During startup - Warning messages:
1: Setting LC_CTYPE failed, using "C" 
2: Setting LC_COLLATE failed, using "C" 
3: Setting LC_TIME failed, using "C" 
4: Setting LC_MESSAGES failed, using "C" 
5: Setting LC_MONETARY failed, using "C" 
6: Setting LC_PAPER failed, using "C" 
7: Setting LC_MEASUREMENT failed, using "C" 

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       \               '        ##_______ _____ ,--,__,=##,__   ///
        ,    __==    ___,-,__,--'#'  ==='      `-'    | ##,-/
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      /__/     \__\ | _| `._____| \______||__|  |__| | _| `._____|
    
ArchR : Version 1.0.2
For more information see our website : www.ArchRProject.com
If you encounter a bug please report : https://github.com/GreenleafLab/ArchR/issues
Loading Required Packages...
	Loading Package : grid v4.2.2
	Loading Package : gridExtra v2.3
	Loading Package : gtools v3.9.4
	Loading Package : gtable v0.3.1
	Loading Package : ggplot2 v3.3.6
	Loading Package : magrittr v2.0.3
	Loading Package : plyr v1.8.8
	Loading Package : stringr v1.5.0
	Loading Package : data.table v1.14.6
	Loading Package : matrixStats v0.63.0
	Loading Package : S4Vectors v0.36.1
	Loading Package : GenomicRanges v1.50.2
	Loading Package : BiocGenerics v0.44.0
	Loading Package : Matrix v1.5.3
	Loading Package : Rcpp v1.0.9
	Loading Package : SummarizedExperiment v1.28.0
	Loading Package : rhdf5 v2.42.0
here() starts at /projects/pfenninggroup/singleCell/BICCN_mouse_CATlas_snATAC-seq

Attaching package: 'here'

The following object is masked from 'package:plyr':

    here

Setting default number of Parallel threads to 8.
Setting default genome to Mm10.
Successfully loaded ArchRProject!

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        ,    __==    ___,-,__,--'#'  ==='      `-'    | ##,-/
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           ___      .______        ______  __    __  .______      
          /   \     |   _  \      /      ||  |  |  | |   _  \     
         /  ^  \    |  |_)  |    |  ,----'|  |__|  | |  |_)  |    
        /  /_\  \   |      /     |  |     |   __   | |      /     
       /  _____  \  |  |\  \\___ |  `----.|  |  |  | |  |\  \\___.
      /__/     \__\ | _| `._____| \______||__|  |__| | _| `._____|
    
Checking Inputs...
ArchR logging to : ArchRLogs/ArchR-addIterativeLSI-4e99447fa5663-Date-2023-04-27_Time-14-05-41.log
If there is an issue, please report to github with logFile!
2023-04-27 14:05:43 : Computing Total Across All Features, 0.033 mins elapsed.
2023-04-27 14:05:55 : Computing Top Features, 0.234 mins elapsed.
###########
2023-04-27 14:05:57 : Running LSI (1 of 4) on Top Features, 0.262 mins elapsed.
###########
2023-04-27 14:05:58 : Creating Partial Matrix, 0.283 mins elapsed.
2023-04-27 14:06:29 : Computing LSI, 0.796 mins elapsed.
2023-04-27 14:07:09 : Identifying Clusters, 1.461 mins elapsed.
2023-04-27 14:07:45 : Identified 9 Clusters, 2.058 mins elapsed.
2023-04-27 14:07:45 : Creating Cluster Matrix on the total Group Features, 2.059 mins elapsed.
2023-04-27 14:08:17 : Computing Variable Features, 2.604 mins elapsed.
###########
2023-04-27 14:08:18 : Running LSI (2 of 4) on Variable Features, 2.611 mins elapsed.
###########
2023-04-27 14:08:18 : Creating Partial Matrix, 2.612 mins elapsed.
2023-04-27 14:08:43 : Computing LSI, 3.037 mins elapsed.
2023-04-27 14:09:24 : Identifying Clusters, 3.713 mins elapsed.
2023-04-27 14:09:49 : Identified 10 Clusters, 4.136 mins elapsed.
2023-04-27 14:09:51 : Creating Cluster Matrix on the total Group Features, 4.157 mins elapsed.
2023-04-27 14:10:23 : Computing Variable Features, 4.693 mins elapsed.
###########
2023-04-27 14:10:23 : Running LSI (3 of 4) on Variable Features, 4.698 mins elapsed.
###########
2023-04-27 14:10:23 : Creating Partial Matrix, 4.698 mins elapsed.
2023-04-27 14:10:51 : Computing LSI, 5.16 mins elapsed.
2023-04-27 14:11:29 : Identifying Clusters, 5.791 mins elapsed.
2023-04-27 14:11:54 : Identified 10 Clusters, 6.221 mins elapsed.
2023-04-27 14:11:56 : Creating Cluster Matrix on the total Group Features, 6.241 mins elapsed.
2023-04-27 14:12:29 : Computing Variable Features, 6.802 mins elapsed.
###########
2023-04-27 14:12:31 : Running LSI (4 of 4) on Variable Features, 6.824 mins elapsed.
###########
2023-04-27 14:12:31 : Creating Partial Matrix, 6.825 mins elapsed.
2023-04-27 14:12:58 : Computing LSI, 7.289 mins elapsed.
2023-04-27 14:13:41 : Finished Running IterativeLSI, 7.998 mins elapsed.
Saving ArchRProject...
Loading ArchRProject...
Successfully loaded ArchRProject!

                                                   / |
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                ==###########>      /                   ||
                 \\##==......\    /                     ||
            ______ =       =|__ /__                     ||      \\\
        ,--' ,----`-,__ ___/'  --,-`-===================##========>
       \               '        ##_______ _____ ,--,__,=##,__   ///
        ,    __==    ___,-,__,--'#'  ==='      `-'    | ##,-/
        -,____,---'       \\####\\________________,--\\_##,/
           ___      .______        ______  __    __  .______      
          /   \     |   _  \      /      ||  |  |  | |   _  \     
         /  ^  \    |  |_)  |    |  ,----'|  |__|  | |  |_)  |    
        /  /_\  \   |      /     |  |     |   __   | |      /     
       /  _____  \  |  |\  \\___ |  `----.|  |  |  | |  |\  \\___.
      /__/     \__\ | _| `._____| \______||__|  |__| | _| `._____|
    
Harmony 1/10
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Harmony 2/10
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Harmony 3/10
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Harmony 4/10
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Harmony converged after 4 iterations
ArchR logging to : ArchRLogs/ArchR-addClusters-4e9945b1b8fe7-Date-2023-04-27_Time-14-14-24.log
If there is an issue, please report to github with logFile!
Overriding previous entry for ClustersX50
2023-04-27 14:14:25 : Running Seurats FindClusters (Stuart et al. Cell 2019), 0.003 mins elapsed.
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 24220
Number of edges: 758253

Running Louvain algorithm...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.8910
Number of communities: 12
Elapsed time: 6 seconds
2023-04-27 14:14:52 : Testing Biased Clusters, 0.447 mins elapsed.
2023-04-27 14:14:52 : Testing Outlier Clusters, 0.448 mins elapsed.
2023-04-27 14:14:52 : Assigning Cluster Names to 12 Clusters, 0.448 mins elapsed.
2023-04-27 14:14:52 : Finished addClusters, 0.45 mins elapsed.
14:14:52 UMAP embedding parameters a = 0.583 b = 1.334
14:14:52 Read 24220 rows and found 30 numeric columns
14:14:52 Using Annoy for neighbor search, n_neighbors = 30
14:14:52 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
14:14:54 Writing NN index file to temp file /tmp/RtmpBMaSdv/file4e99470f0ebfb
14:14:54 Searching Annoy index using 16 threads, search_k = 3000
14:14:56 Annoy recall = 100%
14:14:57 Commencing smooth kNN distance calibration using 16 threads with target n_neighbors = 30
14:14:59 Initializing from normalized Laplacian + noise (using irlba)
14:15:01 Commencing optimization for 200 epochs, with 1120104 positive edges
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
14:15:40 Optimization finished
14:15:40 Creating temp model dir /tmp/RtmpBMaSdv/dir4e994199530f9
14:15:40 Creating dir /tmp/RtmpBMaSdv/dir4e994199530f9
14:15:43 Changing to /tmp/RtmpBMaSdv/dir4e994199530f9
14:15:43 Creating /projects/pfenninggroup/singleCell/BICCN_mouse_CATlas_snATAC-seq/data/tidy_data/ArchRProjects/BICCN_mouse_NAc_snATAC/Embeddings/Save-Uwot-UMAP-Params-HarmonyX50-4e99463ee0021-Date-2023-04-27_Time-14-15-40.tar
ArchR logging to : ArchRLogs/ArchR-addImputeWeights-4e99443620aa1-Date-2023-04-27_Time-14-15-45.log
If there is an issue, please report to github with logFile!
2023-04-27 14:15:45 : Computing Impute Weights Using Magic (Cell 2018), 0 mins elapsed.
Checking Inputs...
ArchR logging to : ArchRLogs/ArchR-addIterativeLSI-4e99440100e2c-Date-2023-04-27_Time-14-16-15.log
If there is an issue, please report to github with logFile!
2023-04-27 14:16:16 : Computing Total Across All Features, 0.011 mins elapsed.
2023-04-27 14:16:21 : Computing Top Features, 0.106 mins elapsed.
###########
2023-04-27 14:16:23 : Running LSI (1 of 4) on Top Features, 0.13 mins elapsed.
###########
2023-04-27 14:16:24 : Creating Partial Matrix, 0.148 mins elapsed.
2023-04-27 14:16:58 : Computing LSI, 0.709 mins elapsed.
2023-04-27 14:17:50 : Identifying Clusters, 1.588 mins elapsed.
2023-04-27 14:18:17 : Identified 10 Clusters, 2.026 mins elapsed.
2023-04-27 14:18:17 : Creating Cluster Matrix on the total Group Features, 2.026 mins elapsed.
2023-04-27 14:18:58 : Computing Variable Features, 2.721 mins elapsed.
###########
2023-04-27 14:18:59 : Running LSI (2 of 4) on Variable Features, 2.726 mins elapsed.
###########
2023-04-27 14:19:00 : Creating Partial Matrix, 2.744 mins elapsed.
2023-04-27 14:19:33 : Computing LSI, 3.294 mins elapsed.
2023-04-27 14:20:16 : Identifying Clusters, 4.016 mins elapsed.
2023-04-27 14:20:41 : Identified 10 Clusters, 4.425 mins elapsed.
2023-04-27 14:20:42 : Creating Cluster Matrix on the total Group Features, 4.446 mins elapsed.
2023-04-27 14:21:20 : Computing Variable Features, 5.079 mins elapsed.
###########
2023-04-27 14:21:20 : Running LSI (3 of 4) on Variable Features, 5.084 mins elapsed.
###########
2023-04-27 14:21:20 : Creating Partial Matrix, 5.085 mins elapsed.
2023-04-27 14:21:54 : Computing LSI, 5.643 mins elapsed.
2023-04-27 14:22:46 : Identifying Clusters, 6.524 mins elapsed.
2023-04-27 14:23:13 : Identified 10 Clusters, 6.965 mins elapsed.
2023-04-27 14:23:14 : Creating Cluster Matrix on the total Group Features, 6.986 mins elapsed.
2023-04-27 14:23:49 : Computing Variable Features, 7.56 mins elapsed.
###########
2023-04-27 14:23:49 : Running LSI (4 of 4) on Variable Features, 7.565 mins elapsed.
###########
2023-04-27 14:23:49 : Creating Partial Matrix, 7.566 mins elapsed.
2023-04-27 14:24:15 : Computing LSI, 7.992 mins elapsed.
2023-04-27 14:25:11 : Finished Running IterativeLSI, 8.93 mins elapsed.
Saving ArchRProject...
Loading ArchRProject...
Successfully loaded ArchRProject!

                                                   / |
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            \\\                              /        |.
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                \\\                      /              |.
                  \                    /                |\
                  \\#####\           /                  ||
                ==###########>      /                   ||
                 \\##==......\    /                     ||
            ______ =       =|__ /__                     ||      \\\
        ,--' ,----`-,__ ___/'  --,-`-===================##========>
       \               '        ##_______ _____ ,--,__,=##,__   ///
        ,    __==    ___,-,__,--'#'  ==='      `-'    | ##,-/
        -,____,---'       \\####\\________________,--\\_##,/
           ___      .______        ______  __    __  .______      
          /   \     |   _  \      /      ||  |  |  | |   _  \     
         /  ^  \    |  |_)  |    |  ,----'|  |__|  | |  |_)  |    
        /  /_\  \   |      /     |  |     |   __   | |      /     
       /  _____  \  |  |\  \\___ |  `----.|  |  |  | |  |\  \\___.
      /__/     \__\ | _| `._____| \______||__|  |__| | _| `._____|
    
Harmony 1/10
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Harmony 2/10
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Harmony 3/10
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Harmony 4/10
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Harmony 5/10
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Harmony 6/10
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Harmony converged after 6 iterations
ArchR logging to : ArchRLogs/ArchR-addClusters-4e994567dc241-Date-2023-04-27_Time-14-26-07.log
If there is an issue, please report to github with logFile!
Overriding previous entry for ClustersX100
2023-04-27 14:26:08 : Running Seurats FindClusters (Stuart et al. Cell 2019), 0.002 mins elapsed.
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 24220
Number of edges: 765040

Running Louvain algorithm...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.8911
Number of communities: 15
Elapsed time: 5 seconds
2023-04-27 14:26:35 : Testing Biased Clusters, 0.451 mins elapsed.
2023-04-27 14:26:36 : Testing Outlier Clusters, 0.47 mins elapsed.
2023-04-27 14:26:36 : Assigning Cluster Names to 15 Clusters, 0.47 mins elapsed.
2023-04-27 14:26:36 : Finished addClusters, 0.471 mins elapsed.
14:26:36 UMAP embedding parameters a = 0.583 b = 1.334
14:26:36 Read 24220 rows and found 30 numeric columns
14:26:36 Using Annoy for neighbor search, n_neighbors = 30
14:26:36 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
14:26:38 Writing NN index file to temp file /tmp/RtmpBMaSdv/file4e99432fbbee3
14:26:38 Searching Annoy index using 16 threads, search_k = 3000
14:26:40 Annoy recall = 100%
14:26:41 Commencing smooth kNN distance calibration using 16 threads with target n_neighbors = 30
14:26:42 Initializing from normalized Laplacian + noise (using irlba)
14:26:45 Commencing optimization for 200 epochs, with 1065756 positive edges
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
14:27:26 Optimization finished
14:27:26 Creating temp model dir /tmp/RtmpBMaSdv/dir4e9942203ea64
14:27:26 Creating dir /tmp/RtmpBMaSdv/dir4e9942203ea64
14:27:28 Changing to /tmp/RtmpBMaSdv/dir4e9942203ea64
14:27:28 Creating /projects/pfenninggroup/singleCell/BICCN_mouse_CATlas_snATAC-seq/data/tidy_data/ArchRProjects/BICCN_mouse_NAc_snATAC/Embeddings/Save-Uwot-UMAP-Params-HarmonyX100-4e9944bd6a7e2-Date-2023-04-27_Time-14-27-26.tar
ArchR logging to : ArchRLogs/ArchR-addImputeWeights-4e99430ff01f0-Date-2023-04-27_Time-14-27-29.log
If there is an issue, please report to github with logFile!
2023-04-27 14:27:29 : Computing Impute Weights Using Magic (Cell 2018), 0 mins elapsed.
Checking Inputs...
ArchR logging to : ArchRLogs/ArchR-addIterativeLSI-4e9947cc6626-Date-2023-04-27_Time-14-28-04.log
If there is an issue, please report to github with logFile!
2023-04-27 14:28:10 : Computing Total Across All Features, 0.069 mins elapsed.
2023-04-27 14:28:20 : Computing Top Features, 0.229 mins elapsed.
###########
2023-04-27 14:28:23 : Running LSI (1 of 4) on Top Features, 0.283 mins elapsed.
###########
2023-04-27 14:28:23 : Creating Partial Matrix, 0.283 mins elapsed.
2023-04-27 14:29:03 : Computing LSI, 0.947 mins elapsed.
2023-04-27 14:30:26 : Identifying Clusters, 2.334 mins elapsed.
2023-04-27 14:30:53 : Identified 12 Clusters, 2.78 mins elapsed.
2023-04-27 14:30:53 : Creating Cluster Matrix on the total Group Features, 2.781 mins elapsed.
2023-04-27 14:31:34 : Computing Variable Features, 3.464 mins elapsed.
###########
2023-04-27 14:31:34 : Running LSI (2 of 4) on Variable Features, 3.47 mins elapsed.
###########
2023-04-27 14:31:35 : Creating Partial Matrix, 3.471 mins elapsed.
2023-04-27 14:32:05 : Computing LSI, 3.982 mins elapsed.
2023-04-27 14:33:14 : Identifying Clusters, 5.135 mins elapsed.
2023-04-27 14:33:42 : Identified 13 Clusters, 5.592 mins elapsed.
2023-04-27 14:33:43 : Creating Cluster Matrix on the total Group Features, 5.612 mins elapsed.
2023-04-27 14:34:21 : Computing Variable Features, 6.253 mins elapsed.
###########
2023-04-27 14:34:23 : Running LSI (3 of 4) on Variable Features, 6.276 mins elapsed.
###########
2023-04-27 14:34:23 : Creating Partial Matrix, 6.277 mins elapsed.
2023-04-27 14:35:02 : Computing LSI, 6.925 mins elapsed.
2023-04-27 14:36:21 : Identifying Clusters, 8.247 mins elapsed.
2023-04-27 14:36:46 : Identified 12 Clusters, 8.656 mins elapsed.
2023-04-27 14:36:47 : Creating Cluster Matrix on the total Group Features, 8.676 mins elapsed.
2023-04-27 14:37:18 : Computing Variable Features, 9.188 mins elapsed.
###########
2023-04-27 14:37:18 : Running LSI (4 of 4) on Variable Features, 9.194 mins elapsed.
###########
2023-04-27 14:37:18 : Creating Partial Matrix, 9.195 mins elapsed.
2023-04-27 14:37:50 : Computing LSI, 9.732 mins elapsed.
2023-04-27 14:39:04 : Finished Running IterativeLSI, 10.955 mins elapsed.
Saving ArchRProject...
Loading ArchRProject...
Successfully loaded ArchRProject!

                                                   / |
                                                 /    \
            .                                  /      |.
            \\\                              /        |.
              \\\                          /           `|.
                \\\                      /              |.
                  \                    /                |\
                  \\#####\           /                  ||
                ==###########>      /                   ||
                 \\##==......\    /                     ||
            ______ =       =|__ /__                     ||      \\\
        ,--' ,----`-,__ ___/'  --,-`-===================##========>
       \               '        ##_______ _____ ,--,__,=##,__   ///
        ,    __==    ___,-,__,--'#'  ==='      `-'    | ##,-/
        -,____,---'       \\####\\________________,--\\_##,/
           ___      .______        ______  __    __  .______      
          /   \     |   _  \      /      ||  |  |  | |   _  \     
         /  ^  \    |  |_)  |    |  ,----'|  |__|  | |  |_)  |    
        /  /_\  \   |      /     |  |     |   __   | |      /     
       /  _____  \  |  |\  \\___ |  `----.|  |  |  | |  |\  \\___.
      /__/     \__\ | _| `._____| \______||__|  |__| | _| `._____|
    
Harmony 1/10
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Harmony 2/10
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Harmony 3/10
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Harmony 4/10
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Harmony converged after 4 iterations
ArchR logging to : ArchRLogs/ArchR-addClusters-4e9946921b209-Date-2023-04-27_Time-14-39-46.log
If there is an issue, please report to github with logFile!
2023-04-27 14:39:47 : Running Seurats FindClusters (Stuart et al. Cell 2019), 0.002 mins elapsed.
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 24220
Number of edges: 773556

Running Louvain algorithm...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.8987
Number of communities: 18
Elapsed time: 6 seconds
2023-04-27 14:40:17 : Testing Biased Clusters, 0.503 mins elapsed.
2023-04-27 14:40:17 : Testing Outlier Clusters, 0.511 mins elapsed.
2023-04-27 14:40:17 : Assigning Cluster Names to 18 Clusters, 0.511 mins elapsed.
2023-04-27 14:40:17 : Finished addClusters, 0.512 mins elapsed.
14:40:17 UMAP embedding parameters a = 0.583 b = 1.334
14:40:17 Read 24220 rows and found 30 numeric columns
14:40:17 Using Annoy for neighbor search, n_neighbors = 30
14:40:17 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
14:40:20 Writing NN index file to temp file /tmp/RtmpBMaSdv/file4e99446ee1cd3
14:40:20 Searching Annoy index using 16 threads, search_k = 3000
14:40:22 Annoy recall = 100%
14:40:23 Commencing smooth kNN distance calibration using 16 threads with target n_neighbors = 30
14:40:24 Initializing from normalized Laplacian + noise (using irlba)
14:40:25 Commencing optimization for 200 epochs, with 1033654 positive edges
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
14:41:02 Optimization finished
14:41:03 Creating temp model dir /tmp/RtmpBMaSdv/dir4e9946663d6b0
14:41:03 Creating dir /tmp/RtmpBMaSdv/dir4e9946663d6b0
14:41:06 Changing to /tmp/RtmpBMaSdv/dir4e9946663d6b0
14:41:06 Creating /projects/pfenninggroup/singleCell/BICCN_mouse_CATlas_snATAC-seq/data/tidy_data/ArchRProjects/BICCN_mouse_NAc_snATAC/Embeddings/Save-Uwot-UMAP-Params-HarmonyX200-4e9942f71f397-Date-2023-04-27_Time-14-41-03.tar
ArchR logging to : ArchRLogs/ArchR-addImputeWeights-4e9947ff9bd0a-Date-2023-04-27_Time-14-41-06.log
If there is an issue, please report to github with logFile!
2023-04-27 14:41:07 : Computing Impute Weights Using Magic (Cell 2018), 0 mins elapsed.
Checking Inputs...
ArchR logging to : ArchRLogs/ArchR-addIterativeLSI-4e9945e68c382-Date-2023-04-27_Time-14-41-34.log
If there is an issue, please report to github with logFile!
2023-04-27 14:41:37 : Computing Total Across All Features, 0.039 mins elapsed.
2023-04-27 14:41:43 : Computing Top Features, 0.132 mins elapsed.
###########
2023-04-27 14:41:45 : Running LSI (1 of 4) on Top Features, 0.168 mins elapsed.
###########
2023-04-27 14:41:47 : Creating Partial Matrix, 0.2 mins elapsed.
2023-04-27 14:42:27 : Computing LSI, 0.87 mins elapsed.
2023-04-27 14:44:00 : Identifying Clusters, 2.421 mins elapsed.
2023-04-27 14:44:26 : Identified 12 Clusters, 2.848 mins elapsed.
2023-04-27 14:44:26 : Creating Cluster Matrix on the total Group Features, 2.848 mins elapsed.
2023-04-27 14:44:59 : Computing Variable Features, 3.409 mins elapsed.
###########
2023-04-27 14:45:00 : Running LSI (2 of 4) on Variable Features, 3.428 mins elapsed.
###########
2023-04-27 14:45:00 : Creating Partial Matrix, 3.429 mins elapsed.
2023-04-27 14:45:37 : Computing LSI, 4.032 mins elapsed.
2023-04-27 14:47:06 : Identifying Clusters, 5.53 mins elapsed.
2023-04-27 14:47:31 : Identified 13 Clusters, 5.934 mins elapsed.
2023-04-27 14:47:32 : Creating Cluster Matrix on the total Group Features, 5.954 mins elapsed.
2023-04-27 14:48:07 : Computing Variable Features, 6.536 mins elapsed.
###########
2023-04-27 14:48:07 : Running LSI (3 of 4) on Variable Features, 6.542 mins elapsed.
###########
2023-04-27 14:48:07 : Creating Partial Matrix, 6.543 mins elapsed.
2023-04-27 14:48:44 : Computing LSI, 7.157 mins elapsed.
2023-04-27 14:50:09 : Identifying Clusters, 8.579 mins elapsed.
2023-04-27 14:50:33 : Identified 13 Clusters, 8.975 mins elapsed.
2023-04-27 14:50:34 : Creating Cluster Matrix on the total Group Features, 8.995 mins elapsed.
2023-04-27 14:51:11 : Computing Variable Features, 9.603 mins elapsed.
###########
2023-04-27 14:51:11 : Running LSI (4 of 4) on Variable Features, 9.613 mins elapsed.
###########
2023-04-27 14:51:11 : Creating Partial Matrix, 9.614 mins elapsed.
2023-04-27 14:51:43 : Computing LSI, 10.146 mins elapsed.
2023-04-27 14:53:07 : Finished Running IterativeLSI, 11.536 mins elapsed.
Saving ArchRProject...
Loading ArchRProject...
Successfully loaded ArchRProject!

                                                   / |
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                  \                    /                |\
                  \\#####\           /                  ||
                ==###########>      /                   ||
                 \\##==......\    /                     ||
            ______ =       =|__ /__                     ||      \\\
        ,--' ,----`-,__ ___/'  --,-`-===================##========>
       \               '        ##_______ _____ ,--,__,=##,__   ///
        ,    __==    ___,-,__,--'#'  ==='      `-'    | ##,-/
        -,____,---'       \\####\\________________,--\\_##,/
           ___      .______        ______  __    __  .______      
          /   \     |   _  \      /      ||  |  |  | |   _  \     
         /  ^  \    |  |_)  |    |  ,----'|  |__|  | |  |_)  |    
        /  /_\  \   |      /     |  |     |   __   | |      /     
       /  _____  \  |  |\  \\___ |  `----.|  |  |  | |  |\  \\___.
      /__/     \__\ | _| `._____| \______||__|  |__| | _| `._____|
    
Harmony 1/10
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Harmony 2/10
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Harmony 3/10
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Harmony converged after 3 iterations
ArchR logging to : ArchRLogs/ArchR-addClusters-4e99443a45210-Date-2023-04-27_Time-14-53-56.log
If there is an issue, please report to github with logFile!
2023-04-27 14:53:56 : Running Seurats FindClusters (Stuart et al. Cell 2019), 0.002 mins elapsed.
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 24220
Number of edges: 776966

Running Louvain algorithm...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.9007
Number of communities: 20
Elapsed time: 5 seconds
2023-04-27 14:54:23 : Testing Biased Clusters, 0.455 mins elapsed.
2023-04-27 14:54:23 : Testing Outlier Clusters, 0.457 mins elapsed.
2023-04-27 14:54:23 : Assigning Cluster Names to 20 Clusters, 0.457 mins elapsed.
2023-04-27 14:54:23 : Finished addClusters, 0.458 mins elapsed.
14:54:24 UMAP embedding parameters a = 0.583 b = 1.334
14:54:24 Read 24220 rows and found 30 numeric columns
14:54:24 Using Annoy for neighbor search, n_neighbors = 30
14:54:24 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
14:54:26 Writing NN index file to temp file /tmp/RtmpBMaSdv/file4e9941cbb8e8c
14:54:26 Searching Annoy index using 16 threads, search_k = 3000
14:54:28 Annoy recall = 100%
14:54:29 Commencing smooth kNN distance calibration using 16 threads with target n_neighbors = 30
14:54:30 Initializing from normalized Laplacian + noise (using irlba)
14:54:33 Commencing optimization for 200 epochs, with 1022882 positive edges
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
14:55:12 Optimization finished
14:55:12 Creating temp model dir /tmp/RtmpBMaSdv/dir4e99421159d60
14:55:12 Creating dir /tmp/RtmpBMaSdv/dir4e99421159d60
14:55:15 Changing to /tmp/RtmpBMaSdv/dir4e99421159d60
14:55:15 Creating /projects/pfenninggroup/singleCell/BICCN_mouse_CATlas_snATAC-seq/data/tidy_data/ArchRProjects/BICCN_mouse_NAc_snATAC/Embeddings/Save-Uwot-UMAP-Params-HarmonyX300-4e9943eab7c1d-Date-2023-04-27_Time-14-55-12.tar
ArchR logging to : ArchRLogs/ArchR-addImputeWeights-4e9944d6b2352-Date-2023-04-27_Time-14-55-16.log
If there is an issue, please report to github with logFile!
2023-04-27 14:55:16 : Computing Impute Weights Using Magic (Cell 2018), 0 mins elapsed.
Checking Inputs...
ArchR logging to : ArchRLogs/ArchR-addIterativeLSI-4e994b1c763e-Date-2023-04-27_Time-14-55-40.log
If there is an issue, please report to github with logFile!
2023-04-27 14:55:43 : Computing Total Across All Features, 0.012 mins elapsed.
2023-04-27 14:55:48 : Computing Top Features, 0.111 mins elapsed.
###########
2023-04-27 14:55:51 : Running LSI (1 of 4) on Top Features, 0.15 mins elapsed.
###########
2023-04-27 14:55:52 : Creating Partial Matrix, 0.165 mins elapsed.
2023-04-27 14:56:36 : Computing LSI, 0.91 mins elapsed.
2023-04-27 14:58:14 : Identifying Clusters, 2.532 mins elapsed.
2023-04-27 14:58:41 : Identified 12 Clusters, 2.987 mins elapsed.
2023-04-27 14:58:41 : Creating Cluster Matrix on the total Group Features, 2.987 mins elapsed.
2023-04-27 14:59:31 : Computing Variable Features, 3.813 mins elapsed.
###########
2023-04-27 14:59:32 : Running LSI (2 of 4) on Variable Features, 3.832 mins elapsed.
###########
2023-04-27 14:59:32 : Creating Partial Matrix, 3.833 mins elapsed.
2023-04-27 15:00:12 : Computing LSI, 4.51 mins elapsed.
2023-04-27 15:02:08 : Identifying Clusters, 6.446 mins elapsed.
2023-04-27 15:02:33 : Identified 12 Clusters, 6.85 mins elapsed.
2023-04-27 15:02:34 : Creating Cluster Matrix on the total Group Features, 6.871 mins elapsed.
2023-04-27 15:03:05 : Computing Variable Features, 7.388 mins elapsed.
###########
2023-04-27 15:03:05 : Running LSI (3 of 4) on Variable Features, 7.394 mins elapsed.
###########
2023-04-27 15:03:06 : Creating Partial Matrix, 7.412 mins elapsed.
2023-04-27 15:03:53 : Computing LSI, 8.185 mins elapsed.
2023-04-27 15:05:47 : Identifying Clusters, 10.095 mins elapsed.
2023-04-27 15:06:13 : Identified 12 Clusters, 10.52 mins elapsed.
2023-04-27 15:06:14 : Creating Cluster Matrix on the total Group Features, 10.54 mins elapsed.
2023-04-27 15:06:46 : Computing Variable Features, 11.077 mins elapsed.
###########
2023-04-27 15:06:47 : Running LSI (4 of 4) on Variable Features, 11.083 mins elapsed.
###########
2023-04-27 15:06:47 : Creating Partial Matrix, 11.084 mins elapsed.
2023-04-27 15:07:35 : Computing LSI, 11.879 mins elapsed.
2023-04-27 15:09:32 : Finished Running IterativeLSI, 13.846 mins elapsed.
Saving ArchRProject...
Loading ArchRProject...
Successfully loaded ArchRProject!

                                                   / |
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            .                                  /      |.
            \\\                              /        |.
              \\\                          /           `|.
                \\\                      /              |.
                  \                    /                |\
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                ==###########>      /                   ||
                 \\##==......\    /                     ||
            ______ =       =|__ /__                     ||      \\\
        ,--' ,----`-,__ ___/'  --,-`-===================##========>
       \               '        ##_______ _____ ,--,__,=##,__   ///
        ,    __==    ___,-,__,--'#'  ==='      `-'    | ##,-/
        -,____,---'       \\####\\________________,--\\_##,/
           ___      .______        ______  __    __  .______      
          /   \     |   _  \      /      ||  |  |  | |   _  \     
         /  ^  \    |  |_)  |    |  ,----'|  |__|  | |  |_)  |    
        /  /_\  \   |      /     |  |     |   __   | |      /     
       /  _____  \  |  |\  \\___ |  `----.|  |  |  | |  |\  \\___.
      /__/     \__\ | _| `._____| \______||__|  |__| | _| `._____|
    
Harmony 1/10
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Harmony 2/10
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Harmony 3/10
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Harmony converged after 3 iterations
ArchR logging to : ArchRLogs/ArchR-addClusters-4e99460e07c05-Date-2023-04-27_Time-15-10-42.log
If there is an issue, please report to github with logFile!
2023-04-27 15:10:42 : Running Seurats FindClusters (Stuart et al. Cell 2019), 0.002 mins elapsed.
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 24220
Number of edges: 779908

Running Louvain algorithm...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.9017
Number of communities: 20
Elapsed time: 4 seconds
2023-04-27 15:11:06 : Testing Biased Clusters, 0.405 mins elapsed.
2023-04-27 15:11:07 : Testing Outlier Clusters, 0.42 mins elapsed.
2023-04-27 15:11:07 : Assigning Cluster Names to 20 Clusters, 0.42 mins elapsed.
2023-04-27 15:11:07 : Finished addClusters, 0.422 mins elapsed.
15:11:07 UMAP embedding parameters a = 0.583 b = 1.334
15:11:07 Read 24220 rows and found 30 numeric columns
15:11:07 Using Annoy for neighbor search, n_neighbors = 30
15:11:07 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
15:11:10 Writing NN index file to temp file /tmp/RtmpBMaSdv/file4e994359bdcb7
15:11:10 Searching Annoy index using 16 threads, search_k = 3000
15:11:11 Annoy recall = 100%
15:11:13 Commencing smooth kNN distance calibration using 16 threads with target n_neighbors = 30
15:11:14 Initializing from normalized Laplacian + noise (using irlba)
15:11:16 Commencing optimization for 200 epochs, with 1022738 positive edges
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
15:11:58 Optimization finished
15:11:58 Creating temp model dir /tmp/RtmpBMaSdv/dir4e9945d375b09
15:11:58 Creating dir /tmp/RtmpBMaSdv/dir4e9945d375b09
15:12:00 Changing to /tmp/RtmpBMaSdv/dir4e9945d375b09
15:12:00 Creating /projects/pfenninggroup/singleCell/BICCN_mouse_CATlas_snATAC-seq/data/tidy_data/ArchRProjects/BICCN_mouse_NAc_snATAC/Embeddings/Save-Uwot-UMAP-Params-HarmonyX400-4e9944a0d309c-Date-2023-04-27_Time-15-11-58.tar
ArchR logging to : ArchRLogs/ArchR-addImputeWeights-4e9946c19e8b2-Date-2023-04-27_Time-15-12-02.log
If there is an issue, please report to github with logFile!
2023-04-27 15:12:03 : Computing Impute Weights Using Magic (Cell 2018), 0 mins elapsed.
Saving ArchRProject...
Loading ArchRProject...
Successfully loaded ArchRProject!

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                ==###########>      /                   ||
                 \\##==......\    /                     ||
            ______ =       =|__ /__                     ||      \\\
        ,--' ,----`-,__ ___/'  --,-`-===================##========>
       \               '        ##_______ _____ ,--,__,=##,__   ///
        ,    __==    ___,-,__,--'#'  ==='      `-'    | ##,-/
        -,____,---'       \\####\\________________,--\\_##,/
           ___      .______        ______  __    __  .______      
          /   \     |   _  \      /      ||  |  |  | |   _  \     
         /  ^  \    |  |_)  |    |  ,----'|  |__|  | |  |_)  |    
        /  /_\  \   |      /     |  |     |   __   | |      /     
       /  _____  \  |  |\  \\___ |  `----.|  |  |  | |  |\  \\___.
      /__/     \__\ | _| `._____| \______||__|  |__| | _| `._____|