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20 hours ago •
GreenleafLab
GreenleafLab
Error during addDoubletScores
Hi! I was running the tutorial code on tutorial data but couldn't get past doublet scoring. I keep seeing this error. Could you help have a look? Thanks!
> ArrowFiles
[1] "ATAC-H134-1.arrow"
> doubScores <- addDoubletScores(input = ArrowFiles,
+ k = 10, #Refers to how many cells near a "pseudo-doublet" to count.
+ knnMethod = "UMAP", #Refers to the embedding to use for nearest neighbor search with doublet projection.
+ LSIMethod = 1,
+ threads = 1)
ArchR logging to : ArchRLogs/ArchR-addDoubletScores-33f37f2a7050bb-Date-2023-10-31_Time-16-39-42.log
If there is an issue, please report to github with logFile!
2023-10-31 16:39:42 : Batch Execution w/ safelapply!, 0 mins elapsed.
2023-10-31 16:39:42 : ATAC-H134-1 (1 of 1) : Computing Doublet Statistics, 0 mins elapsed.
************************************************************
2023-10-31 16:40:20 : ERROR Found in .LSIPartialMatrix for
LogFile = ArchRLogs/ArchR-addDoubletScores-33f37f2a7050bb-Date-2023-10-31_Time-16-39-42.log
<simpleError in validityMethod(as(object, superClass)): 找不到对象'Csparse_validate'>
************************************************************
************************************************************
2023-10-31 16:40:20 : ERROR Found in addIterativeLSI for ATAC-H134-1 (1 of 1) :
LogFile = ArchRLogs/ArchR-addDoubletScores-33f37f2a7050bb-Date-2023-10-31_Time-16-39-42.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
This is the log file:
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
Logging With ArchR!
Start Time : 2023-10-31 16:39:42
------- ArchR Info
ArchRThreads = 1
ArchRGenome = Hg38
------- System Info
Computer OS = unix
Total Cores = 96
------- Session Info
R version 4.1.1 (2021-08-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 20.04.5 LTS
Matrix products: default
BLAS/LAPACK: /home/zhengyuhui/anaconda3/envs/pbmc/lib/libopenblasp-r0.3.17.so
Random number generation:
RNG: L'Ecuyer-CMRG
Normal: Inversion
Sample: Rejection
locale:
[1] LC_CTYPE=zh_CN.UTF-8 LC_NUMERIC=C LC_TIME=zh_CN.UTF-8 LC_COLLATE=zh_CN.UTF-8 LC_MONETARY=zh_CN.UTF-8
[6] LC_MESSAGES=zh_CN.UTF-8 LC_PAPER=zh_CN.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=zh_CN.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel grid stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] BSgenome.Hsapiens.UCSC.hg38_1.4.4 BiocManager_1.30.18 doRNG_1.8.6
[4] rngtools_1.5.2 foreach_1.5.2 GSEABase_1.56.0
[7] graph_1.72.0 annotate_1.72.0 XML_3.99-0.8
[10] AUCell_1.16.0 rsvd_1.0.5 scMetabolism_0.2.1
[13] ggrepel_0.9.4 ggpubr_0.6.0 harmony_0.1.0
[16] reshape2_1.4.4 RColorBrewer_1.1-3 cowplot_1.1.1
[19] BSgenome_1.62.0 rtracklayer_1.54.0 forcats_0.5.2
[22] dplyr_1.1.3 purrr_1.0.2 readr_2.1.3
[25] tidyr_1.3.0 tibble_3.2.1 tidyverse_1.3.2
[28] Rsamtools_2.10.0 Biostrings_2.62.0 XVector_0.34.0
[31] pryr_0.1.5 rhdf5_2.38.1 SummarizedExperiment_1.24.0
[34] MatrixGenerics_1.6.0 Rcpp_1.0.11 Matrix_1.6-1.1
[37] matrixStats_0.63.0 data.table_1.14.8 stringr_1.5.0
[40] plyr_1.8.9 magrittr_2.0.3 gtable_0.3.4
[43] gtools_3.9.3 gridExtra_2.3 ArchR_1.0.2
[46] EnsDb.Hsapiens.v86_2.99.0 ensembldb_2.18.4 AnnotationFilter_1.18.0
[49] GenomicFeatures_1.46.5 AnnotationDbi_1.56.2 Biobase_2.54.0
[52] GenomicRanges_1.46.1 GenomeInfoDb_1.35.15 IRanges_2.28.0
[55] S4Vectors_0.32.4 BiocGenerics_0.40.0 patchwork_1.1.3
[58] ggplot2_3.4.4 SeuratObject_4.1.3 Seurat_4.3.0.1
[61] Signac_1.7.0
loaded via a namespace (and not attached):
[1] rappdirs_0.3.3 scattermore_0.8 R.methodsS3_1.8.2 bit64_4.0.5 irlba_2.3.5
[6] DelayedArray_0.20.0 R.utils_2.12.0 doParallel_1.0.17 KEGGREST_1.34.0 RCurl_1.98-1.8
[11] generics_0.1.3 RSQLite_2.2.17 RANN_2.6.1 future_1.28.0 bit_4.0.4
[16] tzdb_0.4.0 spatstat.data_3.0-0 xml2_1.3.3 lubridate_1.9.0 httpuv_1.6.6
[21] assertthat_0.2.1 gargle_1.2.1 hms_1.1.2 promises_1.2.0.1 fansi_1.0.5
[26] restfulr_0.0.15 progress_1.2.2 dbplyr_2.2.1 readxl_1.4.1 igraph_1.3.4
[31] DBI_1.1.3 htmlwidgets_1.6.2 spatstat.geom_3.0-3 googledrive_2.0.0 ellipsis_0.3.2
[36] backports_1.4.1 biomaRt_2.50.3 deldir_1.0-6 vctrs_0.6.4 Cairo_1.5-12.2
[41] ROCR_1.0-11 abind_1.4-5 cachem_1.0.8 withr_2.5.1 progressr_0.11.0
[46] sctransform_0.3.5 GenomicAlignments_1.30.0 prettyunits_1.2.0 goftest_1.2-3 cluster_2.1.4
[51] lazyeval_0.2.2 crayon_1.5.2 spatstat.explore_3.0-5 labeling_0.4.3 pkgconfig_2.0.3
[56] nlme_3.1-155 ProtGenerics_1.26.0 rlang_1.1.1 globals_0.16.1 lifecycle_1.0.3
[61] miniUI_0.1.1.1 filelock_1.0.2 BiocFileCache_2.2.1 modelr_0.1.10 cellranger_1.1.0
[66] polyclip_1.10-0 lmtest_0.9-40 carData_3.0-5 Rhdf5lib_1.16.0 zoo_1.8-11
[71] reprex_2.0.2 GlobalOptions_0.1.2 ggridges_0.5.3 googlesheets4_1.0.1 png_0.1-7
[76] viridisLite_0.4.2 rjson_0.2.21 bitops_1.0-7 R.oo_1.25.0 KernSmooth_2.23-20
[81] rhdf5filters_1.6.0 blob_1.2.3 shape_1.4.6 parallelly_1.32.1 spatstat.random_3.0-1
[86] rstatix_0.7.2 ggsignif_0.6.4 scales_1.2.1 memoise_2.0.1 ica_1.0-3
[91] zlibbioc_1.40.0 compiler_4.1.1 BiocIO_1.4.0 clue_0.3-61 fitdistrplus_1.1-8
[96] cli_3.6.1 listenv_0.8.0 pbapply_1.7-2 MASS_7.3-58.1 tidyselect_1.2.0
[101] stringi_1.7.6 yaml_2.3.5 fastmatch_1.1-3 tools_4.1.1 timechange_0.1.1
[106] future.apply_1.9.1 circlize_0.4.15 rstudioapi_0.15.0 farver_2.1.1 Rtsne_0.16
[111] digest_0.6.33 rgeos_0.5-9 shiny_1.7.2 car_3.1-2 broom_1.0.5
[116] later_1.3.0 RcppAnnoy_0.0.19 httr_1.4.4 ComplexHeatmap_2.10.0 colorspace_2.1-0
[121] rvest_1.0.3 fs_1.6.3 tensor_1.5 reticulate_1.26 splines_4.1.1
[126] uwot_0.1.14 RcppRoll_0.3.0 spatstat.utils_3.0-1 sp_1.5-0 plotly_4.10.0
[131] xtable_1.8-4 jsonlite_1.8.7 R6_2.5.1 pillar_1.9.0 htmltools_0.5.6
[136] mime_0.12 glue_1.6.2 fastmap_1.1.1 BiocParallel_1.28.3 codetools_0.2-18
[141] utf8_1.2.4 lattice_0.20-45 spatstat.sparse_3.0-0 curl_4.3.2 leiden_0.4.3
[146] survival_3.4-0 munsell_0.5.0 GetoptLong_1.0.5 GenomeInfoDbData_1.2.7 iterators_1.0.14
[151] haven_2.5.1
------- Log Info
2023-10-31 16:39:42 : addDoubletScores Input-Parameters, Class = list
addDoubletScores Input-Parameters$input: length = 1
[1] "ATAC-H134-1.arrow"
addDoubletScores Input-Parameters$useMatrix: length = 1
[1] "TileMatrix"
addDoubletScores Input-Parameters$k: length = 1
[1] 10
addDoubletScores Input-Parameters$nTrials: length = 1
[1] 5
addDoubletScores Input-Parameters$dimsToUse: length = 30
[1] 1 2 3 4 5 6
addDoubletScores Input-Parameters$LSIMethod: length = 1
[1] 1
addDoubletScores Input-Parameters$scaleDims: length = 1
[1] FALSE
addDoubletScores Input-Parameters$corCutOff: length = 1
[1] 0.75
addDoubletScores Input-Parameters$knnMethod: length = 1
[1] "UMAP"
addDoubletScores Input-Parameters$outDir: length = 1
[1] "QualityControl"
addDoubletScores Input-Parameters$threads: length = 1
[1] 1
addDoubletScores Input-Parameters$force: length = 1
[1] FALSE
addDoubletScores Input-Parameters$parallelParam: length = 0
NULL
addDoubletScores Input-Parameters$verbose: length = 1
[1] TRUE
addDoubletScores Input-Parameters$logFile: length = 1
[1] "ArchRLogs/ArchR-addDoubletScores-33f37f2a7050bb-Date-2023-10-31_Time-16-39-42.log"
2023-10-31 16:39:42 : Batch Execution w/ safelapply!, 0 mins elapsed.
2023-10-31 16:39:42 : ATAC-H134-1 (1 of 1) : Computing Doublet Statistics, 0 mins elapsed.
2023-10-31 16:39:43 : Running IterativeLSI, 0.018 mins elapsed.
2023-10-31 16:39:43 : IterativeLSI Input-Parameters, Class = list
IterativeLSI Input-Parameters$ArchRProj: length = 1
IterativeLSI Input-Parameters$useMatrix: length = 1
[1] "TileMatrix"
IterativeLSI Input-Parameters$name: length = 1
[1] "IterativeLSI"
IterativeLSI Input-Parameters$iterations: length = 1
[1] 2
IterativeLSI Input-Parameters$firstSelection: length = 1
[1] "top"
IterativeLSI Input-Parameters$depthCol: length = 1
[1] "nFrags"
IterativeLSI Input-Parameters$varFeatures: length = 1
[1] 25000
IterativeLSI Input-Parameters$dimsToUse: length = 30
[1] 1 2 3 4 5 6
IterativeLSI Input-Parameters$LSIMethod: length = 1
[1] 1
IterativeLSI Input-Parameters$scaleDims: length = 1
[1] FALSE
IterativeLSI Input-Parameters$corCutOff: length = 1
[1] 0.75
IterativeLSI Input-Parameters$binarize: length = 1
[1] TRUE
IterativeLSI Input-Parameters$outlierQuantiles: length = 0
NULL
IterativeLSI Input-Parameters$filterBias: length = 1
[1] FALSE
IterativeLSI Input-Parameters$sampleCellsPre: length = 1
[1] 10000
IterativeLSI Input-Parameters$projectCellsPre: length = 1
[1] FALSE
IterativeLSI Input-Parameters$sampleCellsFinal: length = 0
NULL
IterativeLSI Input-Parameters$selectionMethod: length = 1
[1] "var"
IterativeLSI Input-Parameters$scaleTo: length = 1
[1] 10000
IterativeLSI Input-Parameters$totalFeatures: length = 1
[1] 5e+05
IterativeLSI Input-Parameters$filterQuantile: length = 1
[1] 0.995
IterativeLSI Input-Parameters$excludeChr: length = 0
NULL
IterativeLSI Input-Parameters$saveIterations: length = 1
[1] FALSE
IterativeLSI Input-Parameters$nPlot: length = 1
[1] 10000
IterativeLSI Input-Parameters$outDir: length = 1
[1] "/media/AnalysisTempDisk2/Yangshichen/0_HIV/HIV-ATAC-HDs/tmp/tmp-33f37f5e50a608-Date-2023-10-31_Time-16-39-42"
IterativeLSI Input-Parameters$threads: length = 1
[1] 1
IterativeLSI Input-Parameters$seed: length = 1
[1] 1
IterativeLSI Input-Parameters$verbose: length = 1
[1] FALSE
IterativeLSI Input-Parameters$force: length = 1
[1] TRUE
IterativeLSI Input-Parameters$logFile: length = 1
[1] "ArchRLogs/ArchR-addDoubletScores-33f37f2a7050bb-Date-2023-10-31_Time-16-39-42.log"
2023-10-31 16:39:43 : Computing Total Across All Features, 0.002 mins elapsed.
2023-10-31 16:39:46 : Computing Top Features, 0.05 mins elapsed.
###########
2023-10-31 16:39:49 : Running LSI (1 of 2) on Top Features, 0.107 mins elapsed.
###########
2023-10-31 16:39:49 : Creating Partial Matrix, 0.107 mins elapsed.
2023-10-31 16:40:19 : Computing LSI, 0.607 mins elapsed.
2023-10-31 16:40:19 : LSI Parameters, Class = list
LSI Parameters$: length = 1
1 function (name)
2 .Internal(args(name))
LSI Parameters$mat: nRows = 25000, nCols = 5105
LSI Parameters$mat: NonZeroEntries = 11344310, EntryRange = [ 1 , 1 ]
5 x 5 sparse Matrix of class "dgCMatrix"
************************************************************
2023-10-31 16:40:20 : ERROR Found in .LSIPartialMatrix for
LogFile = ArchRLogs/ArchR-addDoubletScores-33f37f2a7050bb-Date-2023-10-31_Time-16-39-42.log
<simpleError in validityMethod(as(object, superClass)): 找不到对象'Csparse_validate'>
2023-10-31 16:40:20 : errorList, Class = list
errorList$: length = 1
1 function (name)
2 .Internal(args(name))
errorList$ArrowFiles: length = 1
[1] "ATAC-H134-1.arrow"
errorList$useMatrix: length = 1
[1] "TileMatrix"
errorList$cellNames: length = 5105
[1] "ATAC-H134-1#ATAC-H134-1_BC01716_N14" "ATAC-H134-1#ATAC-H134-1_BC01673_N13" "ATAC-H134-1#ATAC-H134-1_BC03254_N14"
[4] "ATAC-H134-1#ATAC-H134-1_BC00150_N05" "ATAC-H134-1#ATAC-H134-1_BC00414_N18" "ATAC-H134-1#ATAC-H134-1_BC00065_N08"
errorList$cellDepth: length = 5105
ATAC-H134-1#ATAC-H134-1_BC01716_N14 ATAC-H134-1#ATAC-H134-1_BC01673_N13 ATAC-H134-1#ATAC-H134-1_BC03254_N14
4.999913 4.999300 4.988563
ATAC-H134-1#ATAC-H134-1_BC00150_N05 ATAC-H134-1#ATAC-H134-1_BC00414_N18 ATAC-H134-1#ATAC-H134-1_BC00065_N08
4.983103 4.982389 4.975073
errorList$sampleNames: length = 5105
[1] "ATAC-H134-1" "ATAC-H134-1" "ATAC-H134-1" "ATAC-H134-1" "ATAC-H134-1" "ATAC-H134-1"
errorList$dimsToUse: length = 30
[1] 1 2 3 4 5 6
errorList$binarize: length = 1
[1] TRUE
errorList$outlierQuantiles: length = 0
NULL
errorList$LSIMethod: length = 1
[1] 1
errorList$scaleTo: length = 1
[1] 10000
errorList$sampleCells: length = 0
NULL
errorList$projectAll: length = 0
logical(0)
errorList$threads: length = 1
[1] 1
errorList$seed: length = 1
[1] 1
errorList$useIndex: length = 1
[1] FALSE
errorList$tstart: length = 1
[1] "2023-10-31 16:39:43 CST"
errorList$verbose: length = 1
[1] FALSE
errorList$logFile: length = 1
[1] "ArchRLogs/ArchR-addDoubletScores-33f37f2a7050bb-Date-2023-10-31_Time-16-39-42.log"
errorList$outLSI: length = 1
[1] "Error with outLSI!"
errorList$matSVD: length = 1
[1] "Error with matSVD!"
************************************************************
************************************************************
2023-10-31 16:40:20 : ERROR Found in addIterativeLSI for ATAC-H134-1 (1 of 1) :
LogFile = ArchRLogs/ArchR-addDoubletScores-33f37f2a7050bb-Date-2023-10-31_Time-16-39-42.log
<simpleError in .logError(e, fn = ".LSIPartialMatrix", info = "", errorList = errorList, logFile = logFile): Exiting See Error Above>
2023-10-31 16:40:20 : errorList, Class = list
errorList$ArrowFile: length = 1
[1] "ATAC-H134-1.arrow"
************************************************************
Hi @yangshichen0713! Thanks for using ArchR! Please make sure that your post belongs in the Issues section. Only bugs and error reports belong in the Issues section. Usage questions and feature requests should be posted in the Discussions section, not in Issues.
It is worth noting that there are very few actual bugs in ArchR. If you are getting an error, it is probably something specific to your dataset, usage, or computational environment, all of which are extremely challenging to troubleshoot. As such, we require reproducible examples (preferably using the tutorial dataset) from users who want assistance. If you cannot reproduce your error, we will not be able to help.
Before going through the work of making a reproducible example, search the previous Issues, Discussions, function definitions, or the ArchR manual and you will likely find the answers you are looking for.
If your post does not contain a reproducible example, it is unlikely to receive a response.
__In addition to a reproducible example, you must do the following things before we help you, unless your original post already contained this information:
1. If you've encountered an error, have you already searched previous Issues to make sure that this hasn't already been solved?
2. Did you post your log file? If not, add it now.
3. Remove any screenshots that contain text and instead copy and paste the text using markdown's codeblock syntax (three consecutive backticks). You can do this by editing your original post.
I solved this problem by re-installing irlba using install.package('irlba').
