
[30] htmlwidgets_1.6.3
[31] spatstat.geom_3.2-7
[32] purrr_1.0.2
[33] ellipsis_0.3.2
[34] RSpectra_0.16-1
[35] dplyr_1.1.4
[36] backports_1.4.1
[37] deldir_2.0-2
[38] artificer.matrix_1.4.1
[39] vctrs_0.6.4
[40] SingleCellExperiment_1.20.1
[41] remotes_2.4.2.1
[42] Cairo_1.6-0
[43] ROCR_1.0-11
[44] abind_1.4-5
[45] cachem_1.0.8
[46] withr_2.5.2
[47] BSgenome.Hsapiens.UCSC.hg38_1.4.5
[48] BSgenome_1.66.3
[49] progressr_0.14.0
[50] sctransform_0.4.1
[51] GenomicAlignments_1.34.1
[52] metacommons_1.10.0
[53] prettyunits_1.2.0
[54] goftest_1.2-3
[55] cluster_2.1.3
[56] dotCall64_1.1-1
[57] lazyeval_0.2.2
[58] crayon_1.5.2
[59] spatstat.explore_3.2-5
[60] pkgconfig_2.0.3
[61] nlme_3.1-162
[62] pkgload_1.3.3
[63] rlang_1.1.2
[64] globals_0.16.2
[65] lifecycle_1.0.4
[66] miniUI_0.1.1.1
[67] artificer.schemas_1.0.0
[68] filelock_1.0.2
[69] artificer.base_1.4.2
[70] fastDummies_1.7.3
[71] polyclip_1.10-6
[72] RcppHNSW_0.5.0
[73] lmtest_0.9-40
[74] Rhdf5lib_1.20.0
[75] zoo_1.8-12
[76] ggridges_0.5.4
[77] GlobalOptions_0.1.2
[78] processx_3.8.2
[79] pheatmap_1.0.12
[80] png_0.1-8
[81] viridisLite_0.4.2
[82] rjson_0.2.21
[83] artificer.ranges_1.4.0
[84] bitops_1.0-7
[85] artificer.se_1.4.0
[86] getPass_0.2-2
[87] KernSmooth_2.23-20
[88] spam_2.10-0
[89] rhdf5filters_1.10.1
[90] Biostrings_2.66.0
[91] blob_1.2.4
[92] shape_1.4.6
[93] spatstat.random_3.2-2
[94] parallelly_1.36.0
[95] scales_1.3.0
[96] memoise_2.0.1
[97] ica_1.0-3
[98] zlibbioc_1.44.0
[99] compiler_4.2.1
[100] BiocIO_1.8.0
[101] RColorBrewer_1.1-3
[102] clue_0.3-65
[103] fitdistrplus_1.1-11
[104] Rsamtools_2.14.0
[105] cli_3.6.1
[106] XVector_0.38.0
[107] urlchecker_1.0.1
[108] listenv_0.9.0
[109] patchwork_1.1.3
[110] pbapply_1.7-2
[111] ps_1.7.5
[112] ArtifactDB_1.10.4
[113] MASS_7.3-58.2
[114] tidyselect_1.2.0
[115] stringi_1.8.2
[116] yaml_2.3.7
[117] ggrepel_0.9.4
[118] tools_4.2.1
[119] future.apply_1.11.0
[120] circlize_0.4.15
[121] rstudioapi_0.15.0
[122] foreach_1.5.2
[123] Rtsne_0.16
[124] digest_0.6.33
[125] shiny_1.8.0
[126] later_1.3.1
[127] RcppAnnoy_0.0.21
[128] gp.auth_1.8.0
[129] httr_1.4.7
[130] ComplexHeatmap_2.14.0
[131] colorspace_2.1-0
[132] XML_3.99-0.16
[133] fs_1.6.3
[134] tensor_1.5
[135] reticulate_1.34.0
[136] splines_4.2.1
[137] uwot_0.1.16
[138] spatstat.utils_3.0-4
[139] plotly_4.10.3
[140] sessioninfo_1.2.2
[141] xtable_1.8-4
[142] jsonlite_1.8.7
[143] ShadowArray_1.8.0
[144] R6_2.5.1
[145] profvis_0.3.8
[146] pillar_1.9.0
[147] htmltools_0.5.7
[148] mime_0.12
[149] glue_1.6.2
[150] fastmap_1.1.1
[151] BiocParallel_1.32.6
[152] codetools_0.2-18
[153] gp.version_1.2.0
[154] pkgbuild_1.4.2
[155] utf8_1.2.4
[156] lattice_0.20-45
[157] spatstat.sparse_3.0-3
[158] tibble_3.2.1
[159] genomitory.schemas_1.0.0
[160] leiden_0.4.3.1
[161] artificer.sce_1.4.1
[162] survival_3.5-3
[163] dsdb.schemas_1.0.0
[164] rmarkdown_2.25
[165] munsell_0.5.0
[166] GetoptLong_1.0.5
[167] GenomeInfoDbData_1.2.9
[168] iterators_1.0.14
[169] HDF5Array_1.26.0
[170] reshape2_1.4.4
------- Log Info
2023-11-30 15:21:27 : addClusters Input-Parameters, Class = list
addClusters Input-Parameters$: length = 1
1 function (name)
2 .Internal(args(name))
addClusters Input-Parameters$input: length = 1
addClusters Input-Parameters$reducedDims: length = 1
[1] "LSI_Combined"
addClusters Input-Parameters$name: length = 1
[1] "Clusters_Combined"
addClusters Input-Parameters$sampleCells: length = 0
NULL
addClusters Input-Parameters$seed: length = 1
[1] 1
addClusters Input-Parameters$method: length = 1
[1] "Seurat"
addClusters Input-Parameters$dimsToUse: length = 0
NULL
addClusters Input-Parameters$scaleDims: length = 0
NULL
addClusters Input-Parameters$corCutOff: length = 1
[1] 0.75
addClusters Input-Parameters$knnAssign: length = 1
[1] 10
addClusters Input-Parameters$nOutlier: length = 1
[1] 5
addClusters Input-Parameters$maxClusters: length = 1
[1] 25
addClusters Input-Parameters$testBias: length = 1
[1] TRUE
addClusters Input-Parameters$filterBias: length = 1
[1] FALSE
addClusters Input-Parameters$biasClusters: length = 1
[1] 0.01
addClusters Input-Parameters$biasCol: length = 1
[1] "nFrags"
addClusters Input-Parameters$biasVals: length = 0
NULL
addClusters Input-Parameters$biasQuantiles: length = 2
[1] 0.05 0.95
addClusters Input-Parameters$biasEnrich: length = 1
[1] 10
addClusters Input-Parameters$biasProportion: length = 1
[1] 0.5
addClusters Input-Parameters$biasPval: length = 1
[1] 0.05
addClusters Input-Parameters$nPerm: length = 1
[1] 500
addClusters Input-Parameters$prefix: length = 1
[1] "C"
addClusters Input-Parameters$FCmethod: length = 0
NULL
addClusters Input-Parameters$ArchRProj: length = 0
NULL
addClusters Input-Parameters$verbose: length = 1
[1] TRUE
addClusters Input-Parameters$tstart: length = 0
NULL
addClusters Input-Parameters$force: length = 1
[1] TRUE
addClusters Input-Parameters$logFile: length = 1
[1] "ArchRLogs/ArchR-addClusters-5f864a184a02-Date-2023-11-30_Time-15-21-26.log"
addClusters Input-Parameters$...: length = 1
2023-11-30 15:21:27 : Running Seurats FindClusters (Stuart et al. Cell 2019), 0.009 mins elapsed.
2023-11-30 15:21:28 : ERROR Found in FindNeighbors for
LogFile = ArchRLogs/ArchR-addClusters-5f864a184a02-Date-2023-11-30_Time-15-21-26.log
<simpleError in validObject(.Object): invalid class “DimReduc” object: dimensions for ‘cell.embeddings’ must be in order>
2023-11-30 15:21:28 : errorList, Class = list
errorList$: length = 1
1 function (name)
2 .Internal(args(name))
errorList$e: length = 2
$message
[1] "invalid class “DimReduc” object: dimensions for ‘cell.embeddings’ must be in order"
$call
validObject(.Object)
2023-11-30 15:21:28 : ERROR Found in runClusters for
LogFile = ArchRLogs/ArchR-addClusters-5f864a184a02-Date-2023-11-30_Time-15-21-26.log
<simpleError in .logError(e, fn = "FindNeighbors", info = "", errorList = errorList, logFile = logFile): Exiting See Error Above>
2023-11-30 15:21:28 : errorList, Class = list
errorList$resolution: length = 1
[1] 0.4
errorList$verbose: length = 1
[1] TRUE
errorList$tstart: length = 1
[1] "2023-11-30 15:21:27 PST"
Beta Was this translation helpful? Give feedback.
All reactions