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Published
20 hours ago •
GreenleafLab
GreenleafLab
Error in addDoubletScores
Hi! When I use the tutorial data to run the sample code, I keep encountering this error. I also try to set threads=1, but it still appear same error. I also used diferent version, like ArchR v1.0.2 and ArchR 1.0.2, but the result is same. Could you please help me? Thanks!
doubScores <- addDoubletScores(
+ input = ArrowFiles,
+ k = 10,
+ knnMethod = "UMAP",
+ LSIMethod = 1
+ )
ArchR logging to : ArchRLogs/ArchR-addDoubletScores-fad5818efe33b-Date-2023-08-23_Time-08-58-48.log
If there is an issue, please report to github with logFile!
2023-08-23 08:58:48 : Batch Execution w/ safelapply!, 0 mins elapsed.
2023-08-23 08:58:48 : scATAC_BMMC_R1 (1 of 3) : Computing Doublet Statistics, 0 mins elapsed.
************************************************************
2023-08-23 08:59:04 : ERROR Found in .LSIPartialMatrix for
LogFile = ArchRLogs/ArchR-addDoubletScores-fad5818efe33b-Date-2023-08-23_Time-08-58-48.log
<simpleError in validityMethod(as(object, superClass)): object 'Csparse_validate' not found>
************************************************************
************************************************************
2023-08-23 08:59:04 : ERROR Found in addIterativeLSI for scATAC_BMMC_R1 (1 of 3) :
LogFile = ArchRLogs/ArchR-addDoubletScores-fad5818efe33b-Date-2023-08-23_Time-08-58-48.log
<simpleError in .logError(e, fn = ".LSIPartialMatrix", info = "", errorList = errorList, logFile = logFile): Exiting See Error Above>
************************************************************
Error in .logError(e, fn = "addIterativeLSI", info = prefix, errorList = list(ArrowFile = ArrowFile), :
Exiting See Error Above
> sessionInfo()
R version 4.2.2 Patched (2022-11-10 r83330)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.5 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
Random number generation:
RNG: L'Ecuyer-CMRG
Normal: Inversion
Sample: Rejection
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 grid stats graphics grDevices utils
[8] datasets methods base
other attached packages:
[1] markdown_1.4 ArchR_1.0.2
[3] SeuratObject_4.1.3 Seurat_4.3.0
[5] BSgenome.Hsapiens.UCSC.hg38_1.4.5 Rsamtools_2.14.0
[7] BSgenome.Hsapiens.UCSC.hg19_1.4.3 BSgenome_1.66.3
[9] rtracklayer_1.58.0 Biostrings_2.66.0
[11] XVector_0.38.0 rhdf5_2.42.1
[13] SummarizedExperiment_1.28.0 Biobase_2.58.0
[15] MatrixGenerics_1.10.0 Rcpp_1.0.11
[17] Matrix_1.6-1 GenomicRanges_1.50.2
[19] GenomeInfoDb_1.34.9 IRanges_2.32.0
[21] S4Vectors_0.36.2 BiocGenerics_0.44.0
[23] matrixStats_1.0.0 data.table_1.14.8
[25] stringr_1.5.0 plyr_1.8.8
[27] magrittr_2.0.3 ggplot2_3.4.3
[29] gtable_0.3.4 gtools_3.9.4
[31] gridExtra_2.3
loaded via a namespace (and not attached):
[1] igraph_1.3.5 lazyeval_0.2.2 sp_1.5-1
[4] splines_4.2.2 BiocParallel_1.32.6 listenv_0.8.0
[7] scattermore_0.8 usethis_2.1.6 digest_0.6.33
[10] htmltools_0.5.6 fansi_1.0.4 memoise_2.0.1
[13] tensor_1.5 cluster_2.1.4 ROCR_1.0-11
[16] remotes_2.4.2 globals_0.16.1 spatstat.sparse_3.0-0
[19] prettyunits_1.1.1 colorspace_2.1-0 ggrepel_0.9.3
[22] xfun_0.40 dplyr_1.1.2 callr_3.7.3
[25] crayon_1.5.2 RCurl_1.98-1.12 jsonlite_1.8.7
[28] progressr_0.11.0 spatstat.data_3.0-0 survival_3.4-0
[31] zoo_1.8-11 glue_1.6.2 polyclip_1.10-4
[34] zlibbioc_1.44.0 leiden_0.4.3 DelayedArray_0.24.0
[37] pkgbuild_1.3.1 Rhdf5lib_1.20.0 future.apply_1.10.0
[40] abind_1.4-5 scales_1.2.1 DBI_1.1.3
[43] spatstat.random_3.0-1 miniUI_0.1.1.1 viridisLite_0.4.2
[46] xtable_1.8-4 reticulate_1.26 profvis_0.3.7
[49] htmlwidgets_1.6.2 httr_1.4.7 RColorBrewer_1.1-3
[52] ellipsis_0.3.2 ica_1.0-3 urlchecker_1.0.1
[55] pkgconfig_2.0.3 XML_3.99-0.14 uwot_0.1.16
[58] deldir_1.0-6 utf8_1.2.3 tidyselect_1.2.0
[61] rlang_1.1.1 reshape2_1.4.4 later_1.3.1
[64] cachem_1.0.8 munsell_0.5.0 tools_4.2.2
[67] cli_3.6.1 generics_0.1.3 devtools_2.4.5
[70] ggridges_0.5.4 fastmap_1.1.1 yaml_2.3.7
[73] goftest_1.2-3 processx_3.8.0 fs_1.6.3
[76] knitr_1.43 fitdistrplus_1.1-8 purrr_1.0.2
[79] RANN_2.6.1 nlme_3.1-160 pbapply_1.6-0
[82] future_1.29.0 mime_0.12 rhandsontable_0.3.8
[85] shinythemes_1.2.0 compiler_4.2.2 rstudioapi_0.14
[88] plotly_4.10.2 png_0.1-8 spatstat.utils_3.0-1
[91] tibble_3.2.1 stringi_1.7.12 ps_1.7.2
[94] lattice_0.20-45 vctrs_0.6.3 pillar_1.9.0
[97] lifecycle_1.0.3 rhdf5filters_1.10.1 BiocManager_1.30.22
[100] spatstat.geom_3.0-3 lmtest_0.9-40 RcppAnnoy_0.0.21
[103] cowplot_1.1.1 bitops_1.0-7 irlba_2.3.5.1
[106] httpuv_1.6.11 patchwork_1.1.2 R6_2.5.1
[109] BiocIO_1.8.0 promises_1.2.1 KernSmooth_2.23-20
[112] parallelly_1.32.1 sessioninfo_1.2.2 codetools_0.2-18
[115] pkgload_1.3.2 MASS_7.3-58.1 rjson_0.2.21
[118] withr_2.5.0 presto_1.0.0 GenomicAlignments_1.34.1
[121] sctransform_0.3.5 harmony_0.1.1 GenomeInfoDbData_1.2.9
[124] tidyr_1.3.0 Cairo_1.6-0 Rtsne_0.16
[127] spatstat.explore_3.0-5 shiny_1.7.5 restfulr_0.0.15
I run the following code
if (!requireNamespace("devtools", quietly = TRUE)) install.packages("devtools")
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
devtools::install_github("GreenleafLab/ArchR", ref="master", repos = BiocManager::repositories())
library(ArchR)
ArchR::installExtraPackages()
set.seed(1)
addArchRThreads(threads = 16)
addArchRGenome("hg19")
inputFiles <- getTutorialData("Hematopoiesis")
inputFiles
ArrowFiles <- createArrowFiles(
inputFiles = inputFiles,
sampleNames = names(inputFiles),
filterTSS = 4,
filterFrags = 1000,
addTileMat = TRUE,
addGeneScoreMat = TRUE
)
ArrowFiles
doubScores <- addDoubletScores(
input = ArrowFiles,
k = 10,
knnMethod = "UMAP",
LSIMethod = 1
)
