runChromVAR() error: Error in isVirtualExt(exti) :
zhaoliyang0429 opened this issue · comments
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 = handle_warning)
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
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
<simpleError in isVirtualExt(exti): trying to get slot "virtual" from an object of a basic class ("NULL") with no slots>
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
<simpleError in .logError(e, fn = ".customDeviationsSingle", info = prefix, errorList = errorList, logFile = logFile): Exiting See Error Above>
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 immunarch_0.6.5 dtplyr_1.0.1
[4] scRepertoire_1.0.0 ggalluvial_0.12.2 CellaRepertorium_1.0.0
[7] monocle3_0.2.3.0 psych_2.0.9 GSVA_1.38.0
[10] scDataviz_1.0.0 sankeywheel_0.1.0 survutils_1.0.2
[13] survminer_0.4.8 genefu_2.22.0 AIMS_1.22.0
[16] e1071_1.7-4 iC10_1.5 iC10TrainingData_1.3.1
[19] impute_1.64.0 pamr_1.56.1 biomaRt_2.46.0
[22] mclust_5.4.6 survcomp_1.40.0 prodlim_2019.11.13
[25] clustree_0.4.3 ggraph_2.0.3 gtools_3.8.2
[28] ggdendro_0.1.22 ggthemes_4.2.0 ggsci_2.9
[31] ggpubr_0.4.0 manipulateWidget_0.10.1 alakazam_1.0.2
[34] wesanderson_0.3.6 kableExtra_1.3.1 car_3.0-10
[37] carData_3.0-4 gridExtra_2.3 cofeatureR_1.1.1
[40] hues_0.2.0 pander_0.6.3 DT_0.16
[43] scran_1.18.1 scater_1.18.3 Matrix.utils_0.9.8
[46] batchelor_1.6.0 limma_3.46.0 DelayedMatrixStats_1.12.0
[49] DelayedArray_0.16.0 org.Dm.eg.db_3.12.0 shape_1.4.5
[52] circlize_0.4.11 ComplexHeatmap_2.6.0 yyplot_0.0.8
[55] ggord_1.1.5 TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.12.0 BSgenome.Dmelanogaster.UCSC.dm6_1.4.1
[58] BSgenome_1.58.0 rtracklayer_1.50.0 Biostrings_2.58.0
[61] XVector_0.30.0 SeuratData_0.2.1 EnsDb.Hsapiens.v75_2.99.0
[64] ensembldb_2.14.0 AnnotationFilter_1.14.0 GenomicFeatures_1.42.0
[67] AnnotationDbi_1.52.0 Signac_1.1.0 multtest_2.46.0
[70] metap_1.4 plyr_1.8.6 reshape2_1.4.4
[73] rgl_0.100.54 future_1.20.1 scatterplot3d_0.3-41
[76] evd_2.3-3 pryr_0.1.4 Hmisc_4.4-1
[79] Formula_1.2-4 survival_3.1-12 RColorBrewer_1.1-2
[82] MASS_7.3-51.6 ggfortify_0.4.11 fpc_2.2-8
[85] cluster_2.1.0 DESeq2_1.30.0 sctransform_0.3.1
[88] patchwork_1.1.0 monocle_2.18.0 DDRTree_0.1.5
[91] irlba_2.3.3 VGAM_1.1-4 vegan_2.5-6
[94] lattice_0.20-41 permute_0.9-5 DatabaseConnector_3.0.0
[97] devtools_2.3.2 usethis_1.6.3 rJava_0.9-13
[100] remotes_2.2.0 SCORPIUS_1.0.7 BUSpaRse_1.3.1
[103] MySeuratWrappers_0.1.0 reticulate_1.18 plotly_4.9.2.1
[106] scales_1.1.1 SingleR_1.4.0 GGally_2.0.0
[109] uwot_0.1.8 forcats_0.5.0 purrr_0.3.4
[112] readr_1.4.0 tidyr_1.1.2 tibble_3.0.4
[115] tidyverse_1.3.0 DropletUtils_1.10.0 SingleCellExperiment_1.12.0
[118] AnnotationHub_2.22.0 BiocFileCache_1.14.0 dbplyr_2.0.0
[121] SeuratWrappers_0.3.0 Seurat_3.2.2.9012 pheatmap_1.0.12
[124] cowplot_1.1.0 viridis_0.5.1 viridisLite_0.3.0
[127] dplyr_1.0.2 ggpointdensity_0.1.0 stringr_1.4.0
[130] ArchR_0.9.5 magrittr_1.5 rhdf5_2.34.0
[133] Matrix_1.2-18 data.table_1.13.2 SummarizedExperiment_1.20.0
[136] Biobase_2.50.0 GenomicRanges_1.42.0 GenomeInfoDb_1.26.0
[139] IRanges_2.24.0 S4Vectors_0.28.0 BiocGenerics_0.36.0
[142] MatrixGenerics_1.2.0 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$registryDir: length = 1
[1] "/mayi/biodata/project/2020/AS_Result3/MotifMatrixDeviationsRegistry"
2020-11-22 06:58:38 : Batch Execution w/ safelapply!, 0 mins elapsed.
2020-11-22 06:58:40 : chromVAR deviations AS_PBMC (1 of 2) Schep (2017), 0.031 mins elapsed.
2020-11-22 06:58:45 : ERROR Found in .customDeviationsSingle for AS_PBMC (1 of 2)
LogFile = ArchRLogs/ArchR-addDeviationsMatrix-a199f9c00de-Date-2020-11-22_Time-06-58-33.log
<simpleError in isVirtualExt(exti): trying to get slot "virtual" from an object of a basic class ("NULL") with no slots>
2020-11-22 06:58:45 : errorList, Class = list
errorList$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$z: length = 1
[1] "z"
2020-11-22 06:58:45 : ERROR Found in .computeDeviations for AS_PBMC (1 of 2)
LogFile = ArchRLogs/ArchR-addDeviationsMatrix-a199f9c00de-Date-2020-11-22_Time-06-58-33.log
<simpleError in .logError(e, fn = ".customDeviationsSingle", info = prefix, errorList = errorList, logFile = logFile): Exiting See Error Above>
2020-11-22 06:58:45 : errorList, Class = list
errorList$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"
I have run into this issue as well. I have tried re-installing R to no avail. Any help would be much appreciated!