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AddDoubletScores makes Rstudio aborted? #2247

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joeyQX opened this issue Dec 17, 2024 · 1 comment
Open

AddDoubletScores makes Rstudio aborted? #2247

joeyQX opened this issue Dec 17, 2024 · 1 comment
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@joeyQX
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joeyQX commented Dec 17, 2024

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I encountered an issue where RStudio aborts when running AddDoubletScores of specific samples, while others run without problems. I am unsure why this happens, especially since my computer has 192 GB of memory.

The ArchRlogs are as follows:
When running the sample "Ang11," RStudio consistently aborts. I have tried several times, but the ArchR log always ends at the same point.

ArchR_1.0.2

2024-12-15 16:00:40.045005 : Ang10 (2 of 16) : Computing Doublet Statistics, 77.398 mins elapsed.
2024-12-15 16:00:40.803713 : Running IterativeLSI, 77.41 mins elapsed.

2024-12-15 16:00:40.804899 : 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 = 50
[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] "E:\scATAC-seq\tmp\tmp-8285f5d4028-Date-2024-12-15_Time-16-00-40.045207"

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-8286ee159b3-Date-2024-12-15_Time-14-43-16.11319.log"

2024-12-15 16:00:40.884007 : Computing Total Across All Features, 0 mins elapsed.
2024-12-15 16:00:41.848786 : Computing Top Features, 0.016 mins elapsed.
###########
2024-12-15 16:00:43.591331 : Running LSI (1 of 2) on Top Features, 0.045 mins elapsed.
###########
2024-12-15 16:00:43.726186 : Sampling Cells (N = 10000) for Estimated LSI, 0.047 mins elapsed.
2024-12-15 16:00:43.726777 : Creating Sampled Partial Matrix, 0.048 mins elapsed.
2024-12-15 16:00:47.032476 : Computing Estimated LSI (projectAll = FALSE), 0.103 mins elapsed.

2024-12-15 16:00:47.033115 : LSI Parameters, Class = list

LSI Parameters$: length = 1

1 function (name)
2 .Internal(args(name))

LSI Parameters$mat: nRows = 25000, nCols = 10000
LSI Parameters$mat: NonZeroEntries = 824864, EntryRange = [ 1 , 1 ]
5 x 5 sparse Matrix of class "dgCMatrix"
Ang10#AAACGAAAGAACAGGA-1 Ang10#AAACGAAAGAACGACC-1 Ang10#AAACGAAAGAATACTG-1 Ang10#AAACGAAAGAGAGGTA-1 Ang10#AAACGAAAGATGCGCA-1
[1,] . . . . .
[2,] . . . . .
[3,] . . . . .
[4,] . . . . .
[5,] . . . . .

LSI Parameters$LSIMethod: length = 1
[1] 1

LSI Parameters$scaleTo: length = 1
[1] 10000

LSI Parameters$nDimensions: length = 1
[1] 50

LSI Parameters$binarize: length = 1
[1] TRUE

LSI Parameters$outlierQuantiles: length = 0
NULL

LSI Parameters$seed: length = 1
[1] 1

LSI Parameters$verbose: length = 1
[1] FALSE

LSI Parameters$tstart: length = 1
[1] "2024-12-15 16:00:40 CST"

LSI Parameters$logFile: length = 1
[1] "ArchRLogs\ArchR-addDoubletScores-8286ee159b3-Date-2024-12-15_Time-14-43-16.11319.log"

2024-12-15 16:00:47.040944 : Running LSI, Input Matrix = 0.011 GB, 0.103 mins elapsed.
2024-12-15 16:00:47.041794 : Binarizing Matrix, 0.103 mins elapsed.
2024-12-15 16:00:47.046419 : Computing Term Frequency, 0.103 mins elapsed.
2024-12-15 16:00:47.051032 : Removing 0 Sum Rows, 0.103 mins elapsed.
2024-12-15 16:00:47.056721 : Computing Inverse Document Frequency, 0.103 mins elapsed.
2024-12-15 16:00:47.057944 : Computing TF-IDF Matrix, 0.103 mins elapsed.
2024-12-15 16:00:48.419358 : Computing SVD using irlba, 0.126 mins elapsed.
2024-12-15 16:00:51.702875 : Finished LSI (TF-IDF SVD) using irlba, 0.18 mins elapsed.

2024-12-15 16:00:54.502156 : outLSI-1, Class = SimpleList

outLSI-1$matSVD: nRows = 6131, nCols = 50
LSI1 LSI2 LSI3 LSI4 LSI5
Ang10#AAACGAAAGAACAGGA-1 2.803639e-07 8.562099e-07 1.276423e-05 -1.222417e-05 -4.362075e-09
Ang10#AAACGAAAGATGCGCA-1 2.765396e-07 7.853001e-07 9.091395e-07 -2.646900e-06 -1.254862e-07
Ang10#AAACGAACAAGAGCGT-1 1.099042e-06 1.477499e-06 2.106828e-06 -2.686546e-06 -9.122517e-07
Ang10#AAACGAACAAGTAACA-1 1.300231e-06 2.005853e-06 2.214296e-06 -1.870760e-06 -5.277139e-07
Ang10#AAACGAACACGCGACT-1 2.734347e-07 2.742727e-05 2.161207e-06 -1.151224e-06 -4.252459e-07

outLSI-1$rowSm: length = 25000
[1] 21 50 38 22 11 16

outLSI-1$nCol: length = 1
[1] 6131

outLSI-1$exclude: length = 3869
Ang10#AAACGAAAGAACGACC-1 Ang10#AAACGAAAGAATACTG-1 Ang10#AAACGAAAGAGAGGTA-1 Ang10#AAACGAAAGCCCATGC-1 Ang10#AAACGAAAGGCGTAGT-1
2 3 4 6 7
Ang10#AAACGAACAGATTGTC-1
12

outLSI-1$idx: length = 25000
[1] 1 2 3 4 5 6

outLSI-1$u: nRows = 25000, nCols = 50
[,1] [,2] [,3] [,4] [,5]
[1,] 1.864579e-08 1.150033e-07 8.846264e-08 -5.520343e-08 -4.963960e-09
[2,] 2.263589e-07 1.307140e-07 1.018959e-07 -1.399754e-07 -2.457590e-07
[3,] 1.683178e-07 9.633686e-08 1.317327e-07 -1.502311e-07 -6.929415e-08
[4,] 3.022884e-08 3.070345e-08 6.220437e-08 -3.715084e-08 -4.022985e-08
[5,] 1.849464e-08 3.550430e-08 8.067237e-08 -3.802822e-08 -4.898427e-09

outLSI-1$v: nRows = 6131, nCols = 50
[,1] [,2] [,3] [,4] [,5]
[1,] 3.058186e-08 9.886662e-08 1.490359e-06 -1.429550e-06 -5.127501e-10
[2,] 3.016471e-08 9.067866e-08 1.061517e-07 -3.095406e-07 -1.475056e-08
[3,] 1.198826e-07 1.706069e-07 2.459946e-07 -3.141770e-07 -1.072327e-07
[4,] 1.418281e-07 2.316160e-07 2.585427e-07 -2.187752e-07 -6.203134e-08
[5,] 2.982603e-08 3.167029e-06 2.523440e-07 -1.346294e-07 -4.998651e-08

outLSI-1$binarize: length = 1
[1] TRUE

outLSI-1$scaleTo: length = 1
[1] 10000

outLSI-1$nDimensions: length = 1
[1] 50

outLSI-1$LSIMethod: length = 1
[1] 1

outLSI-1$outliers: length = 1
[1] NA

outLSI-1$date: length = 1
[1] "2024-12-15"

outLSI-1$seed: length = 1
[1] 1

outLSI-1$scaleDims: length = 1
[1] FALSE

outLSI-1$useMatrix: length = 1
[1] "TileMatrix"

outLSI-1$tileSize: length = 1
[1] 500

2024-12-15 16:00:54.514106 : Cluster Params, Class = list

Cluster Params$: length = 1

1 function (name)
2 .Internal(args(name))

Cluster Params$matSVD: nRows = 6131, nCols = 50
LSI1 LSI2 LSI3 LSI4 LSI5
Ang10#AAACGAAAGAACAGGA-1 2.803639e-07 8.562099e-07 1.276423e-05 -1.222417e-05 -4.362075e-09
Ang10#AAACGAAAGATGCGCA-1 2.765396e-07 7.853001e-07 9.091395e-07 -2.646900e-06 -1.254862e-07
Ang10#AAACGAACAAGAGCGT-1 1.099042e-06 1.477499e-06 2.106828e-06 -2.686546e-06 -9.122517e-07
Ang10#AAACGAACAAGTAACA-1 1.300231e-06 2.005853e-06 2.214296e-06 -1.870760e-06 -5.277139e-07
Ang10#AAACGAACACGCGACT-1 2.734347e-07 2.742727e-05 2.161207e-06 -1.151224e-06 -4.252459e-07

Cluster Params$corCutOff: length = 1
[1] 0.75

Cluster Params$dimsToUse: length = 50
[1] 1 2 3 4 5 6

Cluster Params$scaleDims: length = 1
[1] FALSE

Cluster Params$verbose: length = 1
[1] FALSE

Cluster Params$j: length = 1
[1] 1

Cluster Params$filterBias: length = 1
[1] FALSE

Cluster Params$cellNames: length = 487787
[1] "Ang10#ACCAAACAGTCCTTCC-1" "Ang10#AACTTGGAGGTTACAA-1" "Ang10#TTAGCTTTCTCTGCGT-1" "Ang10#CTTTGCGAGCTCGTTA-1"
[5] "Ang10#CATAACGCACCTCGTT-1" "Ang10#CACTAAGCAACGGGTA-1"

Cluster Params$cellDepth: length = 487787
Ang10#ACCAAACAGTCCTTCC-1 Ang10#AACTTGGAGGTTACAA-1 Ang10#TTAGCTTTCTCTGCGT-1 Ang10#CTTTGCGAGCTCGTTA-1 Ang10#CATAACGCACCTCGTT-1
4.993052 4.925090 4.912647 4.911818 4.907664
Ang10#CACTAAGCAACGGGTA-1
4.904926

Cluster Params$tstart: length = 1
[1] "2024-12-15 16:00:40 CST"

Cluster Params$logFile: length = 1
[1] "ArchRLogs\ArchR-addDoubletScores-8286ee159b3-Date-2024-12-15_Time-14-43-16.11319.log"

2024-12-15 16:00:54.518982 : Identifying Clusters, 0.227 mins elapsed.

2024-12-15 16:00:54.54776 : addClusters Input-Parameters, Class = list

addClusters Input-Parameters$: length = 1

1 function (name)
2 .Internal(args(name))

addClusters Input-Parameters$input: nRows = 6131, nCols = 50
LSI1 LSI2 LSI3 LSI4 LSI5
Ang10#AAACGAAAGAACAGGA-1 2.803639e-07 8.562099e-07 1.276423e-05 -1.222417e-05 -4.362075e-09
Ang10#AAACGAAAGATGCGCA-1 2.765396e-07 7.853001e-07 9.091395e-07 -2.646900e-06 -1.254862e-07
Ang10#AAACGAACAAGAGCGT-1 1.099042e-06 1.477499e-06 2.106828e-06 -2.686546e-06 -9.122517e-07
Ang10#AAACGAACAAGTAACA-1 1.300231e-06 2.005853e-06 2.214296e-06 -1.870760e-06 -5.277139e-07
Ang10#AAACGAACACGCGACT-1 2.734347e-07 2.742727e-05 2.161207e-06 -1.151224e-06 -4.252459e-07

addClusters Input-Parameters$reducedDims: length = 1
[1] "IterativeLSI"

addClusters Input-Parameters$name: length = 1
[1] "Clusters"

addClusters Input-Parameters$sampleCells: length = 1
[1] 10000

addClusters Input-Parameters$seed: length = 1
[1] 1

addClusters Input-Parameters$method: length = 1
[1] "Seurat"

addClusters Input-Parameters$dimsToUse: length = 0
NULL

addClusters Input-Parameters$scaleDims: length = 0
NULL

addClusters Input-Parameters$corCutOff: length = 1
[1] 0.75

addClusters Input-Parameters$knnAssign: length = 1
[1] 10

addClusters Input-Parameters$nOutlier: length = 1
[1] 5

addClusters Input-Parameters$maxClusters: length = 1
[1] 6

addClusters Input-Parameters$testBias: length = 1
[1] TRUE

addClusters Input-Parameters$filterBias: length = 1
[1] FALSE

addClusters Input-Parameters$biasClusters: length = 1
[1] 0.01

addClusters Input-Parameters$biasCol: length = 1
[1] "nFrags"

addClusters Input-Parameters$biasVals: length = 6131
[1] 0.3010300 0.6989700 0.6020600 2.3463530 0.4771213 1.3979400

addClusters Input-Parameters$biasQuantiles: length = 2
[1] 0.05 0.95

addClusters Input-Parameters$biasEnrich: length = 1
[1] 10

addClusters Input-Parameters$biasProportion: length = 1
[1] 0.5

addClusters Input-Parameters$biasPval: length = 1
[1] 0.05

addClusters Input-Parameters$nPerm: length = 1
[1] 500

addClusters Input-Parameters$prefix: length = 1
[1] "C"

addClusters Input-Parameters$ArchRProj: length = 0
NULL

addClusters Input-Parameters$verbose: length = 1
[1] FALSE

addClusters Input-Parameters$tstart: length = 0
NULL

addClusters Input-Parameters$force: length = 1
[1] FALSE

addClusters Input-Parameters$logFile: length = 1
[1] "ArchRLogs\ArchR-addDoubletScores-8286ee159b3-Date-2024-12-15_Time-14-43-16.11319.log"

addClusters Input-Parameters$...: length = 2

2024-12-15 16:00:54.55925 : Running Seurats FindClusters (Stuart et al. Cell 2019), 0 mins elapsed.
2024-12-15 16:01:04.19908 : Testing Biased Clusters, 0.161 mins elapsed.
2024-12-15 16:01:04.2071 : Testing Outlier Clusters, 0.161 mins elapsed.
2024-12-15 16:01:04.207913 : Identified more clusters than maxClusters allowed (n = 0). Merging clusters to maxClusters (n = 6).
If this is not desired set maxClusters = NULL!, 0.161 mins elapsed.
2024-12-15 16:01:04.211959 : Assigning Cluster Names to 6 Clusters, 0.161 mins elapsed.
2024-12-15 16:01:04.214912 : Finished addClusters, 0.161 mins elapsed.
2024-12-15 16:01:04.216799 : Identified 6 Clusters, 0.389 mins elapsed.

2024-12-15 16:01:04.21726 : clusterDF-1, Class = DFrame
DataFrame with 6131 rows and 2 columns
cellNames clusters

1 Ang10#AAACGAAAGAACAG.. C5
2 Ang10#AAACGAAAGATGCG.. C5
3 Ang10#AAACGAACAAGAGC.. C5
4 Ang10#AAACGAACAAGTAA.. C5
5 Ang10#AAACGAACACGCGA.. C5
... ... ...
6127 Ang10#TTTGTGTAGCGTAT.. C5
6128 Ang10#TTTGTGTAGTTCGT.. C5
6129 Ang10#TTTGTGTCATTACT.. C5
6130 Ang10#TTTGTGTTCAGCAC.. C5
6131 Ang10#TTTGTGTTCCAGAA.. C5

2024-12-15 16:01:04.220075 : Creating Cluster Matrix on the total Group Features, 0.389 mins elapsed.
2024-12-15 16:01:43.187787 : Computing Variable Features, 1.039 mins elapsed.
###########
2024-12-15 16:01:43.299739 : Running LSI (2 of 2) on Variable Features, 1.04 mins elapsed.
###########
2024-12-15 16:01:43.355603 : Creating Partial Matrix, 1.041 mins elapsed.
2024-12-15 16:01:55.336845 : Computing LSI, 1.241 mins elapsed.

2024-12-15 16:01:55.33761 : LSI Parameters, Class = list

LSI Parameters$: length = 1

1 function (name)
2 .Internal(args(name))

LSI Parameters$mat: nRows = 25000, nCols = 487787
LSI Parameters$mat: NonZeroEntries = 32677070, EntryRange = [ 1 , 1 ]
5 x 5 sparse Matrix of class "dgCMatrix"
Ang10#ACCAAACAGTCCTTCC-1 Ang10#AACTTGGAGGTTACAA-1 Ang10#TTAGCTTTCTCTGCGT-1 Ang10#CTTTGCGAGCTCGTTA-1 Ang10#CATAACGCACCTCGTT-1
[1,] . . . . .
[2,] . 1 . 1 .
[3,] . 1 . 1 1
[4,] . 1 . 1 1
[5,] . . 1 1 .

LSI Parameters$LSIMethod: length = 1
[1] 1

LSI Parameters$scaleTo: length = 1
[1] 10000

LSI Parameters$nDimensions: length = 1
[1] 50

LSI Parameters$binarize: length = 1
[1] TRUE

LSI Parameters$outlierQuantiles: length = 0
NULL

LSI Parameters$seed: length = 1
[1] 1

LSI Parameters$verbose: length = 1
[1] FALSE

LSI Parameters$tstart: length = 1
[1] "2024-12-15 16:00:40 CST"

LSI Parameters$logFile: length = 1
[1] "ArchRLogs\ArchR-addDoubletScores-8286ee159b3-Date-2024-12-15_Time-14-43-16.11319.log"

2024-12-15 16:01:55.47217 : Running LSI, Input Matrix = 0.437 GB, 1.243 mins elapsed.
2024-12-15 16:01:55.479017 : Binarizing Matrix, 1.243 mins elapsed.
2024-12-15 16:01:55.629578 : Computing Term Frequency, 1.246 mins elapsed.
2024-12-15 16:01:55.772372 : Removing 0 Sum Rows, 1.248 mins elapsed.
2024-12-15 16:01:55.941208 : Computing Inverse Document Frequency, 1.251 mins elapsed.
2024-12-15 16:01:55.942472 : Computing TF-IDF Matrix, 1.251 mins elapsed.
2024-12-15 16:01:57.409959 : Computing SVD using irlba, 1.276 mins elapsed.
2024-12-15 16:04:39.124078 : Finished LSI (TF-IDF SVD) using irlba, 3.971 mins elapsed.

2024-12-15 16:04:40.747753 : outLSI-2, Class = SimpleList

outLSI-2$matSVD: nRows = 278731, nCols = 50
LSI1 LSI2 LSI3 LSI4 LSI5
Ang10#ACCAAACAGTCCTTCC-1 0.0004277673 -0.0003627436 -0.0013758331 0.0005720289 -0.007136091
Ang10#AACTTGGAGGTTACAA-1 0.0010075568 -0.0010465750 -0.0012926285 0.0010494250 -0.001447100
Ang10#TTAGCTTTCTCTGCGT-1 0.0006062246 -0.0018162360 -0.0008679921 0.0018187516 -0.001107673
Ang10#CTTTGCGAGCTCGTTA-1 0.0009731813 -0.0010069793 -0.0012568067 0.0009960013 -0.001404395
Ang10#CATAACGCACCTCGTT-1 0.0009137606 -0.0009416399 -0.0011638715 0.0009289805 -0.001311815

outLSI-2$rowSm: length = 25000
[1] 349 1624 2053 984 1047 4009

outLSI-2$nCol: length = 1
[1] 278731

outLSI-2$exclude: length = 209056
Ang10#TCAAGCAAGAGTGGTC-1 Ang10#TATTGCTTCTCTGCAC-1 Ang10#ACTCGGGAGTTGTCCA-1 Ang10#CGCGCAAGTCACATTG-1 Ang10#GGCGTTGTCTTAGTGG-1
8286 17467 17687 19580 20851
Ang10#GCTTGCTGTCGCTAGC-1
23054

outLSI-2$idx: length = 25000
[1] 1 2 3 4 5 6

outLSI-2$u: nRows = 25000, nCols = 50
[,1] [,2] [,3] [,4] [,5]
[1,] 1.179230e-05 -7.642679e-06 -1.220049e-05 9.474139e-06 -3.189839e-05
[2,] 2.951826e-05 -3.138011e-05 -4.534307e-05 2.851975e-05 -6.649319e-05
[3,] 3.414399e-05 -4.388274e-05 -6.678402e-05 4.534615e-05 -8.659786e-05
[4,] 1.292884e-05 -1.181075e-05 -2.504519e-05 2.263389e-05 -3.263369e-05
[5,] 3.106104e-05 -1.636229e-03 2.977561e-05 1.314025e-05 -2.215058e-05

outLSI-2$v: nRows = 278731, nCols = 50
[,1] [,2] [,3] [,4] [,5]
[1,] 1.389229e-05 -1.188334e-05 -4.521887e-05 1.891460e-05 -2.384039e-04
[2,] 3.272171e-05 -3.428538e-05 -4.248422e-05 3.470009e-05 -4.834501e-05
[3,] 1.968792e-05 -5.949917e-05 -2.852789e-05 6.013850e-05 -3.700534e-05
[4,] 3.160532e-05 -3.298824e-05 -4.130688e-05 3.293359e-05 -4.691829e-05
[5,] 2.967555e-05 -3.084775e-05 -3.825242e-05 3.071749e-05 -4.382535e-05

outLSI-2$binarize: length = 1
[1] TRUE

outLSI-2$scaleTo: length = 1
[1] 10000

outLSI-2$nDimensions: length = 1
[1] 50

outLSI-2$LSIMethod: length = 1
[1] 1

outLSI-2$outliers: length = 1
[1] NA

outLSI-2$date: length = 1
[1] "2024-12-15"

outLSI-2$seed: length = 1
[1] 1

outLSI-2$scaleDims: length = 1
[1] FALSE

outLSI-2$useMatrix: length = 1
[1] "TileMatrix"

outLSI-2$tileSize: length = 1
[1] 500

2024-12-15 16:04:42.107015 : Finished Running IterativeLSI, 4.021 mins elapsed.
2024-12-15 16:04:42.109515 : Constructing Partial Matrix for Projection, 81.432 mins elapsed.

2024-12-15 16:04:42.152796 : Ang10 (2 of 16) : LSI Result, Class = SimpleList

Ang10 (2 of 16) : LSI Result$matSVD: nRows = 278731, nCols = 50
LSI1 LSI2 LSI3 LSI4 LSI5
Ang10#ACCAAACAGTCCTTCC-1 0.0004277673 -0.0003627436 -0.0013758331 0.0005720289 -0.007136091
Ang10#AACTTGGAGGTTACAA-1 0.0010075568 -0.0010465750 -0.0012926285 0.0010494250 -0.001447100
Ang10#TTAGCTTTCTCTGCGT-1 0.0006062246 -0.0018162360 -0.0008679921 0.0018187516 -0.001107673
Ang10#CTTTGCGAGCTCGTTA-1 0.0009731813 -0.0010069793 -0.0012568067 0.0009960013 -0.001404395
Ang10#CATAACGCACCTCGTT-1 0.0009137606 -0.0009416399 -0.0011638715 0.0009289805 -0.001311815

Ang10 (2 of 16) : LSI Result$rowSm: length = 25000
[1] 349 1624 2053 984 1047 4009

Ang10 (2 of 16) : LSI Result$nCol: length = 1
[1] 278731

Ang10 (2 of 16) : LSI Result$exclude: length = 209056
Ang10#TCAAGCAAGAGTGGTC-1 Ang10#TATTGCTTCTCTGCAC-1 Ang10#ACTCGGGAGTTGTCCA-1 Ang10#CGCGCAAGTCACATTG-1 Ang10#GGCGTTGTCTTAGTGG-1
8286 17467 17687 19580 20851
Ang10#GCTTGCTGTCGCTAGC-1
23054

Ang10 (2 of 16) : LSI Result$idx: length = 25000
[1] 1 2 3 4 5 6

Ang10 (2 of 16) : LSI Result$u: nRows = 25000, nCols = 50
[,1] [,2] [,3] [,4] [,5]
[1,] 1.179230e-05 -7.642679e-06 -1.220049e-05 9.474139e-06 -3.189839e-05
[2,] 2.951826e-05 -3.138011e-05 -4.534307e-05 2.851975e-05 -6.649319e-05
[3,] 3.414399e-05 -4.388274e-05 -6.678402e-05 4.534615e-05 -8.659786e-05
[4,] 1.292884e-05 -1.181075e-05 -2.504519e-05 2.263389e-05 -3.263369e-05
[5,] 3.106104e-05 -1.636229e-03 2.977561e-05 1.314025e-05 -2.215058e-05

Ang10 (2 of 16) : LSI Result$v: nRows = 278731, nCols = 50
[,1] [,2] [,3] [,4] [,5]
[1,] 1.389229e-05 -1.188334e-05 -4.521887e-05 1.891460e-05 -2.384039e-04
[2,] 3.272171e-05 -3.428538e-05 -4.248422e-05 3.470009e-05 -4.834501e-05
[3,] 1.968792e-05 -5.949917e-05 -2.852789e-05 6.013850e-05 -3.700534e-05
[4,] 3.160532e-05 -3.298824e-05 -4.130688e-05 3.293359e-05 -4.691829e-05
[5,] 2.967555e-05 -3.084775e-05 -3.825242e-05 3.071749e-05 -4.382535e-05

Ang10 (2 of 16) : LSI Result$binarize: length = 1
[1] TRUE

Ang10 (2 of 16) : LSI Result$scaleTo: length = 1
[1] 10000

Ang10 (2 of 16) : LSI Result$nDimensions: length = 1
[1] 50

Ang10 (2 of 16) : LSI Result$LSIMethod: length = 1
[1] 1

Ang10 (2 of 16) : LSI Result$outliers: length = 1
[1] NA

Ang10 (2 of 16) : LSI Result$date: length = 1
[1] "2024-12-15"

Ang10 (2 of 16) : LSI Result$seed: length = 1
[1] 1

Ang10 (2 of 16) : LSI Result$scaleDims: length = 1
[1] FALSE

Ang10 (2 of 16) : LSI Result$useMatrix: length = 1
[1] "TileMatrix"

Ang10 (2 of 16) : LSI Result$tileSize: length = 1
[1] 500

Ang10 (2 of 16) : LSI Result$dimsKept: length = 50
[1] 1 2 3 4 5 6

2024-12-15 16:04:54.061 : Running LSI UMAP, 81.631 mins elapsed.

2024-12-15 16:04:54.061837 : Ang10 (2 of 16) : UMAP Params, Class = list

Ang10 (2 of 16) : UMAP Params$n_neighbors: length = 1
[1] 30

Ang10 (2 of 16) : UMAP Params$min_dist: length = 1
[1] 0.3

Ang10 (2 of 16) : UMAP Params$metric: length = 1
[1] "cosine"

Ang10 (2 of 16) : UMAP Params$verbose: length = 1
[1] FALSE

Ang10 (2 of 16) : UMAP Params$X: nRows = 278731, nCols = 50
LSI1 LSI2 LSI3 LSI4 LSI5
Ang10#ACCAAACAGTCCTTCC-1 0.0004277673 -0.0003627436 -0.0013758331 0.0005720289 -0.007136091
Ang10#AACTTGGAGGTTACAA-1 0.0010075568 -0.0010465750 -0.0012926285 0.0010494250 -0.001447100
Ang10#TTAGCTTTCTCTGCGT-1 0.0006062246 -0.0018162360 -0.0008679921 0.0018187516 -0.001107673
Ang10#CTTTGCGAGCTCGTTA-1 0.0009731813 -0.0010069793 -0.0012568067 0.0009960013 -0.001404395
Ang10#CATAACGCACCTCGTT-1 0.0009137606 -0.0009416399 -0.0011638715 0.0009289805 -0.001311815

Ang10 (2 of 16) : UMAP Params$ret_nn: length = 1
[1] TRUE

Ang10 (2 of 16) : UMAP Params$ret_model: length = 1
[1] TRUE

Ang10 (2 of 16) : UMAP Params$n_threads: length = 1
[1] 1

2024-12-15 16:15:55.292995 : Simulating and Projecting Doublets, 92.652 mins elapsed.

2024-12-15 17:23:22.834092 : Ang10 (2 of 16) : SimulatedLSI, Class = matrix

2024-12-15 17:23:22.834092 : Ang10 (2 of 16) : SimulatedLSI, Class = array
LSI1 LSI2 LSI3 LSI4 LSI5
[1,] 0.0005188030 -0.0003520069 -0.0015981061 0.0006196878 -0.0003159474
[2,] 0.0008559924 -0.0009343077 -0.0069776817 0.0008628541 -0.0006163202
[3,] 0.0003085856 -0.0006546585 -0.0010805449 0.0004159364 -0.0051236283
[4,] 0.0001884121 -0.0003500704 -0.0003038052 0.0002384285 -0.0004928688
[5,] 0.0004688319 -0.0004332997 -0.0006147534 0.0005343652 -0.0014986912

Ang10 (2 of 16) : SimulatedLSI: nRows = 1653365, nCols = 50

2024-12-15 17:23:26.432692 : Ang10 (2 of 16) : OriginalLSI, Class = matrix

2024-12-15 17:23:26.432692 : Ang10 (2 of 16) : OriginalLSI, Class = array
LSI1 LSI2 LSI3 LSI4 LSI5
Ang10#ACCAAACAGTCCTTCC-1 0.0004277673 -0.0003627436 -0.0013758331 0.0005720289 -0.007136091
Ang10#AACTTGGAGGTTACAA-1 0.0010075568 -0.0010465750 -0.0012926285 0.0010494250 -0.001447100
Ang10#TTAGCTTTCTCTGCGT-1 0.0006062246 -0.0018162360 -0.0008679921 0.0018187516 -0.001107673
Ang10#CTTTGCGAGCTCGTTA-1 0.0009731813 -0.0010069793 -0.0012568067 0.0009960013 -0.001404395
Ang10#CATAACGCACCTCGTT-1 0.0009137606 -0.0009416399 -0.0011638715 0.0009289805 -0.001311815

Ang10 (2 of 16) : OriginalLSI: nRows = 278731, nCols = 50

2024-12-15 17:23:26.433998 : Ang10 (2 of 16) : OriginalReProjectedLSI, Class = matrix

2024-12-15 17:23:26.433998 : Ang10 (2 of 16) : OriginalReProjectedLSI, Class = array
LSI1 LSI2 LSI3 LSI4 LSI5
Ang10#ACCAAACAGTCCTTCC-1 0.0004277673 -0.0003627436 -0.0013758331 0.0005720289 -0.007136091
Ang10#AACTTGGAGGTTACAA-1 0.0010075568 -0.0010465750 -0.0012926285 0.0010494250 -0.001447100
Ang10#TTAGCTTTCTCTGCGT-1 0.0006062246 -0.0018162360 -0.0008679921 0.0018187516 -0.001107673
Ang10#CTTTGCGAGCTCGTTA-1 0.0009731813 -0.0010069793 -0.0012568067 0.0009960013 -0.001404395
Ang10#CATAACGCACCTCGTT-1 0.0009137606 -0.0009416399 -0.0011638715 0.0009289805 -0.001311815

Ang10 (2 of 16) : OriginalReProjectedLSI: nRows = 278731, nCols = 50

2024-12-15 17:37:37.186411 : Ang10 (2 of 16) : OriginalUMAP, Class = matrix

2024-12-15 17:37:37.186411 : Ang10 (2 of 16) : OriginalUMAP, Class = array
[,1] [,2]
Ang10#ACCAAACAGTCCTTCC-1 -4.4525063 -3.8344782
Ang10#AACTTGGAGGTTACAA-1 0.2765908 -0.4427993
Ang10#TTAGCTTTCTCTGCGT-1 0.4313479 -1.1073339
Ang10#CTTTGCGAGCTCGTTA-1 0.8946131 -0.6036769
Ang10#CATAACGCACCTCGTT-1 0.4958196 -0.6398484

Ang10 (2 of 16) : OriginalUMAP: nRows = 278731, nCols = 2

2024-12-15 17:37:37.18743 : Ang10 (2 of 16) : OriginalReProjectedUMAP, Class = matrix

2024-12-15 17:37:37.18743 : Ang10 (2 of 16) : OriginalReProjectedUMAP, Class = array
[,1] [,2]
Ang10#ACCAAACAGTCCTTCC-1 -4.4465575 -3.8318865
Ang10#AACTTGGAGGTTACAA-1 0.8342067 -0.9140998
Ang10#TTAGCTTTCTCTGCGT-1 0.5628061 -1.3031087
Ang10#CTTTGCGAGCTCGTTA-1 0.8522189 -1.1778014
Ang10#CATAACGCACCTCGTT-1 0.9637401 -0.7666059

Ang10 (2 of 16) : OriginalReProjectedUMAP: nRows = 278731, nCols = 2

2024-12-15 17:37:37.197806 : Ang10 (2 of 16) : UMAP Projection R^2 = 0.97734

2024-12-15 19:57:59.253828 : Ang10 (2 of 16) : Number of Nearby Simulated Doublets, Class = numeric

Ang10 (2 of 16) : Number of Nearby Simulated Doublets: length = 278731
Ang10#ACCAAACAGTCCTTCC-1 Ang10#AACTTGGAGGTTACAA-1 Ang10#TTAGCTTTCTCTGCGT-1 Ang10#CTTTGCGAGCTCGTTA-1 Ang10#CATAACGCACCTCGTT-1
0 0 0 0 0
Ang10#CACTAAGCAACGGGTA-1
0

2024-12-15 19:58:39.7189 : Ang10 (2 of 16) : DoubletScoresLSI, Class = numeric

Ang10 (2 of 16) : DoubletScoresLSI: length = 278731
Ang10#ACCAAACAGTCCTTCC-1 Ang10#AACTTGGAGGTTACAA-1 Ang10#TTAGCTTTCTCTGCGT-1 Ang10#CTTTGCGAGCTCGTTA-1 Ang10#CATAACGCACCTCGTT-1
0 0 0 0 0
Ang10#CACTAAGCAACGGGTA-1
0

2024-12-15 19:58:39.720483 : Ang10 (2 of 16) : DoubletEnrichLSI, Class = numeric

Ang10 (2 of 16) : DoubletEnrichLSI: length = 278731
Ang10#ACCAAACAGTCCTTCC-1 Ang10#AACTTGGAGGTTACAA-1 Ang10#TTAGCTTTCTCTGCGT-1 Ang10#CTTTGCGAGCTCGTTA-1 Ang10#CATAACGCACCTCGTT-1
0 0 0 0 0
Ang10#CACTAAGCAACGGGTA-1
0

2024-12-15 19:59:24.464527 : Ang10 (2 of 16) : DoubletScoresUMAP, Class = numeric

Ang10 (2 of 16) : DoubletScoresUMAP: length = 278731
Ang10#ACCAAACAGTCCTTCC-1 Ang10#AACTTGGAGGTTACAA-1 Ang10#TTAGCTTTCTCTGCGT-1 Ang10#CTTTGCGAGCTCGTTA-1 Ang10#CATAACGCACCTCGTT-1
0 0 0 0 0
Ang10#CACTAAGCAACGGGTA-1
0

2024-12-15 19:59:24.465823 : Ang10 (2 of 16) : DoubletEnrichUMAP, Class = numeric

Ang10 (2 of 16) : DoubletEnrichUMAP: length = 278731
Ang10#ACCAAACAGTCCTTCC-1 Ang10#AACTTGGAGGTTACAA-1 Ang10#TTAGCTTTCTCTGCGT-1 Ang10#CTTTGCGAGCTCGTTA-1 Ang10#CATAACGCACCTCGTT-1
0.00000000 0.06290202 0.06955512 0.05806340 0.05443444
Ang10#CACTAAGCAACGGGTA-1
0.04657169

2024-12-15 19:59:24.47068 : Ang10 (2 of 16) : SimulationResults, Class = SimpleList

Ang10 (2 of 16) : SimulationResults$doubletUMAP: nRows = 1653365, nCols = 2
[,1] [,2]
-6.5237527 2.8266714
1.7729748 1.6282195
-2.8345025 -3.1130834
-0.7860867 -11.6198654
0.6690965 -0.4757369

Ang10 (2 of 16) : SimulationResults$doubletScore: length = 278731
Ang10#ACCAAACAGTCCTTCC-1 Ang10#AACTTGGAGGTTACAA-1 Ang10#TTAGCTTTCTCTGCGT-1 Ang10#CTTTGCGAGCTCGTTA-1 Ang10#CATAACGCACCTCGTT-1
0 0 0 0 0
Ang10#CACTAAGCAACGGGTA-1
0

Ang10 (2 of 16) : SimulationResults$doubletEnrich: length = 278731
Ang10#ACCAAACAGTCCTTCC-1 Ang10#AACTTGGAGGTTACAA-1 Ang10#TTAGCTTTCTCTGCGT-1 Ang10#CTTTGCGAGCTCGTTA-1 Ang10#CATAACGCACCTCGTT-1
0.00000000 0.06290202 0.06955512 0.05806340 0.05443444
Ang10#CACTAAGCAACGGGTA-1
0.04657169

2024-12-15 20:00:04.318681 : Ang10 (2 of 16) : Sample UMAP, Class = data.frame
Ang10 (2 of 16) : Sample UMAP: nRows = 278731, nCols = 5
X1 X2 type score enrichment
Ang10#ACCAAACAGTCCTTCC-1 -4.4525063 -3.8344782 experiment 0 0.00000000
Ang10#AACTTGGAGGTTACAA-1 0.2765908 -0.4427993 experiment 0 0.06290202
Ang10#TTAGCTTTCTCTGCGT-1 0.4313479 -1.1073339 experiment 0 0.06955512
Ang10#CTTTGCGAGCTCGTTA-1 0.8946131 -0.6036769 experiment 0 0.05806340
Ang10#CATAACGCACCTCGTT-1 0.4958196 -0.6398484 experiment 0 0.05443444
Ang10#CACTAAGCAACGGGTA-1 0.5193334 -0.6686975 experiment 0 0.04657169

2024-12-15 20:00:04.321404 : Ang10 (2 of 16) : Simulated Doublet UMAP, Class = data.frame
Ang10 (2 of 16) : Simulated Doublet UMAP: nRows = 1653365, nCols = 5
x y density type color
doublet_566394 -11.11171341 -6.785820 4.160437e-07 simulated_doublet 4.160437e-07
doublet_756514 -12.67309666 -6.470299 7.385835e-07 simulated_doublet 7.385835e-07
doublet_718977 -0.21614346 11.396702 8.626038e-07 simulated_doublet 8.626038e-07
doublet_630707 0.03986001 12.351623 9.320182e-07 simulated_doublet 9.320182e-07
doublet_1108044 0.59577644 10.226229 9.571769e-07 simulated_doublet 9.571769e-07
doublet_1636195 4.79880381 -6.265242 1.025162e-06 simulated_doublet 1.025162e-06

2024-12-15 20:00:15.890607 : ERROR Found in ggplot for Ang10 (2 of 16) :
LogFile = ArchRLogs\ArchR-addDoubletScores-8286ee159b3-Date-2024-12-15_Time-14-43-16.11319.log

<simpleError in g$grobs[[legend]]: 在2层没有这一索引

2024-12-15 20:00:15.891527 : errorList, Class = list

errorList$df: nRows = 278731, nCols = 5
X1 X2 type score enrichment
Ang10#ACCAAACAGTCCTTCC-1 -4.4525063 -3.8344782 experiment 0 0.00000000
Ang10#AACTTGGAGGTTACAA-1 0.2765908 -0.4427993 experiment 0 0.06290202
Ang10#TTAGCTTTCTCTGCGT-1 0.4313479 -1.1073339 experiment 0 0.06955512
Ang10#CTTTGCGAGCTCGTTA-1 0.8946131 -0.6036769 experiment 0 0.05806340
Ang10#CATAACGCACCTCGTT-1 0.4958196 -0.6398484 experiment 0 0.05443444
Ang10#CACTAAGCAACGGGTA-1 0.5193334 -0.6686975 experiment 0 0.04657169

errorList$dfDoub: nRows = 1653365, nCols = 5
x y density type color
doublet_566394 -11.11171341 -6.785820 4.160437e-07 simulated_doublet 4.160437e-07
doublet_756514 -12.67309666 -6.470299 7.385835e-07 simulated_doublet 7.385835e-07
doublet_718977 -0.21614346 11.396702 8.626038e-07 simulated_doublet 8.626038e-07
doublet_630707 0.03986001 12.351623 9.320182e-07 simulated_doublet 9.320182e-07
doublet_1108044 0.59577644 10.226229 9.571769e-07 simulated_doublet 9.571769e-07
doublet_1636195 4.79880381 -6.265242 1.025162e-06 simulated_doublet 1.025162e-06

2024-12-15 20:00:18.097328 : Ang11 (3 of 16) : Computing Doublet Statistics, 317.032 mins elapsed.
2024-12-15 20:00:18.883121 : Running IterativeLSI, 317.045 mins elapsed.

2024-12-15 20:00:18.884347 : 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 = 50
[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] "E:\scATAC-seq\tmp\tmp-82816a66e0b-Date-2024-12-15_Time-20-00-18.097553"

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-8286ee159b3-Date-2024-12-15_Time-14-43-16.11319.log"

2024-12-15 20:00:18.979158 : Computing Total Across All Features, 0 mins elapsed.
2024-12-15 20:00:19.296527 : Computing Top Features, 0.005 mins elapsed.
###########
2024-12-15 20:00:21.145757 : Running LSI (1 of 2) on Top Features, 0.036 mins elapsed.
###########
2024-12-15 20:00:21.308175 : Sampling Cells (N = 10000) for Estimated LSI, 0.039 mins elapsed.
2024-12-15 20:00:21.308744 : Creating Sampled Partial Matrix, 0.039 mins elapsed.
2024-12-15 20:00:24.947126 : Computing Estimated LSI (projectAll = FALSE), 0.1 mins elapsed.

2024-12-15 20:00:24.94795 : LSI Parameters, Class = list

LSI Parameters$: length = 1

1 function (name)
2 .Internal(args(name))

LSI Parameters$mat: nRows = 25000, nCols = 10000
LSI Parameters$mat: NonZeroEntries = 736200, EntryRange = [ 1 , 1 ]
5 x 5 sparse Matrix of class "dgCMatrix"
Ang11#AAACGAAAGACTAGGC-1 Ang11#AAACGAAAGCCTATAC-1 Ang11#AAACGAAAGGCAGTGT-1 Ang11#AAACGAAAGGCTTAAA-1 Ang11#AAACGAAAGGTTCTCA-1
[1,] . . . . .
[2,] . . . . .
[3,] . . . . .
[4,] . . . . .
[5,] . . . . .

LSI Parameters$LSIMethod: length = 1
[1] 1

LSI Parameters$scaleTo: length = 1
[1] 10000

LSI Parameters$nDimensions: length = 1
[1] 50

LSI Parameters$binarize: length = 1
[1] TRUE

LSI Parameters$outlierQuantiles: length = 0
NULL

LSI Parameters$seed: length = 1
[1] 1

LSI Parameters$verbose: length = 1
[1] FALSE

LSI Parameters$tstart: length = 1
[1] "2024-12-15 20:00:18 CST"

LSI Parameters$logFile: length = 1
[1] "ArchRLogs\ArchR-addDoubletScores-8286ee159b3-Date-2024-12-15_Time-14-43-16.11319.log"

2024-12-15 20:00:24.955243 : Running LSI, Input Matrix = 0.01 GB, 0.1 mins elapsed.
2024-12-15 20:00:24.956116 : Binarizing Matrix, 0.1 mins elapsed.
2024-12-15 20:00:24.960024 : Computing Term Frequency, 0.1 mins elapsed.
2024-12-15 20:00:24.964053 : Removing 0 Sum Rows, 0.1 mins elapsed.
2024-12-15 20:00:24.969291 : Computing Inverse Document Frequency, 0.1 mins elapsed.
2024-12-15 20:00:24.97047 : Computing TF-IDF Matrix, 0.1 mins elapsed.
2024-12-15 20:00:26.386279 : Computing SVD using irlba, 0.124 mins elapsed.
2024-12-15 20:00:29.533783 : Finished LSI (TF-IDF SVD) using irlba, 0.176 mins elapsed.

2024-12-15 20:00:32.495209 : outLSI-1, Class = SimpleList

outLSI-1$matSVD: nRows = 5022, nCols = 50
LSI1 LSI2 LSI3 LSI4 LSI5
Ang11#AAACGAAAGGCAGTGT-1 3.119091e-07 -5.039169e-07 7.484641e-07 4.684546e-07 -1.557774e-06
Ang11#AAACGAACACCTACCT-1 4.068413e-07 -1.243062e-08 4.420917e-07 4.174515e-07 -6.124253e-07
Ang11#AAACGAAGTCCCTAAA-1 5.522224e-07 -2.052763e-07 8.901391e-07 3.427923e-07 -1.793216e-06
Ang11#AAACGAAGTCTGATTG-1 2.747045e-07 -1.064332e-09 7.874881e-07 7.982996e-07 -3.613612e-06
Ang11#AAACGAATCCTCCTGA-1 3.501255e-07 -2.094183e-07 1.509373e-06 6.912165e-07 -1.416456e-06

outLSI-1$rowSm: length = 25000
[1] 32 19 43 42 14 19

outLSI-1$nCol: length = 1
[1] 5022

outLSI-1$exclude: length = 4978
Ang11#AAACGAAAGACTAGGC-1 Ang11#AAACGAAAGCCTATAC-1 Ang11#AAACGAAAGGCTTAAA-1 Ang11#AAACGAAAGGTTCTCA-1 Ang11#AAACGAAAGTCTCTAG-1
1 2 4 5 6
Ang11#AAACGAACAACGACAG-1
7

outLSI-1$idx: length = 25000
[1] 1 2 3 4 5 6

outLSI-1$u: nRows = 25000, nCols = 50
[,1] [,2] [,3] [,4] [,5]
[1,] 1.882700e-07 -1.058495e-07 5.760693e-08 3.401999e-08 -2.865769e-07
[2,] 2.330871e-08 -2.156093e-08 6.717424e-08 2.280960e-08 -4.427199e-08
[3,] 7.896339e-08 -5.750032e-08 1.743470e-07 2.702032e-08 -2.099376e-07
[4,] 4.331426e-07 -3.366481e-08 1.005783e-07 2.127298e-08 -2.469195e-07
[5,] 3.938506e-08 -1.013152e-08 1.764121e-07 2.131382e-08 -1.701873e-07

outLSI-1$v: nRows = 5022, nCols = 50
[,1] [,2] [,3] [,4] [,5]
[1,] 3.445613e-08 -5.979357e-08 8.966646e-08 5.625670e-08 -1.943217e-07
[2,] 4.494314e-08 -1.474988e-09 5.296286e-08 5.013174e-08 -7.639586e-08
[3,] 6.100317e-08 -2.435759e-08 1.066392e-07 4.116592e-08 -2.236915e-07
[4,] 3.034619e-08 -1.262911e-10 9.434157e-08 9.586779e-08 -4.507733e-07
[5,] 3.867783e-08 -2.484908e-08 1.808239e-07 8.300818e-08 -1.766932e-07

outLSI-1$binarize: length = 1
[1] TRUE

outLSI-1$scaleTo: length = 1
[1] 10000

outLSI-1$nDimensions: length = 1
[1] 50

outLSI-1$LSIMethod: length = 1
[1] 1

outLSI-1$outliers: length = 1
[1] NA

outLSI-1$date: length = 1
[1] "2024-12-15"

outLSI-1$seed: length = 1
[1] 1

outLSI-1$scaleDims: length = 1
[1] FALSE

outLSI-1$useMatrix: length = 1
[1] "TileMatrix"

outLSI-1$tileSize: length = 1
[1] 500

2024-12-15 20:00:32.507182 : Cluster Params, Class = list

Cluster Params$: length = 1

1 function (name)
2 .Internal(args(name))

Cluster Params$matSVD: nRows = 5022, nCols = 50
LSI1 LSI2 LSI3 LSI4 LSI5
Ang11#AAACGAAAGGCAGTGT-1 3.119091e-07 -5.039169e-07 7.484641e-07 4.684546e-07 -1.557774e-06
Ang11#AAACGAACACCTACCT-1 4.068413e-07 -1.243062e-08 4.420917e-07 4.174515e-07 -6.124253e-07
Ang11#AAACGAAGTCCCTAAA-1 5.522224e-07 -2.052763e-07 8.901391e-07 3.427923e-07 -1.793216e-06
Ang11#AAACGAAGTCTGATTG-1 2.747045e-07 -1.064332e-09 7.874881e-07 7.982996e-07 -3.613612e-06
Ang11#AAACGAATCCTCCTGA-1 3.501255e-07 -2.094183e-07 1.509373e-06 6.912165e-07 -1.416456e-06

Cluster Params$corCutOff: length = 1
[1] 0.75

Cluster Params$dimsToUse: length = 50
[1] 1 2 3 4 5 6

Cluster Params$scaleDims: length = 1
[1] FALSE

Cluster Params$verbose: length = 1
[1] FALSE

Cluster Params$j: length = 1
[1] 1

Cluster Params$filterBias: length = 1
[1] FALSE

Cluster Params$cellNames: length = 514558
[1] "Ang11#TTTGGCCTCTCCCTTT-1" "Ang11#GTAGGAGAGGAATGGA-1" "Ang11#CTTTGCGCAGTATCTG-1" "Ang11#AACAAAGGTGATGCTT-1"
[5] "Ang11#GCATTGACAAATAGTG-1" "Ang11#AAGGAGCAGAAACGCC-1"

Cluster Params$cellDepth: length = 514558
Ang11#TTTGGCCTCTCCCTTT-1 Ang11#GTAGGAGAGGAATGGA-1 Ang11#CTTTGCGCAGTATCTG-1 Ang11#AACAAAGGTGATGCTT-1 Ang11#GCATTGACAAATAGTG-1
4.991576 4.979908 4.974572 4.973576 4.973183
Ang11#AAGGAGCAGAAACGCC-1
4.963637

Cluster Params$tstart: length = 1
[1] "2024-12-15 20:00:18 CST"

Cluster Params$logFile: length = 1
[1] "ArchRLogs\ArchR-addDoubletScores-8286ee159b3-Date-2024-12-15_Time-14-43-16.11319.log"

2024-12-15 20:00:32.513278 : Identifying Clusters, 0.226 mins elapsed.

2024-12-15 20:00:32.549325 : addClusters Input-Parameters, Class = list

addClusters Input-Parameters$: length = 1

1 function (name)
2 .Internal(args(name))

addClusters Input-Parameters$input: nRows = 5022, nCols = 50
LSI1 LSI2 LSI3 LSI4 LSI5
Ang11#AAACGAAAGGCAGTGT-1 3.119091e-07 -5.039169e-07 7.484641e-07 4.684546e-07 -1.557774e-06
Ang11#AAACGAACACCTACCT-1 4.068413e-07 -1.243062e-08 4.420917e-07 4.174515e-07 -6.124253e-07
Ang11#AAACGAAGTCCCTAAA-1 5.522224e-07 -2.052763e-07 8.901391e-07 3.427923e-07 -1.793216e-06
Ang11#AAACGAAGTCTGATTG-1 2.747045e-07 -1.064332e-09 7.874881e-07 7.982996e-07 -3.613612e-06
Ang11#AAACGAATCCTCCTGA-1 3.501255e-07 -2.094183e-07 1.509373e-06 6.912165e-07 -1.416456e-06

addClusters Input-Parameters$reducedDims: length = 1
[1] "IterativeLSI"

addClusters Input-Parameters$name: length = 1
[1] "Clusters"

addClusters Input-Parameters$sampleCells: length = 1
[1] 10000

addClusters Input-Parameters$seed: length = 1
[1] 1

addClusters Input-Parameters$method: length = 1
[1] "Seurat"

addClusters Input-Parameters$dimsToUse: length = 0
NULL

addClusters Input-Parameters$scaleDims: length = 0
NULL

addClusters Input-Parameters$corCutOff: length = 1
[1] 0.75

addClusters Input-Parameters$knnAssign: length = 1
[1] 10

addClusters Input-Parameters$nOutlier: length = 1
[1] 5

addClusters Input-Parameters$maxClusters: length = 1
[1] 6

addClusters Input-Parameters$testBias: length = 1
[1] TRUE

addClusters Input-Parameters$filterBias: length = 1
[1] FALSE

addClusters Input-Parameters$biasClusters: length = 1
[1] 0.01

addClusters Input-Parameters$biasCol: length = 1
[1] "nFrags"

addClusters Input-Parameters$biasVals: length = 5022
[1] 0.3010300 0.3010300 2.4517864 0.6020600 0.8450980 0.4771213

addClusters Input-Parameters$biasQuantiles: length = 2
[1] 0.05 0.95

addClusters Input-Parameters$biasEnrich: length = 1
[1] 10

addClusters Input-Parameters$biasProportion: length = 1
[1] 0.5

addClusters Input-Parameters$biasPval: length = 1
[1] 0.05

addClusters Input-Parameters$nPerm: length = 1
[1] 500

addClusters Input-Parameters$prefix: length = 1
[1] "C"

addClusters Input-Parameters$ArchRProj: length = 0
NULL

addClusters Input-Parameters$verbose: length = 1
[1] FALSE

addClusters Input-Parameters$tstart: length = 0
NULL

addClusters Input-Parameters$force: length = 1
[1] FALSE

addClusters Input-Parameters$logFile: length = 1
[1] "ArchRLogs\ArchR-addDoubletScores-8286ee159b3-Date-2024-12-15_Time-14-43-16.11319.log"

addClusters Input-Parameters$...: length = 2

2024-12-15 20:00:32.560956 : Running Seurats FindClusters (Stuart et al. Cell 2019), 0 mins elapsed.
2024-12-15 20:00:40.429561 : Testing Biased Clusters, 0.131 mins elapsed.
2024-12-15 20:00:40.444235 : Testing Outlier Clusters, 0.131 mins elapsed.
2024-12-15 20:00:40.44504 : Identified more clusters than maxClusters allowed (n = 0). Merging clusters to maxClusters (n = 6).
If this is not desired set maxClusters = NULL!, 0.131 mins elapsed.
2024-12-15 20:00:40.448711 : Assigning Cluster Names to 6 Clusters, 0.132 mins elapsed.
2024-12-15 20:00:40.451622 : Finished addClusters, 0.132 mins elapsed.
2024-12-15 20:00:40.453548 : Identified 6 Clusters, 0.358 mins elapsed.

2024-12-15 20:00:40.454028 : clusterDF-1, Class = DFrame
DataFrame with 5022 rows and 2 columns
cellNames clusters

1 Ang11#AAACGAAAGGCAGT.. C5
2 Ang11#AAACGAACACCTAC.. C5
3 Ang11#AAACGAAGTCCCTA.. C5
4 Ang11#AAACGAAGTCTGAT.. C5
5 Ang11#AAACGAATCCTCCT.. C6
... ... ...
5018 Ang11#TTTGTGTCACTGAT.. C5
5019 Ang11#TTTGTGTGTAGAAC.. C5
5020 Ang11#TTTGTGTGTTTGTG.. C5
5021 Ang11#TTTGTGTTCGGGTC.. C5
5022 Ang11#TTTGTGTTCTGGCC.. C5

2024-12-15 20:00:40.457175 : Creating Cluster Matrix on the total Group Features, 0.358 mins elapsed.
2024-12-15 20:01:20.674089 : Computing Variable Features, 1.028 mins elapsed.
###########
2024-12-15 20:01:20.78247 : Running LSI (2 of 2) on Variable Features, 1.03 mins elapsed.
###########
2024-12-15 20:01:20.854325 : Creating Partial Matrix, 1.031 mins elapsed.
2024-12-15 20:01:34.147929 : Computing LSI, 1.253 mins elapsed.

2024-12-15 20:01:34.148837 : LSI Parameters, Class = list

LSI Parameters$: length = 1

1 function (name)
2 .Internal(args(name))

LSI Parameters$mat: nRows = 25000, nCols = 514558
LSI Parameters$mat: NonZeroEntries = 33651231, EntryRange = [ 1 , 1 ]
5 x 5 sparse Matrix of class "dgCMatrix"
Ang11#TTTGGCCTCTCCCTTT-1 Ang11#GTAGGAGAGGAATGGA-1 Ang11#CTTTGCGCAGTATCTG-1 Ang11#AACAAAGGTGATGCTT-1 Ang11#GCATTGACAAATAGTG-1
[1,] . 1 . . .
[2,] . . . . .
[3,] . . . . .
[4,] . 1 . 1 .
[5,] . . . . .

LSI Parameters$LSIMethod: length = 1
[1] 1

LSI Parameters$scaleTo: length = 1
[1] 10000

LSI Parameters$nDimensions: length = 1
[1] 50

LSI Parameters$binarize: length = 1
[1] TRUE

LSI Parameters$outlierQuantiles: length = 0
NULL

LSI Parameters$seed: length = 1
[1] 1

LSI Parameters$verbose: length = 1
[1] FALSE

LSI Parameters$tstart: length = 1
[1] "2024-12-15 20:00:18 CST"

LSI Parameters$logFile: length = 1
[1] "ArchRLogs\ArchR-addDoubletScores-8286ee159b3-Date-2024-12-15_Time-14-43-16.11319.log"

2024-12-15 20:01:34.287991 : Running LSI, Input Matrix = 0.451 GB, 1.255 mins elapsed.
2024-12-15 20:01:34.295294 : Binarizing Matrix, 1.255 mins elapsed.
2024-12-15 20:01:34.459287 : Computing Term Frequency, 1.258 mins elapsed.
2024-12-15 20:01:34.6112 : Removing 0 Sum Rows, 1.261 mins elapsed.
2024-12-15 20:01:34.787551 : Computing Inverse Document Frequency, 1.264 mins elapsed.
2024-12-15 20:01:34.789099 : Computing TF-IDF Matrix, 1.264 mins elapsed.
2024-12-15 20:01:36.338096 : Computing SVD using irlba, 1.289 mins elapsed.
2024-12-15 20:03:48.464021 : Finished LSI (TF-IDF SVD) using irlba, 3.492 mins elapsed.

2024-12-15 20:03:50.216579 : outLSI-2, Class = SimpleList

outLSI-2$matSVD: nRows = 247466, nCols = 50
LSI1 LSI2 LSI3 LSI4 LSI5
Ang11#TTTGGCCTCTCCCTTT-1 0.0012412156 0.0006242996 0.0011592353 0.0006170853 -0.0013806892
Ang11#GTAGGAGAGGAATGGA-1 0.0006303025 0.0007785215 0.0005170682 0.0008834823 -0.0006768914
Ang11#CTTTGCGCAGTATCTG-1 0.0003232040 0.0020403788 -0.0000434681 0.0006534769 -0.0003780666
Ang11#AACAAAGGTGATGCTT-1 0.0009525052 0.0010235260 0.0001970237 0.0012604624 -0.0010423615
Ang11#GCATTGACAAATAGTG-1 0.0003697105 0.0002842416 0.0002945889 0.0004566009 -0.0003182365

outLSI-2$rowSm: length = 25000
[1] 521 166 129 1509 121 95

outLSI-2$nCol: length = 1
[1] 247466

outLSI-2$exclude: length = 267092
Ang11#TCGAGCGAGACGAAAG-1 Ang11#ACAAGCTAGAGTGGTC-1 Ang11#AACGAGGCATGCCCTT-1 Ang11#ACCGGGTCAAATGTCC-1 Ang11#ACCATCCGTGCGCATC-1
47336 63834 67324 67330 68192
Ang11#CAGTGTAGTGAGAGTC-1
68687

outLSI-2$idx: length = 25000
[1] 1 2 3 4 5 6

outLSI-2$u: nRows = 25000, nCols = 50
[,1] [,2] [,3] [,4] [,5]
[1,] 5.453806e-06 2.405669e-05 7.920024e-05 9.302645e-06 -7.470796e-06
[2,] 7.317706e-07 1.216742e-06 6.558896e-07 1.610903e-06 -1.018371e-06
[3,] 1.493166e-06 4.713718e-06 1.305872e-06 5.364986e-06 -3.563304e-06
[4,] 1.260841e-05 1.810047e-05 8.438801e-06 2.789812e-05 -1.412372e-05
[5,] 4.000196e-06 6.687166e-06 1.649683e-05 6.794235e-06 -3.155624e-06

outLSI-2$v: nRows = 247466, nCols = 50
[,1] [,2] [,3] [,4] [,5]
[1,] 4.102732e-05 2.156062e-05 4.004161e-05 2.240645e-05 -5.084534e-05
[2,] 2.083411e-05 2.688677e-05 1.786026e-05 3.207936e-05 -2.492724e-05
[3,] 1.068323e-05 7.046588e-05 -1.501449e-06 2.372783e-05 -1.392270e-05
[4,] 3.148424e-05 3.534818e-05 6.805473e-06 4.576756e-05 -3.838606e-05
[5,] 1.222046e-05 9.816478e-06 1.017551e-05 1.657924e-05 -1.171939e-05

outLSI-2$binarize: length = 1
[1] TRUE

outLSI-2$scaleTo: length = 1
[1] 10000

outLSI-2$nDimensions: length = 1
[1] 50

outLSI-2$LSIMethod: length = 1
[1] 1

outLSI-2$outliers: length = 1
[1] NA

outLSI-2$date: length = 1
[1] "2024-12-15"

outLSI-2$seed: length = 1
[1] 1

outLSI-2$scaleDims: length = 1
[1] FALSE

outLSI-2$useMatrix: length = 1
[1] "TileMatrix"

outLSI-2$tileSize: length = 1
[1] 500

2024-12-15 20:03:51.671868 : Finished Running IterativeLSI, 3.545 mins elapsed.
2024-12-15 20:03:51.67446 : Constructing Partial Matrix for Projection, 320.592 mins elapsed.

2024-12-15 20:03:51.717543 : Ang11 (3 of 16) : LSI Result, Class = SimpleList

Ang11 (3 of 16) : LSI Result$matSVD: nRows = 247466, nCols = 50
LSI1 LSI2 LSI3 LSI4 LSI5
Ang11#TTTGGCCTCTCCCTTT-1 0.0012412156 0.0006242996 0.0011592353 0.0006170853 -0.0013806892
Ang11#GTAGGAGAGGAATGGA-1 0.0006303025 0.0007785215 0.0005170682 0.0008834823 -0.0006768914
Ang11#CTTTGCGCAGTATCTG-1 0.0003232040 0.0020403788 -0.0000434681 0.0006534769 -0.0003780666
Ang11#AACAAAGGTGATGCTT-1 0.0009525052 0.0010235260 0.0001970237 0.0012604624 -0.0010423615
Ang11#GCATTGACAAATAGTG-1 0.0003697105 0.0002842416 0.0002945889 0.0004566009 -0.0003182365

Ang11 (3 of 16) : LSI Result$rowSm: length = 25000
[1] 521 166 129 1509 121 95

Ang11 (3 of 16) : LSI Result$nCol: length = 1
[1] 247466

Ang11 (3 of 16) : LSI Result$exclude: length = 267092
Ang11#TCGAGCGAGACGAAAG-1 Ang11#ACAAGCTAGAGTGGTC-1 Ang11#AACGAGGCATGCCCTT-1 Ang11#ACCGGGTCAAATGTCC-1 Ang11#ACCATCCGTGCGCATC-1
47336 63834 67324 67330 68192
Ang11#CAGTGTAGTGAGAGTC-1
68687

Ang11 (3 of 16) : LSI Result$idx: length = 25000
[1] 1 2 3 4 5 6

Ang11 (3 of 16) : LSI Result$u: nRows = 25000, nCols = 50
[,1] [,2] [,3] [,4] [,5]
[1,] 5.453806e-06 2.405669e-05 7.920024e-05 9.302645e-06 -7.470796e-06
[2,] 7.317706e-07 1.216742e-06 6.558896e-07 1.610903e-06 -1.018371e-06
[3,] 1.493166e-06 4.713718e-06 1.305872e-06 5.364986e-06 -3.563304e-06
[4,] 1.260841e-05 1.810047e-05 8.438801e-06 2.789812e-05 -1.412372e-05
[5,] 4.000196e-06 6.687166e-06 1.649683e-05 6.794235e-06 -3.155624e-06

Ang11 (3 of 16) : LSI Result$v: nRows = 247466, nCols = 50
[,1] [,2] [,3] [,4] [,5]
[1,] 4.102732e-05 2.156062e-05 4.004161e-05 2.240645e-05 -5.084534e-05
[2,] 2.083411e-05 2.688677e-05 1.786026e-05 3.207936e-05 -2.492724e-05
[3,] 1.068323e-05 7.046588e-05 -1.501449e-06 2.372783e-05 -1.392270e-05
[4,] 3.148424e-05 3.534818e-05 6.805473e-06 4.576756e-05 -3.838606e-05
[5,] 1.222046e-05 9.816478e-06 1.017551e-05 1.657924e-05 -1.171939e-05

Ang11 (3 of 16) : LSI Result$binarize: length = 1
[1] TRUE

Ang11 (3 of 16) : LSI Result$scaleTo: length = 1
[1] 10000

Ang11 (3 of 16) : LSI Result$nDimensions: length = 1
[1] 50

Ang11 (3 of 16) : LSI Result$LSIMethod: length = 1
[1] 1

Ang11 (3 of 16) : LSI Result$outliers: length = 1
[1] NA

Ang11 (3 of 16) : LSI Result$date: length = 1
[1] "2024-12-15"

Ang11 (3 of 16) : LSI Result$seed: length = 1
[1] 1

Ang11 (3 of 16) : LSI Result$scaleDims: length = 1
[1] FALSE

Ang11 (3 of 16) : LSI Result$useMatrix: length = 1
[1] "TileMatrix"

Ang11 (3 of 16) : LSI Result$tileSize: length = 1
[1] 500

Ang11 (3 of 16) : LSI Result$dimsKept: length = 50
[1] 1 2 3 4 5 6

2024-12-15 20:04:05.006294 : Running LSI UMAP, 320.814 mins elapsed.

2024-12-15 20:04:05.007167 : Ang11 (3 of 16) : UMAP Params, Class = list

Ang11 (3 of 16) : UMAP Params$n_neighbors: length = 1
[1] 30

Ang11 (3 of 16) : UMAP Params$min_dist: length = 1
[1] 0.3

Ang11 (3 of 16) : UMAP Params$metric: length = 1
[1] "cosine"

Ang11 (3 of 16) : UMAP Params$verbose: length = 1
[1] FALSE

Ang11 (3 of 16) : UMAP Params$X: nRows = 247466, nCols = 50
LSI1 LSI2 LSI3 LSI4 LSI5
Ang11#TTTGGCCTCTCCCTTT-1 0.0012412156 0.0006242996 0.0011592353 0.0006170853 -0.0013806892
Ang11#GTAGGAGAGGAATGGA-1 0.0006303025 0.0007785215 0.0005170682 0.0008834823 -0.0006768914
Ang11#CTTTGCGCAGTATCTG-1 0.0003232040 0.0020403788 -0.0000434681 0.0006534769 -0.0003780666
Ang11#AACAAAGGTGATGCTT-1 0.0009525052 0.0010235260 0.0001970237 0.0012604624 -0.0010423615
Ang11#GCATTGACAAATAGTG-1 0.0003697105 0.0002842416 0.0002945889 0.0004566009 -0.0003182365

Ang11 (3 of 16) : UMAP Params$ret_nn: length = 1
[1] TRUE

Ang11 (3 of 16) : UMAP Params$ret_model: length = 1
[1] TRUE

Ang11 (3 of 16) : UMAP Params$n_threads: length = 1
[1] 1
@joeyQX joeyQX added the bug Something isn't working label Dec 17, 2024
@rcorces
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rcorces commented Dec 17, 2024

Hi @joeyQX! Thanks for using ArchR! Lately, it has been very challenging for me to keep up with maintenance of this package and all of my other
responsibilities as a PI. I have not been responding to issue posts and I have not been pushing updates to the software. We are actively searching to hire
a computational biologist to continue to develop and maintain ArchR and related tools. If you know someone who might be a good fit, please let us know!
In the meantime, your issue will likely go without a reply. Most issues with ArchR right not relate to compatibility. Try reverting to R 4.1 and Bioconductor 3.15.
Newer versions of Seurat and Matrix also are causing issues. Sorry for not being able to provide active support for this package at this time.

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