AddDoubletScore in ArchR throws error irlba : <simpleError in irlba::irlba(mat, nDimensions, nDimensions): function 'as_cholmod_sparse' not provided by package 'Matrix'>
Opened this issue · 2 comments
Hey. I have the same error showing up. Please note that i have run ArchR on the same dataset previously and it had worked. Here is the error and the sessioninfo along with output of the logfile. I get the error when i try to run DoubletScores.
Please note, i have tried installing RSpectre, tried using 1 thread and nothing has worked so far. Please help me..
The error :
2024-02-22 17:07:55 : ERROR Found in .computeLSI for
LogFile = ArchRLogs/ArchR-addDoubletScores-2ee32a9b951d-Date-2024-02-22_Time-17-07-46.log
<simpleError in irlba::irlba(mat, nDimensions, nDimensions): function 'as_cholmod_sparse' not provided by package 'Matrix'>
2024-02-22 17:07:55 : ERROR Found in .LSIPartialMatrix for
LogFile = ArchRLogs/ArchR-addDoubletScores-2ee32a9b951d-Date-2024-02-22_Time-17-07-46.log
<simpleError in .logError(e, fn = ".computeLSI", info = "", errorList = errorList, logFile = logFile): Exiting See Error Above>
2024-02-22 17:07:55 : ERROR Found in addIterativeLSI for Sample1 (1 of 5) :
LogFile = ArchRLogs/ArchR-addDoubletScores-2ee32a9b951d-Date-2024-02-22_Time-17-07-46.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
Here is the sessioninfo()
─ Session info ───────────────────────────────────────────────────────────────────────
setting value
version R version 4.2.3 (2023-03-15)
os macOS Big Sur 11.0.1
system x86_64, darwin17.0
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/New_York
date 2024-02-22
rstudio 2023.03.0+386 Cherry Blossom (desktop)
pandoc 2.11.3.2 @ /usr/local/bin/pandoc
─ Packages ───────────────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
ArchR * 1.0.3 2023-11-08 [1] Github (GreenleafLab/ArchR@65968a4)
Biobase * 2.58.0 2022-11-01 [1] Bioconductor
BiocGenerics * 0.44.0 2022-11-01 [1] Bioconductor
BiocIO 1.8.0 2022-11-01 [1] Bioconductor
BiocManager 1.30.22 2023-08-08 [1] CRAN (R 4.2.0)
BiocParallel 1.32.6 2023-03-17 [1] Bioconductor
Biostrings * 2.66.0 2022-11-01 [1] Bioconductor
bitops 1.0-7 2021-04-24 [1] CRAN (R 4.2.0)
BSgenome * 1.66.3 2023-02-16 [1] Bioconductor
BSgenome.Hsapiens.UCSC.hg38 * 1.4.5 2023-07-11 [1] Bioconductor
cachem 1.0.8 2023-05-01 [1] CRAN (R 4.2.0)
Cairo 1.6-2 2023-11-28 [1] CRAN (R 4.2.3)
cli 3.6.2 2023-12-11 [1] CRAN (R 4.2.3)
codetools 0.2-19 2023-02-01 [1] CRAN (R 4.2.3)
colorspace 2.1-0 2023-01-23 [1] CRAN (R 4.2.0)
crayon 1.5.2 2022-09-29 [1] CRAN (R 4.2.0)
data.table * 1.15.0 2024-01-30 [1] CRAN (R 4.2.3)
DelayedArray 0.24.0 2022-11-01 [1] Bioconductor
devtools * 2.4.5 2022-10-11 [1] CRAN (R 4.2.0)
digest 0.6.34 2024-01-11 [1] CRAN (R 4.2.3)
dplyr 1.1.4 2023-11-17 [1] CRAN (R 4.2.3)
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.2.0)
fansi 1.0.6 2023-12-08 [1] CRAN (R 4.2.3)
fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.2.0)
fs 1.6.3 2023-07-20 [1] CRAN (R 4.2.0)
generics 0.1.3 2022-07-05 [1] CRAN (R 4.2.0)
GenomeInfoDb * 1.34.9 2023-02-02 [1] Bioconductor
GenomeInfoDbData 1.2.9 2023-03-26 [1] Bioconductor
GenomicAlignments 1.34.1 2023-03-09 [1] Bioconductor
GenomicRanges * 1.50.2 2022-12-16 [1] Bioconductor
ggplot2 * 3.4.4 2023-10-12 [1] CRAN (R 4.2.0)
glue 1.7.0 2024-01-09 [1] CRAN (R 4.2.3)
gridExtra * 2.3 2017-09-09 [1] CRAN (R 4.2.0)
gtable * 0.3.4 2023-08-21 [1] CRAN (R 4.2.0)
gtools * 3.9.5 2023-11-20 [1] CRAN (R 4.2.3)
htmltools 0.5.7 2023-11-03 [1] CRAN (R 4.2.3)
htmlwidgets 1.6.4 2023-12-06 [1] CRAN (R 4.2.3)
httpuv 1.6.14 2024-01-26 [1] CRAN (R 4.2.3)
IRanges * 2.32.0 2022-11-01 [1] Bioconductor
irlba * 2.3.5.1 2022-10-03 [1] CRAN (R 4.2.0)
later 1.3.2 2023-12-06 [1] CRAN (R 4.2.3)
lattice 0.22-5 2023-10-24 [1] CRAN (R 4.2.3)
lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.2.3)
magrittr * 2.0.3 2022-03-30 [1] CRAN (R 4.2.0)
Matrix * 1.6-4 2023-11-30 [1] CRAN (R 4.2.0)
MatrixGenerics * 1.10.0 2022-11-01 [1] Bioconductor
matrixStats * 1.2.0 2023-12-11 [1] CRAN (R 4.2.0)
memoise 2.0.1 2021-11-26 [1] CRAN (R 4.2.0)
mime 0.12 2021-09-28 [1] CRAN (R 4.2.0)
miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.2.0)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.2.0)
pillar 1.9.0 2023-03-22 [1] CRAN (R 4.2.0)
pkgbuild 1.4.3 2023-12-10 [1] CRAN (R 4.2.3)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.0)
pkgload 1.3.4 2024-01-16 [1] CRAN (R 4.2.3)
plyr * 1.8.9 2023-10-02 [1] CRAN (R 4.2.0)
profvis 0.3.8 2023-05-02 [1] CRAN (R 4.2.0)
promises 1.2.1 2023-08-10 [1] CRAN (R 4.2.0)
purrr 1.0.2 2023-08-10 [1] CRAN (R 4.2.0)
R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.0)
Rcpp * 1.0.12 2024-01-09 [1] CRAN (R 4.2.3)
RcppArmadillo * 0.12.6.6.1 2023-12-04 [1] CRAN (R 4.2.0)
RCurl 1.98-1.14 2024-01-09 [1] CRAN (R 4.2.3)
remotes 2.4.2.1 2023-07-18 [1] CRAN (R 4.2.0)
restfulr 0.0.15 2022-06-16 [1] CRAN (R 4.2.0)
rhdf5 * 2.42.1 2023-04-07 [1] Bioconductor
rhdf5filters 1.10.1 2023-03-24 [1] Bioconductor
Rhdf5lib 1.20.0 2022-11-01 [1] Bioconductor
rjson 0.2.21 2022-01-09 [1] CRAN (R 4.2.0)
rlang 1.1.3 2024-01-10 [1] CRAN (R 4.2.3)
Rsamtools * 2.14.0 2022-11-01 [1] Bioconductor
RSpectra * 0.16-1 2022-04-24 [1] CRAN (R 4.2.0)
rstudioapi 0.15.0 2023-07-07 [1] CRAN (R 4.2.0)
rtracklayer * 1.58.0 2022-11-01 [1] Bioconductor
S4Vectors * 0.36.2 2023-02-26 [1] Bioconductor
scales 1.3.0 2023-11-28 [1] CRAN (R 4.2.3)
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.0)
shiny 1.8.0 2023-11-17 [1] CRAN (R 4.2.3)
sparseMatrixStats * 1.10.0 2022-11-01 [1] Bioconductor
stringi 1.8.3 2023-12-11 [1] CRAN (R 4.2.3)
stringr * 1.5.1 2023-11-14 [1] CRAN (R 4.2.3)
SummarizedExperiment * 1.28.0 2022-11-01 [1] Bioconductor
tibble 3.2.1 2023-03-20 [1] CRAN (R 4.2.0)
tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.2.0)
urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.2.0)
usethis * 2.2.2 2023-07-06 [1] CRAN (R 4.2.0)
utf8 1.2.4 2023-10-22 [1] CRAN (R 4.2.3)
vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.2.3)
withr 3.0.0 2024-01-16 [1] CRAN (R 4.2.3)
XML 3.99-0.16.1 2024-01-22 [1] CRAN (R 4.2.3)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.2.0)
XVector * 0.38.0 2022-11-01 [1] Bioconductor
yaml 2.3.8 2023-12-11 [1] CRAN (R 4.2.3)
zlibbioc 1.44.0 2022-11-01 [1] Bioconductor
[1] /Library/Frameworks/R.framework/Versions/4.2/Resources/library
──────────────────────────────────────────────────────────────────────────────────────
And here is the output of the logfile
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \___ | ----.| | | | | |\ \\___. /__/ \__\ | _| .| _||| || | _| `._____|
Logging With ArchR!
Start Time : 2024-02-22 17:07:46
------- ArchR Info
ArchRThreads = 1
ArchRGenome = Hg38
------- System Info
Computer OS = unix
------- Session Info
R version 4.2.3 (2023-03-15)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.0.1
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
Random number generation:
RNG: L'Ecuyer-CMRG
Normal: Inversion
Sample: Rejection
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats4 grid stats graphics grDevices utils datasets methods
[9] base
other attached packages:
[1] Rsamtools_2.14.0 BSgenome.Hsapiens.UCSC.hg38_1.4.5
[3] BSgenome_1.66.3 rtracklayer_1.58.0
[5] Biostrings_2.66.0 XVector_0.38.0
[7] rhdf5_2.42.1 SummarizedExperiment_1.28.0
[9] Biobase_2.58.0 RcppArmadillo_0.12.6.6.1
[11] Rcpp_1.0.12 GenomicRanges_1.50.2
[13] GenomeInfoDb_1.34.9 IRanges_2.32.0
[15] S4Vectors_0.36.2 BiocGenerics_0.44.0
[17] sparseMatrixStats_1.10.0 MatrixGenerics_1.10.0
[19] matrixStats_1.2.0 data.table_1.15.0
[21] stringr_1.5.1 plyr_1.8.9
[23] magrittr_2.0.3 ggplot2_3.4.4
[25] gtable_0.3.4 gtools_3.9.5
[27] gridExtra_2.3 devtools_2.4.5
[29] usethis_2.2.2 ArchR_1.0.3
[31] RSpectra_0.16-1 irlba_2.3.5.1
[33] Matrix_1.6-4
loaded via a namespace (and not attached):
[1] bitops_1.0-7 fs_1.6.3 tools_4.2.3
[4] profvis_0.3.8 utf8_1.2.4 R6_2.5.1
[7] colorspace_2.1-0 rhdf5filters_1.10.1 urlchecker_1.0.1
[10] withr_3.0.0 tidyselect_1.2.0 compiler_4.2.3
[13] cli_3.6.2 Cairo_1.6-2 DelayedArray_0.24.0
[16] scales_1.3.0 digest_0.6.34 pkgconfig_2.0.3
[19] htmltools_0.5.7 sessioninfo_1.2.2 fastmap_1.1.1
[22] htmlwidgets_1.6.4 rlang_1.1.3 rstudioapi_0.15.0
[25] shiny_1.8.0 BiocIO_1.8.0 generics_0.1.3
[28] BiocParallel_1.32.6 dplyr_1.1.4 RCurl_1.98-1.14
[31] GenomeInfoDbData_1.2.9 munsell_0.5.0 Rhdf5lib_1.20.0
[34] fansi_1.0.6 lifecycle_1.0.4 yaml_2.3.8
[37] stringi_1.8.3 zlibbioc_1.44.0 pkgbuild_1.4.3
[40] parallel_4.2.3 promises_1.2.1 crayon_1.5.2
[43] miniUI_0.1.1.1 lattice_0.22-5 pillar_1.9.0
[46] rjson_0.2.21 codetools_0.2-19 pkgload_1.3.4
[49] XML_3.99-0.16.1 glue_1.7.0 remotes_2.4.2.1
[52] BiocManager_1.30.22 vctrs_0.6.5 httpuv_1.6.14
[55] purrr_1.0.2 cachem_1.0.8 mime_0.12
[58] xtable_1.8-4 restfulr_0.0.15 later_1.3.2
[61] tibble_3.2.1 GenomicAlignments_1.34.1 memoise_2.0.1
[64] ellipsis_0.3.2
------- Log Info
2024-02-22 17:07:46 : addDoubletScores Input-Parameters, Class = list
addDoubletScores Input-Parameters$input: length = 5
[1] "Sample1.arrow" "Sample2.arrow" "Sample3.arrow"
[4] "Sample4.arrow" "Sample5.arrow"
addDoubletScores Input-Parameters$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$logFile: length = 1
[1] "ArchRLogs/ArchR-addDoubletScores-2ee32a9b951d-Date-2024-02-22_Time-17-07-46.log"
2024-02-22 17:07:46 : Batch Execution w/ safelapply!, 0 mins elapsed.
2024-02-22 17:07:46 : Sample1(1 of 5) : Computing Doublet Statistics, 0 mins elapsed.
2024-02-22 17:07:46 : Running IterativeLSI, 0.004 mins elapsed.
2024-02-22 17:07:46 : IterativeLSI Input-Parameters, Class = list
IterativeLSI Input-Parameters$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$excludeChr: length = 0
NULL
IterativeLSI Input-Parameters$keep0lsi: length = 1
[1] FALSE
IterativeLSI Input-Parameters$saveIterations: length = 1
[1] FALSE
IterativeLSI Input-Parameters$nPlot: length = 1
[1] 10000
IterativeLSI Input-Parameters$outDir: length = 1
[1] "/Users/hiraanis/Desktop/PhD/Hira-multiome/ArchR_analysis/tmp/tmp-2ee34c5ab8c5-Date-2024-02-22_Time-17-07-46"
IterativeLSI Input-Parameters$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-2ee32a9b951d-Date-2024-02-22_Time-17-07-46.log"
2024-02-22 17:07:46 : Computing Total Across All Features, 0 mins elapsed.
2024-02-22 17:07:47 : Computing Top Features, 0.023 mins elapsed.
###########
2024-02-22 17:07:48 : Running LSI (1 of 2) on Top Features, 0.038 mins elapsed.
###########
2024-02-22 17:07:48 : Creating Partial Matrix, 0.038 mins elapsed.
2024-02-22 17:07:54 : Computing LSI, 0.13 mins elapsed.
2024-02-22 17:07:54 : LSI Parameters, Class = list
LSI Parameters$: length = 1
1 function (name)
2 .Internal(args(name))
LSI Parameters$mat: nRows = 25000, nCols = 1788
LSI Parameters$mat: NonZeroEntries = 10513861, EntryRange = [ 1 , 1 ]
5 x 5 sparse Matrix of class "dgCMatrix"
Sample1#GTCTTGCTCATGGTTA-1 Sample1#GACCTTTGTGTCCTGC-1
[1,] 1 1
[2,] 1 1
[3,] . 1
[4,] 1 1
[5,] 1 1
Sample1#CCCAGTTTCTTGATGA-1 Sample1#CCGCAAATCGATTATG-1
[1,] 1 .
[2,] 1 .
[3,] . 1
[4,] 1 1
[5,] 1 1
Sample1#CCAAGTTAGCCACATG-1
[1,] 1
[2,] 1
[3,] .
[4,] .
[5,] 1
LSI Parameters$LSIMethod: length = 1
[1] 1
LSI Parameters$scaleTo: length = 1
[1] 10000
LSI Parameters$nDimensions: length = 1
[1] 30
LSI Parameters$binarize: length = 1
[1] TRUE
LSI Parameters$outlierQuantiles: length = 0
NULL
LSI Parameters$keep0lsi: length = 1
[1] FALSE
LSI Parameters$seed: length = 1
[1] 1
LSI Parameters$verbose: length = 1
[1] FALSE
LSI Parameters$tstart: length = 1
[1] "2024-02-22 17:07:46 EST"
LSI Parameters$logFile: length = 1
[1] "ArchRLogs/ArchR-addDoubletScores-2ee32a9b951d-Date-2024-02-22_Time-17-07-46.log"
2024-02-22 17:07:54 : Running LSI, Input Matrix = 0.126 GB, 0.132 mins elapsed.
2024-02-22 17:07:54 : Binarizing Matrix, 0.132 mins elapsed.
2024-02-22 17:07:54 : Computing Term Frequency, 0.133 mins elapsed.
2024-02-22 17:07:54 : Removing 0 Sum Rows, 0.133 mins elapsed.
2024-02-22 17:07:54 : Computing Inverse Document Frequency, 0.135 mins elapsed.
2024-02-22 17:07:54 : Computing TF-IDF Matrix, 0.135 mins elapsed.
2024-02-22 17:07:55 : Computing SVD using irlba, 0.145 mins elapsed.
2024-02-22 17:07:55 : ERROR Found in .computeLSI for
LogFile = ArchRLogs/ArchR-addDoubletScores-2ee32a9b951d-Date-2024-02-22_Time-17-07-46.log
<simpleError in irlba::irlba(mat, nDimensions, nDimensions): function 'as_cholmod_sparse' not provided by package 'Matrix'>
2024-02-22 17:07:55 : errorList, Class = list
errorList$mat: nRows = 25000, nCols = 1788
errorList$mat: NonZeroEntries = 10513861, EntryRange = [ 6.05921387773296e-05 , 0.019743480836276 ]
5 x 5 sparse Matrix of class "dgCMatrix"
Sample1#GTCTTGCTCATGGTTA-1 Sample1#GACCTTTGTGTCCTGC-1
[1,] 1.003779e-04 9.683009e-05
[2,] 8.973452e-05 8.656289e-05
[3,] . 9.005340e-05
[4,] 7.383138e-05 7.122185e-05
[5,] 9.618878e-05 9.278904e-05
Sample1#CCCAGTTTCTTGATGA-1 Sample1#CCGCAAATCGATTATG-1
[1,] 1.026353e-04 .
[2,] 9.175255e-05 .
[3,] . 9.387405e-05
[4,] 7.549177e-05 7.424354e-05
[5,] 9.835197e-05 9.672575e-05
Sample1#CCAAGTTAGCCACATG-1
[1,] 9.992355e-05
[2,] 8.932835e-05
[3,] .
[4,] .
[5,] 9.575340e-05
errorList$colSm: length = 1
[1] "Error with colSm!"
errorList$idf: length = 1
[1] "Error with idf!"
errorList$V: length = 1
[1] "Error with V!"
errorList$matSVD: length = 1
[1] "Error with matSVD!"
errorList$out: length = 1
[1] "Error with out!"
2024-02-22 17:07:55 : ERROR Found in .LSIPartialMatrix for
LogFile = ArchRLogs/ArchR-addDoubletScores-2ee32a9b951d-Date-2024-02-22_Time-17-07-46.log
<simpleError in .logError(e, fn = ".computeLSI", info = "", errorList = errorList, logFile = logFile): Exiting See Error Above>
2024-02-22 17:07:55 : errorList, Class = list
errorList$: length = 1
1 function (name)
2 .Internal(args(name))
errorList$ArrowFiles: length = 1
[1] "Sample1.arrow"
errorList$useMatrix: length = 1
[1] "TileMatrix"
errorList$cellNames: length = 1788
[1] "Sample1#GTCTTGCTCATGGTTA-1" "Sample1#GACCTTTGTGTCCTGC-1"
[3] "Sample1#CCCAGTTTCTTGATGA-1" "Sample1#CCGCAAATCGATTATG-1"
[5] "Sample1#CCAAGTTAGCCACATG-1" "Sample1#AACCTAATCTTGTCCA-1"
errorList$cellDepth: length = 1788
Sample1#GTCTTGCTCATGGTTA-1 Sample1#GACCTTTGTGTCCTGC-1
4.982931 4.980317
Sample1#CCCAGTTTCTTGATGA-1Sample1#CCGCAAATCGATTATG-1
4.965225 4.961654
Sample1#CCAAGTTAGCCACATG-1 Sample1#AACCTAATCTTGTCCA-1
4.961169 4.958750
errorList$sampleNames: length = 1788
[1] "Sample1" "Sample1" "Sample1" "Sample1" "Sample1"
[6] "Sample1"
errorList$dimsToUse: length = 30
[1] 1 2 3 4 5 6
errorList$binarize: length = 1
[1] TRUE
errorList$outlierQuantiles: length = 0
NULL
errorList$keep0lsi: length = 1
[1] FALSE
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] "2024-02-22 17:07:46 EST"
errorList$verbose: length = 1
[1] FALSE
errorList$logFile: length = 1
[1] "ArchRLogs/ArchR-addDoubletScores-2ee32a9b951d-Date-2024-02-22_Time-17-07-46.log"
errorList$outLSI: length = 1
[1] "Error with outLSI!"
errorList$matSVD: length = 1
[1] "Error with matSVD!"
2024-02-22 17:07:55 : ERROR Found in addIterativeLSI for Sample1 (1 of 5) :
LogFile = ArchRLogs/ArchR-addDoubletScores-2ee32a9b951d-Date-2024-02-22_Time-17-07-46.log
<simpleError in .logError(e, fn = ".LSIPartialMatrix", info = "", errorList = errorList, logFile = logFile): Exiting See Error Above>
2024-02-22 17:07:55 : errorList, Class = list
errorList$ArrowFile: length = 1
[1] "Sample1.arrow"
Is there any solutions now ? I meet the same problem and it does not work . even I changed Matrix version changes to 1.6.5
irlba v 2.3.51 ArchR v1.0.3