runChromVAR() error: Error in isVirtualExt(exti) :

zhaoliyang0429 commented 3 years ago

Hello, when I was running the example of 10X_brain_5k in the step of runChromVAR(), an error occurred:

x.sp@mmat = runChromVAR(

obj=x.sp,

input.mat="pmat",

genome=BSgenome.Mmusculus.UCSC.mm10,

min.count=10,

species="Homo sapiens"

) Epoch: checking depedent packages ... Epoch: checking input parameters ... Epoch: creating chromVAR object ... Epoch: computing GC bias ... Epoch: getting JASPAR motifs ... Epoch: scanning motifs in the peaks ... Epoch: calculating motif variability between cells ... Error: BiocParallel errors element index: 1, 2, 3, 4, 5, 6, ... first error: trying to get slot "virtual" from an object of a basic class ("NULL") with no slots

traceback() is below:

traceback() 10: stop(.error_bplist(res)) 9: bplapply(X, FUN, ..., BPREDO = BPREDO, BPPARAM = BPPARAM) 8: bplapply(X, FUN, ..., BPREDO = BPREDO, BPPARAM = BPPARAM) 7: bplapply(peak_indices, compute_deviations_single, counts_mat = counts_mat, background_peaks = background_peaks, expectation = expectation) 6: bplapply(peak_indices, compute_deviations_single, counts_mat = counts_mat, background_peaks = background_peaks, expectation = expectation) 5: compute_deviations_core(counts(object), peak_indices, background_peaks, expectation, colData = colData(object), rowData = colData(annotations)) 4: .local(object, annotations, ...) 3: computeDeviations(object = rse, annotations = motif_mm) 2: computeDeviations(object = rse, annotations = motif_mm) 1: runChromVAR(obj = x.sp, input.mat = "pmat", genome = BSgenome.Mmusculus.UCSC.mm10, min.count = 10, species = "Homo sapiens")

then I add library(BiocParallel) register(SerialParam()) ,and tried again,it went out a new error:

Epoch: checking depedent packages ... Epoch: checking input parameters ... Epoch: creating chromVAR object ... Epoch: computing GC bias ... Epoch: getting JASPAR motifs ... Epoch: scanning motifs in the peaks ... Epoch: calculating motif variability between cells ... Error in isVirtualExt(exti) : trying to get slot "virtual" from an object of a basic class ("NULL") with no slots

Below is the traceback()

traceback() 18: stop(e) 17: value[3L] 16: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15: tryCatchList(expr, classes, parentenv, handlers) 14: tryCatch({ FUN(...) }, error = handle_error) 13: withCallingHandlers({ tryCatch({ FUN(...) }, error = handle_error) }, warning = handlewarning) 12: FUN(...) 11: FUN(X[[i]], ...) 10: lapply(X, FUN, ...) 9: bplapply(X, FUN, ..., BPREDO = BPREDO, BPPARAM = BPPARAM) 8: bplapply(X, FUN, ..., BPREDO = BPREDO, BPPARAM = BPPARAM) 7: bplapply(peak_indices, compute_deviations_single, counts_mat = counts_mat, background_peaks = background_peaks, expectation = expectation) 6: bplapply(peak_indices, compute_deviations_single, counts_mat = counts_mat, background_peaks = background_peaks, expectation = expectation) 5: compute_deviations_core(counts(object), peak_indices, background_peaks, expectation, colData = colData(object), rowData = colData(annotations)) 4: .local(object, annotations, ...) 3: computeDeviations(object = rse, annotations = motif_mm) 2: computeDeviations(object = rse, annotations = motif_mm) 1: runChromVAR(obj = x.sp, input.mat = "pmat", genome = BSgenome.Mmusculus.UCSC.mm10, min.count = 10, species = "Homo sapiens")

Below is the session info: R version 4.0.3 (2020-10-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.5 LTS [1] JASPAR2016_1.16.0 GO.db_3.11.4 [3] AnnotationDbi_1.50.3 chromVARmotifs_0.2.0 [5] ggplot2_3.3.2 viridisLite_0.3.0 [7] BiocParallel_1.22.0 BSgenome.Mmusculus.UCSC.mm10_1.4.0 [9] BSgenome_1.56.0 rtracklayer_1.48.0 [11] Biostrings_2.56.0 XVector_0.28.0 [13] SummarizedExperiment_1.18.2 DelayedArray_0.14.1 [15] matrixStats_0.57.0 Biobase_2.48.0 [17] GenomicRanges_1.40.0 GenomeInfoDb_1.24.2 [19] IRanges_2.22.2 S4Vectors_0.26.1 [21] BiocGenerics_0.34.0 motifmatchr_1.1.1 [23] chromVAR_1.10.0 SnapATAC_1.0.0 [25] rhdf5_2.32.4 Matrix_1.2-18 [27] TFBSTools_1.26.0

How can I handle this problem? Anxiously waiting for feedback！ Thanks, ZHAOLIYANG

liaoshengyou commented 3 years ago

I was also see this error, my ArchR log is 👍

error is : Using Previous Background Peaks! ArchR logging to : ArchRLogs/ArchR-addDeviationsMatrix-a199f9c00de-Date-2020-11-22_Time-06-58-33.log If there is an issue, please report to github with logFile! NULL 2020-11-22 06:58:38 : Batch Execution w/ safelapply!, 0 mins elapsed. Can not create group. Object with name 'MotifMatrix' already exists. 2020-11-22 06:58:40 : chromVAR deviations AS_PBMC (1 of 2) Schep (2017), 0.031 mins elapsed.

2020-11-22 06:58:45 : ERROR Found in .customDeviationsSingle for AS_PBMC (1 of 2) LogFile = ArchRLogs/ArchR-addDeviationsMatrix-a199f9c00de-Date-2020-11-22_Time-06-58-33.log

2020-11-22 06:58:45 : ERROR Found in .computeDeviations for AS_PBMC (1 of 2) LogFile = ArchRLogs/ArchR-addDeviationsMatrix-a199f9c00de-Date-2020-11-22_Time-06-58-33.log

Error in .logError(e, fn = ".computeDeviations", info = prefix, errorList = errorList, : Exiting See Error Above

detail see below:

       ___      .______        ______  __    __  .______      
      /   \     |   _  \      /      ||  |  |  | |   _  \     
     /  ^  \    |  |_)  |    |  ,----'|  |__|  | |  |_)  |    
    /  /_\  \   |      /     |  |     |   __   | |      /     
   /  _____  \  |  |\  \\___ |  `----.|  |  |  | |  |\  \\___.
  /__/     \__\ | _| `._____| \______||__|  |__| | _| `._____|

Logging With ArchR!

Start Time : 2020-11-22 06:58:33

------- ArchR Info

ArchRThreads = 1

------- System Info

Computer OS = unix Total Cores = 16

------- Session Info

R version 4.0.2 (2020-06-22) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 8 (Core)

Matrix products: default BLAS: /mayi/biodata/softs/R/R-4.0.2/lib64/R/lib/libRblas.so LAPACK: /mayi/biodata/softs/R/R-4.0.2/lib64/R/lib/libRlapack.so

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=en_US.UTF-8 LC_ADDRESS=en_US.UTF-8 LC_TELEPHONE=en_US.UTF-8
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=en_US.UTF-8

attached base packages: [1] grid splines parallel stats4 stats graphics grDevices utils datasets methods base

other attached packages: [1] chromVAR_1.13.0 [4] scRepertoire_1.0.0 [7] monocle3_0.2.3.0 [10] scDataviz_1.0.0 [13] survminer_0.4.8 [16] e1071_1.7-4 [19] impute_1.64.0 [22] mclust_5.4.6 [25] clustree_0.4.3 [28] ggdendro_0.1.22 [31] ggpubr_0.4.0 [34] wesanderson_0.3.6 [37] carData_3.0-4 [40] hues_0.2.0 [43] scran_1.18.1 [46] batchelor_1.6.0 [49] DelayedArray_0.16.0 [52] circlize_0.4.11 [55] ggord_1.1.5 [58] BSgenome_1.58.0 [61] XVector_0.30.0 [64] ensembldb_2.14.0 [67] AnnotationDbi_1.52.0 [70] metap_1.4 [73] rgl_0.100.54 [76] evd_2.3-3 [79] Formula_1.2-4 [82] MASS_7.3-51.6 [85] cluster_2.1.0 [88] patchwork_1.1.0 [91] irlba_2.3.3 [94] lattice_0.20-41 [97] devtools_2.3.2 [100] remotes_2.2.0 [103] MySeuratWrappers_0.1.0 [106] scales_1.1.1 [109] uwot_0.1.8 [112] readr_1.4.0 [115] tidyverse_1.3.0 [118] AnnotationHub_2.22.0 [121] SeuratWrappers_0.3.0 [124] cowplot_1.1.0 [127] dplyr_1.0.2 [130] ArchR_0.9.5 [133] Matrix_1.2-18 [136] Biobase_2.50.0 [139] IRanges_2.24.0 [142] MatrixGenerics_1.2.0 immunarch_0.6.5 dtplyr_1.0.1
ggalluvial_0.12.2 CellaRepertorium_1.0.0
psych_2.0.9 GSVA_1.38.0
sankeywheel_0.1.0 survutils_1.0.2
genefu_2.22.0 AIMS_1.22.0
iC10_1.5 iC10TrainingData_1.3.1
pamr_1.56.1 biomaRt_2.46.0
survcomp_1.40.0 prodlim_2019.11.13
ggraph_2.0.3 gtools_3.8.2
ggthemes_4.2.0 ggsci_2.9
manipulateWidget_0.10.1 alakazam_1.0.2
kableExtra_1.3.1 car_3.0-10
gridExtra_2.3 cofeatureR_1.1.1
pander_0.6.3 DT_0.16
scater_1.18.3 Matrix.utils_0.9.8
limma_3.46.0 DelayedMatrixStats_1.12.0
org.Dm.eg.db_3.12.0 shape_1.4.5
ComplexHeatmap_2.6.0 yyplot_0.0.8
TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.12.0 BSgenome.Dmelanogaster.UCSC.dm6_1.4.1
rtracklayer_1.50.0 Biostrings_2.58.0
SeuratData_0.2.1 EnsDb.Hsapiens.v75_2.99.0
AnnotationFilter_1.14.0 GenomicFeatures_1.42.0
Signac_1.1.0 multtest_2.46.0
plyr_1.8.6 reshape2_1.4.4
future_1.20.1 scatterplot3d_0.3-41
pryr_0.1.4 Hmisc_4.4-1
survival_3.1-12 RColorBrewer_1.1-2
ggfortify_0.4.11 fpc_2.2-8
DESeq2_1.30.0 sctransform_0.3.1
monocle_2.18.0 DDRTree_0.1.5
VGAM_1.1-4 vegan_2.5-6
permute_0.9-5 DatabaseConnector_3.0.0
usethis_1.6.3 rJava_0.9-13
SCORPIUS_1.0.7 BUSpaRse_1.3.1
reticulate_1.18 plotly_4.9.2.1
SingleR_1.4.0 GGally_2.0.0
forcats_0.5.0 purrr_0.3.4
tidyr_1.1.2 tibble_3.0.4
DropletUtils_1.10.0 SingleCellExperiment_1.12.0
BiocFileCache_1.14.0 dbplyr_2.0.0
Seurat_3.2.2.9012 pheatmap_1.0.12
viridis_0.5.1 viridisLite_0.3.0
ggpointdensity_0.1.0 stringr_1.4.0
magrittr_1.5 rhdf5_2.34.0
data.table_1.13.2 SummarizedExperiment_1.20.0
GenomicRanges_1.42.0 GenomeInfoDb_1.26.0
S4Vectors_0.28.0 BiocGenerics_0.36.0
matrixStats_0.57.0 ggplot2_3.3.2

loaded via a namespace (and not attached): [1] graph_1.68.0 abind_1.4-5 harmony_1.0 fastICA_1.2-2 GO.db_3.12.1
[6] dqrng_0.2.1 RProtoBufLib_2.2.0 HDF5Array_1.18.0 CNEr_1.26.0 RANN_2.6.1
[11] modelr_0.1.8 ellipsis_0.3.1 memoise_1.1.0 munsell_0.5.0 grr_0.9.5
[16] locfit_1.5-9.4 ggridges_0.5.2 seqinr_4.2-4 listenv_0.8.0 blob_1.2.1
[21] interactiveDisplayBase_1.28.0 gsl_2.1-6 km.ci_0.5-2 sparseMatrixStats_1.2.0 RcppRoll_0.3.0
[26] jpeg_0.1-8.1 dynwrap_1.2.1 htmltools_0.5.0 presto_1.0.0 vipor_0.4.5
[31] doSNOW_1.0.19 Rsamtools_2.6.0 ggplotify_0.0.5 fastmatch_1.1-0 bigmemory_4.5.36
[36] leiden_0.3.5 XML_3.99-0.5 foreach_1.5.1 openssl_1.4.3 tcltk_4.0.2
[41] crayon_1.3.4 tidyselect_1.1.0 lsa_0.73.2 withr_2.3.0 RcppParallel_5.0.2
[46] amap_0.8-18 qlcMatrix_0.9.7 densityClust_0.3 future.apply_1.6.0 DEoptimR_1.0-8
[51] shiny_1.5.0 snow_0.4-3 ape_5.4-1 BiocManager_1.30.10 Rdpack_2.1
[56] lmds_0.1.0 SparseM_1.78 multcomp_1.4-14 graphlayouts_0.7.1 SnapATAC_1.0.0
[61] rappdirs_0.3.1 doParallel_1.0.16 UpSetR_1.4.0 proxyC_0.1.5 diptest_0.75-7
[66] DBI_1.1.0 rprojroot_1.3-2 httr_1.4.2 spatstat.data_1.4-3 parallelly_1.21.0
[71] xml2_1.3.2 babelwhale_1.0.1 mnormt_2.0.2 ggseqlogo_0.1 deldir_0.2-3
[76] RISmed_2.2 fastmap_1.0.1 glue_1.4.2 flexmix_2.3-17 bootstrap_2019.6
[81] tidygraph_1.2.0 cytolib_2.2.0 rlang_0.4.8 fs_1.5.0 clue_0.3-57
[86] rvcheck_0.1.8 mvtnorm_1.1-1 cli_2.1.0 princurve_2.1.5 misc3d_0.9-0
[91] plyranges_1.10.0 magick_2.5.1 latticeExtra_0.6-29 SnowballC_0.7.0 RCurl_1.98-1.2
[96] scholar_0.1.7 openxlsx_4.2.3 polyclip_1.10-0 ggimage_0.2.8 tmvnsim_1.0-2
[101] pillar_1.4.6 prettyunits_1.1.1 R6_2.5.0 KMsurv_0.1-5 ROCR_1.0-11
[106] bit64_4.0.5 dichromat_2.0-0 gtable_0.3.0 xfun_0.19 lava_1.6.8.1
[111] tweenr_1.0.1 miniUI_0.1.1.1 slam_0.1-47 RBGL_1.66.0 lifecycle_0.2.0
[116] dynutils_1.0.5 Gviz_1.34.0 KernSmooth_2.23-17 DirichletMultinomial_1.32.0 ggfittext_0.9.0
[121] testthat_3.0.0 globals_0.13.1 spatstat.utils_1.17-0 mgcv_1.8-31 backports_1.2.0
[126] jsonlite_1.7.1 rpart_4.1-15 GetoptLong_1.0.4 Rtsne_0.15 prabclus_2.3-2
[131] fitdistrplus_1.1-1 stringi_1.5.3 BiocParallel_1.24.1 generics_0.1.0 cubature_2.0.4.1
[136] stringdist_0.9.6.3 askpass_1.1 mutoss_0.1-12 zlibbioc_1.36.0 htmlTable_2.1.0
[141] sessioninfo_1.1.1 ResidualMatrix_1.0.0 ggrepel_0.8.2 scuttle_1.0.0 qrcode_0.1.1
[146] hms_0.5.3 ggbio_1.38.0 png_0.1-7 pbapply_1.4-3 rmarkdown_2.5
[151] assertthat_0.2.1 lazyeval_0.2.2 tcR_2.3.2 numDeriv_2016.8-1.1 sandwich_3.0-0
[156] broom_0.7.2 htmlwidgets_1.5.2 annotate_1.68.0 OrganismDbi_1.32.0 flowCore_2.2.0
[161] R.oo_1.24.0 bluster_1.0.0 callr_3.5.1 beachmat_2.6.1 BiocNeighbors_1.8.0
[166] evmix_2.12 caTools_1.18.0 rbibutils_1.4 rsvd_1.0.3 beeswarm_0.2.3
[171] ggforce_0.3.2 zip_2.1.1 rio_0.5.16 R.methodsS3_1.8.1 rsvg_2.1
[176] fansi_0.4.1 ade4_1.7-16 bit_4.0.4 TFMPvalue_0.0.8 rjson_0.2.20
[181] robustbase_0.93-6 knitr_1.30 ranger_0.12.1 tools_4.0.2 RcppAnnoy_0.0.16
[186] rhdf5filters_1.2.0 gbRd_0.4-11 GSEABase_1.52.0 statmod_1.4.35 spatstat_1.64-1
[191] plotrix_3.7-8 carrier_0.1.0 ps_1.4.0 GlobalOptions_0.1.2 Rcpp_1.0.5
[196] ica_1.0-2 shinythemes_1.1.2 TFBSTools_1.28.0 combinat_0.0-8 bitops_1.0-6
[201] zeallot_0.1.0 nabor_0.5.0 digest_0.6.27 pkgload_1.1.0 dbscan_1.1-5
[206] Rhdf5lib_1.12.0 dynparam_1.0.1 TH.data_1.0-10 VariantAnnotation_1.36.0 haven_2.3.1
[211] rstudioapi_0.11 edgeR_3.32.0 sparsesvd_0.2 survMisc_0.5.5 ggbeeswarm_0.6.0
[216] geneplotter_1.68.0 rhandsontable_0.3.7 modeltools_0.2-23 sn_1.6-2 igraph_1.2.6
[221] survivalROC_1.0.3 vctrs_0.3.4 zoo_1.8-8 crosstalk_1.1.0.1 powerTCR_1.10.0
[226] dlstats_0.1.3 R.cache_0.14.0 colorspace_1.4-1 SuppDists_1.1-9.5 curl_4.3
[231] httpuv_1.5.4 BiocVersion_3.12.0 GenomicAlignments_1.26.0 desc_1.2.0 base64enc_0.1-3
[236] lubridate_1.7.9.2 genefilter_1.72.0 class_7.3-17 ProtGenerics_1.22.0 nnet_7.3-14
[241] mathjaxr_1.0-1 reprex_0.3.0 pracma_2.2.9 poweRlaw_0.70.6 colorRamps_2.3
[246] biovizBase_1.38.0 later_1.1.0.1 reshape_0.8.8 TFisher_0.2.0 tensor_1.5
[251] nlme_3.1-148 kernlab_0.9-29 Cairo_1.5-12.2 bigmemory.sri_0.1.3 TSP_1.1-10
[256] pkgbuild_1.1.0 corrplot_0.84 checkmate_2.0.0 rvest_0.3.6 compiler_4.0.2
[261] xtable_1.8-4 farver_2.0.3 codetools_0.2-16 rstatix_0.6.0 gridGraphics_0.5-0
[266] evaluate_0.14 yaml_2.2.1 goftest_1.2-2 docopt_0.7.1 gglayer_0.0.4
[271] cellranger_1.1.0 GenomeInfoDbData_1.2.4 plot3D_1.3 RSpectra_0.16-0 promises_1.1.1
[276] RSQLite_2.2.1 factoextra_1.0.7 truncdist_1.0-2 ggsignif_0.6.0 FNN_1.1.3
[281] lmtest_0.9-38 readxl_1.3.1 BiocSingular_1.6.0 webshot_0.5.2 seqLogo_1.56.0
[286] R.utils_2.10.1 rmeta_3.0 KEGGREST_1.30.0 HSMMSingleCell_1.10.0 iterators_1.0.13
[291] umap_0.2.7.0 progress_1.2.2 processx_3.4.4 foreign_0.8-80 mime_0.9
[296] pkgconfig_2.0.3

------- Log Info

2020-11-22 06:58:37 : Deviations-Args, Class = list

Deviations-Args$bgdPeaks: length = 69152 class: RangedSummarizedExperiment dim: 6 50 metadata(0): assays(1): bgdPeaks rownames: NULL rowData names(2): value GC colnames: NULL colData names(0):

Deviations-Args$matrixName: length = 1 [1] "MotifMatrix"

Deviations-Args$out: length = 2 [1] "z" "deviations"

Deviations-Args$binarize: length = 1 [1] FALSE

Deviations-Args$threads: length = 1 [1] 1

Deviations-Args$verbose: length = 1 [1] TRUE

Deviations-Args$parallelParam: length = 0 NULL

Deviations-Args$force: length = 1 [1] TRUE

Deviations-Args$logFile: length = 1 [1] "ArchRLogs/ArchR-addDeviationsMatrix-a199f9c00de-Date-2020-11-22_Time-06-58-33.log"

Deviations-Args$annotationsMatrix: nRows = 69152, nCols = 870 Deviations-Args$annotationsMatrix: NonZeroEntries = 4064800, EntryRange = [ 1 , 1 ] 5 x 5 sparse Matrix of class "dgCMatrix" TFAP2B_1 TFAP2D_2 TFAP2C_3 TFAP2E_4 TFAP2A_5 chr1_817102_817602 . . . . . chr1_827269_827769 . 1 . . . chr1_869634_870134 . . 1 . . chr1_904496_904996 . . . . . chr1_906626_907126 . . . . .

Deviations-Args$useMatrix: length = 1 [1] "PeakMatrix"

Deviations-Args$ArrowFiles: length = 2 AS_PBMC "/mayi/biodata/project/2020/AS_Result3/ArrowFiles/AS_PBMC.arrow" NC_PBMC "/mayi/biodata/project/2020/AS_Result3/ArrowFiles/NC_PBMC.arrow"

Deviations-Args$allCells: length = 6799 [1] "NC_PBMC#ATCCTGCAGAGGCAGG-1" "NC_PBMC#ATGCATGGTGTCCTTC-1" "NC_PBMC#GCCTAGGCAAGCAGGT-1" "NC_PBMC#CCACGTTAGATTCCGT-1" "NC_PBMC#ATTACCTAGTGGTGTG-1" [6] "NC_PBMC#GAAATGATCGCTACCT-1"

Deviations-Args$X: length = 2 [1] 1 2

Deviations-Args$FUN: length = 1

1 function (i = NULL, ArrowFiles = NULL, annotationsMatrix = NULL,
2 out = c("z", "deviations"), cellNames = NULL, allCells = NULL,
3 featureDF = NULL, bgdPeaks = NULL, binarize = FALSE, useMatrix = "PeakMatrix", 4 matrixName = "Motif", force = FALSE, verbose = TRUE, tstart = NULL,
5 subThreads = 1, logFile = NULL)
6 {

Deviations-Args$registryDir: length = 1 [1] "/mayi/biodata/project/2020/AS_Result3/MotifMatrixDeviationsRegistry"

2020-11-22 06:58:38 : Batch Execution w/ safelapply!, 0 mins elapsed. 2020-11-22 06:58:40 : chromVAR deviations AS_PBMC (1 of 2) Schep (2017), 0.031 mins elapsed.

2020-11-22 06:58:45 : ERROR Found in .customDeviationsSingle for AS_PBMC (1 of 2) LogFile = ArchRLogs/ArchR-addDeviationsMatrix-a199f9c00de-Date-2020-11-22_Time-06-58-33.log

2020-11-22 06:58:45 : errorList, Class = list

errorList$annotationsVector: nRows = 69152, nCols = 1 errorList$annotationsVector: NonZeroEntries = 4702, EntryRange = [ 1 , 1 ] 5 x 1 sparse Matrix of class "dgCMatrix" TFAP2B_1 chr1_817102_817602 . chr1_827269_827769 . chr1_869634_870134 . chr1_904496_904996 . chr1_906626_907126 .

errorList$observed: length = 1 [1] "observed"

errorList$expected: length = 1 [1] "expected"

errorList$sampleMat: length = 1 [1] "sampleMat"

errorList$sampleMat2: length = 1 [1] "sampleMat2"

errorList$sampledDeviation: length = 1 [1] "sampledDeviation"

errorList$sampledDeviation2: length = 1 [1] "sampledDeviation2"

errorList$normdev: length = 1 [1] "normdev"

errorList$z: length = 1 [1] "z"

2020-11-22 06:58:45 : ERROR Found in .computeDeviations for AS_PBMC (1 of 2) LogFile = ArchRLogs/ArchR-addDeviationsMatrix-a199f9c00de-Date-2020-11-22_Time-06-58-33.log

2020-11-22 06:58:45 : errorList, Class = list

errorList$annotationsMatrix: nRows = 69152, nCols = 870 errorList$annotationsMatrix: NonZeroEntries = 4064800, EntryRange = [ 1 , 1 ] 5 x 5 sparse Matrix of class "dgCMatrix" TFAP2B_1 TFAP2D_2 TFAP2C_3 TFAP2E_4 TFAP2A_5 chr1_817102_817602 . . . . . chr1_827269_827769 . 1 . . . chr1_869634_870134 . . 1 . . chr1_904496_904996 . . . . . chr1_906626_907126 . . . . .

errorList$prefix: length = 1 [1] "AS_PBMC (1 of 2)"

errorList$backgroudPeaks: nRows = 69152, nCols = 50 [,1] [,2] [,3] [,4] [,5] [1,] 41253 62021 28846 12277 56308 [2,] 64901 57747 27937 54309 6862 [3,] 3 68024 7395 68024 62998 [4,] 99 30108 37069 15210 1747 [5,] 10047 36980 62460 55480 14928

errorList$expectation: length = 69152 [1] 4.394758e-06 3.869829e-05 1.322497e-05 1.424227e-05 4.760988e-06 3.532083e-05

errorList$out: length = 2 [1] "z" "deviations"

errorList$verbose: length = 1 [1] TRUE

errorList$threads: length = 1 [1] 1

errorList$logFile: length = 1 [1] "ArchRLogs/ArchR-addDeviationsMatrix-a199f9c00de-Date-2020-11-22_Time-06-58-33.log"

leeanapeters commented 3 years ago

I have run into this issue as well. I have tried re-installing R to no avail. Any help would be much appreciated!

r3fang / SnapATAC

runChromVAR() error: Error in isVirtualExt(exti) : #211