`createArrowFiles` can't generate "QualityControl" plots

[danli349]

I run the codes in the documents: https://www.archrproject.com/bookdown/per-cell-quality-control.html

ArrowFiles <- createArrowFiles(
  inputFiles = inputFiles,
  sampleNames = names(inputFiles),
  minTSS = 4, #Dont set this too high because you can always increase later
  minFrags = 1000, 
  addTileMat = TRUE,
  addGeneScoreMat = TRUE
)

But createArrowFiles can't generate "QualityControl" plots (the plots are empty):

           ___      .______        ______  __    __  .______      
          /   \     |   _  \      /      ||  |  |  | |   _  \     
         /  ^  \    |  |_)  |    |  ,----'|  |__|  | |  |_)  |    
        /  /_\  \   |      /     |  |     |   __   | |      /     
       /  _____  \  |  |\  \\___ |  `----.|  |  |  | |  |\  \\___.
      /__/     \__\ | _| `._____| \______||__|  |__| | _| `._____|

Logging With ArchR!

Start Time : 2024-09-28 21:14:29.923374

------- ArchR Info

ArchRThreads = 10
ArchRGenome = Hg19

------- System Info

Computer OS = unix
Total Cores = 12

------- Session Info

R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 20.04.1 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3;  LAPACK version 3.9.0

Random number generation:
 RNG:     L'Ecuyer-CMRG 
 Normal:  Inversion 
 Sample:  Rejection 

locale:
 [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
 [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
 [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
[10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   

time zone: America/New_York
tzcode source: system (glibc)

attached base packages:
 [1] parallel  stats4    grid      stats     graphics  grDevices utils    
 [8] datasets  methods   base     

other attached packages:
 [1] BSgenome.Hsapiens.UCSC.hg19_1.4.3 BSgenome_1.72.0                  
 [3] rtracklayer_1.64.0                BiocIO_1.14.0                    
 [5] Biostrings_2.72.1                 XVector_0.44.0                   
 [7] rhdf5_2.48.0                      SummarizedExperiment_1.34.0      
 [9] Biobase_2.64.0                    MatrixGenerics_1.16.0            
[11] Rcpp_1.0.13                       Matrix_1.7-0                     
[13] GenomicRanges_1.56.1              GenomeInfoDb_1.40.1              
[15] IRanges_2.38.1                    S4Vectors_0.42.1                 
[17] BiocGenerics_0.50.0               matrixStats_1.4.1                
[19] data.table_1.16.0                 stringr_1.5.1                    
[21] plyr_1.8.9                        magrittr_2.0.3                   
[23] ggplot2_3.5.1                     gtable_0.3.5                     
[25] gtools_3.9.5                      gridExtra_2.3                    
[27] ArchR_1.0.2                      

loaded via a namespace (and not attached):
 [1] rjson_0.2.23             lattice_0.22-6           bitops_1.0-8            
 [4] rhdf5filters_1.16.0      vctrs_0.6.5              tools_4.4.1             
 [7] generics_0.1.3           curl_5.2.3               tibble_3.2.1            
[10] fansi_1.0.6              pkgconfig_2.0.3          uuid_1.2-1              
[13] lifecycle_1.0.4          GenomeInfoDbData_1.2.12  compiler_4.4.1          
[16] Rsamtools_2.20.0         munsell_0.5.1            repr_1.1.7              
[19] codetools_0.2-20         htmltools_0.5.8.1        yaml_2.3.10             
[22] RCurl_1.98-1.16          pillar_1.9.0             crayon_1.5.3            
[25] BiocParallel_1.38.0      DelayedArray_0.30.1      abind_1.4-8             
[28] tidyselect_1.2.1         digest_0.6.37            stringi_1.8.4           
[31] restfulr_0.0.15          dplyr_1.1.4              fastmap_1.2.0           
[34] colorspace_2.1-1         cli_3.6.3                SparseArray_1.4.8       
[37] S4Arrays_1.4.1           base64enc_0.1-3          XML_3.99-0.17           
[40] utf8_1.2.4               IRdisplay_1.1            withr_3.0.1             
[43] scales_1.3.0             UCSC.utils_1.0.0         IRkernel_1.3.2          
[46] httr_1.4.7               pbdZMQ_0.3-11            evaluate_1.0.0          
[49] rlang_1.1.4              glue_1.7.0               jsonlite_1.8.9          
[52] R6_2.5.1                 Rhdf5lib_1.26.0          GenomicAlignments_1.40.0
[55] zlibbioc_1.50.0         

------- Log Info

2024-09-28 21:14:29.990213 : createArrowFiles Input-Parameters, Class = list

createArrowFiles Input-Parameters$inputFiles: length = 3
                                      scATAC_BMMC_R1 
     "HemeFragments/scATAC_BMMC_R1.fragments.tsv.gz" 
                                 scATAC_CD34_BMMC_R1 
"HemeFragments/scATAC_CD34_BMMC_R1.fragments.tsv.gz" 
                                      scATAC_PBMC_R1 
     "HemeFragments/scATAC_PBMC_R1.fragments.tsv.gz" 

createArrowFiles Input-Parameters$sampleNames: length = 3
[1] "scATAC_BMMC_R1"      "scATAC_CD34_BMMC_R1" "scATAC_PBMC_R1"     

createArrowFiles Input-Parameters$outputNames: length = 3
[1] "scATAC_BMMC_R1"      "scATAC_CD34_BMMC_R1" "scATAC_PBMC_R1"     

createArrowFiles Input-Parameters$validBarcodes: length = 0
NULL

createArrowFiles Input-Parameters$minTSS: length = 1
[1] 4

createArrowFiles Input-Parameters$minFrags: length = 1
[1] 1000

createArrowFiles Input-Parameters$maxFrags: length = 1
[1] 1e+05

createArrowFiles Input-Parameters$minFragSize: length = 1
[1] 10

createArrowFiles Input-Parameters$maxFragSize: length = 1
[1] 2000

createArrowFiles Input-Parameters$QCDir: length = 1
[1] "QualityControl"

createArrowFiles Input-Parameters$nucLength: length = 1
[1] 147

createArrowFiles Input-Parameters$promoterRegion: length = 2
[1] 2000  100

createArrowFiles Input-Parameters$excludeChr: length = 2
[1] "chrM" "chrY"

createArrowFiles Input-Parameters$nChunk: length = 1
[1] 5

createArrowFiles Input-Parameters$bcTag: length = 1
[1] "qname"

createArrowFiles Input-Parameters$gsubExpression: length = 0
NULL

createArrowFiles Input-Parameters$bamFlag: length = 0
NULL

createArrowFiles Input-Parameters$offsetPlus: length = 1
[1] 4

createArrowFiles Input-Parameters$offsetMinus: length = 1
[1] -5

createArrowFiles Input-Parameters$addTileMat: length = 1
[1] TRUE

createArrowFiles Input-Parameters$addGeneScoreMat: length = 1
[1] TRUE

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

createArrowFiles Input-Parameters$threads: length = 1
[1] 10

createArrowFiles Input-Parameters$parallelParam: length = 0
NULL

createArrowFiles Input-Parameters$subThreading: length = 1
[1] TRUE

createArrowFiles Input-Parameters$verbose: length = 1
[1] TRUE

createArrowFiles Input-Parameters$cleanTmp: length = 1
[1] TRUE

createArrowFiles Input-Parameters$logFile: length = 1
[1] "ArchRLogs/ArchR-createArrows-3ad2f20f7fe-Date-2024-09-28_Time-21-14-29.920487.log"

createArrowFiles Input-Parameters$filterFrags: length = 1
[1] 1000

createArrowFiles Input-Parameters$filterTSS: length = 1
[1] 4

2024-09-28 21:14:30.024427 : 
2024-09-28 21:14:30.028486 : Batch Execution w/ safelapply!, 0 mins elapsed.

###########
2024-09-28 21:14:30.125745 : Creating Arrow File scATAC_BMMC_R1.arrow (scATAC_BMMC_R1 : 1 of 3)
###########

2024-09-28 21:14:30.127657 : validBC, Class = NULL

validBC: length = 0
NULL

###########
2024-09-28 21:14:30.192353 : Creating Arrow File scATAC_CD34_BMMC_R1.arrow (scATAC_CD34_BMMC_R1 : 2 of 3)
###########

2024-09-28 21:14:30.195114 : validBC, Class = NULL

validBC: length = 0
NULL

2024-09-28 21:14:30.219077 : 

###########
2024-09-28 21:14:30.255793 : Creating Arrow File scATAC_PBMC_R1.arrow (scATAC_PBMC_R1 : 3 of 3)
###########

2024-09-28 21:14:30.258033 : validBC, Class = NULL

validBC: length = 0
NULL

2024-09-28 21:14:30.303941 : 

2024-09-28 21:14:30.373695 : 
2024-09-28 21:14:34.743106 : (scATAC_PBMC_R1 : 3 of 3) Reading In Fragments from inputFiles (readMethod = tabix), 0.079 mins elapsed.
2024-09-28 21:14:34.764987 : (scATAC_PBMC_R1 : 3 of 3) Tabix Bed To Temporary File, 0.079 mins elapsed.

2024-09-28 21:14:34.966274 : tileChromSizes, Class = GRanges
GRanges object with 120 ranges and 1 metadata column:
        seqnames              ranges strand |     chunkName
           <Rle>           <IRanges>  <Rle> |   <character>
    [1]     chr1          1-49850124      * |   chr1#chunk1
    [2]     chr1   49850125-99700248      * |   chr1#chunk2
    [3]     chr1  99700249-149550372      * |   chr1#chunk3
    [4]     chr1 149550373-199400496      * |   chr1#chunk4
    [5]     chr1 199400497-249250621      * |   chr1#chunk5
    ...      ...                 ...    ... .           ...
  [116]     chrY          1-11874713      * | chrY#chunk116
  [117]     chrY   11874714-23749426      * | chrY#chunk117
  [118]     chrY   23749427-35624139      * | chrY#chunk118
  [119]     chrY   35624140-47498852      * | chrY#chunk119
  [120]     chrY   47498853-59373566      * | chrY#chunk120
  -------
  seqinfo: 24 sequences from an unspecified genome; no seqlengths

2024-09-28 21:14:35.283716 : (scATAC_CD34_BMMC_R1 : 2 of 3) Reading In Fragments from inputFiles (readMethod = tabix), 0.087 mins elapsed.
2024-09-28 21:14:35.307267 : (scATAC_CD34_BMMC_R1 : 2 of 3) Tabix Bed To Temporary File, 0.088 mins elapsed.

2024-09-28 21:14:35.488381 : tileChromSizes, Class = GRanges
GRanges object with 120 ranges and 1 metadata column:
        seqnames              ranges strand |     chunkName
           <Rle>           <IRanges>  <Rle> |   <character>
    [1]     chr1          1-49850124      * |   chr1#chunk1
    [2]     chr1   49850125-99700248      * |   chr1#chunk2
    [3]     chr1  99700249-149550372      * |   chr1#chunk3
    [4]     chr1 149550373-199400496      * |   chr1#chunk4
    [5]     chr1 199400497-249250621      * |   chr1#chunk5
    ...      ...                 ...    ... .           ...
  [116]     chrY          1-11874713      * | chrY#chunk116
  [117]     chrY   11874714-23749426      * | chrY#chunk117
  [118]     chrY   23749427-35624139      * | chrY#chunk118
  [119]     chrY   35624140-47498852      * | chrY#chunk119
  [120]     chrY   47498853-59373566      * | chrY#chunk120
  -------
  seqinfo: 24 sequences from an unspecified genome; no seqlengths

2024-09-28 21:14:36.472437 : (scATAC_BMMC_R1 : 1 of 3) Reading In Fragments from inputFiles (readMethod = tabix), 0.107 mins elapsed.
2024-09-28 21:14:36.503757 : (scATAC_BMMC_R1 : 1 of 3) Tabix Bed To Temporary File, 0.108 mins elapsed.

2024-09-28 21:14:36.735945 : tileChromSizes, Class = GRanges
GRanges object with 120 ranges and 1 metadata column:
        seqnames              ranges strand |     chunkName
           <Rle>           <IRanges>  <Rle> |   <character>
    [1]     chr1          1-49850124      * |   chr1#chunk1
    [2]     chr1   49850125-99700248      * |   chr1#chunk2
    [3]     chr1  99700249-149550372      * |   chr1#chunk3
    [4]     chr1 149550373-199400496      * |   chr1#chunk4
    [5]     chr1 199400497-249250621      * |   chr1#chunk5
    ...      ...                 ...    ... .           ...
  [116]     chrY          1-11874713      * | chrY#chunk116
  [117]     chrY   11874714-23749426      * | chrY#chunk117
  [118]     chrY   23749427-35624139      * | chrY#chunk118
  [119]     chrY   35624140-47498852      * | chrY#chunk119
  [120]     chrY   47498853-59373566      * | chrY#chunk120
  -------
  seqinfo: 24 sequences from an unspecified genome; no seqlengths

2024-09-28 21:14:36.941219 : (scATAC_PBMC_R1 : 3 of 3) .tabixToTmp Fragments-Chunk-(1 of 120)-chr1:1-49850124, Class = data.table

2024-09-28 21:14:36.941219 : (scATAC_PBMC_R1 : 3 of 3) .tabixToTmp Fragments-Chunk-(1 of 120)-chr1:1-49850124, Class = data.frame
(scATAC_PBMC_R1 : 3 of 3) .tabixToTmp Fragments-Chunk-(1 of 120)-chr1:1-49850124: nRows = 384110, nCols = 3
      V2    V3                 V4
   <num> <int>             <char>
1: 10072 10279 CAGGGCTTCTTTCGAT-1
2: 10388 10565 GATGATCCACGTTACA-1
3: 10445 10548 TTTGCGCTCTATCTAC-1
4: 10518 10569 ATGTACGAGTATGCTC-1
5: 16227 16261 ACCGAATCAACGGGTA-1
6: 17171 17525 CCGTGAGAGACCATAA-1

2024-09-28 21:14:36.988463 : (scATAC_PBMC_R1 : 3 of 3) .tabixToTmp Barcodes-Chunk-(1 of 120)-chr1:1-49850124, Class = character

(scATAC_PBMC_R1 : 3 of 3) .tabixToTmp Barcodes-Chunk-(1 of 120)-chr1:1-49850124: length = 2966
[1] "CAGGGCTTCTTTCGAT-1" "GATGATCCACGTTACA-1" "TTTGCGCTCTATCTAC-1"
[4] "ATGTACGAGTATGCTC-1" "ACCGAATCAACGGGTA-1" "CCGTGAGAGACCATAA-1"

2024-09-28 21:14:38.338534 : (scATAC_CD34_BMMC_R1 : 2 of 3) .tabixToTmp Fragments-Chunk-(1 of 120)-chr1:1-49850124, Class = data.table

2024-09-28 21:14:38.338534 : (scATAC_CD34_BMMC_R1 : 2 of 3) .tabixToTmp Fragments-Chunk-(1 of 120)-chr1:1-49850124, Class = data.frame
(scATAC_CD34_BMMC_R1 : 2 of 3) .tabixToTmp Fragments-Chunk-(1 of 120)-chr1:1-49850124: nRows = 456085, nCols = 3
      V2    V3                 V4
   <num> <int>             <char>
1: 10103 10197 ATTTGTCTCAATCGTG-1
2: 10498 10536 CACATGAGTGATAAGT-1
3: 10595 10654 GCATTCCTCGTTGTTT-1
4: 17298 17508 TGTACAGAGGTAGGAA-1
5: 87244 87302 GTGGATTCAATGACTC-1
6: 87353 87572 TGCTTTAGTAACAATG-1

2024-09-28 21:14:38.378499 : (scATAC_CD34_BMMC_R1 : 2 of 3) .tabixToTmp Barcodes-Chunk-(1 of 120)-chr1:1-49850124, Class = character

(scATAC_CD34_BMMC_R1 : 2 of 3) .tabixToTmp Barcodes-Chunk-(1 of 120)-chr1:1-49850124: length = 3700
[1] "ATTTGTCTCAATCGTG-1" "CACATGAGTGATAAGT-1" "GCATTCCTCGTTGTTT-1"
[4] "TGTACAGAGGTAGGAA-1" "GTGGATTCAATGACTC-1" "TGCTTTAGTAACAATG-1"

2024-09-28 21:14:42.456348 : (scATAC_BMMC_R1 : 1 of 3) .tabixToTmp Fragments-Chunk-(1 of 120)-chr1:1-49850124, Class = data.table

2024-09-28 21:14:42.456348 : (scATAC_BMMC_R1 : 1 of 3) .tabixToTmp Fragments-Chunk-(1 of 120)-chr1:1-49850124, Class = data.frame
(scATAC_BMMC_R1 : 1 of 3) .tabixToTmp Fragments-Chunk-(1 of 120)-chr1:1-49850124: nRows = 505916, nCols = 3
      V2    V3                 V4
   <num> <int>             <char>
1: 10080 10209 TAGGAGGGTTAACCGT-1
2: 10091 10278 CCTTGGTAGTTCTCCC-1
3: 10158 10204 GCCAGCAGTTCTGAGT-1
4: 10223 10333 TAGCATGGTGACCAGA-1
5: 10298 10614 GCCCAGAAGTGTCACT-1
6: 10352 10533 GTGCCAGTCAAGGCAG-1

2024-09-28 21:14:42.495992 : (scATAC_PBMC_R1 : 3 of 3) Reading TabixFile 6 Percent, 0.207 mins elapsed.

2024-09-28 21:14:42.483586 : (scATAC_BMMC_R1 : 1 of 3) .tabixToTmp Barcodes-Chunk-(1 of 120)-chr1:1-49850124, Class = character

(scATAC_BMMC_R1 : 1 of 3) .tabixToTmp Barcodes-Chunk-(1 of 120)-chr1:1-49850124: length = 5000
[1] "TAGGAGGGTTAACCGT-1" "CCTTGGTAGTTCTCCC-1" "GCCAGCAGTTCTGAGT-1"
[4] "TAGCATGGTGACCAGA-1" "GCCCAGAAGTGTCACT-1" "GTGCCAGTCAAGGCAG-1"

2024-09-28 21:14:43.465777 : (scATAC_CD34_BMMC_R1 : 2 of 3) Reading TabixFile 6 Percent, 0.223 mins elapsed.
2024-09-28 21:14:46.513228 : (scATAC_BMMC_R1 : 1 of 3) Reading TabixFile 6 Percent, 0.274 mins elapsed.
2024-09-28 21:14:50.486445 : (scATAC_PBMC_R1 : 3 of 3) Reading TabixFile 12 Percent, 0.34 mins elapsed.
2024-09-28 21:14:52.067255 : (scATAC_CD34_BMMC_R1 : 2 of 3) Reading TabixFile 12 Percent, 0.367 mins elapsed.
2024-09-28 21:14:55.577246 : (scATAC_BMMC_R1 : 1 of 3) Reading TabixFile 12 Percent, 0.425 mins elapsed.
2024-09-28 21:14:59.044526 : (scATAC_PBMC_R1 : 3 of 3) Reading TabixFile 18 Percent, 0.483 mins elapsed.
2024-09-28 21:15:01.255398 : (scATAC_CD34_BMMC_R1 : 2 of 3) Reading TabixFile 18 Percent, 0.52 mins elapsed.
2024-09-28 21:15:04.881347 : (scATAC_BMMC_R1 : 1 of 3) Reading TabixFile 18 Percent, 0.58 mins elapsed.
2024-09-28 21:15:07.549631 : (scATAC_PBMC_R1 : 3 of 3) Reading TabixFile 23 Percent, 0.625 mins elapsed.
2024-09-28 21:15:09.734545 : (scATAC_CD34_BMMC_R1 : 2 of 3) Reading TabixFile 23 Percent, 0.661 mins elapsed.
2024-09-28 21:15:14.472571 : (scATAC_BMMC_R1 : 1 of 3) Reading TabixFile 23 Percent, 0.74 mins elapsed.
2024-09-28 21:15:15.137267 : (scATAC_PBMC_R1 : 3 of 3) Reading TabixFile 29 Percent, 0.751 mins elapsed.
2024-09-28 21:15:17.580071 : (scATAC_CD34_BMMC_R1 : 2 of 3) Reading TabixFile 29 Percent, 0.792 mins elapsed.
2024-09-28 21:15:24.018237 : (scATAC_BMMC_R1 : 1 of 3) Reading TabixFile 29 Percent, 0.899 mins elapsed.
2024-09-28 21:15:24.654294 : (scATAC_PBMC_R1 : 3 of 3) Reading TabixFile 35 Percent, 0.91 mins elapsed.
2024-09-28 21:15:27.769298 : (scATAC_CD34_BMMC_R1 : 2 of 3) Reading TabixFile 35 Percent, 0.962 mins elapsed.
2024-09-28 21:15:32.866544 : (scATAC_PBMC_R1 : 3 of 3) Reading TabixFile 41 Percent, 1.047 mins elapsed.
2024-09-28 21:15:33.365472 : (scATAC_BMMC_R1 : 1 of 3) Reading TabixFile 35 Percent, 1.055 mins elapsed.
2024-09-28 21:15:36.120216 : (scATAC_CD34_BMMC_R1 : 2 of 3) Reading TabixFile 41 Percent, 1.101 mins elapsed.
2024-09-28 21:15:41.264702 : (scATAC_PBMC_R1 : 3 of 3) Reading TabixFile 47 Percent, 1.187 mins elapsed.
2024-09-28 21:15:42.457581 : (scATAC_BMMC_R1 : 1 of 3) Reading TabixFile 41 Percent, 1.206 mins elapsed.
2024-09-28 21:15:44.995439 : (scATAC_CD34_BMMC_R1 : 2 of 3) Reading TabixFile 47 Percent, 1.249 mins elapsed.
2024-09-28 21:15:50.173129 : (scATAC_PBMC_R1 : 3 of 3) Reading TabixFile 52 Percent, 1.335 mins elapsed.
2024-09-28 21:15:52.437088 : (scATAC_BMMC_R1 : 1 of 3) Reading TabixFile 47 Percent, 1.373 mins elapsed.
2024-09-28 21:15:54.437287 : (scATAC_CD34_BMMC_R1 : 2 of 3) Reading TabixFile 52 Percent, 1.406 mins elapsed.
2024-09-28 21:15:57.469686 : (scATAC_PBMC_R1 : 3 of 3) Reading TabixFile 58 Percent, 1.457 mins elapsed.
2024-09-28 21:16:01.932538 : (scATAC_BMMC_R1 : 1 of 3) Reading TabixFile 52 Percent, 1.531 mins elapsed.
2024-09-28 21:16:02.313703 : (scATAC_CD34_BMMC_R1 : 2 of 3) Reading TabixFile 58 Percent, 1.537 mins elapsed.
2024-09-28 21:16:05.375772 : (scATAC_PBMC_R1 : 3 of 3) Reading TabixFile 64 Percent, 1.588 mins elapsed.
2024-09-28 21:16:09.139982 : (scATAC_BMMC_R1 : 1 of 3) Reading TabixFile 58 Percent, 1.651 mins elapsed.
2024-09-28 21:16:10.199786 : (scATAC_CD34_BMMC_R1 : 2 of 3) Reading TabixFile 64 Percent, 1.669 mins elapsed.
2024-09-28 21:16:13.3353 : (scATAC_PBMC_R1 : 3 of 3) Reading TabixFile 70 Percent, 1.721 mins elapsed.
2024-09-28 21:16:18.074141 : (scATAC_CD34_BMMC_R1 : 2 of 3) Reading TabixFile 70 Percent, 1.8 mins elapsed.
2024-09-28 21:16:18.406574 : (scATAC_BMMC_R1 : 1 of 3) Reading TabixFile 64 Percent, 1.806 mins elapsed.
2024-09-28 21:16:22.536443 : (scATAC_PBMC_R1 : 3 of 3) Reading TabixFile 76 Percent, 1.874 mins elapsed.
2024-09-28 21:16:26.842185 : (scATAC_BMMC_R1 : 1 of 3) Reading TabixFile 70 Percent, 1.946 mins elapsed.
2024-09-28 21:16:27.763774 : (scATAC_CD34_BMMC_R1 : 2 of 3) Reading TabixFile 76 Percent, 1.962 mins elapsed.
2024-09-28 21:16:30.238433 : (scATAC_PBMC_R1 : 3 of 3) Reading TabixFile 82 Percent, 2.003 mins elapsed.
2024-09-28 21:16:35.667975 : (scATAC_CD34_BMMC_R1 : 2 of 3) Reading TabixFile 82 Percent, 2.093 mins elapsed.
2024-09-28 21:16:36.420333 : (scATAC_BMMC_R1 : 1 of 3) Reading TabixFile 76 Percent, 2.106 mins elapsed.
2024-09-28 21:16:37.19443 : (scATAC_PBMC_R1 : 3 of 3) Reading TabixFile 88 Percent, 2.119 mins elapsed.
2024-09-28 21:16:43.275632 : (scATAC_CD34_BMMC_R1 : 2 of 3) Reading TabixFile 88 Percent, 2.22 mins elapsed.
2024-09-28 21:16:43.803773 : (scATAC_PBMC_R1 : 3 of 3) Reading TabixFile 93 Percent, 2.229 mins elapsed.
2024-09-28 21:16:45.144185 : (scATAC_BMMC_R1 : 1 of 3) Reading TabixFile 82 Percent, 2.251 mins elapsed.
2024-09-28 21:16:51.22909 : (scATAC_CD34_BMMC_R1 : 2 of 3) Reading TabixFile 93 Percent, 2.353 mins elapsed.
2024-09-28 21:16:52.084188 : (scATAC_BMMC_R1 : 1 of 3) Reading TabixFile 88 Percent, 2.367 mins elapsed.
2024-09-28 21:16:52.47349 : (scATAC_PBMC_R1 : 3 of 3) Reading TabixFile 99 Percent, 2.373 mins elapsed.
2024-09-28 21:16:55.16415 : (scATAC_PBMC_R1 : 3 of 3) Parallel Hdf5 Linkage Temporary File, 2.419 mins elapsed.
2024-09-28 21:16:57.132397 : (scATAC_PBMC_R1 : 3 of 3) Successful creation of Temporary File, 2.452 mins elapsed.
2024-09-28 21:16:57.144088 : (scATAC_PBMC_R1 : 3 of 3) Creating ArrowFile From Temporary File, 2.452 mins elapsed.
2024-09-28 21:16:57.588449 : (scATAC_CD34_BMMC_R1 : 2 of 3) Reading TabixFile 99 Percent, 2.459 mins elapsed.

2024-09-28 21:16:57.873237 : (scATAC_PBMC_R1 : 3 of 3) chunkChrNames, Class = data.frame
(scATAC_PBMC_R1 : 3 of 3) chunkChrNames: nRows = 118, nCols = 1
     chunkNames
1   chr1#chunk1
2   chr1#chunk2
3   chr1#chunk3
4   chr1#chunk4
5   chr1#chunk5
6 chr10#chunk46

2024-09-28 21:16:57.885386 : (scATAC_PBMC_R1 : 3 of 3) Counting Unique Barcodes From Temporary File, 2.464 mins elapsed.
2024-09-28 21:16:58.480584 : (scATAC_BMMC_R1 : 1 of 3) Reading TabixFile 93 Percent, 2.474 mins elapsed.
2024-09-28 21:17:00.071484 : (scATAC_CD34_BMMC_R1 : 2 of 3) Parallel Hdf5 Linkage Temporary File, 2.501 mins elapsed.

2024-09-28 21:17:01.39207 : (scATAC_PBMC_R1 : 3 of 3) BarcodeFrequencyTable, Class = data.table

2024-09-28 21:17:01.39207 : (scATAC_PBMC_R1 : 3 of 3) BarcodeFrequencyTable, Class = data.frame
(scATAC_PBMC_R1 : 3 of 3) BarcodeFrequencyTable: nRows = 3000, nCols = 2
            values.V1     V1
               <char>  <int>
1: GTGCACGGTGTTGTTG-1 109035
2: AACTGGTAGCTCCGGT-1  97234
3: CCGTGAGAGACCATAA-1  91194
4: TGCACCTTCGGCTATA-1  83428
5: GACTAACAGCAACGGT-1  79122
6: ATAGGCTCAAACCGAG-1  76515

2024-09-28 21:17:01.40552 : (scATAC_PBMC_R1 : 3 of 3) BarcodesMinMaxFrags, Class = data.frame
(scATAC_PBMC_R1 : 3 of 3) BarcodesMinMaxFrags: nRows = 2495, nCols = 1
                  bc
1 AACTGGTAGCTCCGGT-1
2 CCGTGAGAGACCATAA-1
3 TGCACCTTCGGCTATA-1
4 GACTAACAGCAACGGT-1
5 ATAGGCTCAAACCGAG-1
6 TCGAGCGAGAGCACTG-1

2024-09-28 21:17:01.662415 : (scATAC_CD34_BMMC_R1 : 2 of 3) Successful creation of Temporary File, 2.527 mins elapsed.
2024-09-28 21:17:01.673022 : (scATAC_CD34_BMMC_R1 : 2 of 3) Creating ArrowFile From Temporary File, 2.527 mins elapsed.

2024-09-28 21:17:01.947472 : (scATAC_PBMC_R1 : 3 of 3) Unique Chromosomes, Class = data.frame
(scATAC_PBMC_R1 : 3 of 3) Unique Chromosomes: nRows = 24, nCols = 1
   chr
1 chr1
2 chr2
3 chr3
4 chr4
5 chr5
6 chr6

2024-09-28 21:17:02.075678 : (scATAC_PBMC_R1 : 3 of 3) Adding Chromosome 1 of 24, 2.534 mins elapsed.
2024-09-28 21:17:02.184663 : (scATAC_PBMC_R1 : 3 of 3) Adding Chromosome 2 of 24, 2.536 mins elapsed.
2024-09-28 21:17:02.277286 : (scATAC_PBMC_R1 : 3 of 3) Adding Chromosome 3 of 24, 2.538 mins elapsed.

2024-09-28 21:17:02.286187 : (scATAC_CD34_BMMC_R1 : 2 of 3) chunkChrNames, Class = data.frame
(scATAC_CD34_BMMC_R1 : 2 of 3) chunkChrNames: nRows = 118, nCols = 1
     chunkNames
1   chr1#chunk1
2   chr1#chunk2
3   chr1#chunk3
4   chr1#chunk4
5   chr1#chunk5
6 chr10#chunk46

2024-09-28 21:17:02.297006 : (scATAC_CD34_BMMC_R1 : 2 of 3) Counting Unique Barcodes From Temporary File, 2.538 mins elapsed.
2024-09-28 21:17:05.610376 : (scATAC_BMMC_R1 : 1 of 3) Reading TabixFile 99 Percent, 2.592 mins elapsed.

2024-09-28 21:17:06.211982 : (scATAC_CD34_BMMC_R1 : 2 of 3) BarcodeFrequencyTable, Class = data.table

2024-09-28 21:17:06.211982 : (scATAC_CD34_BMMC_R1 : 2 of 3) BarcodeFrequencyTable, Class = data.frame
(scATAC_CD34_BMMC_R1 : 2 of 3) BarcodeFrequencyTable: nRows = 3723, nCols = 2
            values.V1     V1
               <char>  <int>
1: CGCTGGAAGCATTGGG-1 101939
2: GCGATCGTCCAGTACA-1  50131
3: GCTTAAGAGCAGGAGG-1  41408
4: GTTCAAGAGGTGTTGG-1  34964
5: GCGTTGGGTTACGGAG-1  29044
6: CAACGGCGTACCCACG-1  28840

2024-09-28 21:17:06.232527 : (scATAC_CD34_BMMC_R1 : 2 of 3) BarcodesMinMaxFrags, Class = data.frame
(scATAC_CD34_BMMC_R1 : 2 of 3) BarcodesMinMaxFrags: nRows = 3392, nCols = 1
                  bc
1 GCGATCGTCCAGTACA-1
2 GCTTAAGAGCAGGAGG-1
3 GTTCAAGAGGTGTTGG-1
4 GCGTTGGGTTACGGAG-1
5 CAACGGCGTACCCACG-1
6 ATTCGTTTCTCGTGAA-1

2024-09-28 21:17:06.378715 : (scATAC_PBMC_R1 : 3 of 3) .tmpToArrow Fragments-Chr-(1 of 24)-chr1, Class = IRanges

(scATAC_PBMC_R1 : 3 of 3) .tmpToArrow Fragments-Chr-(1 of 24)-chr1: length = 1096301
IRanges object with 6 ranges and 1 metadata column:
          start       end     width |                 RG
      <integer> <integer> <integer> |              <Rle>
  [1]    714475    714499        25 | AACTGGTAGCTCCGGT-1
  [2]    843408    843606       199 | AACTGGTAGCTCCGGT-1
  [3]    915566    915767       202 | AACTGGTAGCTCCGGT-1
  [4]    916584    916970       387 | AACTGGTAGCTCCGGT-1
  [5]    946422    946624       203 | AACTGGTAGCTCCGGT-1
  [6]    950589    950773       185 | AACTGGTAGCTCCGGT-1

2024-09-28 21:17:06.394784 : (scATAC_PBMC_R1 : 3 of 3) .tmpToArrow Barcodes-Chr-(1 of 24)-chr1, Class = data.frame
(scATAC_PBMC_R1 : 3 of 3) .tmpToArrow Barcodes-Chr-(1 of 24)-chr1: nRows = 2495, nCols = 1
                  bc
1 AACTGGTAGCTCCGGT-1
2 CCGTGAGAGACCATAA-1
3 TGCACCTTCGGCTATA-1
4 GACTAACAGCAACGGT-1
5 ATAGGCTCAAACCGAG-1
6 TCGAGCGAGAGCACTG-1

2024-09-28 21:17:06.839508 : (scATAC_CD34_BMMC_R1 : 2 of 3) Unique Chromosomes, Class = data.frame
(scATAC_CD34_BMMC_R1 : 2 of 3) Unique Chromosomes: nRows = 24, nCols = 1
   chr
1 chr1
2 chr2
3 chr3
4 chr4
5 chr5
6 chr6

2024-09-28 21:17:07.002036 : (scATAC_CD34_BMMC_R1 : 2 of 3) Adding Chromosome 1 of 24, 2.616 mins elapsed.
2024-09-28 21:17:07.10352 : (scATAC_CD34_BMMC_R1 : 2 of 3) Adding Chromosome 2 of 24, 2.618 mins elapsed.
2024-09-28 21:17:07.208457 : (scATAC_CD34_BMMC_R1 : 2 of 3) Adding Chromosome 3 of 24, 2.62 mins elapsed.
2024-09-28 21:17:08.249406 : (scATAC_BMMC_R1 : 1 of 3) Parallel Hdf5 Linkage Temporary File, 2.637 mins elapsed.
2024-09-28 21:17:08.476361 : (scATAC_PBMC_R1 : 3 of 3) Adding Chromosome 4 of 24, 2.641 mins elapsed.
2024-09-28 21:17:08.585844 : (scATAC_PBMC_R1 : 3 of 3) Adding Chromosome 5 of 24, 2.643 mins elapsed.
2024-09-28 21:17:08.817794 : (scATAC_PBMC_R1 : 3 of 3) Adding Chromosome 6 of 24, 2.647 mins elapsed.
2024-09-28 21:17:10.353483 : (scATAC_BMMC_R1 : 1 of 3) Successful creation of Temporary File, 2.672 mins elapsed.
2024-09-28 21:17:10.448609 : (scATAC_BMMC_R1 : 1 of 3) Creating ArrowFile From Temporary File, 2.672 mins elapsed.

2024-09-28 21:17:11.034226 : (scATAC_BMMC_R1 : 1 of 3) chunkChrNames, Class = data.frame
(scATAC_BMMC_R1 : 1 of 3) chunkChrNames: nRows = 118, nCols = 1
     chunkNames
1   chr1#chunk1
2   chr1#chunk2
3   chr1#chunk3
4   chr1#chunk4
5   chr1#chunk5
6 chr10#chunk46

2024-09-28 21:17:11.04453 : (scATAC_BMMC_R1 : 1 of 3) Counting Unique Barcodes From Temporary File, 2.684 mins elapsed.

2024-09-28 21:17:11.656989 : (scATAC_CD34_BMMC_R1 : 2 of 3) .tmpToArrow Fragments-Chr-(1 of 24)-chr1, Class = IRanges

(scATAC_CD34_BMMC_R1 : 2 of 3) .tmpToArrow Fragments-Chr-(1 of 24)-chr1: length = 1252903
IRanges object with 6 ranges and 1 metadata column:
          start       end     width |                 RG
      <integer> <integer> <integer> |              <Rle>
  [1]    862397    862437        41 | GCGATCGTCCAGTACA-1
  [2]    919688    919724        37 | GCGATCGTCCAGTACA-1
  [3]    947336    947439       104 | GCGATCGTCCAGTACA-1
  [4]    953498    953780       283 | GCGATCGTCCAGTACA-1
  [5]   1026618   1026671        54 | GCGATCGTCCAGTACA-1
  [6]   1167120   1167165        46 | GCGATCGTCCAGTACA-1

2024-09-28 21:17:11.681178 : (scATAC_CD34_BMMC_R1 : 2 of 3) .tmpToArrow Barcodes-Chr-(1 of 24)-chr1, Class = data.frame
(scATAC_CD34_BMMC_R1 : 2 of 3) .tmpToArrow Barcodes-Chr-(1 of 24)-chr1: nRows = 3392, nCols = 1
                  bc
1 GCGATCGTCCAGTACA-1
2 GCTTAAGAGCAGGAGG-1
3 GTTCAAGAGGTGTTGG-1
4 GCGTTGGGTTACGGAG-1
5 CAACGGCGTACCCACG-1
6 ATTCGTTTCTCGTGAA-1

2024-09-28 21:17:13.846888 : (scATAC_CD34_BMMC_R1 : 2 of 3) Adding Chromosome 4 of 24, 2.73 mins elapsed.
2024-09-28 21:17:14.033148 : (scATAC_CD34_BMMC_R1 : 2 of 3) Adding Chromosome 5 of 24, 2.733 mins elapsed.
2024-09-28 21:17:14.143138 : (scATAC_CD34_BMMC_R1 : 2 of 3) Adding Chromosome 6 of 24, 2.735 mins elapsed.
2024-09-28 21:17:14.928335 : (scATAC_PBMC_R1 : 3 of 3) Adding Chromosome 7 of 24, 2.748 mins elapsed.
2024-09-28 21:17:15.040278 : (scATAC_PBMC_R1 : 3 of 3) Adding Chromosome 8 of 24, 2.75 mins elapsed.
2024-09-28 21:17:15.18621 : (scATAC_PBMC_R1 : 3 of 3) Adding Chromosome 9 of 24, 2.753 mins elapsed.

2024-09-28 21:17:15.347695 : (scATAC_BMMC_R1 : 1 of 3) BarcodeFrequencyTable, Class = data.table

2024-09-28 21:17:15.347695 : (scATAC_BMMC_R1 : 1 of 3) BarcodeFrequencyTable, Class = data.frame
(scATAC_BMMC_R1 : 1 of 3) BarcodeFrequencyTable: nRows = 5000, nCols = 2
            values.V1    V1
               <char> <int>
1: TTATGTCAGTGATTAG-1 26189
2: GGAACCCAGGCACCTC-1 25975
3: CTGAATGCAAGGACCA-1 24565
4: ACTAACGGTGTCCTTC-1 22245
5: GCGGTGTTCTCCACTG-1 22124
6: GAAGTGGCATTAGCAC-1 21218

2024-09-28 21:17:15.376105 : (scATAC_BMMC_R1 : 1 of 3) BarcodesMinMaxFrags, Class = data.frame
(scATAC_BMMC_R1 : 1 of 3) BarcodesMinMaxFrags: nRows = 5000, nCols = 1
                  bc
1 TTATGTCAGTGATTAG-1
2 GGAACCCAGGCACCTC-1
3 CTGAATGCAAGGACCA-1
4 ACTAACGGTGTCCTTC-1
5 GCGGTGTTCTCCACTG-1
6 GAAGTGGCATTAGCAC-1

2024-09-28 21:17:15.991276 : (scATAC_BMMC_R1 : 1 of 3) Unique Chromosomes, Class = data.frame
(scATAC_BMMC_R1 : 1 of 3) Unique Chromosomes: nRows = 24, nCols = 1
   chr
1 chr1
2 chr2
3 chr3
4 chr4
5 chr5
6 chr6

2024-09-28 21:17:16.175294 : (scATAC_BMMC_R1 : 1 of 3) Adding Chromosome 1 of 24, 2.769 mins elapsed.
2024-09-28 21:17:16.312622 : (scATAC_BMMC_R1 : 1 of 3) Adding Chromosome 2 of 24, 2.771 mins elapsed.
2024-09-28 21:17:16.443313 : (scATAC_BMMC_R1 : 1 of 3) Adding Chromosome 3 of 24, 2.774 mins elapsed.
2024-09-28 21:17:20.89147 : (scATAC_CD34_BMMC_R1 : 2 of 3) Adding Chromosome 7 of 24, 2.848 mins elapsed.
2024-09-28 21:17:21.163958 : (scATAC_CD34_BMMC_R1 : 2 of 3) Adding Chromosome 8 of 24, 2.852 mins elapsed.
2024-09-28 21:17:21.495722 : (scATAC_CD34_BMMC_R1 : 2 of 3) Adding Chromosome 9 of 24, 2.858 mins elapsed.

2024-09-28 21:17:22.0259 : (scATAC_BMMC_R1 : 1 of 3) .tmpToArrow Fragments-Chr-(1 of 24)-chr1, Class = IRanges

(scATAC_BMMC_R1 : 1 of 3) .tmpToArrow Fragments-Chr-(1 of 24)-chr1: length = 1544829
IRanges object with 6 ranges and 1 metadata column:
          start       end     width |                 RG
      <integer> <integer> <integer> |              <Rle>
  [1]    713735    713974       240 | TTATGTCAGTGATTAG-1
  [2]    737018    737244       227 | TTATGTCAGTGATTAG-1
  [3]    883042    883206       165 | TTATGTCAGTGATTAG-1
  [4]    886245    886566       322 | TTATGTCAGTGATTAG-1
  [5]    926613    926678        66 | TTATGTCAGTGATTAG-1
  [6]    954774    954927       154 | TTATGTCAGTGATTAG-1

2024-09-28 21:17:22.058193 : (scATAC_BMMC_R1 : 1 of 3) .tmpToArrow Barcodes-Chr-(1 of 24)-chr1, Class = data.frame
(scATAC_BMMC_R1 : 1 of 3) .tmpToArrow Barcodes-Chr-(1 of 24)-chr1: nRows = 5000, nCols = 1
                  bc
1 TTATGTCAGTGATTAG-1
2 GGAACCCAGGCACCTC-1
3 CTGAATGCAAGGACCA-1
4 ACTAACGGTGTCCTTC-1
5 GCGGTGTTCTCCACTG-1
6 GAAGTGGCATTAGCAC-1

2024-09-28 21:17:22.07996 : (scATAC_PBMC_R1 : 3 of 3) Adding Chromosome 10 of 24, 2.868 mins elapsed.
2024-09-28 21:17:22.209878 : (scATAC_PBMC_R1 : 3 of 3) Adding Chromosome 11 of 24, 2.87 mins elapsed.
2024-09-28 21:17:22.414382 : (scATAC_PBMC_R1 : 3 of 3) Adding Chromosome 12 of 24, 2.873 mins elapsed.
2024-09-28 21:17:24.486198 : (scATAC_BMMC_R1 : 1 of 3) Adding Chromosome 4 of 24, 2.908 mins elapsed.
2024-09-28 21:17:24.634159 : (scATAC_BMMC_R1 : 1 of 3) Adding Chromosome 5 of 24, 2.91 mins elapsed.
2024-09-28 21:17:24.800504 : (scATAC_BMMC_R1 : 1 of 3) Adding Chromosome 6 of 24, 2.913 mins elapsed.
2024-09-28 21:17:28.266234 : (scATAC_CD34_BMMC_R1 : 2 of 3) Adding Chromosome 10 of 24, 2.971 mins elapsed.
2024-09-28 21:17:28.452292 : (scATAC_CD34_BMMC_R1 : 2 of 3) Adding Chromosome 11 of 24, 2.974 mins elapsed.
2024-09-28 21:17:28.901381 : (scATAC_CD34_BMMC_R1 : 2 of 3) Adding Chromosome 12 of 24, 2.981 mins elapsed.
2024-09-28 21:17:29.30861 : (scATAC_PBMC_R1 : 3 of 3) Adding Chromosome 13 of 24, 2.988 mins elapsed.
2024-09-28 21:17:29.451861 : (scATAC_PBMC_R1 : 3 of 3) Adding Chromosome 14 of 24, 2.99 mins elapsed.
2024-09-28 21:17:29.746456 : (scATAC_PBMC_R1 : 3 of 3) Adding Chromosome 15 of 24, 2.995 mins elapsed.
2024-09-28 21:17:31.951734 : (scATAC_BMMC_R1 : 1 of 3) Adding Chromosome 7 of 24, 3.032 mins elapsed.
2024-09-28 21:17:32.194492 : (scATAC_BMMC_R1 : 1 of 3) Adding Chromosome 8 of 24, 3.036 mins elapsed.
2024-09-28 21:17:32.34451 : (scATAC_BMMC_R1 : 1 of 3) Adding Chromosome 9 of 24, 3.039 mins elapsed.
2024-09-28 21:17:35.63678 : (scATAC_CD34_BMMC_R1 : 2 of 3) Adding Chromosome 13 of 24, 3.093 mins elapsed.
2024-09-28 21:17:36.013047 : (scATAC_CD34_BMMC_R1 : 2 of 3) Adding Chromosome 14 of 24, 3.1 mins elapsed.
2024-09-28 21:17:36.335868 : (scATAC_PBMC_R1 : 3 of 3) Adding Chromosome 16 of 24, 3.105 mins elapsed.
2024-09-28 21:17:36.515877 : (scATAC_CD34_BMMC_R1 : 2 of 3) Adding Chromosome 15 of 24, 3.108 mins elapsed.
2024-09-28 21:17:36.717203 : (scATAC_PBMC_R1 : 3 of 3) Adding Chromosome 17 of 24, 3.112 mins elapsed.
2024-09-28 21:17:36.888603 : (scATAC_PBMC_R1 : 3 of 3) Adding Chromosome 18 of 24, 3.114 mins elapsed.
2024-09-28 21:17:39.697403 : (scATAC_BMMC_R1 : 1 of 3) Adding Chromosome 10 of 24, 3.161 mins elapsed.
2024-09-28 21:17:39.839545 : (scATAC_BMMC_R1 : 1 of 3) Adding Chromosome 11 of 24, 3.164 mins elapsed.
2024-09-28 21:17:39.983172 : (scATAC_BMMC_R1 : 1 of 3) Adding Chromosome 12 of 24, 3.166 mins elapsed.
2024-09-28 21:17:42.697325 : (scATAC_CD34_BMMC_R1 : 2 of 3) Adding Chromosome 16 of 24, 3.211 mins elapsed.
2024-09-28 21:17:43.272912 : (scATAC_CD34_BMMC_R1 : 2 of 3) Adding Chromosome 17 of 24, 3.221 mins elapsed.
2024-09-28 21:17:43.872718 : (scATAC_PBMC_R1 : 3 of 3) Adding Chromosome 19 of 24, 3.231 mins elapsed.
2024-09-28 21:17:44.033329 : (scATAC_CD34_BMMC_R1 : 2 of 3) Adding Chromosome 18 of 24, 3.233 mins elapsed.
2024-09-28 21:17:44.055435 : (scATAC_PBMC_R1 : 3 of 3) Adding Chromosome 20 of 24, 3.234 mins elapsed.
2024-09-28 21:17:44.490638 : (scATAC_PBMC_R1 : 3 of 3) Adding Chromosome 21 of 24, 3.241 mins elapsed.
2024-09-28 21:17:47.69064 : (scATAC_BMMC_R1 : 1 of 3) Adding Chromosome 13 of 24, 3.294 mins elapsed.
2024-09-28 21:17:47.868848 : (scATAC_BMMC_R1 : 1 of 3) Adding Chromosome 14 of 24, 3.297 mins elapsed.
2024-09-28 21:17:48.015423 : (scATAC_BMMC_R1 : 1 of 3) Adding Chromosome 15 of 24, 3.3 mins elapsed.
2024-09-28 21:17:50.544477 : (scATAC_CD34_BMMC_R1 : 2 of 3) Adding Chromosome 19 of 24, 3.342 mins elapsed.
2024-09-28 21:17:51.232776 : (scATAC_CD34_BMMC_R1 : 2 of 3) Adding Chromosome 20 of 24, 3.353 mins elapsed.
2024-09-28 21:17:51.463839 : (scATAC_CD34_BMMC_R1 : 2 of 3) Adding Chromosome 21 of 24, 3.357 mins elapsed.
2024-09-28 21:17:51.51376 : (scATAC_PBMC_R1 : 3 of 3) Adding Chromosome 22 of 24, 3.358 mins elapsed.
2024-09-28 21:17:51.664369 : (scATAC_PBMC_R1 : 3 of 3) Adding Chromosome 23 of 24, 3.361 mins elapsed.
2024-09-28 21:17:51.792788 : (scATAC_PBMC_R1 : 3 of 3) Adding Chromosome 24 of 24, 3.363 mins elapsed.
2024-09-28 21:17:55.27052 : (scATAC_BMMC_R1 : 1 of 3) Adding Chromosome 16 of 24, 3.421 mins elapsed.
2024-09-28 21:17:55.406774 : (scATAC_BMMC_R1 : 1 of 3) Adding Chromosome 17 of 24, 3.423 mins elapsed.
2024-09-28 21:17:55.554797 : (scATAC_BMMC_R1 : 1 of 3) Adding Chromosome 18 of 24, 3.425 mins elapsed.
2024-09-28 21:17:58.039741 : (scATAC_CD34_BMMC_R1 : 2 of 3) Adding Chromosome 22 of 24, 3.467 mins elapsed.
2024-09-28 21:17:58.143648 : (scATAC_CD34_BMMC_R1 : 2 of 3) Adding Chromosome 23 of 24, 3.469 mins elapsed.
2024-09-28 21:17:58.233733 : (scATAC_PBMC_R1 : 3 of 3) Parallel Hdf5 Linkage Arrow File, 3.47 mins elapsed.
2024-09-28 21:17:58.367778 : (scATAC_CD34_BMMC_R1 : 2 of 3) Adding Chromosome 24 of 24, 3.472 mins elapsed.
2024-09-28 21:17:58.754346 : (scATAC_PBMC_R1 : 3 of 3) Successful creation of Arrow File, 3.479 mins elapsed.
2024-09-28 21:18:00.055331 : (scATAC_PBMC_R1 : 3 of 3) Adding Fragment Summary, 3.5 mins elapsed.
2024-09-28 21:18:01.7797 : (scATAC_BMMC_R1 : 1 of 3) Adding Chromosome 19 of 24, 3.529 mins elapsed.
2024-09-28 21:18:01.915427 : (scATAC_BMMC_R1 : 1 of 3) Adding Chromosome 20 of 24, 3.531 mins elapsed.
2024-09-28 21:18:02.231693 : (scATAC_BMMC_R1 : 1 of 3) Adding Chromosome 21 of 24, 3.537 mins elapsed.
2024-09-28 21:18:03.785684 : (scATAC_CD34_BMMC_R1 : 2 of 3) Parallel Hdf5 Linkage Arrow File, 3.563 mins elapsed.
2024-09-28 21:18:04.179726 : (scATAC_CD34_BMMC_R1 : 2 of 3) Successful creation of Arrow File, 3.569 mins elapsed.
2024-09-28 21:18:05.311252 : (scATAC_CD34_BMMC_R1 : 2 of 3) Adding Fragment Summary, 3.588 mins elapsed.
2024-09-28 21:18:05.331532 : (scATAC_PBMC_R1 : 3 of 3) Plotting Fragment Size Distribution, 3.588 mins elapsed.
2024-09-28 21:18:05.575597 : Continuing through after error ggplot for Fragment Size Distribution, 3.592 mins elapsed.
2024-09-28 21:18:06.103077 : (scATAC_PBMC_R1 : 3 of 3) Computing TSS Enrichment Scores, 3.601 mins elapsed.
2024-09-28 21:18:07.257528 : (scATAC_BMMC_R1 : 1 of 3) Adding Chromosome 22 of 24, 3.621 mins elapsed.
2024-09-28 21:18:07.392152 : (scATAC_BMMC_R1 : 1 of 3) Adding Chromosome 23 of 24, 3.623 mins elapsed.
2024-09-28 21:18:07.743718 : (scATAC_BMMC_R1 : 1 of 3) Adding Chromosome 24 of 24, 3.629 mins elapsed.
2024-09-28 21:18:11.066951 : (scATAC_CD34_BMMC_R1 : 2 of 3) Plotting Fragment Size Distribution, 3.684 mins elapsed.
2024-09-28 21:18:11.413534 : Continuing through after error ggplot for Fragment Size Distribution, 3.69 mins elapsed.
2024-09-28 21:18:12.011085 : (scATAC_CD34_BMMC_R1 : 2 of 3) Computing TSS Enrichment Scores, 3.7 mins elapsed.
2024-09-28 21:18:13.488859 : (scATAC_BMMC_R1 : 1 of 3) Parallel Hdf5 Linkage Arrow File, 3.724 mins elapsed.
2024-09-28 21:18:14.020149 : (scATAC_BMMC_R1 : 1 of 3) Successful creation of Arrow File, 3.733 mins elapsed.
2024-09-28 21:18:15.6287 : (scATAC_BMMC_R1 : 1 of 3) Adding Fragment Summary, 3.76 mins elapsed.
2024-09-28 21:18:23.180269 : (scATAC_BMMC_R1 : 1 of 3) Plotting Fragment Size Distribution, 3.886 mins elapsed.
2024-09-28 21:18:23.431591 : Continuing through after error ggplot for Fragment Size Distribution, 3.89 mins elapsed.
2024-09-28 21:18:24.163934 : (scATAC_BMMC_R1 : 1 of 3) Computing TSS Enrichment Scores, 3.902 mins elapsed.
2024-09-28 21:18:50.022397 : (scATAC_PBMC_R1 : 3 of 3) Computed TSS Scores!, 0.732 mins elapsed.
2024-09-28 21:18:50.049403 : (scATAC_PBMC_R1 : 3 of 3) CellStats : Number of Cells Pass Filter = 2453 , 4.334 mins elapsed.
2024-09-28 21:18:50.061877 : (scATAC_PBMC_R1 : 3 of 3) CellStats : Median Frags = 3348 , 4.334 mins elapsed.
2024-09-28 21:18:50.072231 : (scATAC_PBMC_R1 : 3 of 3) CellStats : Median TSS Enrichment = 19.972 , 4.334 mins elapsed.
2024-09-28 21:18:50.07311 : (scATAC_PBMC_R1 : 3 of 3) Plotting TSS Enrichment Scores, 4.334 mins elapsed.
2024-09-28 21:18:50.853744 : Continuing through after error ggplot for TSS by Frags, 4.347 mins elapsed.
2024-09-28 21:18:50.857539 : (scATAC_PBMC_R1 : 3 of 3) Adding Metadata to Fragments, 4.347 mins elapsed.
2024-09-28 21:18:51.732987 : (scATAC_PBMC_R1 : 3 of 3) Adding Additional Feature Counts!, 4.362 mins elapsed.
2024-09-28 21:18:56.798326 : (scATAC_CD34_BMMC_R1 : 2 of 3) Computed TSS Scores!, 0.746 mins elapsed.
2024-09-28 21:18:56.821473 : (scATAC_CD34_BMMC_R1 : 2 of 3) CellStats : Number of Cells Pass Filter = 3275 , 4.446 mins elapsed.
2024-09-28 21:18:56.831433 : (scATAC_CD34_BMMC_R1 : 2 of 3) CellStats : Median Frags = 3178 , 4.447 mins elapsed.
2024-09-28 21:18:56.843154 : (scATAC_CD34_BMMC_R1 : 2 of 3) CellStats : Median TSS Enrichment = 16.708 , 4.447 mins elapsed.
2024-09-28 21:18:56.845019 : (scATAC_CD34_BMMC_R1 : 2 of 3) Plotting TSS Enrichment Scores, 4.447 mins elapsed.
2024-09-28 21:18:57.860883 : Continuing through after error ggplot for TSS by Frags, 4.464 mins elapsed.
2024-09-28 21:18:57.865508 : (scATAC_CD34_BMMC_R1 : 2 of 3) Adding Metadata to Fragments, 4.464 mins elapsed.
2024-09-28 21:18:58.70674 : (scATAC_CD34_BMMC_R1 : 2 of 3) Adding Additional Feature Counts!, 4.478 mins elapsed.
2024-09-28 21:19:11.718685 : (scATAC_BMMC_R1 : 1 of 3) Computed TSS Scores!, 0.793 mins elapsed.
2024-09-28 21:19:11.741985 : (scATAC_BMMC_R1 : 1 of 3) CellStats : Number of Cells Pass Filter = 4932 , 4.695 mins elapsed.
2024-09-28 21:19:11.754 : (scATAC_BMMC_R1 : 1 of 3) CellStats : Median Frags = 2771 , 4.695 mins elapsed.
2024-09-28 21:19:11.76518 : (scATAC_BMMC_R1 : 1 of 3) CellStats : Median TSS Enrichment = 15.2575 , 4.695 mins elapsed.
2024-09-28 21:19:11.76652 : (scATAC_BMMC_R1 : 1 of 3) Plotting TSS Enrichment Scores, 4.696 mins elapsed.
2024-09-28 21:19:12.748336 : Continuing through after error ggplot for TSS by Frags, 4.712 mins elapsed.
2024-09-28 21:19:12.755 : (scATAC_BMMC_R1 : 1 of 3) Adding Metadata to Fragments, 4.712 mins elapsed.
2024-09-28 21:19:13.76161 : (scATAC_BMMC_R1 : 1 of 3) Adding Additional Feature Counts!, 4.729 mins elapsed.
2024-09-28 21:19:35.635754 : (scATAC_PBMC_R1 : 3 of 3) Finished Adding Additional Feature Counts!, 5.093 mins elapsed.

2024-09-28 21:19:35.637664 : (scATAC_PBMC_R1 : 3 of 3) Metadata, Class = DFrame
DataFrame with 2495 rows and 12 columns
                  cellNames    nFrags nMonoFrags  nDiFrags nMultiFrags
                <character> <numeric>  <numeric> <numeric>   <numeric>
1    scATAC_PBMC_R1#AACTG..     97233      14445     54566       28222
2    scATAC_PBMC_R1#CCGTG..     91194      19918     47936       23340
3    scATAC_PBMC_R1#TGCAC..     83427      14361     46671       22395
4    scATAC_PBMC_R1#GACTA..     79122      28315     34125       16682
5    scATAC_PBMC_R1#ATAGG..     76513      11901     45508       19104
...                     ...       ...        ...       ...         ...
2491 scATAC_PBMC_R1#GCTGC..      1038        485       368         185
2492 scATAC_PBMC_R1#GCAGC..      1037        481       350         206
2493 scATAC_PBMC_R1#GCAGA..      1033        525       369         139
2494 scATAC_PBMC_R1#TTCGT..      1033        603       274         156
2495 scATAC_PBMC_R1#CGCTA..      1002        440       371         191
     TSSEnrichment ReadsInTSS      Keep ReadsInPromoter PromoterRatio
         <numeric>  <numeric> <numeric>       <numeric>     <numeric>
1            2.066        651         0            3879     0.0199469
2            6.652       2926         1           11746     0.0644012
3            4.699       1571         1            7126     0.0427080
4            1.457        309         0            2395     0.0151349
5            3.473        705         0            3460     0.0226105
...            ...        ...       ...             ...           ...
2491        24.257        245         1             840      0.404624
2492        22.537        239         1             768      0.370299
2493        19.888        231         1             801      0.387706
2494        30.000        303         1             947      0.458374
2495        21.287        215         1             728      0.363273
     ReadsInBlacklist BlacklistRatio
            <numeric>      <numeric>
1                1690     0.00869047
2                1861     0.01020352
3                1349     0.00808491
4                1545     0.00976340
5                1540     0.01006365
...               ...            ...
2491               24     0.01156069
2492               30     0.01446480
2493               18     0.00871249
2494               23     0.01113262
2495               30     0.01497006

2024-09-28 21:19:35.743474 : (scATAC_PBMC_R1 : 3 of 3) Removing Fragments from Filtered Cells, 5.095 mins elapsed.
2024-09-28 21:19:35.761626 : (scATAC_PBMC_R1 : 3 of 3) Creating Filtered Arrow File, 5.095 mins elapsed.

2024-09-28 21:19:36.517842 : (scATAC_PBMC_R1 : 3 of 3) .filterCellsFromArrow Fragments-Chr-(1 of 24)-chr1, Class = GRanges
GRanges object with 1043953 ranges and 1 metadata column:
            seqnames              ranges strand |                     RG
               <Rle>           <IRanges>  <Rle> |                  <Rle>
        [1]     chr1         17171-17525      * | scATAC_PBMC_R1#CCGTG..
        [2]     chr1       138313-138532      * | scATAC_PBMC_R1#CCGTG..
        [3]     chr1       531909-532087      * | scATAC_PBMC_R1#CCGTG..
        [4]     chr1       538911-538944      * | scATAC_PBMC_R1#CCGTG..
        [5]     chr1       568247-568377      * | scATAC_PBMC_R1#CCGTG..
        ...      ...                 ...    ... .                    ...
  [1043949]     chr1 236010833-236010905      * | scATAC_PBMC_R1#CGCTA..
  [1043950]     chr1 236706997-236707092      * | scATAC_PBMC_R1#CGCTA..
  [1043951]     chr1 244001648-244001730      * | scATAC_PBMC_R1#CGCTA..
  [1043952]     chr1 246670637-246670682      * | scATAC_PBMC_R1#CGCTA..
  [1043953]     chr1 247241899-247242201      * | scATAC_PBMC_R1#CGCTA..
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths

2024-09-28 21:19:36.541641 : (scATAC_PBMC_R1 : 3 of 3) .filterCellsFromArrow Barcodes-Chr-(1 of 24)-chr1, Class = data.frame
(scATAC_PBMC_R1 : 3 of 3) .filterCellsFromArrow Barcodes-Chr-(1 of 24)-chr1: nRows = 2453, nCols = 1
                                 bc
1 scATAC_PBMC_R1#CCGTGAGAGACCATAA-1
2 scATAC_PBMC_R1#TGCACCTTCGGCTATA-1
3 scATAC_PBMC_R1#TATCTGTAGACAGCTG-1
4 scATAC_PBMC_R1#ATGGATCCAGGCAAGT-1
5 scATAC_PBMC_R1#CACATGAAGGCCTAAG-1
6 scATAC_PBMC_R1#CAAAGCTGTCTGATTG-1

2024-09-28 21:19:43.103574 : (scATAC_CD34_BMMC_R1 : 2 of 3) Finished Adding Additional Feature Counts!, 5.218 mins elapsed.

2024-09-28 21:19:43.105094 : (scATAC_CD34_BMMC_R1 : 2 of 3) Metadata, Class = DFrame
DataFrame with 3392 rows and 12 columns
                  cellNames    nFrags nMonoFrags  nDiFrags nMultiFrags
                <character> <numeric>  <numeric> <numeric>   <numeric>
1    scATAC_CD34_BMMC_R1#..     50131      37609     10619        1903
2    scATAC_CD34_BMMC_R1#..     41408      34022      6804         582
3    scATAC_CD34_BMMC_R1#..     34964      17458     16198        1308
4    scATAC_CD34_BMMC_R1#..     29044      14815     13000        1229
5    scATAC_CD34_BMMC_R1#..     28840      23469      4862         509
...                     ...       ...        ...       ...         ...
3388 scATAC_CD34_BMMC_R1#..      1017        663       301          53
3389 scATAC_CD34_BMMC_R1#..      1016        663       293          60
3390 scATAC_CD34_BMMC_R1#..      1012        827       171          14
3391 scATAC_CD34_BMMC_R1#..      1006        844       153           9
3392 scATAC_CD34_BMMC_R1#..      1003        611       347          45
     TSSEnrichment ReadsInTSS      Keep ReadsInPromoter PromoterRatio
         <numeric>  <numeric> <numeric>       <numeric>     <numeric>
1            1.953        431         0            2912     0.0290439
2            2.662        484         0            2838     0.0342687
3            7.952       1767         1            7251     0.1036924
4            9.072       2199         1            8436     0.1452279
5           10.438       2198         1            8375     0.1451976
...            ...        ...       ...             ...           ...
3388        14.455        146         1             564     0.2772861
3389        15.743        159         1             568     0.2795276
3390         0.198          2         0              45     0.0222332
3391         0.693          7         0              44     0.0218688
3392         3.740         51         0             246     0.1226321
     ReadsInBlacklist BlacklistRatio
            <numeric>      <numeric>
1                1255     0.01251720
2                 919     0.01109689
3                 592     0.00846585
4                 502     0.00864206
5                 574     0.00995146
...               ...            ...
3388               18     0.00884956
3389               22     0.01082677
3390               22     0.01086957
3391               16     0.00795229
3392               20     0.00997009

2024-09-28 21:19:43.212678 : (scATAC_CD34_BMMC_R1 : 2 of 3) Removing Fragments from Filtered Cells, 5.22 mins elapsed.
2024-09-28 21:19:43.224267 : (scATAC_CD34_BMMC_R1 : 2 of 3) Creating Filtered Arrow File, 5.22 mins elapsed.

2024-09-28 21:19:43.802734 : (scATAC_CD34_BMMC_R1 : 2 of 3) .filterCellsFromArrow Fragments-Chr-(1 of 24)-chr1, Class = GRanges
GRanges object with 1198781 ranges and 1 metadata column:
            seqnames              ranges strand |                     RG
               <Rle>           <IRanges>  <Rle> |                  <Rle>
        [1]     chr1       792180-792221      * | scATAC_CD34_BMMC_R1#..
        [2]     chr1       805326-805364      * | scATAC_CD34_BMMC_R1#..
        [3]     chr1       805527-805595      * | scATAC_CD34_BMMC_R1#..
        [4]     chr1       878828-879125      * | scATAC_CD34_BMMC_R1#..
        [5]     chr1       904299-904343      * | scATAC_CD34_BMMC_R1#..
        ...      ...                 ...    ... .                    ...
  [1198777]     chr1 233443071-233443231      * | scATAC_CD34_BMMC_R1#..
  [1198778]     chr1 235434186-235434263      * | scATAC_CD34_BMMC_R1#..
  [1198779]     chr1 235668171-235668404      * | scATAC_CD34_BMMC_R1#..
  [1198780]     chr1 248786000-248786224      * | scATAC_CD34_BMMC_R1#..
  [1198781]     chr1 249200409-249200661      * | scATAC_CD34_BMMC_R1#..
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths

2024-09-28 21:19:43.822424 : (scATAC_CD34_BMMC_R1 : 2 of 3) .filterCellsFromArrow Barcodes-Chr-(1 of 24)-chr1, Class = data.frame
(scATAC_CD34_BMMC_R1 : 2 of 3) .filterCellsFromArrow Barcodes-Chr-(1 of 24)-chr1: nRows = 3275, nCols = 1
                                      bc
1 scATAC_CD34_BMMC_R1#GTTCAAGAGGTGTTGG-1
2 scATAC_CD34_BMMC_R1#GCGTTGGGTTACGGAG-1
3 scATAC_CD34_BMMC_R1#CAACGGCGTACCCACG-1
4 scATAC_CD34_BMMC_R1#ATTCGTTTCTCGTGAA-1
5 scATAC_CD34_BMMC_R1#CAAGGCCAGGCTTTAC-1
6 scATAC_CD34_BMMC_R1#TAATCGGGTTCGGGAA-1

2024-09-28 21:19:55.657678 : (scATAC_BMMC_R1 : 1 of 3) Finished Adding Additional Feature Counts!, 5.427 mins elapsed.

2024-09-28 21:19:55.658871 : (scATAC_BMMC_R1 : 1 of 3) Metadata, Class = DFrame
DataFrame with 5000 rows and 12 columns
                  cellNames    nFrags nMonoFrags  nDiFrags nMultiFrags
                <character> <numeric>  <numeric> <numeric>   <numeric>
1    scATAC_BMMC_R1#TTATG..     26189       6196     16192        3801
2    scATAC_BMMC_R1#GGAAC..     25975      15182      6822        3971
3    scATAC_BMMC_R1#CTGAA..     24565       6761     12819        4985
4    scATAC_BMMC_R1#ACTAA..     22245       9873      7990        4382
5    scATAC_BMMC_R1#GCGGT..     22124       3499     14608        4017
...                     ...       ...        ...       ...         ...
4996 scATAC_BMMC_R1#GTGAT..      1005        536       342         127
4997 scATAC_BMMC_R1#GCGGT..      1003         52       528         423
4998 scATAC_BMMC_R1#AGCTG..      1002        410       442         150
4999 scATAC_BMMC_R1#GTTGG..      1001        346       466         189
5000 scATAC_BMMC_R1#TGAGT..      1001        449       411         141
     TSSEnrichment ReadsInTSS      Keep ReadsInPromoter PromoterRatio
         <numeric>  <numeric> <numeric>       <numeric>     <numeric>
1            7.204       1146         1            4306    0.08221009
2            1.823         93         0             625    0.01203080
3            3.359        402         0            2007    0.04085080
4            1.972        233         0            1661    0.03733423
5            1.743         66         0             441    0.00996655
...            ...        ...       ...             ...           ...
4996         0.594          6         0              45     0.0223881
4997         6.931         70         1             310     0.1545364
4998        15.545        157         1             555     0.2769461
4999        10.297        104         1             446     0.2227772
5000        19.010        192         1             558     0.2787213
     ReadsInBlacklist BlacklistRatio
            <numeric>      <numeric>
1                 611      0.0116652
2                 641      0.0123388
3                 828      0.0168532
4                 527      0.0118454
5                 827      0.0186901
...               ...            ...
4996               90     0.04477612
4997               32     0.01595214
4998               22     0.01097804
4999               22     0.01098901
5000               20     0.00999001

2024-09-28 21:19:55.756449 : (scATAC_BMMC_R1 : 1 of 3) Removing Fragments from Filtered Cells, 5.429 mins elapsed.
2024-09-28 21:19:55.767202 : (scATAC_BMMC_R1 : 1 of 3) Creating Filtered Arrow File, 5.429 mins elapsed.

2024-09-28 21:19:56.337682 : (scATAC_BMMC_R1 : 1 of 3) .filterCellsFromArrow Fragments-Chr-(1 of 24)-chr1, Class = GRanges
GRanges object with 1509044 ranges and 1 metadata column:
            seqnames              ranges strand |                     RG
               <Rle>           <IRanges>  <Rle> |                  <Rle>
        [1]     chr1       713735-713974      * | scATAC_BMMC_R1#TTATG..
        [2]     chr1       737018-737244      * | scATAC_BMMC_R1#TTATG..
        [3]     chr1       883042-883206      * | scATAC_BMMC_R1#TTATG..
        [4]     chr1       886245-886566      * | scATAC_BMMC_R1#TTATG..
        [5]     chr1       926613-926678      * | scATAC_BMMC_R1#TTATG..
        ...      ...                 ...    ... .                    ...
  [1509040]     chr1 235147637-235147833      * | scATAC_BMMC_R1#TGAGT..
  [1509041]     chr1 236958562-236958979      * | scATAC_BMMC_R1#TGAGT..
  [1509042]     chr1 244211450-244211598      * | scATAC_BMMC_R1#TGAGT..
  [1509043]     chr1 245026366-245026390      * | scATAC_BMMC_R1#TGAGT..
  [1509044]     chr1 247267687-247267722      * | scATAC_BMMC_R1#TGAGT..
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths

2024-09-28 21:19:56.353689 : (scATAC_BMMC_R1 : 1 of 3) .filterCellsFromArrow Barcodes-Chr-(1 of 24)-chr1, Class = data.frame
(scATAC_BMMC_R1 : 1 of 3) .filterCellsFromArrow Barcodes-Chr-(1 of 24)-chr1: nRows = 4932, nCols = 1
                                 bc
1 scATAC_BMMC_R1#TTATGTCAGTGATTAG-1
2 scATAC_BMMC_R1#AAGATAGTCACCGCGA-1
3 scATAC_BMMC_R1#GCATTGAAGATTCCGT-1
4 scATAC_BMMC_R1#TATGTTCAGGGTTCCC-1
5 scATAC_BMMC_R1#TCCATCGGTCCCGTGA-1
6 scATAC_BMMC_R1#AGTTACGAGAACGTCG-1

2024-09-28 21:19:59.685025 : (scATAC_PBMC_R1 : 3 of 3) Finished Constructing Filtered Arrow File!, 5.494 mins elapsed.
2024-09-28 21:19:59.844307 : (scATAC_PBMC_R1 : 3 of 3) Adding TileMatrix!, 5.497 mins elapsed.

2024-09-28 21:20:04.637828 : scATAC_PBMC_R1 .addTileMat FeatureDF, Class = DFrame
DataFrame with 6072620 rows and 3 columns
           seqnames       idx     start
        <character> <integer> <numeric>
1              chr1         1         0
2              chr1         2       500
3              chr1         3      1000
4              chr1         4      1500
5              chr1         5      2000
...             ...       ...       ...
6072616        chrX    310538 155268500
6072617        chrX    310539 155269000
6072618        chrX    310540 155269500
6072619        chrX    310541 155270000
6072620        chrX    310542 155270500

2024-09-28 21:20:05.35237 : (scATAC_CD34_BMMC_R1 : 2 of 3) Finished Constructing Filtered Arrow File!, 5.589 mins elapsed.
2024-09-28 21:20:05.524545 : (scATAC_CD34_BMMC_R1 : 2 of 3) Adding TileMatrix!, 5.592 mins elapsed.

2024-09-28 21:20:09.845663 : scATAC_CD34_BMMC_R1 .addTileMat FeatureDF, Class = DFrame
DataFrame with 6072620 rows and 3 columns
           seqnames       idx     start
        <character> <integer> <numeric>
1              chr1         1         0
2              chr1         2       500
3              chr1         3      1000
4              chr1         4      1500
5              chr1         5      2000
...             ...       ...       ...
6072616        chrX    310538 155268500
6072617        chrX    310539 155269000
6072618        chrX    310540 155269500
6072619        chrX    310541 155270000
6072620        chrX    310542 155270500

2024-09-28 21:20:13.156458 : Adding TileMatrix to scATAC_PBMC_R1 for Chr (1 of 23)!, 0.222 mins elapsed.

2024-09-28 21:20:13.295287 : NTiles_TileMatrix_1_chr1, Class = numeric

NTiles_TileMatrix_1_chr1: length = 1
  chr1 
498502 

2024-09-28 21:20:13.297268 : NCells_TileMatrix_1_chr1, Class = integer

NCells_TileMatrix_1_chr1: length = 1
[1] 2453

2024-09-28 21:20:13.299226 : MinTile_TileMatrix_1_chr1, Class = numeric

MinTile_TileMatrix_1_chr1: length = 1
[1] 21

2024-09-28 21:20:13.301901 : MaxTile_TileMatrix_1_chr1, Class = numeric

MaxTile_TileMatrix_1_chr1: length = 1
[1] 498481

2024-09-28 21:20:13.310146 : MinCell_TileMatrix_1_chr1, Class = integer

MinCell_TileMatrix_1_chr1: length = 1
[1] 1

2024-09-28 21:20:13.312487 : MaxCell_TileMatrix_1_chr1, Class = integer

MaxCell_TileMatrix_1_chr1: length = 1
[1] 2453

2024-09-28 21:20:15.222917 : (scATAC_BMMC_R1 : 1 of 3) Finished Constructing Filtered Arrow File!, 5.753 mins elapsed.
2024-09-28 21:20:15.371097 : (scATAC_BMMC_R1 : 1 of 3) Adding TileMatrix!, 5.756 mins elapsed.
2024-09-28 21:20:18.28887 : Adding TileMatrix to scATAC_PBMC_R1 for Chr (2 of 23)!, 0.307 mins elapsed.
2024-09-28 21:20:18.347407 : Adding TileMatrix to scATAC_CD34_BMMC_R1 for Chr (1 of 23)!, 0.213 mins elapsed.

2024-09-28 21:20:18.376048 : NTiles_TileMatrix_2_chr2, Class = numeric

NTiles_TileMatrix_2_chr2: length = 1
  chr2 
486399 

2024-09-28 21:20:18.378518 : NCells_TileMatrix_2_chr2, Class = integer

NCells_TileMatrix_2_chr2: length = 1
[1] 2453

2024-09-28 21:20:18.3806 : MinTile_TileMatrix_2_chr2, Class = numeric

MinTile_TileMatrix_2_chr2: length = 1
[1] 22

2024-09-28 21:20:18.383038 : MaxTile_TileMatrix_2_chr2, Class = numeric

MaxTile_TileMatrix_2_chr2: length = 1
[1] 486371

2024-09-28 21:20:18.389685 : MinCell_TileMatrix_2_chr2, Class = integer

MinCell_TileMatrix_2_chr2: length = 1
[1] 1

2024-09-28 21:20:18.391963 : MaxCell_TileMatrix_2_chr2, Class = integer

MaxCell_TileMatrix_2_chr2: length = 1
[1] 2453

2024-09-28 21:20:18.472686 : NTiles_TileMatrix_1_chr1, Class = numeric

NTiles_TileMatrix_1_chr1: length = 1
  chr1 
498502 

2024-09-28 21:20:18.475856 : NCells_TileMatrix_1_chr1, Class = integer

NCells_TileMatrix_1_chr1: length = 1
[1] 3275

2024-09-28 21:20:18.479003 : MinTile_TileMatrix_1_chr1, Class = numeric

MinTile_TileMatrix_1_chr1: length = 1
[1] 21

2024-09-28 21:20:18.483846 : MaxTile_TileMatrix_1_chr1, Class = numeric

MaxTile_TileMatrix_1_chr1: length = 1
[1] 498480

2024-09-28 21:20:18.497822 : MinCell_TileMatrix_1_chr1, Class = integer

MinCell_TileMatrix_1_chr1: length = 1
[1] 1

2024-09-28 21:20:18.500757 : MaxCell_TileMatrix_1_chr1, Class = integer

MaxCell_TileMatrix_1_chr1: length = 1
[1] 3275

2024-09-28 21:20:19.839167 : scATAC_BMMC_R1 .addTileMat FeatureDF, Class = DFrame
DataFrame with 6072620 rows and 3 columns
           seqnames       idx     start
        <character> <integer> <numeric>
1              chr1         1         0
2              chr1         2       500
3              chr1         3      1000
4              chr1         4      1500
5              chr1         5      2000
...             ...       ...       ...
6072616        chrX    310538 155268500
6072617        chrX    310539 155269000
6072618        chrX    310540 155269500
6072619        chrX    310541 155270000
6072620        chrX    310542 155270500

2024-09-28 21:20:22.512311 : Adding TileMatrix to scATAC_PBMC_R1 for Chr (3 of 23)!, 0.377 mins elapsed.

2024-09-28 21:20:22.598999 : NTiles_TileMatrix_3_chr3, Class = numeric

NTiles_TileMatrix_3_chr3: length = 1
  chr3 
396045 

2024-09-28 21:20:22.601574 : NCells_TileMatrix_3_chr3, Class = integer

NCells_TileMatrix_3_chr3: length = 1
[1] 2453

2024-09-28 21:20:22.603656 : MinTile_TileMatrix_3_chr3, Class = numeric

MinTile_TileMatrix_3_chr3: length = 1
[1] 123

2024-09-28 21:20:22.606186 : MaxTile_TileMatrix_3_chr3, Class = numeric

MaxTile_TileMatrix_3_chr3: length = 1
[1] 395800

2024-09-28 21:20:22.611815 : MinCell_TileMatrix_3_chr3, Class = integer

MinCell_TileMatrix_3_chr3: length = 1
[1] 1

2024-09-28 21:20:22.614148 : MaxCell_TileMatrix_3_chr3, Class = integer

MaxCell_TileMatrix_3_chr3: length = 1
[1] 2453

2024-09-28 21:20:23.791363 : Adding TileMatrix to scATAC_CD34_BMMC_R1 for Chr (2 of 23)!, 0.304 mins elapsed.

2024-09-28 21:20:23.899193 : NTiles_TileMatrix_2_chr2, Class = numeric

NTiles_TileMatrix_2_chr2: length = 1
  chr2 
486399 

2024-09-28 21:20:23.901202 : NCells_TileMatrix_2_chr2, Class = integer

NCells_TileMatrix_2_chr2: length = 1
[1] 3275

2024-09-28 21:20:23.903161 : MinTile_TileMatrix_2_chr2, Class = numeric

MinTile_TileMatrix_2_chr2: length = 1
[1] 22

2024-09-28 21:20:23.905762 : MaxTile_TileMatrix_2_chr2, Class = numeric

MaxTile_TileMatrix_2_chr2: length = 1
[1] 486309

2024-09-28 21:20:23.912602 : MinCell_TileMatrix_2_chr2, Class = integer

MinCell_TileMatrix_2_chr2: length = 1
[1] 1

2024-09-28 21:20:23.914596 : MaxCell_TileMatrix_2_chr2, Class = integer

MaxCell_TileMatrix_2_chr2: length = 1
[1] 3275

2024-09-28 21:20:25.539612 : Adding TileMatrix to scATAC_PBMC_R1 for Chr (4 of 23)!, 0.428 mins elapsed.

2024-09-28 21:20:25.603737 : NTiles_TileMatrix_4_chr4, Class = numeric

NTiles_TileMatrix_4_chr4: length = 1
  chr4 
382309 

2024-09-28 21:20:25.60599 : NCells_TileMatrix_4_chr4, Class = integer

NCells_TileMatrix_4_chr4: length = 1
[1] 2453

2024-09-28 21:20:25.608203 : MinTile_TileMatrix_4_chr4, Class = numeric

MinTile_TileMatrix_4_chr4: length = 1
[1] 23

2024-09-28 21:20:25.610695 : MaxTile_TileMatrix_4_chr4, Class = numeric

MaxTile_TileMatrix_4_chr4: length = 1
[1] 382089

2024-09-28 21:20:25.615117 : MinCell_TileMatrix_4_chr4, Class = integer

MinCell_TileMatrix_4_chr4: length = 1
[1] 1

2024-09-28 21:20:25.617233 : MaxCell_TileMatrix_4_chr4, Class = integer

MaxCell_TileMatrix_4_chr4: length = 1
[1] 2453

2024-09-28 21:20:27.772638 : Adding TileMatrix to scATAC_CD34_BMMC_R1 for Chr (3 of 23)!, 0.37 mins elapsed.

2024-09-28 21:20:27.867261 : NTiles_TileMatrix_3_chr3, Class = numeric

NTiles_TileMatrix_3_chr3: length = 1
  chr3 
396045 

2024-09-28 21:20:27.869561 : NCells_TileMatrix_3_chr3, Class = integer

NCells_TileMatrix_3_chr3: length = 1
[1] 3275

2024-09-28 21:20:27.871523 : MinTile_TileMatrix_3_chr3, Class = numeric

MinTile_TileMatrix_3_chr3: length = 1
[1] 130

2024-09-28 21:20:27.87397 : MaxTile_TileMatrix_3_chr3, Class = numeric

MaxTile_TileMatrix_3_chr3: length = 1
[1] 395814

2024-09-28 21:20:27.880032 : MinCell_TileMatrix_3_chr3, Class = integer

MinCell_TileMatrix_3_chr3: length = 1
[1] 1

2024-09-28 21:20:27.881893 : MaxCell_TileMatrix_3_chr3, Class = integer

MaxCell_TileMatrix_3_chr3: length = 1
[1] 3275

2024-09-28 21:20:28.385212 : Adding TileMatrix to scATAC_PBMC_R1 for Chr (5 of 23)!, 0.475 mins elapsed.
2024-09-28 21:20:28.397519 : Adding TileMatrix to scATAC_BMMC_R1 for Chr (1 of 23)!, 0.217 mins elapsed.

2024-09-28 21:20:28.465291 : NTiles_TileMatrix_5_chr5, Class = numeric

NTiles_TileMatrix_5_chr5: length = 1
  chr5 
361831 

2024-09-28 21:20:28.467966 : NCells_TileMatrix_5_chr5, Class = integer

NCells_TileMatrix_5_chr5: length = 1
[1] 2453

2024-09-28 21:20:28.470612 : MinTile_TileMatrix_5_chr5, Class = numeric

MinTile_TileMatrix_5_chr5: length = 1
[1] 24

2024-09-28 21:20:28.473946 : MaxTile_TileMatrix_5_chr5, Class = numeric

MaxTile_TileMatrix_5_chr5: length = 1
[1] 361463

2024-09-28 21:20:28.481248 : MinCell_TileMatrix_5_chr5, Class = integer

MinCell_TileMatrix_5_chr5: length = 1
[1] 1

2024-09-28 21:20:28.483204 : MaxCell_TileMatrix_5_chr5, Class = integer

MaxCell_TileMatrix_5_chr5: length = 1
[1] 2453

2024-09-28 21:20:28.550258 : NTiles_TileMatrix_1_chr1, Class = numeric

NTiles_TileMatrix_1_chr1: length = 1
  chr1 
498502 

2024-09-28 21:20:28.552437 : NCells_TileMatrix_1_chr1, Class = integer

NCells_TileMatrix_1_chr1: length = 1
[1] 4932

2024-09-28 21:20:28.55435 : MinTile_TileMatrix_1_chr1, Class = numeric

MinTile_TileMatrix_1_chr1: length = 1
[1] 21

2024-09-28 21:20:28.557624 : MaxTile_TileMatrix_1_chr1, Class = numeric

MaxTile_TileMatrix_1_chr1: length = 1
[1] 498482

2024-09-28 21:20:28.568516 : MinCell_TileMatrix_1_chr1, Class = integer

MinCell_TileMatrix_1_chr1: length = 1
[1] 1

2024-09-28 21:20:28.571169 : MaxCell_TileMatrix_1_chr1, Class = integer

MaxCell_TileMatrix_1_chr1: length = 1
[1] 4932

2024-09-28 21:20:31.384459 : Adding TileMatrix to scATAC_CD34_BMMC_R1 for Chr (4 of 23)!, 0.431 mins elapsed.

2024-09-28 21:20:31.466644 : NTiles_TileMatrix_4_chr4, Class = numeric

NTiles_TileMatrix_4_chr4: length = 1
  chr4 
382309 

2024-09-28 21:20:31.469112 : NCells_TileMatrix_4_chr4, Class = integer

NCells_TileMatrix_4_chr4: length = 1
[1] 3275

2024-09-28 21:20:31.471156 : MinTile_TileMatrix_4_chr4, Class = numeric

MinTile_TileMatrix_4_chr4: length = 1
[1] 21

2024-09-28 21:20:31.47363 : MaxTile_TileMatrix_4_chr4, Class = numeric

MaxTile_TileMatrix_4_chr4: length = 1
[1] 382089

2024-09-28 21:20:31.47849 : MinCell_TileMatrix_4_chr4, Class = integer

MinCell_TileMatrix_4_chr4: length = 1
[1] 1

2024-09-28 21:20:31.480385 : MaxCell_TileMatrix_4_chr4, Class = integer

MaxCell_TileMatrix_4_chr4: length = 1
[1] 3275

2024-09-28 21:20:31.694498 : Adding TileMatrix to scATAC_PBMC_R1 for Chr (6 of 23)!, 0.531 mins elapsed.

2024-09-28 21:20:31.782657 : NTiles_TileMatrix_6_chr6, Class = numeric

NTiles_TileMatrix_6_chr6: length = 1
  chr6 
342231 

2024-09-28 21:20:31.784908 : NCells_TileMatrix_6_chr6, Class = integer

NCells_TileMatrix_6_chr6: length = 1
[1] 2453

2024-09-28 21:20:31.787057 : MinTile_TileMatrix_6_chr6, Class = numeric

MinTile_TileMatrix_6_chr6: length = 1
[1] 406

2024-09-28 21:20:31.789881 : MaxTile_TileMatrix_6_chr6, Class = numeric

MaxTile_TileMatrix_6_chr6: length = 1
[1] 342045

2024-09-28 21:20:31.795684 : MinCell_TileMatrix_6_chr6, Class = integer

MinCell_TileMatrix_6_chr6: length = 1
[1] 1

2024-09-28 21:20:31.797936 : MaxCell_TileMatrix_6_chr6, Class = integer

MaxCell_TileMatrix_6_chr6: length = 1
[1] 2453

2024-09-28 21:20:34.69241 : Adding TileMatrix to scATAC_CD34_BMMC_R1 for Chr (5 of 23)!, 0.486 mins elapsed.

2024-09-28 21:20:34.794362 : NTiles_TileMatrix_5_chr5, Class = numeric

NTiles_TileMatrix_5_chr5: length = 1
  chr5 
361831 

2024-09-28 21:20:34.796982 : NCells_TileMatrix_5_chr5, Class = integer

NCells_TileMatrix_5_chr5: length = 1
[1] 3275

2024-09-28 21:20:34.79905 : MinTile_TileMatrix_5_chr5, Class = numeric

MinTile_TileMatrix_5_chr5: length = 1
[1] 24

2024-09-28 21:20:34.801456 : MaxTile_TileMatrix_5_chr5, Class = numeric

MaxTile_TileMatrix_5_chr5: length = 1
[1] 361568

2024-09-28 21:20:34.806885 : MinCell_TileMatrix_5_chr5, Class = integer

MinCell_TileMatrix_5_chr5: length = 1
[1] 1

2024-09-28 21:20:34.808945 : MaxCell_TileMatrix_5_chr5, Class = integer

MaxCell_TileMatrix_5_chr5: length = 1
[1] 3275

2024-09-28 21:20:34.979624 : Adding TileMatrix to scATAC_BMMC_R1 for Chr (2 of 23)!, 0.326 mins elapsed.
2024-09-28 21:20:35.045404 : Adding TileMatrix to scATAC_PBMC_R1 for Chr (7 of 23)!, 0.586 mins elapsed.

2024-09-28 21:20:35.122192 : NTiles_TileMatrix_7_chr7, Class = numeric

NTiles_TileMatrix_7_chr7: length = 1
  chr7 
318278 

2024-09-28 21:20:35.124072 : NCells_TileMatrix_7_chr7, Class = integer

NCells_TileMatrix_7_chr7: length = 1
[1] 2453

2024-09-28 21:20:35.125873 : MinTile_TileMatrix_7_chr7, Class = numeric

MinTile_TileMatrix_7_chr7: length = 1
[1] 21

2024-09-28 21:20:35.128973 : NTiles_TileMatrix_2_chr2, Class = numeric

NTiles_TileMatrix_2_chr2: length = 1
  chr2 
486399 

2024-09-28 21:20:35.130584 : NCells_TileMatrix_2_chr2, Class = integer

NCells_TileMatrix_2_chr2: length = 1

2024-09-28 21:20:35.128376 : MaxTile_TileMatrix_7_chr7, Class = numeric
[1] 4932

MaxTile_TileMatrix_7_chr7: length = 1
[1] 318258

2024-09-28 21:20:35.133482 : MinCell_TileMatrix_7_chr7, Class = integer

2024-09-28 21:20:35.132825 : MinTile_TileMatrix_2_chr2, Class = numeric

MinCell_TileMatrix_7_chr7: length = 1

MinTile_TileMatrix_2_chr2: length = 1
[1] 1
[1] 22

2024-09-28 21:20:35.135582 : MaxCell_TileMatrix_7_chr7, Class = integer

MaxCell_TileMatrix_7_chr7: length = 1
[1] 2453

2024-09-28 21:20:35.136033 : MaxTile_TileMatrix_2_chr2, Class = numeric

MaxTile_TileMatrix_2_chr2: length = 1
[1] 486370

2024-09-28 21:20:35.145579 : MinCell_TileMatrix_2_chr2, Class = integer

MinCell_TileMatrix_2_chr2: length = 1
[1] 1

2024-09-28 21:20:35.148197 : MaxCell_TileMatrix_2_chr2, Class = integer

MaxCell_TileMatrix_2_chr2: length = 1
[1] 4932

2024-09-28 21:20:37.926648 : Adding TileMatrix to scATAC_CD34_BMMC_R1 for Chr (6 of 23)!, 0.54 mins elapsed.

2024-09-28 21:20:38.012384 : NTiles_TileMatrix_6_chr6, Class = numeric

NTiles_TileMatrix_6_chr6: length = 1
  chr6 
342231 

2024-09-28 21:20:38.014711 : NCells_TileMatrix_6_chr6, Class = integer

NCells_TileMatrix_6_chr6: length = 1
[1] 3275

2024-09-28 21:20:38.016936 : MinTile_TileMatrix_6_chr6, Class = numeric

MinTile_TileMatrix_6_chr6: length = 1
[1] 406

2024-09-28 21:20:38.019835 : MaxTile_TileMatrix_6_chr6, Class = numeric

MaxTile_TileMatrix_6_chr6: length = 1
[1] 342093

2024-09-28 21:20:38.029192 : MinCell_TileMatrix_6_chr6, Class = integer

MinCell_TileMatrix_6_chr6: length = 1
[1] 1

2024-09-28 21:20:38.033394 : MaxCell_TileMatrix_6_chr6, Class = integer

MaxCell_TileMatrix_6_chr6: length = 1
[1] 3275

2024-09-28 21:20:38.063342 : Adding TileMatrix to scATAC_PBMC_R1 for Chr (8 of 23)!, 0.637 mins elapsed.

2024-09-28 21:20:38.123744 : NTiles_TileMatrix_8_chr8, Class = numeric

NTiles_TileMatrix_8_chr8: length = 1
  chr8 
292729 

2024-09-28 21:20:38.125911 : NCells_TileMatrix_8_chr8, Class = integer

NCells_TileMatrix_8_chr8: length = 1
[1] 2453

2024-09-28 21:20:38.127949 : MinTile_TileMatrix_8_chr8, Class = numeric

MinTile_TileMatrix_8_chr8: length = 1
[1] 227

2024-09-28 21:20:38.130281 : MaxTile_TileMatrix_8_chr8, Class = numeric

MaxTile_TileMatrix_8_chr8: length = 1
[1] 292603

2024-09-28 21:20:38.134718 : MinCell_TileMatrix_8_chr8, Class = integer

MinCell_TileMatrix_8_chr8: length = 1
[1] 1

2024-09-28 21:20:38.136831 : MaxCell_TileMatrix_8_chr8, Class = integer

MaxCell_TileMatrix_8_chr8: length = 1
[1] 2453

2024-09-28 21:20:40.587691 : Adding TileMatrix to scATAC_BMMC_R1 for Chr (3 of 23)!, 0.42 mins elapsed.

2024-09-28 21:20:40.718356 : NTiles_TileMatrix_3_chr3, Class = numeric

NTiles_TileMatrix_3_chr3: length = 1
  chr3 
396045 

2024-09-28 21:20:40.720304 : NCells_TileMatrix_3_chr3, Class = integer

NCells_TileMatrix_3_chr3: length = 1
[1] 4932

2024-09-28 21:20:40.722181 : MinTile_TileMatrix_3_chr3, Class = numeric

MinTile_TileMatrix_3_chr3: length = 1
[1] 121

2024-09-28 21:20:40.724917 : MaxTile_TileMatrix_3_chr3, Class = numeric

MaxTile_TileMatrix_3_chr3: length = 1
[1] 395802

2024-09-28 21:20:40.737304 : MinCell_TileMatrix_3_chr3, Class = integer

MinCell_TileMatrix_3_chr3: length = 1
[1] 1

2024-09-28 21:20:40.740008 : MaxCell_TileMatrix_3_chr3, Class = integer

MaxCell_TileMatrix_3_chr3: length = 1
[1] 4932

2024-09-28 21:20:40.812285 : Adding TileMatrix to scATAC_PBMC_R1 for Chr (9 of 23)!, 0.682 mins elapsed.

2024-09-28 21:20:40.877031 : NTiles_TileMatrix_9_chr9, Class = numeric

NTiles_TileMatrix_9_chr9: length = 1
  chr9 
282427 

2024-09-28 21:20:40.879158 : NCells_TileMatrix_9_chr9, Class = integer

NCells_TileMatrix_9_chr9: length = 1
[1] 2453

2024-09-28 21:20:40.88126 : MinTile_TileMatrix_9_chr9, Class = numeric

MinTile_TileMatrix_9_chr9: length = 1
[1] 21

2024-09-28 21:20:40.883651 : MaxTile_TileMatrix_9_chr9, Class = numeric

MaxTile_TileMatrix_9_chr9: length = 1
[1] 282223

2024-09-28 21:20:40.888149 : MinCell_TileMatrix_9_chr9, Class = integer

MinCell_TileMatrix_9_chr9: length = 1
[1] 1

2024-09-28 21:20:40.890222 : MaxCell_TileMatrix_9_chr9, Class = integer

MaxCell_TileMatrix_9_chr9: length = 1
[1] 2453

2024-09-28 21:20:41.407112 : Adding TileMatrix to scATAC_CD34_BMMC_R1 for Chr (7 of 23)!, 0.598 mins elapsed.

2024-09-28 21:20:41.489558 : NTiles_TileMatrix_7_chr7, Class = numeric

NTiles_TileMatrix_7_chr7: length = 1
  chr7 
318278 

2024-09-28 21:20:41.491801 : NCells_TileMatrix_7_chr7, Class = integer

NCells_TileMatrix_7_chr7: length = 1
[1] 3275

2024-09-28 21:20:41.494216 : MinTile_TileMatrix_7_chr7, Class = numeric

MinTile_TileMatrix_7_chr7: length = 1
[1] 34

2024-09-28 21:20:41.497916 : MaxTile_TileMatrix_7_chr7, Class = numeric

MaxTile_TileMatrix_7_chr7: length = 1
[1] 318258

2024-09-28 21:20:41.505615 : MinCell_TileMatrix_7_chr7, Class = integer

MinCell_TileMatrix_7_chr7: length = 1
[1] 1

2024-09-28 21:20:41.508556 : MaxCell_TileMatrix_7_chr7, Class = integer

MaxCell_TileMatrix_7_chr7: length = 1
[1] 3275

2024-09-28 21:20:43.542351 : Adding TileMatrix to scATAC_PBMC_R1 for Chr (10 of 23)!, 0.728 mins elapsed.

2024-09-28 21:20:43.615247 : NTiles_TileMatrix_10_chr10, Class = numeric

NTiles_TileMatrix_10_chr10: length = 1
 chr10 
271070 

2024-09-28 21:20:43.617408 : NCells_TileMatrix_10_chr10, Class = integer

NCells_TileMatrix_10_chr10: length = 1
[1] 2453

2024-09-28 21:20:43.619623 : MinTile_TileMatrix_10_chr10, Class = numeric

MinTile_TileMatrix_10_chr10: length = 1
[1] 190

2024-09-28 21:20:43.622108 : MaxTile_TileMatrix_10_chr10, Class = numeric

MaxTile_TileMatrix_10_chr10: length = 1
[1] 271050

2024-09-28 21:20:43.626922 : MinCell_TileMatrix_10_chr10, Class = integer

MinCell_TileMatrix_10_chr10: length = 1
[1] 1

2024-09-28 21:20:43.628967 : MaxCell_TileMatrix_10_chr10, Class = integer

MaxCell_TileMatrix_10_chr10: length = 1
[1] 2453

2024-09-28 21:20:44.569728 : Adding TileMatrix to scATAC_CD34_BMMC_R1 for Chr (8 of 23)!, 0.65 mins elapsed.

2024-09-28 21:20:44.655547 : NTiles_TileMatrix_8_chr8, Class = numeric

NTiles_TileMatrix_8_chr8: length = 1
  chr8 
292729 

2024-09-28 21:20:44.657454 : NCells_TileMatrix_8_chr8, Class = integer

NCells_TileMatrix_8_chr8: length = 1
[1] 3275

2024-09-28 21:20:44.65949 : MinTile_TileMatrix_8_chr8, Class = numeric

MinTile_TileMatrix_8_chr8: length = 1
[1] 43

2024-09-28 21:20:44.661842 : MaxTile_TileMatrix_8_chr8, Class = numeric

MaxTile_TileMatrix_8_chr8: length = 1
[1] 292608

2024-09-28 21:20:44.666618 : MinCell_TileMatrix_8_chr8, Class = integer

MinCell_TileMatrix_8_chr8: length = 1
[1] 1

2024-09-28 21:20:44.668604 : MaxCell_TileMatrix_8_chr8, Class = integer

MaxCell_TileMatrix_8_chr8: length = 1
[1] 3275

2024-09-28 21:20:44.918626 : Adding TileMatrix to scATAC_BMMC_R1 for Chr (4 of 23)!, 0.492 mins elapsed.

2024-09-28 21:20:45.008339 : NTiles_TileMatrix_4_chr4, Class = numeric

NTiles_TileMatrix_4_chr4: length = 1
  chr4 
382309 

2024-09-28 21:20:45.010457 : NCells_TileMatrix_4_chr4, Class = integer

NCells_TileMatrix_4_chr4: length = 1
[1] 4932

2024-09-28 21:20:45.012495 : MinTile_TileMatrix_4_chr4, Class = numeric

MinTile_TileMatrix_4_chr4: length = 1
[1] 21

2024-09-28 21:20:45.015167 : MaxTile_TileMatrix_4_chr4, Class = numeric

MaxTile_TileMatrix_4_chr4: length = 1
[1] 382089

2024-09-28 21:20:45.020957 : MinCell_TileMatrix_4_chr4, Class = integer

MinCell_TileMatrix_4_chr4: length = 1
[1] 1

2024-09-28 21:20:45.022935 : MaxCell_TileMatrix_4_chr4, Class = integer

MaxCell_TileMatrix_4_chr4: length = 1
[1] 4932

2024-09-28 21:20:46.237306 : Adding TileMatrix to scATAC_PBMC_R1 for Chr (11 of 23)!, 0.773 mins elapsed.

2024-09-28 21:20:46.338708 : NTiles_TileMatrix_11_chr11, Class = numeric

NTiles_TileMatrix_11_chr11: length = 1
 chr11 
270014 

2024-09-28 21:20:46.341676 : NCells_TileMatrix_11_chr11, Class = integer

NCells_TileMatrix_11_chr11: length = 1
[1] 2453

2024-09-28 21:20:46.345659 : MinTile_TileMatrix_11_chr11, Class = numeric

MinTile_TileMatrix_11_chr11: length = 1
[1] 154

2024-09-28 21:20:46.348296 : MaxTile_TileMatrix_11_chr11, Class = numeric

MaxTile_TileMatrix_11_chr11: length = 1
[1] 269892

2024-09-28 21:20:46.353429 : MinCell_TileMatrix_11_chr11, Class = integer

MinCell_TileMatrix_11_chr11: length = 1
[1] 1

2024-09-28 21:20:46.355402 : MaxCell_TileMatrix_11_chr11, Class = integer

MaxCell_TileMatrix_11_chr11: length = 1
[1] 2453

2024-09-28 21:20:47.403824 : Adding TileMatrix to scATAC_CD34_BMMC_R1 for Chr (9 of 23)!, 0.698 mins elapsed.

2024-09-28 21:20:47.487885 : NTiles_TileMatrix_9_chr9, Class = numeric

NTiles_TileMatrix_9_chr9: length = 1
  chr9 
282427 

2024-09-28 21:20:47.490609 : NCells_TileMatrix_9_chr9, Class = integer

NCells_TileMatrix_9_chr9: length = 1
[1] 3275

2024-09-28 21:20:47.493214 : MinTile_TileMatrix_9_chr9, Class = numeric

MinTile_TileMatrix_9_chr9: length = 1
[1] 21

2024-09-28 21:20:47.496516 : MaxTile_TileMatrix_9_chr9, Class = numeric

MaxTile_TileMatrix_9_chr9: length = 1
[1] 282223

2024-09-28 21:20:47.504637 : MinCell_TileMatrix_9_chr9, Class = integer

MinCell_TileMatrix_9_chr9: length = 1
[1] 1

2024-09-28 21:20:47.506974 : MaxCell_TileMatrix_9_chr9, Class = integer

MaxCell_TileMatrix_9_chr9: length = 1
[1] 3275

2024-09-28 21:20:48.660711 : Adding TileMatrix to scATAC_BMMC_R1 for Chr (5 of 23)!, 0.554 mins elapsed.

2024-09-28 21:20:48.759208 : NTiles_TileMatrix_5_chr5, Class = numeric

NTiles_TileMatrix_5_chr5: length = 1
  chr5 
361831 

2024-09-28 21:20:48.762421 : NCells_TileMatrix_5_chr5, Class = integer

NCells_TileMatrix_5_chr5: length = 1
[1] 4932

2024-09-28 21:20:48.764439 : MinTile_TileMatrix_5_chr5, Class = numeric

MinTile_TileMatrix_5_chr5: length = 1
[1] 24

2024-09-28 21:20:48.767345 : MaxTile_TileMatrix_5_chr5, Class = numeric

MaxTile_TileMatrix_5_chr5: length = 1
[1] 361572

2024-09-28 21:20:48.773841 : MinCell_TileMatrix_5_chr5, Class = integer

MinCell_TileMatrix_5_chr5: length = 1
[1] 1

2024-09-28 21:20:48.776019 : MaxCell_TileMatrix_5_chr5, Class = integer

MaxCell_TileMatrix_5_chr5: length = 1
[1] 4932

2024-09-28 21:20:49.153676 : Adding TileMatrix to scATAC_PBMC_R1 for Chr (12 of 23)!, 0.821 mins elapsed.

2024-09-28 21:20:49.254856 : NTiles_TileMatrix_12_chr12, Class = numeric

NTiles_TileMatrix_12_chr12: length = 1
 chr12 
267704 

2024-09-28 21:20:49.257524 : NCells_TileMatrix_12_chr12, Class = integer

NCells_TileMatrix_12_chr12: length = 1
[1] 2453

2024-09-28 21:20:49.259994 : MinTile_TileMatrix_12_chr12, Class = numeric

MinTile_TileMatrix_12_chr12: length = 1
[1] 121

2024-09-28 21:20:49.262898 : MaxTile_TileMatrix_12_chr12, Class = numeric

MaxTile_TileMatrix_12_chr12: length = 1
[1] 267674

2024-09-28 21:20:49.268802 : MinCell_TileMatrix_12_chr12, Class = integer

MinCell_TileMatrix_12_chr12: length = 1
[1] 1

2024-09-28 21:20:49.270946 : MaxCell_TileMatrix_12_chr12, Class = integer

MaxCell_TileMatrix_12_chr12: length = 1
[1] 2453

2024-09-28 21:20:50.261178 : Adding TileMatrix to scATAC_CD34_BMMC_R1 for Chr (10 of 23)!, 0.745 mins elapsed.

2024-09-28 21:20:50.353401 : NTiles_TileMatrix_10_chr10, Class = numeric

NTiles_TileMatrix_10_chr10: length = 1
 chr10 
271070 

2024-09-28 21:20:50.355486 : NCells_TileMatrix_10_chr10, Class = integer

NCells_TileMatrix_10_chr10: length = 1
[1] 3275

2024-09-28 21:20:50.357582 : MinTile_TileMatrix_10_chr10, Class = numeric

MinTile_TileMatrix_10_chr10: length = 1
[1] 156

2024-09-28 21:20:50.360085 : MaxTile_TileMatrix_10_chr10, Class = numeric

MaxTile_TileMatrix_10_chr10: length = 1
[1] 271049

2024-09-28 21:20:50.365314 : MinCell_TileMatrix_10_chr10, Class = integer

MinCell_TileMatrix_10_chr10: length = 1
[1] 1

2024-09-28 21:20:50.367377 : MaxCell_TileMatrix_10_chr10, Class = integer

MaxCell_TileMatrix_10_chr10: length = 1
[1] 3275

2024-09-28 21:20:52.022084 : Adding TileMatrix to scATAC_PBMC_R1 for Chr (13 of 23)!, 0.869 mins elapsed.

2024-09-28 21:20:52.080677 : NTiles_TileMatrix_13_chr13, Class = numeric

NTiles_TileMatrix_13_chr13: length = 1
 chr13 
230340 

2024-09-28 21:20:52.0829 : NCells_TileMatrix_13_chr13, Class = integer

NCells_TileMatrix_13_chr13: length = 1
[1] 2453

2024-09-28 21:20:52.084841 : MinTile_TileMatrix_13_chr13, Class = numeric

MinTile_TileMatrix_13_chr13: length = 1
[1] 38045

2024-09-28 21:20:52.086926 : MaxTile_TileMatrix_13_chr13, Class = numeric

MaxTile_TileMatrix_13_chr13: length = 1
[1] 230220

2024-09-28 21:20:52.090047 : MinCell_TileMatrix_13_chr13, Class = integer

MinCell_TileMatrix_13_chr13: length = 1
[1] 1

2024-09-28 21:20:52.09208 : MaxCell_TileMatrix_13_chr13, Class = integer

MaxCell_TileMatrix_13_chr13: length = 1
[1] 2453

2024-09-28 21:20:52.418025 : Adding TileMatrix to scATAC_BMMC_R1 for Chr (6 of 23)!, 0.617 mins elapsed.

2024-09-28 21:20:52.529567 : NTiles_TileMatrix_6_chr6, Class = numeric

NTiles_TileMatrix_6_chr6: length = 1
  chr6 
342231 

2024-09-28 21:20:52.53153 : NCells_TileMatrix_6_chr6, Class = integer

NCells_TileMatrix_6_chr6: length = 1
[1] 4932

2024-09-28 21:20:52.53351 : MinTile_TileMatrix_6_chr6, Class = numeric

MinTile_TileMatrix_6_chr6: length = 1
[1] 201

2024-09-28 21:20:52.536306 : MaxTile_TileMatrix_6_chr6, Class = numeric

MaxTile_TileMatrix_6_chr6: length = 1
[1] 342094

2024-09-28 21:20:52.543492 : MinCell_TileMatrix_6_chr6, Class = integer

MinCell_TileMatrix_6_chr6: length = 1
[1] 1

2024-09-28 21:20:52.545428 : MaxCell_TileMatrix_6_chr6, Class = integer

MaxCell_TileMatrix_6_chr6: length = 1
[1] 4932

2024-09-28 21:20:53.25181 : Adding TileMatrix to scATAC_CD34_BMMC_R1 for Chr (11 of 23)!, 0.795 mins elapsed.

2024-09-28 21:20:53.347015 : NTiles_TileMatrix_11_chr11, Class = numeric

NTiles_TileMatrix_11_chr11: length = 1
 chr11 
270014 

2024-09-28 21:20:53.349283 : NCells_TileMatrix_11_chr11, Class = integer

NCells_TileMatrix_11_chr11: length = 1
[1] 3275

2024-09-28 21:20:53.351502 : MinTile_TileMatrix_11_chr11, Class = numeric

MinTile_TileMatrix_11_chr11: length = 1
[1] 353

2024-09-28 21:20:53.354151 : MaxTile_TileMatrix_11_chr11, Class = numeric

MaxTile_TileMatrix_11_chr11: length = 1
[1] 269893

2024-09-28 21:20:53.360741 : MinCell_TileMatrix_11_chr11, Class = integer

MinCell_TileMatrix_11_chr11: length = 1
[1] 1

2024-09-28 21:20:53.363859 : MaxCell_TileMatrix_11_chr11, Class = integer

MaxCell_TileMatrix_11_chr11: length = 1
[1] 3275

2024-09-28 21:20:54.403611 : Adding TileMatrix to scATAC_PBMC_R1 for Chr (14 of 23)!, 0.909 mins elapsed.

2024-09-28 21:20:54.464297 : NTiles_TileMatrix_14_chr14, Class = numeric

NTiles_TileMatrix_14_chr14: length = 1
 chr14 
214700 

2024-09-28 21:20:54.466652 : NCells_TileMatrix_14_chr14, Class = integer

NCells_TileMatrix_14_chr14: length = 1
[1] 2453

2024-09-28 21:20:54.468812 : MinTile_TileMatrix_14_chr14, Class = numeric

MinTile_TileMatrix_14_chr14: length = 1
[1] 38001

2024-09-28 21:20:54.471275 : MaxTile_TileMatrix_14_chr14, Class = numeric

MaxTile_TileMatrix_14_chr14: length = 1
[1] 214579

2024-09-28 21:20:54.4757 : MinCell_TileMatrix_14_chr14, Class = integer

MinCell_TileMatrix_14_chr14: length = 1
[1] 1

2024-09-28 21:20:54.477815 : MaxCell_TileMatrix_14_chr14, Class = integer

MaxCell_TileMatrix_14_chr14: length = 1
[1] 2453

2024-09-28 21:20:56.303592 : Adding TileMatrix to scATAC_CD34_BMMC_R1 for Chr (12 of 23)!, 0.846 mins elapsed.
2024-09-28 21:20:56.319603 : Adding TileMatrix to scATAC_BMMC_R1 for Chr (7 of 23)!, 0.682 mins elapsed.

2024-09-28 21:20:56.396151 : NTiles_TileMatrix_12_chr12, Class = numeric

NTiles_TileMatrix_12_chr12: length = 1
 chr12 
267704 

2024-09-28 21:20:56.398149 : NCells_TileMatrix_12_chr12, Class = integer

NCells_TileMatrix_12_chr12: length = 1
[1] 3275

2024-09-28 21:20:56.400258 : MinTile_TileMatrix_12_chr12, Class = numeric

MinTile_TileMatrix_12_chr12: length = 1
[1] 134

2024-09-28 21:20:56.402779 : MaxTile_TileMatrix_12_chr12, Class = numeric

MaxTile_TileMatrix_12_chr12: length = 1
[1] 267682

2024-09-28 21:20:56.408068 : MinCell_TileMatrix_12_chr12, Class = integer

MinCell_TileMatrix_12_chr12: length = 1
[1] 1

2024-09-28 21:20:56.409985 : MaxCell_TileMatrix_12_chr12, Class = integer

MaxCell_TileMatrix_12_chr12: length = 1
[1] 3275

2024-09-28 21:20:56.420772 : NTiles_TileMatrix_7_chr7, Class = numeric

NTiles_TileMatrix_7_chr7: length = 1
  chr7 
318278 

2024-09-28 21:20:56.422702 : NCells_TileMatrix_7_chr7, Class = integer

NCells_TileMatrix_7_chr7: length = 1
[1] 4932

2024-09-28 21:20:56.424442 : MinTile_TileMatrix_7_chr7, Class = numeric

MinTile_TileMatrix_7_chr7: length = 1
[1] 21

2024-09-28 21:20:56.426824 : MaxTile_TileMatrix_7_chr7, Class = numeric

MaxTile_TileMatrix_7_chr7: length = 1
[1] 318258

2024-09-28 21:20:56.434088 : MinCell_TileMatrix_7_chr7, Class = integer

MinCell_TileMatrix_7_chr7: length = 1
[1] 1

2024-09-28 21:20:56.435952 : MaxCell_TileMatrix_7_chr7, Class = integer

MaxCell_TileMatrix_7_chr7: length = 1
[1] 4932

2024-09-28 21:20:56.985047 : Adding TileMatrix to scATAC_PBMC_R1 for Chr (15 of 23)!, 0.952 mins elapsed.

2024-09-28 21:20:57.050503 : NTiles_TileMatrix_15_chr15, Class = numeric

NTiles_TileMatrix_15_chr15: length = 1
 chr15 
205063 

2024-09-28 21:20:57.052714 : NCells_TileMatrix_15_chr15, Class = integer

NCells_TileMatrix_15_chr15: length = 1
[1] 2453

2024-09-28 21:20:57.054873 : MinTile_TileMatrix_15_chr15, Class = numeric

MinTile_TileMatrix_15_chr15: length = 1
[1] 40001

2024-09-28 21:20:57.057974 : MaxTile_TileMatrix_15_chr15, Class = numeric

MaxTile_TileMatrix_15_chr15: length = 1
[1] 205043

2024-09-28 21:20:57.063545 : MinCell_TileMatrix_15_chr15, Class = integer

MinCell_TileMatrix_15_chr15: length = 1
[1] 1

2024-09-28 21:20:57.066291 : MaxCell_TileMatrix_15_chr15, Class = integer

MaxCell_TileMatrix_15_chr15: length = 1
[1] 2453

2024-09-28 21:20:59.259303 : Adding TileMatrix to scATAC_CD34_BMMC_R1 for Chr (13 of 23)!, 0.895 mins elapsed.

2024-09-28 21:20:59.33181 : NTiles_TileMatrix_13_chr13, Class = numeric

NTiles_TileMatrix_13_chr13: length = 1
 chr13 
230340 

2024-09-28 21:20:59.334564 : NCells_TileMatrix_13_chr13, Class = integer

NCells_TileMatrix_13_chr13: length = 1
[1] 3275

2024-09-28 21:20:59.337179 : MinTile_TileMatrix_13_chr13, Class = numeric

MinTile_TileMatrix_13_chr13: length = 1
[1] 38152

2024-09-28 21:20:59.340082 : MaxTile_TileMatrix_13_chr13, Class = numeric

MaxTile_TileMatrix_13_chr13: length = 1
[1] 230220

2024-09-28 21:20:59.344772 : MinCell_TileMatrix_13_chr13, Class = integer

MinCell_TileMatrix_13_chr13: length = 1
[1] 1

2024-09-28 21:20:59.347249 : MaxCell_TileMatrix_13_chr13, Class = integer

MaxCell_TileMatrix_13_chr13: length = 1
[1] 3275

2024-09-28 21:20:59.352638 : Adding TileMatrix to scATAC_PBMC_R1 for Chr (16 of 23)!, 0.991 mins elapsed.

2024-09-28 21:20:59.425312 : NTiles_TileMatrix_16_chr16, Class = numeric

NTiles_TileMatrix_16_chr16: length = 1
 chr16 
180710 

2024-09-28 21:20:59.428167 : NCells_TileMatrix_16_chr16, Class = integer

NCells_TileMatrix_16_chr16: length = 1
[1] 2453

2024-09-28 21:20:59.43096 : MinTile_TileMatrix_16_chr16, Class = numeric

MinTile_TileMatrix_16_chr16: length = 1
[1] 120

2024-09-28 21:20:59.4343 : MaxTile_TileMatrix_16_chr16, Class = numeric

MaxTile_TileMatrix_16_chr16: length = 1
[1] 180564

2024-09-28 21:20:59.440138 : MinCell_TileMatrix_16_chr16, Class = integer

MinCell_TileMatrix_16_chr16: length = 1
[1] 1

2024-09-28 21:20:59.44228 : MaxCell_TileMatrix_16_chr16, Class = integer

MaxCell_TileMatrix_16_chr16: length = 1
[1] 2453

2024-09-28 21:20:59.878052 : Adding TileMatrix to scATAC_BMMC_R1 for Chr (8 of 23)!, 0.741 mins elapsed.

2024-09-28 21:20:59.981673 : NTiles_TileMatrix_8_chr8, Class = numeric

NTiles_TileMatrix_8_chr8: length = 1
  chr8 
292729 

2024-09-28 21:20:59.984757 : NCells_TileMatrix_8_chr8, Class = integer

NCells_TileMatrix_8_chr8: length = 1
[1] 4932

2024-09-28 21:20:59.987161 : MinTile_TileMatrix_8_chr8, Class = numeric

MinTile_TileMatrix_8_chr8: length = 1
[1] 43

2024-09-28 21:20:59.989743 : MaxTile_TileMatrix_8_chr8, Class = numeric

MaxTile_TileMatrix_8_chr8: length = 1
[1] 292608

2024-09-28 21:20:59.995438 : MinCell_TileMatrix_8_chr8, Class = integer

MinCell_TileMatrix_8_chr8: length = 1
[1] 1

2024-09-28 21:20:59.997481 : MaxCell_TileMatrix_8_chr8, Class = integer

MaxCell_TileMatrix_8_chr8: length = 1
[1] 4932

2024-09-28 21:21:01.675113 : Adding TileMatrix to scATAC_CD34_BMMC_R1 for Chr (14 of 23)!, 0.936 mins elapsed.
2024-09-28 21:21:01.745915 : Adding TileMatrix to scATAC_PBMC_R1 for Chr (17 of 23)!, 1.031 mins elapsed.

2024-09-28 21:21:01.75292 : NTiles_TileMatrix_14_chr14, Class = numeric

NTiles_TileMatrix_14_chr14: length = 1
 chr14 
214700 

2024-09-28 21:21:01.755856 : NCells_TileMatrix_14_chr14, Class = integer

NCells_TileMatrix_14_chr14: length = 1
[1] 3275

2024-09-28 21:21:01.758643 : MinTile_TileMatrix_14_chr14, Class = numeric

MinTile_TileMatrix_14_chr14: length = 1
[1] 38003

2024-09-28 21:21:01.762132 : MaxTile_TileMatrix_14_chr14, Class = numeric

MaxTile_TileMatrix_14_chr14: length = 1
[1] 214578

2024-09-28 21:21:01.769113 : MinCell_TileMatrix_14_chr14, Class = integer

MinCell_TileMatrix_14_chr14: length = 1
[1] 1

2024-09-28 21:21:01.772107 : MaxCell_TileMatrix_14_chr14, Class = integer

MaxCell_TileMatrix_14_chr14: length = 1
[1] 3275

2024-09-28 21:21:01.853413 : NTiles_TileMatrix_17_chr17, Class = numeric

NTiles_TileMatrix_17_chr17: length = 1
 chr17 
162391 

2024-09-28 21:21:01.856133 : NCells_TileMatrix_17_chr17, Class = integer

NCells_TileMatrix_17_chr17: length = 1
[1] 2453

2024-09-28 21:21:01.858448 : MinTile_TileMatrix_17_chr17, Class = numeric

MinTile_TileMatrix_17_chr17: length = 1
[1] 1

2024-09-28 21:21:01.86114 : MaxTile_TileMatrix_17_chr17, Class = numeric

MaxTile_TileMatrix_17_chr17: length = 1
[1] 162391

2024-09-28 21:21:01.866429 : MinCell_TileMatrix_17_chr17, Class = integer

MinCell_TileMatrix_17_chr17: length = 1
[1] 1

2024-09-28 21:21:01.868327 : MaxCell_TileMatrix_17_chr17, Class = integer

MaxCell_TileMatrix_17_chr17: length = 1
[1] 2453

2024-09-28 21:21:03.020666 : Adding TileMatrix to scATAC_BMMC_R1 for Chr (9 of 23)!, 0.794 mins elapsed.

2024-09-28 21:21:03.138749 : NTiles_TileMatrix_9_chr9, Class = numeric

NTiles_TileMatrix_9_chr9: length = 1
  chr9 
282427 

2024-09-28 21:21:03.141993 : NCells_TileMatrix_9_chr9, Class = integer

NCells_TileMatrix_9_chr9: length = 1
[1] 4932

2024-09-28 21:21:03.144776 : MinTile_TileMatrix_9_chr9, Class = numeric

MinTile_TileMatrix_9_chr9: length = 1
[1] 21

2024-09-28 21:21:03.148746 : MaxTile_TileMatrix_9_chr9, Class = numeric

MaxTile_TileMatrix_9_chr9: length = 1
[1] 282256

2024-09-28 21:21:03.157684 : MinCell_TileMatrix_9_chr9, Class = integer

MinCell_TileMatrix_9_chr9: length = 1
[1] 1

2024-09-28 21:21:03.159883 : MaxCell_TileMatrix_9_chr9, Class = integer

MaxCell_TileMatrix_9_chr9: length = 1
[1] 4932

2024-09-28 21:21:04.315345 : Adding TileMatrix to scATAC_CD34_BMMC_R1 for Chr (15 of 23)!, 0.98 mins elapsed.

2024-09-28 21:21:04.379605 : NTiles_TileMatrix_15_chr15, Class = numeric

NTiles_TileMatrix_15_chr15: length = 1
 chr15 
205063 

2024-09-28 21:21:04.381868 : NCells_TileMatrix_15_chr15, Class = integer

NCells_TileMatrix_15_chr15: length = 1
[1] 3275

2024-09-28 21:21:04.383718 : MinTile_TileMatrix_15_chr15, Class = numeric

MinTile_TileMatrix_15_chr15: length = 1
[1] 40007

2024-09-28 21:21:04.385878 : MaxTile_TileMatrix_15_chr15, Class = numeric

MaxTile_TileMatrix_15_chr15: length = 1
[1] 205042

2024-09-28 21:21:04.389721 : MinCell_TileMatrix_15_chr15, Class = integer

MinCell_TileMatrix_15_chr15: length = 1
[1] 1

2024-09-28 21:21:04.391524 : MaxCell_TileMatrix_15_chr15, Class = integer

MaxCell_TileMatrix_15_chr15: length = 1
[1] 3275

2024-09-28 21:21:04.402957 : Adding TileMatrix to scATAC_PBMC_R1 for Chr (18 of 23)!, 1.076 mins elapsed.

2024-09-28 21:21:04.458313 : NTiles_TileMatrix_18_chr18, Class = numeric

NTiles_TileMatrix_18_chr18: length = 1
 chr18 
156155 

2024-09-28 21:21:04.460304 : NCells_TileMatrix_18_chr18, Class = integer

NCells_TileMatrix_18_chr18: length = 1
[1] 2453

2024-09-28 21:21:04.4622 : MinTile_TileMatrix_18_chr18, Class = numeric

MinTile_TileMatrix_18_chr18: length = 1
[1] 21

2024-09-28 21:21:04.464581 : MaxTile_TileMatrix_18_chr18, Class = numeric

MaxTile_TileMatrix_18_chr18: length = 1
[1] 156035

2024-09-28 21:21:04.467988 : MinCell_TileMatrix_18_chr18, Class = integer

MinCell_TileMatrix_18_chr18: length = 1
[1] 1

2024-09-28 21:21:04.470219 : MaxCell_TileMatrix_18_chr18, Class = integer

MaxCell_TileMatrix_18_chr18: length = 1
[1] 2453

2024-09-28 21:21:06.277168 : Adding TileMatrix to scATAC_BMMC_R1 for Chr (10 of 23)!, 0.848 mins elapsed.

2024-09-28 21:21:06.394693 : NTiles_TileMatrix_10_chr10, Class = numeric

NTiles_TileMatrix_10_chr10: length = 1
 chr10 
271070 

2024-09-28 21:21:06.396907 : NCells_TileMatrix_10_chr10, Class = integer

NCells_TileMatrix_10_chr10: length = 1
[1] 4932

2024-09-28 21:21:06.399036 : MinTile_TileMatrix_10_chr10, Class = numeric

MinTile_TileMatrix_10_chr10: length = 1
[1] 167

2024-09-28 21:21:06.40188 : MaxTile_TileMatrix_10_chr10, Class = numeric

MaxTile_TileMatrix_10_chr10: length = 1
[1] 271050

2024-09-28 21:21:06.408345 : MinCell_TileMatrix_10_chr10, Class = integer

MinCell_TileMatrix_10_chr10: length = 1
[1] 1

2024-09-28 21:21:06.410585 : MaxCell_TileMatrix_10_chr10, Class = integer

MaxCell_TileMatrix_10_chr10: length = 1
[1] 4932

2024-09-28 21:21:06.592928 : Adding TileMatrix to scATAC_PBMC_R1 for Chr (19 of 23)!, 1.112 mins elapsed.

2024-09-28 21:21:06.694358 : NTiles_TileMatrix_19_chr19, Class = numeric

NTiles_TileMatrix_19_chr19: length = 1
 chr19 
118258 

2024-09-28 21:21:06.696505 : NCells_TileMatrix_19_chr19, Class = integer

NCells_TileMatrix_19_chr19: length = 1
[1] 2453

2024-09-28 21:21:06.698555 : MinTile_TileMatrix_19_chr19, Class = numeric

MinTile_TileMatrix_19_chr19: length = 1
[1] 179

2024-09-28 21:21:06.701238 : MaxTile_TileMatrix_19_chr19, Class = numeric

MaxTile_TileMatrix_19_chr19: length = 1
[1] 118238

2024-09-28 21:21:06.708507 : MinCell_TileMatrix_19_chr19, Class = integer

MinCell_TileMatrix_19_chr19: length = 1
[1] 1

2024-09-28 21:21:06.711345 : MaxCell_TileMatrix_19_chr19, Class = integer

MaxCell_TileMatrix_19_chr19: length = 1
[1] 2453

2024-09-28 21:21:06.792139 : Adding TileMatrix to scATAC_CD34_BMMC_R1 for Chr (16 of 23)!, 1.021 mins elapsed.

2024-09-28 21:21:06.868993 : NTiles_TileMatrix_16_chr16, Class = numeric

NTiles_TileMatrix_16_chr16: length = 1
 chr16 
180710 

2024-09-28 21:21:06.871163 : NCells_TileMatrix_16_chr16, Class = integer

NCells_TileMatrix_16_chr16: length = 1
[1] 3275

2024-09-28 21:21:06.873147 : MinTile_TileMatrix_16_chr16, Class = numeric

MinTile_TileMatrix_16_chr16: length = 1
[1] 121

2024-09-28 21:21:06.875557 : MaxTile_TileMatrix_16_chr16, Class = numeric

MaxTile_TileMatrix_16_chr16: length = 1
[1] 180550

2024-09-28 21:21:06.880391 : MinCell_TileMatrix_16_chr16, Class = integer

MinCell_TileMatrix_16_chr16: length = 1
[1] 1

2024-09-28 21:21:06.882256 : MaxCell_TileMatrix_16_chr16, Class = integer

MaxCell_TileMatrix_16_chr16: length = 1
[1] 3275

2024-09-28 21:21:09.127075 : Adding TileMatrix to scATAC_PBMC_R1 for Chr (20 of 23)!, 1.154 mins elapsed.

2024-09-28 21:21:09.211368 : NTiles_TileMatrix_20_chr20, Class = numeric

NTiles_TileMatrix_20_chr20: length = 1
 chr20 
126052 

2024-09-28 21:21:09.213747 : NCells_TileMatrix_20_chr20, Class = integer

NCells_TileMatrix_20_chr20: length = 1
[1] 2453

2024-09-28 21:21:09.215852 : MinTile_TileMatrix_20_chr20, Class = numeric

MinTile_TileMatrix_20_chr20: length = 1
[1] 121

2024-09-28 21:21:09.218302 : MaxTile_TileMatrix_20_chr20, Class = numeric

MaxTile_TileMatrix_20_chr20: length = 1
[1] 125930

2024-09-28 21:21:09.222117 : MinCell_TileMatrix_20_chr20, Class = integer

MinCell_TileMatrix_20_chr20: length = 1
[1] 1

2024-09-28 21:21:09.224383 : MaxCell_TileMatrix_20_chr20, Class = integer

MaxCell_TileMatrix_20_chr20: length = 1
[1] 2453

2024-09-28 21:21:09.297848 : Adding TileMatrix to scATAC_CD34_BMMC_R1 for Chr (17 of 23)!, 1.063 mins elapsed.

2024-09-28 21:21:09.403142 : NTiles_TileMatrix_17_chr17, Class = numeric

NTiles_TileMatrix_17_chr17: length = 1
 chr17 
162391 

2024-09-28 21:21:09.405408 : NCells_TileMatrix_17_chr17, Class = integer

NCells_TileMatrix_17_chr17: length = 1
[1] 3275

2024-09-28 21:21:09.407551 : MinTile_TileMatrix_17_chr17, Class = numeric

MinTile_TileMatrix_17_chr17: length = 1
[1] 2

2024-09-28 21:21:09.41034 : MaxTile_TileMatrix_17_chr17, Class = numeric

MaxTile_TileMatrix_17_chr17: length = 1
[1] 162320

2024-09-28 21:21:09.416757 : MinCell_TileMatrix_17_chr17, Class = integer

MinCell_TileMatrix_17_chr17: length = 1
[1] 1

2024-09-28 21:21:09.418859 : MaxCell_TileMatrix_17_chr17, Class = integer

MaxCell_TileMatrix_17_chr17: length = 1
[1] 3275

2024-09-28 21:21:09.554534 : Adding TileMatrix to scATAC_BMMC_R1 for Chr (11 of 23)!, 0.903 mins elapsed.

2024-09-28 21:21:09.660781 : NTiles_TileMatrix_11_chr11, Class = numeric

NTiles_TileMatrix_11_chr11: length = 1
 chr11 
270014 

2024-09-28 21:21:09.663203 : NCells_TileMatrix_11_chr11, Class = integer

NCells_TileMatrix_11_chr11: length = 1
[1] 4932

2024-09-28 21:21:09.665528 : MinTile_TileMatrix_11_chr11, Class = numeric

MinTile_TileMatrix_11_chr11: length = 1
[1] 247

2024-09-28 21:21:09.668402 : MaxTile_TileMatrix_11_chr11, Class = numeric

MaxTile_TileMatrix_11_chr11: length = 1
[1] 269893

2024-09-28 21:21:09.675732 : MinCell_TileMatrix_11_chr11, Class = integer

MinCell_TileMatrix_11_chr11: length = 1
[1] 1

2024-09-28 21:21:09.677879 : MaxCell_TileMatrix_11_chr11, Class = integer

MaxCell_TileMatrix_11_chr11: length = 1
[1] 4932

2024-09-28 21:21:11.262415 : Adding TileMatrix to scATAC_PBMC_R1 for Chr (21 of 23)!, 1.19 mins elapsed.

2024-09-28 21:21:11.317127 : NTiles_TileMatrix_21_chr21, Class = numeric

NTiles_TileMatrix_21_chr21: length = 1
chr21 
96260 

2024-09-28 21:21:11.319488 : NCells_TileMatrix_21_chr21, Class = integer

NCells_TileMatrix_21_chr21: length = 1
[1] 2453

2024-09-28 21:21:11.321858 : MinTile_TileMatrix_21_chr21, Class = numeric

MinTile_TileMatrix_21_chr21: length = 1
[1] 18831

2024-09-28 21:21:11.324105 : MaxTile_TileMatrix_21_chr21, Class = numeric

MaxTile_TileMatrix_21_chr21: length = 1
[1] 96200

2024-09-28 21:21:11.326865 : MinCell_TileMatrix_21_chr21, Class = integer

MinCell_TileMatrix_21_chr21: length = 1
[1] 1

2024-09-28 21:21:11.328882 : MaxCell_TileMatrix_21_chr21, Class = integer

MaxCell_TileMatrix_21_chr21: length = 1
[1] 2453

2024-09-28 21:21:11.847677 : Adding TileMatrix to scATAC_CD34_BMMC_R1 for Chr (18 of 23)!, 1.105 mins elapsed.

2024-09-28 21:21:11.917452 : NTiles_TileMatrix_18_chr18, Class = numeric

NTiles_TileMatrix_18_chr18: length = 1
 chr18 
156155 

2024-09-28 21:21:11.919788 : NCells_TileMatrix_18_chr18, Class = integer

NCells_TileMatrix_18_chr18: length = 1
[1] 3275

2024-09-28 21:21:11.921981 : MinTile_TileMatrix_18_chr18, Class = numeric

MinTile_TileMatrix_18_chr18: length = 1
[1] 21

2024-09-28 21:21:11.924383 : MaxTile_TileMatrix_18_chr18, Class = numeric

MaxTile_TileMatrix_18_chr18: length = 1
[1] 156033

2024-09-28 21:21:11.928036 : MinCell_TileMatrix_18_chr18, Class = integer

MinCell_TileMatrix_18_chr18: length = 1
[1] 1

2024-09-28 21:21:11.930255 : MaxCell_TileMatrix_18_chr18, Class = integer

MaxCell_TileMatrix_18_chr18: length = 1
[1] 3275

2024-09-28 21:21:12.915782 : Adding TileMatrix to scATAC_BMMC_R1 for Chr (12 of 23)!, 0.959 mins elapsed.

2024-09-28 21:21:13.031986 : NTiles_TileMatrix_12_chr12, Class = numeric

NTiles_TileMatrix_12_chr12: length = 1
 chr12 
267704 

2024-09-28 21:21:13.035376 : NCells_TileMatrix_12_chr12, Class = integer

NCells_TileMatrix_12_chr12: length = 1
[1] 4932

2024-09-28 21:21:13.038604 : MinTile_TileMatrix_12_chr12, Class = numeric

MinTile_TileMatrix_12_chr12: length = 1
[1] 124

2024-09-28 21:21:13.043092 : MaxTile_TileMatrix_12_chr12, Class = numeric

MaxTile_TileMatrix_12_chr12: length = 1
[1] 267683

2024-09-28 21:21:13.05449 : MinCell_TileMatrix_12_chr12, Class = integer

MinCell_TileMatrix_12_chr12: length = 1
[1] 1

2024-09-28 21:21:13.057606 : MaxCell_TileMatrix_12_chr12, Class = integer

MaxCell_TileMatrix_12_chr12: length = 1
[1] 4932

2024-09-28 21:21:13.335917 : Adding TileMatrix to scATAC_PBMC_R1 for Chr (22 of 23)!, 1.225 mins elapsed.

2024-09-28 21:21:13.404748 : NTiles_TileMatrix_22_chr22, Class = numeric

NTiles_TileMatrix_22_chr22: length = 1
 chr22 
102610 

2024-09-28 21:21:13.406909 : NCells_TileMatrix_22_chr22, Class = integer

NCells_TileMatrix_22_chr22: length = 1
[1] 2453

2024-09-28 21:21:13.409073 : MinTile_TileMatrix_22_chr22, Class = numeric

MinTile_TileMatrix_22_chr22: length = 1
[1] 32108

2024-09-28 21:21:13.411444 : MaxTile_TileMatrix_22_chr22, Class = numeric

MaxTile_TileMatrix_22_chr22: length = 1
[1] 102449

2024-09-28 21:21:13.414975 : MinCell_TileMatrix_22_chr22, Class = integer

MinCell_TileMatrix_22_chr22: length = 1
[1] 1

2024-09-28 21:21:13.417158 : MaxCell_TileMatrix_22_chr22, Class = integer

MaxCell_TileMatrix_22_chr22: length = 1
[1] 2453

2024-09-28 21:21:14.155235 : Adding TileMatrix to scATAC_CD34_BMMC_R1 for Chr (19 of 23)!, 1.144 mins elapsed.

2024-09-28 21:21:14.244174 : NTiles_TileMatrix_19_chr19, Class = numeric

NTiles_TileMatrix_19_chr19: length = 1
 chr19 
118258 

2024-09-28 21:21:14.246462 : NCells_TileMatrix_19_chr19, Class = integer

NCells_TileMatrix_19_chr19: length = 1
[1] 3275

2024-09-28 21:21:14.248318 : MinTile_TileMatrix_19_chr19, Class = numeric

MinTile_TileMatrix_19_chr19: length = 1
[1] 179

2024-09-28 21:21:14.250613 : MaxTile_TileMatrix_19_chr19, Class = numeric

MaxTile_TileMatrix_19_chr19: length = 1
[1] 118238

2024-09-28 21:21:14.256119 : MinCell_TileMatrix_19_chr19, Class = integer

MinCell_TileMatrix_19_chr19: length = 1
[1] 1

2024-09-28 21:21:14.25785 : MaxCell_TileMatrix_19_chr19, Class = integer

MaxCell_TileMatrix_19_chr19: length = 1
[1] 3275

2024-09-28 21:21:15.413336 : Adding TileMatrix to scATAC_PBMC_R1 for Chr (23 of 23)!, 1.259 mins elapsed.

2024-09-28 21:21:15.475359 : NTiles_TileMatrix_23_chrX, Class = numeric

NTiles_TileMatrix_23_chrX: length = 1
  chrX 
310542 

2024-09-28 21:21:15.477324 : NCells_TileMatrix_23_chrX, Class = integer

NCells_TileMatrix_23_chrX: length = 1
[1] 2453

2024-09-28 21:21:15.479223 : MinTile_TileMatrix_23_chrX, Class = numeric

MinTile_TileMatrix_23_chrX: length = 1
[1] 121

2024-09-28 21:21:15.481348 : MaxTile_TileMatrix_23_chrX, Class = numeric

MaxTile_TileMatrix_23_chrX: length = 1
[1] 310521

2024-09-28 21:21:15.484753 : MinCell_TileMatrix_23_chrX, Class = integer

MinCell_TileMatrix_23_chrX: length = 1
[1] 1

2024-09-28 21:21:15.486643 : MaxCell_TileMatrix_23_chrX, Class = integer

MaxCell_TileMatrix_23_chrX: length = 1
[1] 2453

2024-09-28 21:21:16.413553 : Adding TileMatrix to scATAC_BMMC_R1 for Chr (13 of 23)!, 1.017 mins elapsed.

2024-09-28 21:21:16.493522 : NTiles_TileMatrix_13_chr13, Class = numeric

NTiles_TileMatrix_13_chr13: length = 1
 chr13 
230340 

2024-09-28 21:21:16.495684 : NCells_TileMatrix_13_chr13, Class = integer

NCells_TileMatrix_13_chr13: length = 1
[1] 4932

2024-09-28 21:21:16.497687 : MinTile_TileMatrix_13_chr13, Class = numeric

MinTile_TileMatrix_13_chr13: length = 1
[1] 38059

2024-09-28 21:21:16.49995 : MaxTile_TileMatrix_13_chr13, Class = numeric

MaxTile_TileMatrix_13_chr13: length = 1
[1] 230220

2024-09-28 21:21:16.504354 : MinCell_TileMatrix_13_chr13, Class = integer

MinCell_TileMatrix_13_chr13: length = 1
[1] 1

2024-09-28 21:21:16.506237 : MaxCell_TileMatrix_13_chr13, Class = integer

MaxCell_TileMatrix_13_chr13: length = 1
[1] 4932

2024-09-28 21:21:16.74973 : Adding TileMatrix to scATAC_CD34_BMMC_R1 for Chr (20 of 23)!, 1.187 mins elapsed.

2024-09-28 21:21:16.823451 : NTiles_TileMatrix_20_chr20, Class = numeric

NTiles_TileMatrix_20_chr20: length = 1
 chr20 
126052 

2024-09-28 21:21:16.826055 : NCells_TileMatrix_20_chr20, Class = integer

NCells_TileMatrix_20_chr20: length = 1
[1] 3275

2024-09-28 21:21:16.829302 : MinTile_TileMatrix_20_chr20, Class = numeric

MinTile_TileMatrix_20_chr20: length = 1
[1] 121

2024-09-28 21:21:16.832838 : MaxTile_TileMatrix_20_chr20, Class = numeric

MaxTile_TileMatrix_20_chr20: length = 1
[1] 125931

2024-09-28 21:21:16.83972 : MinCell_TileMatrix_20_chr20, Class = integer

MinCell_TileMatrix_20_chr20: length = 1
[1] 1

2024-09-28 21:21:16.842905 : MaxCell_TileMatrix_20_chr20, Class = integer

MaxCell_TileMatrix_20_chr20: length = 1
[1] 3275

2024-09-28 21:21:18.638887 : (scATAC_PBMC_R1 : 3 of 3) Finished Adding TileMatrix!, 6.81 mins elapsed.
2024-09-28 21:21:18.644715 : (scATAC_PBMC_R1 : 3 of 3) Adding GeneScoreMatrix!, 6.81 mins elapsed.

2024-09-28 21:21:18.825714 : scATAC_PBMC_R1 .addGeneScoreMat geneRegions, Class = GRanges
GRanges object with 23127 ranges and 5 metadata columns:
          seqnames              ranges strand |     gene_id       symbol
             <Rle>           <IRanges>  <Rle> | <character>  <character>
      [1]     chr1          6874-14409      + |   100287102      DDX11L1
      [2]     chr1         14362-34961      - |      653635       WASH7P
      [3]     chr1         64091-70008      + |       79501        OR4F5
      [4]     chr1       134773-145566      - |      729737    LOC729737
      [5]     chr1       700245-719068      - |   100288069 LOC100288069
      ...      ...                 ...    ... .         ...          ...
  [23123]     chrX 154294695-154351349      + |       79184        BRCC3
  [23124]     chrX 154439701-154468098      + |        7411         VBP1
  [23125]     chrX 154487526-154498852      - |      116442       RAB39B
  [23126]     chrX 154505500-154568986      - |        1193        CLIC2
  [23127]     chrX 154718673-154847622      - |       55217        TMLHE
          geneStart   geneEnd geneWeight
          <integer> <integer>  <numeric>
      [1]     11874     14409    3.66510
      [2]     29961     14362    1.97496
      [3]     69091     70008    4.39374
      [4]    140566    134773    2.86068
      [5]    714068    700245    2.06694
      ...       ...       ...        ...
  [23123] 154299695 154351349    1.35450
  [23124] 154444701 154468098    1.70724
  [23125] 154493852 154487526    2.77312
  [23126] 154563986 154505500    1.31635
  [23127] 154842622 154718673    1.15575
  -------
  seqinfo: 23 sequences from hg19 genome

2024-09-28 21:21:19.014822 : Adding TileMatrix to scATAC_BMMC_R1 for Chr (14 of 23)!, 1.06 mins elapsed.
2024-09-28 21:21:19.075712 : Adding TileMatrix to scATAC_CD34_BMMC_R1 for Chr (21 of 23)!, 1.226 mins elapsed.

2024-09-28 21:21:19.112168 : NTiles_TileMatrix_14_chr14, Class = numeric

NTiles_TileMatrix_14_chr14: length = 1
 chr14 
214700 

2024-09-28 21:21:19.11418 : NCells_TileMatrix_14_chr14, Class = integer

NCells_TileMatrix_14_chr14: length = 1
[1] 4932

2024-09-28 21:21:19.116066 : MinTile_TileMatrix_14_chr14, Class = numeric

MinTile_TileMatrix_14_chr14: length = 1
[1] 38001

2024-09-28 21:21:19.118418 : MaxTile_TileMatrix_14_chr14, Class = numeric

MaxTile_TileMatrix_14_chr14: length = 1
[1] 214579

2024-09-28 21:21:19.123336 : MinCell_TileMatrix_14_chr14, Class = integer

MinCell_TileMatrix_14_chr14: length = 1
[1] 1

2024-09-28 21:21:19.125336 : MaxCell_TileMatrix_14_chr14, Class = integer

MaxCell_TileMatrix_14_chr14: length = 1
[1] 4932

2024-09-28 21:21:19.133592 : NTiles_TileMatrix_21_chr21, Class = numeric

NTiles_TileMatrix_21_chr21: length = 1
chr21 
96260 

2024-09-28 21:21:19.135911 : NCells_TileMatrix_21_chr21, Class = integer

NCells_TileMatrix_21_chr21: length = 1
[1] 3275

2024-09-28 21:21:19.137814 : MinTile_TileMatrix_21_chr21, Class = numeric

MinTile_TileMatrix_21_chr21: length = 1
[1] 18897

2024-09-28 21:21:19.13985 : MaxTile_TileMatrix_21_chr21, Class = numeric

MaxTile_TileMatrix_21_chr21: length = 1
[1] 96201

2024-09-28 21:21:19.142582 : MinCell_TileMatrix_21_chr21, Class = integer

MinCell_TileMatrix_21_chr21: length = 1
[1] 1

2024-09-28 21:21:19.144447 : MaxCell_TileMatrix_21_chr21, Class = integer

MaxCell_TileMatrix_21_chr21: length = 1
[1] 3275

2024-09-28 21:21:19.169612 : Creating Temp GeneScoreMatrix for scATAC_PBMC_R1, Chr (1 of 23)!, 0.003 mins elapsed.
2024-09-28 21:21:19.306044 : Creating Temp GeneScoreMatrix for scATAC_PBMC_R1, Chr (2 of 23)!, 0.005 mins elapsed.
2024-09-28 21:21:19.445246 : Creating Temp GeneScoreMatrix for scATAC_PBMC_R1, Chr (3 of 23)!, 0.008 mins elapsed.
2024-09-28 21:21:21.259773 : Adding TileMatrix to scATAC_CD34_BMMC_R1 for Chr (22 of 23)!, 1.262 mins elapsed.

2024-09-28 21:21:21.359222 : NTiles_TileMatrix_22_chr22, Class = numeric

NTiles_TileMatrix_22_chr22: length = 1
 chr22 
102610 

2024-09-28 21:21:21.362114 : NCells_TileMatrix_22_chr22, Class = integer

NCells_TileMatrix_22_chr22: length = 1
[1] 3275

2024-09-28 21:21:21.364564 : MinTile_TileMatrix_22_chr22, Class = numeric

MinTile_TileMatrix_22_chr22: length = 1
[1] 32106

2024-09-28 21:21:21.367373 : MaxTile_TileMatrix_22_chr22, Class = numeric

MaxTile_TileMatrix_22_chr22: length = 1
[1] 102480

2024-09-28 21:21:21.371883 : MinCell_TileMatrix_22_chr22, Class = integer

MinCell_TileMatrix_22_chr22: length = 1
[1] 1

2024-09-28 21:21:21.374159 : MaxCell_TileMatrix_22_chr22, Class = integer

MaxCell_TileMatrix_22_chr22: length = 1
[1] 3275

2024-09-28 21:21:22.058041 : Adding TileMatrix to scATAC_BMMC_R1 for Chr (15 of 23)!, 1.111 mins elapsed.

2024-09-28 21:21:22.160099 : NTiles_TileMatrix_15_chr15, Class = numeric

NTiles_TileMatrix_15_chr15: length = 1
 chr15 
205063 

2024-09-28 21:21:22.163064 : NCells_TileMatrix_15_chr15, Class = integer

NCells_TileMatrix_15_chr15: length = 1
[1] 4932

2024-09-28 21:21:22.166079 : MinTile_TileMatrix_15_chr15, Class = numeric

MinTile_TileMatrix_15_chr15: length = 1
[1] 40002

2024-09-28 21:21:22.169384 : MaxTile_TileMatrix_15_chr15, Class = numeric

MaxTile_TileMatrix_15_chr15: length = 1
[1] 205043

2024-09-28 21:21:22.176398 : MinCell_TileMatrix_15_chr15, Class = integer

MinCell_TileMatrix_15_chr15: length = 1
[1] 1

2024-09-28 21:21:22.179016 : MaxCell_TileMatrix_15_chr15, Class = integer

MaxCell_TileMatrix_15_chr15: length = 1
[1] 4932

2024-09-28 21:21:23.887897 : Adding TileMatrix to scATAC_CD34_BMMC_R1 for Chr (23 of 23)!, 1.306 mins elapsed.

2024-09-28 21:21:23.984671 : NTiles_TileMatrix_23_chrX, Class = numeric

NTiles_TileMatrix_23_chrX: length = 1
  chrX 
310542 

2024-09-28 21:21:23.988182 : NCells_TileMatrix_23_chrX, Class = integer

NCells_TileMatrix_23_chrX: length = 1
[1] 3275

2024-09-28 21:21:23.991941 : MinTile_TileMatrix_23_chrX, Class = numeric

MinTile_TileMatrix_23_chrX: length = 1
[1] 121

2024-09-28 21:21:23.99612 : MaxTile_TileMatrix_23_chrX, Class = numeric

MaxTile_TileMatrix_23_chrX: length = 1
[1] 310518

2024-09-28 21:21:24.002957 : MinCell_TileMatrix_23_chrX, Class = integer

MinCell_TileMatrix_23_chrX: length = 1
[1] 1

2024-09-28 21:21:24.006507 : MaxCell_TileMatrix_23_chrX, Class = integer

MaxCell_TileMatrix_23_chrX: length = 1
[1] 3275

2024-09-28 21:21:24.159694 : Creating Temp GeneScoreMatrix for scATAC_PBMC_R1, Chr (4 of 23)!, 0.086 mins elapsed.
2024-09-28 21:21:24.318451 : Creating Temp GeneScoreMatrix for scATAC_PBMC_R1, Chr (5 of 23)!, 0.089 mins elapsed.
2024-09-28 21:21:24.652847 : Creating Temp GeneScoreMatrix for scATAC_PBMC_R1, Chr (6 of 23)!, 0.094 mins elapsed.
2024-09-28 21:21:25.207483 : Adding TileMatrix to scATAC_BMMC_R1 for Chr (16 of 23)!, 1.164 mins elapsed.

2024-09-28 21:21:25.304632 : NTiles_TileMatrix_16_chr16, Class = numeric

NTiles_TileMatrix_16_chr16: length = 1
 chr16 
180710 

2024-09-28 21:21:25.307317 : NCells_TileMatrix_16_chr16, Class = integer

NCells_TileMatrix_16_chr16: length = 1
[1] 4932

2024-09-28 21:21:25.309309 : MinTile_TileMatrix_16_chr16, Class = numeric

MinTile_TileMatrix_16_chr16: length = 1
[1] 121

2024-09-28 21:21:25.311782 : MaxTile_TileMatrix_16_chr16, Class = numeric

MaxTile_TileMatrix_16_chr16: length = 1
[1] 180586

2024-09-28 21:21:25.317415 : MinCell_TileMatrix_16_chr16, Class = integer

MinCell_TileMatrix_16_chr16: length = 1
[1] 1

2024-09-28 21:21:25.319349 : MaxCell_TileMatrix_16_chr16, Class = integer

MaxCell_TileMatrix_16_chr16: length = 1
[1] 4932

2024-09-28 21:21:27.421296 : (scATAC_CD34_BMMC_R1 : 2 of 3) Finished Adding TileMatrix!, 6.957 mins elapsed.
2024-09-28 21:21:27.426425 : (scATAC_CD34_BMMC_R1 : 2 of 3) Adding GeneScoreMatrix!, 6.957 mins elapsed.

2024-09-28 21:21:27.650541 : scATAC_CD34_BMMC_R1 .addGeneScoreMat geneRegions, Class = GRanges
GRanges object with 23127 ranges and 5 metadata columns:
          seqnames              ranges strand |     gene_id       symbol
             <Rle>           <IRanges>  <Rle> | <character>  <character>
      [1]     chr1          6874-14409      + |   100287102      DDX11L1
      [2]     chr1         14362-34961      - |      653635       WASH7P
      [3]     chr1         64091-70008      + |       79501        OR4F5
      [4]     chr1       134773-145566      - |      729737    LOC729737
      [5]     chr1       700245-719068      - |   100288069 LOC100288069
      ...      ...                 ...    ... .         ...          ...
  [23123]     chrX 154294695-154351349      + |       79184        BRCC3
  [23124]     chrX 154439701-154468098      + |        7411         VBP1
  [23125]     chrX 154487526-154498852      - |      116442       RAB39B
  [23126]     chrX 154505500-154568986      - |        1193        CLIC2
  [23127]     chrX 154718673-154847622      - |       55217        TMLHE
          geneStart   geneEnd geneWeight
          <integer> <integer>  <numeric>
      [1]     11874     14409    3.66510
      [2]     29961     14362    1.97496
      [3]     69091     70008    4.39374
      [4]    140566    134773    2.86068
      [5]    714068    700245    2.06694
      ...       ...       ...        ...
  [23123] 154299695 154351349    1.35450
  [23124] 154444701 154468098    1.70724
  [23125] 154493852 154487526    2.77312
  [23126] 154563986 154505500    1.31635
  [23127] 154842622 154718673    1.15575
  -------
  seqinfo: 23 sequences from hg19 genome

2024-09-28 21:21:28.134934 : Creating Temp GeneScoreMatrix for scATAC_CD34_BMMC_R1, Chr (1 of 23)!, 0.004 mins elapsed.
2024-09-28 21:21:28.299227 : Creating Temp GeneScoreMatrix for scATAC_CD34_BMMC_R1, Chr (2 of 23)!, 0.007 mins elapsed.
2024-09-28 21:21:28.411727 : Adding TileMatrix to scATAC_BMMC_R1 for Chr (17 of 23)!, 1.217 mins elapsed.
2024-09-28 21:21:28.484145 : Creating Temp GeneScoreMatrix for scATAC_CD34_BMMC_R1, Chr (3 of 23)!, 0.01 mins elapsed.

2024-09-28 21:21:28.59573 : NTiles_TileMatrix_17_chr17, Class = numeric

NTiles_TileMatrix_17_chr17: length = 1
 chr17 
162391 

2024-09-28 21:21:28.598547 : NCells_TileMatrix_17_chr17, Class = integer

NCells_TileMatrix_17_chr17: length = 1
[1] 4932

2024-09-28 21:21:28.600986 : MinTile_TileMatrix_17_chr17, Class = numeric

MinTile_TileMatrix_17_chr17: length = 1
[1] 1

2024-09-28 21:21:28.605426 : MaxTile_TileMatrix_17_chr17, Class = numeric

MaxTile_TileMatrix_17_chr17: length = 1
[1] 162391

2024-09-28 21:21:28.618472 : MinCell_TileMatrix_17_chr17, Class = integer

MinCell_TileMatrix_17_chr17: length = 1
[1] 1

2024-09-28 21:21:28.622024 : MaxCell_TileMatrix_17_chr17, Class = integer

MaxCell_TileMatrix_17_chr17: length = 1
[1] 4932

2024-09-28 21:21:28.652545 : Creating Temp GeneScoreMatrix for scATAC_PBMC_R1, Chr (7 of 23)!, 0.161 mins elapsed.
2024-09-28 21:21:29.074667 : Creating Temp GeneScoreMatrix for scATAC_PBMC_R1, Chr (8 of 23)!, 0.168 mins elapsed.
2024-09-28 21:21:29.402402 : Creating Temp GeneScoreMatrix for scATAC_PBMC_R1, Chr (9 of 23)!, 0.174 mins elapsed.
2024-09-28 21:21:32.146647 : Adding TileMatrix to scATAC_BMMC_R1 for Chr (18 of 23)!, 1.279 mins elapsed.

2024-09-28 21:21:32.269975 : NTiles_TileMatrix_18_chr18, Class = numeric

NTiles_TileMatrix_18_chr18: length = 1
 chr18 
156155 

2024-09-28 21:21:32.273862 : NCells_TileMatrix_18_chr18, Class = integer

NCells_TileMatrix_18_chr18: length = 1
[1] 4932

2024-09-28 21:21:32.277431 : MinTile_TileMatrix_18_chr18, Class = numeric

MinTile_TileMatrix_18_chr18: length = 1
[1] 21

2024-09-28 21:21:32.281749 : MaxTile_TileMatrix_18_chr18, Class = numeric

MaxTile_TileMatrix_18_chr18: length = 1
[1] 156033

2024-09-28 21:21:32.289001 : MinCell_TileMatrix_18_chr18, Class = integer

MinCell_TileMatrix_18_chr18: length = 1
[1] 1

2024-09-28 21:21:32.292638 : MaxCell_TileMatrix_18_chr18, Class = integer

MaxCell_TileMatrix_18_chr18: length = 1
[1] 4932

2024-09-28 21:21:33.883065 : Creating Temp GeneScoreMatrix for scATAC_PBMC_R1, Chr (10 of 23)!, 0.248 mins elapsed.
2024-09-28 21:21:34.208801 : Creating Temp GeneScoreMatrix for scATAC_CD34_BMMC_R1, Chr (4 of 23)!, 0.105 mins elapsed.
2024-09-28 21:21:34.410274 : Creating Temp GeneScoreMatrix for scATAC_CD34_BMMC_R1, Chr (5 of 23)!, 0.109 mins elapsed.
2024-09-28 21:21:34.506649 : Creating Temp GeneScoreMatrix for scATAC_PBMC_R1, Chr (11 of 23)!, 0.259 mins elapsed.
2024-09-28 21:21:34.688688 : Creating Temp GeneScoreMatrix for scATAC_CD34_BMMC_R1, Chr (6 of 23)!, 0.113 mins elapsed.
2024-09-28 21:21:34.833999 : Creating Temp GeneScoreMatrix for scATAC_PBMC_R1, Chr (12 of 23)!, 0.264 mins elapsed.
2024-09-28 21:21:35.49585 : Adding TileMatrix to scATAC_BMMC_R1 for Chr (19 of 23)!, 1.335 mins elapsed.

2024-09-28 21:21:35.628601 : NTiles_TileMatrix_19_chr19, Class = numeric

NTiles_TileMatrix_19_chr19: length = 1
 chr19 
118258 

2024-09-28 21:21:35.631404 : NCells_TileMatrix_19_chr19, Class = integer

NCells_TileMatrix_19_chr19: length = 1
[1] 4932

2024-09-28 21:21:35.634223 : MinTile_TileMatrix_19_chr19, Class = numeric

MinTile_TileMatrix_19_chr19: length = 1
[1] 179

2024-09-28 21:21:35.638264 : MaxTile_TileMatrix_19_chr19, Class = numeric

MaxTile_TileMatrix_19_chr19: length = 1
[1] 118238

2024-09-28 21:21:35.650245 : MinCell_TileMatrix_19_chr19, Class = integer

MinCell_TileMatrix_19_chr19: length = 1
[1] 1

2024-09-28 21:21:35.652956 : MaxCell_TileMatrix_19_chr19, Class = integer

MaxCell_TileMatrix_19_chr19: length = 1
[1] 4932

2024-09-28 21:21:39.134984 : Creating Temp GeneScoreMatrix for scATAC_PBMC_R1, Chr (13 of 23)!, 0.336 mins elapsed.
2024-09-28 21:21:39.389343 : Adding TileMatrix to scATAC_BMMC_R1 for Chr (20 of 23)!, 1.4 mins elapsed.

2024-09-28 21:21:39.543781 : NTiles_TileMatrix_20_chr20, Class = numeric

NTiles_TileMatrix_20_chr20: length = 1
 chr20 
126052 

2024-09-28 21:21:39.547987 : NCells_TileMatrix_20_chr20, Class = integer

NCells_TileMatrix_20_chr20: length = 1
[1] 4932

2024-09-28 21:21:39.551718 : MinTile_TileMatrix_20_chr20, Class = numeric

MinTile_TileMatrix_20_chr20: length = 1
[1] 121

2024-09-28 21:21:39.556671 : MaxTile_TileMatrix_20_chr20, Class = numeric

MaxTile_TileMatrix_20_chr20: length = 1
[1] 125924

2024-09-28 21:21:39.566376 : MinCell_TileMatrix_20_chr20, Class = integer

MinCell_TileMatrix_20_chr20: length = 1
[1] 1

2024-09-28 21:21:39.570119 : MaxCell_TileMatrix_20_chr20, Class = integer

MaxCell_TileMatrix_20_chr20: length = 1
[1] 4932

2024-09-28 21:21:39.684343 : Creating Temp GeneScoreMatrix for scATAC_CD34_BMMC_R1, Chr (7 of 23)!, 0.197 mins elapsed.
2024-09-28 21:21:39.860363 : Creating Temp GeneScoreMatrix for scATAC_CD34_BMMC_R1, Chr (8 of 23)!, 0.2 mins elapsed.
2024-09-28 21:21:40.050838 : Creating Temp GeneScoreMatrix for scATAC_PBMC_R1, Chr (14 of 23)!, 0.351 mins elapsed.
2024-09-28 21:21:40.263417 : Creating Temp GeneScoreMatrix for scATAC_PBMC_R1, Chr (15 of 23)!, 0.355 mins elapsed.
2024-09-28 21:21:40.320254 : Creating Temp GeneScoreMatrix for scATAC_CD34_BMMC_R1, Chr (9 of 23)!, 0.207 mins elapsed.
2024-09-28 21:21:42.412525 : Adding TileMatrix to scATAC_BMMC_R1 for Chr (21 of 23)!, 1.45 mins elapsed.

2024-09-28 21:21:42.499747 : NTiles_TileMatrix_21_chr21, Class = numeric

NTiles_TileMatrix_21_chr21: length = 1
chr21 
96260 

2024-09-28 21:21:42.502872 : NCells_TileMatrix_21_chr21, Class = integer

NCells_TileMatrix_21_chr21: length = 1
[1] 4932

2024-09-28 21:21:42.505589 : MinTile_TileMatrix_21_chr21, Class = numeric

MinTile_TileMatrix_21_chr21: length = 1
[1] 18826

2024-09-28 21:21:42.508966 : MaxTile_TileMatrix_21_chr21, Class = numeric

MaxTile_TileMatrix_21_chr21: length = 1
[1] 96240

2024-09-28 21:21:42.515054 : MinCell_TileMatrix_21_chr21, Class = integer

MinCell_TileMatrix_21_chr21: length = 1
[1] 1

2024-09-28 21:21:42.518465 : MaxCell_TileMatrix_21_chr21, Class = integer

MaxCell_TileMatrix_21_chr21: length = 1
[1] 4932

2024-09-28 21:21:44.127871 : Creating Temp GeneScoreMatrix for scATAC_PBMC_R1, Chr (16 of 23)!, 0.419 mins elapsed.
2024-09-28 21:21:45.19261 : Creating Temp GeneScoreMatrix for scATAC_PBMC_R1, Chr (17 of 23)!, 0.437 mins elapsed.
2024-09-28 21:21:45.231668 : Creating Temp GeneScoreMatrix for scATAC_CD34_BMMC_R1, Chr (10 of 23)!, 0.289 mins elapsed.
2024-09-28 21:21:45.353667 : Creating Temp GeneScoreMatrix for scATAC_PBMC_R1, Chr (18 of 23)!, 0.439 mins elapsed.
2024-09-28 21:21:45.420974 : Creating Temp GeneScoreMatrix for scATAC_CD34_BMMC_R1, Chr (11 of 23)!, 0.292 mins elapsed.
2024-09-28 21:21:45.629655 : Adding TileMatrix to scATAC_BMMC_R1 for Chr (22 of 23)!, 1.504 mins elapsed.

2024-09-28 21:21:45.741571 : NTiles_TileMatrix_22_chr22, Class = numeric

NTiles_TileMatrix_22_chr22: length = 1
 chr22 
102610 

2024-09-28 21:21:45.74473 : NCells_TileMatrix_22_chr22, Class = integer

NCells_TileMatrix_22_chr22: length = 1
[1] 4932

2024-09-28 21:21:45.748122 : MinTile_TileMatrix_22_chr22, Class = numeric

MinTile_TileMatrix_22_chr22: length = 1
[1] 32140

2024-09-28 21:21:45.752048 : MaxTile_TileMatrix_22_chr22, Class = numeric

MaxTile_TileMatrix_22_chr22: length = 1
[1] 102469

2024-09-28 21:21:45.758855 : MinCell_TileMatrix_22_chr22, Class = integer

MinCell_TileMatrix_22_chr22: length = 1
[1] 1

2024-09-28 21:21:45.762579 : MaxCell_TileMatrix_22_chr22, Class = integer

MaxCell_TileMatrix_22_chr22: length = 1
[1] 4932

2024-09-28 21:21:45.800041 : Creating Temp GeneScoreMatrix for scATAC_CD34_BMMC_R1, Chr (12 of 23)!, 0.299 mins elapsed.
2024-09-28 21:21:48.637022 : Adding TileMatrix to scATAC_BMMC_R1 for Chr (23 of 23)!, 1.554 mins elapsed.

2024-09-28 21:21:48.747159 : NTiles_TileMatrix_23_chrX, Class = numeric

NTiles_TileMatrix_23_chrX: length = 1
  chrX 
310542 

2024-09-28 21:21:48.75043 : NCells_TileMatrix_23_chrX, Class = integer

NCells_TileMatrix_23_chrX: length = 1
[1] 4932

2024-09-28 21:21:48.76174 : MinTile_TileMatrix_23_chrX, Class = numeric

MinTile_TileMatrix_23_chrX: length = 1
[1] 120

2024-09-28 21:21:48.766269 : MaxTile_TileMatrix_23_chrX, Class = numeric

MaxTile_TileMatrix_23_chrX: length = 1
[1] 310521

2024-09-28 21:21:48.773529 : MinCell_TileMatrix_23_chrX, Class = integer

MinCell_TileMatrix_23_chrX: length = 1
[1] 1

2024-09-28 21:21:48.776916 : MaxCell_TileMatrix_23_chrX, Class = integer

MaxCell_TileMatrix_23_chrX: length = 1
[1] 4932

2024-09-28 21:21:49.504193 : Creating Temp GeneScoreMatrix for scATAC_PBMC_R1, Chr (19 of 23)!, 0.509 mins elapsed.
2024-09-28 21:21:50.340519 : Creating Temp GeneScoreMatrix for scATAC_PBMC_R1, Chr (20 of 23)!, 0.522 mins elapsed.
2024-09-28 21:21:50.680825 : Creating Temp GeneScoreMatrix for scATAC_PBMC_R1, Chr (21 of 23)!, 0.528 mins elapsed.
2024-09-28 21:21:50.829811 : Creating Temp GeneScoreMatrix for scATAC_CD34_BMMC_R1, Chr (13 of 23)!, 0.382 mins elapsed.
2024-09-28 21:21:51.190292 : Creating Temp GeneScoreMatrix for scATAC_CD34_BMMC_R1, Chr (14 of 23)!, 0.388 mins elapsed.
2024-09-28 21:21:51.346846 : Creating Temp GeneScoreMatrix for scATAC_CD34_BMMC_R1, Chr (15 of 23)!, 0.391 mins elapsed.
2024-09-28 21:21:53.385374 : (scATAC_BMMC_R1 : 1 of 3) Finished Adding TileMatrix!, 7.389 mins elapsed.
2024-09-28 21:21:53.393914 : (scATAC_BMMC_R1 : 1 of 3) Adding GeneScoreMatrix!, 7.389 mins elapsed.

2024-09-28 21:21:53.656117 : scATAC_BMMC_R1 .addGeneScoreMat geneRegions, Class = GRanges
GRanges object with 23127 ranges and 5 metadata columns:
          seqnames              ranges strand |     gene_id       symbol
             <Rle>           <IRanges>  <Rle> | <character>  <character>
      [1]     chr1          6874-14409      + |   100287102      DDX11L1
      [2]     chr1         14362-34961      - |      653635       WASH7P
      [3]     chr1         64091-70008      + |       79501        OR4F5
      [4]     chr1       134773-145566      - |      729737    LOC729737
      [5]     chr1       700245-719068      - |   100288069 LOC100288069
      ...      ...                 ...    ... .         ...          ...
  [23123]     chrX 154294695-154351349      + |       79184        BRCC3
  [23124]     chrX 154439701-154468098      + |        7411         VBP1
  [23125]     chrX 154487526-154498852      - |      116442       RAB39B
  [23126]     chrX 154505500-154568986      - |        1193        CLIC2
  [23127]     chrX 154718673-154847622      - |       55217        TMLHE
          geneStart   geneEnd geneWeight
          <integer> <integer>  <numeric>
      [1]     11874     14409    3.66510
      [2]     29961     14362    1.97496
      [3]     69091     70008    4.39374
      [4]    140566    134773    2.86068
      [5]    714068    700245    2.06694
      ...       ...       ...        ...
  [23123] 154299695 154351349    1.35450
  [23124] 154444701 154468098    1.70724
  [23125] 154493852 154487526    2.77312
  [23126] 154563986 154505500    1.31635
  [23127] 154842622 154718673    1.15575
  -------
  seqinfo: 23 sequences from hg19 genome

2024-09-28 21:21:54.213453 : Creating Temp GeneScoreMatrix for scATAC_BMMC_R1, Chr (1 of 23)!, 0.005 mins elapsed.
2024-09-28 21:21:54.40433 : Creating Temp GeneScoreMatrix for scATAC_BMMC_R1, Chr (2 of 23)!, 0.008 mins elapsed.
2024-09-28 21:21:54.623122 : Creating Temp GeneScoreMatrix for scATAC_BMMC_R1, Chr (3 of 23)!, 0.011 mins elapsed.
2024-09-28 21:21:54.988075 : Creating Temp GeneScoreMatrix for scATAC_PBMC_R1, Chr (22 of 23)!, 0.6 mins elapsed.
2024-09-28 21:21:55.350108 : Creating Temp GeneScoreMatrix for scATAC_PBMC_R1, Chr (23 of 23)!, 0.606 mins elapsed.
2024-09-28 21:21:55.851202 : Creating Temp GeneScoreMatrix for scATAC_CD34_BMMC_R1, Chr (16 of 23)!, 0.466 mins elapsed.
2024-09-28 21:21:56.328296 : Creating Temp GeneScoreMatrix for scATAC_CD34_BMMC_R1, Chr (17 of 23)!, 0.474 mins elapsed.
2024-09-28 21:21:56.483184 : Creating Temp GeneScoreMatrix for scATAC_CD34_BMMC_R1, Chr (18 of 23)!, 0.477 mins elapsed.
2024-09-28 21:22:01.240504 : Creating Temp GeneScoreMatrix for scATAC_BMMC_R1, Chr (4 of 23)!, 0.122 mins elapsed.
2024-09-28 21:22:01.464831 : Creating Temp GeneScoreMatrix for scATAC_CD34_BMMC_R1, Chr (19 of 23)!, 0.56 mins elapsed.
2024-09-28 21:22:01.542116 : Creating Temp GeneScoreMatrix for scATAC_BMMC_R1, Chr (5 of 23)!, 0.127 mins elapsed.

2024-09-28 21:22:01.823714 : scATAC_PBMC_R1 .addGeneScoreMat FeatureDF, Class = data.frame
scATAC_PBMC_R1 .addGeneScoreMat FeatureDF: nRows = 23127, nCols = 6
  seqnames  start    end strand         name idx
1     chr1  11874  14409      1      DDX11L1   1
2     chr1  29961  14362      2       WASH7P   2
3     chr1  69091  70008      1        OR4F5   3
4     chr1 140566 134773      2    LOC729737   4
5     chr1 714068 700245      2 LOC100288069   5
6     chr1 762971 794826      1    LINC01128   6

2024-09-28 21:22:01.854111 : Creating Temp GeneScoreMatrix for scATAC_BMMC_R1, Chr (6 of 23)!, 0.132 mins elapsed.
2024-09-28 21:22:01.924266 : Creating Temp GeneScoreMatrix for scATAC_CD34_BMMC_R1, Chr (20 of 23)!, 0.567 mins elapsed.
2024-09-28 21:22:02.361617 : Creating Temp GeneScoreMatrix for scATAC_CD34_BMMC_R1, Chr (21 of 23)!, 0.575 mins elapsed.
2024-09-28 21:22:03.279457 : Adding GeneScoreMatrix to scATAC_PBMC_R1 for Chr (1 of 23)!, 0.738 mins elapsed.
2024-09-28 21:22:04.628091 : Adding GeneScoreMatrix to scATAC_PBMC_R1 for Chr (2 of 23)!, 0.761 mins elapsed.
2024-09-28 21:22:05.994343 : Adding GeneScoreMatrix to scATAC_PBMC_R1 for Chr (3 of 23)!, 0.783 mins elapsed.
2024-09-28 21:22:07.025744 : Creating Temp GeneScoreMatrix for scATAC_CD34_BMMC_R1, Chr (22 of 23)!, 0.652 mins elapsed.
2024-09-28 21:22:07.212531 : Creating Temp GeneScoreMatrix for scATAC_BMMC_R1, Chr (7 of 23)!, 0.221 mins elapsed.
2024-09-28 21:22:07.22122 : Creating Temp GeneScoreMatrix for scATAC_CD34_BMMC_R1, Chr (23 of 23)!, 0.656 mins elapsed.
2024-09-28 21:22:07.642381 : Creating Temp GeneScoreMatrix for scATAC_BMMC_R1, Chr (8 of 23)!, 0.228 mins elapsed.
2024-09-28 21:22:08.004613 : Creating Temp GeneScoreMatrix for scATAC_BMMC_R1, Chr (9 of 23)!, 0.234 mins elapsed.
2024-09-28 21:22:08.070723 : Adding GeneScoreMatrix to scATAC_PBMC_R1 for Chr (4 of 23)!, 0.818 mins elapsed.
2024-09-28 21:22:08.923992 : Adding GeneScoreMatrix to scATAC_PBMC_R1 for Chr (5 of 23)!, 0.832 mins elapsed.
2024-09-28 21:22:09.956488 : Adding GeneScoreMatrix to scATAC_PBMC_R1 for Chr (6 of 23)!, 0.849 mins elapsed.
2024-09-28 21:22:11.972014 : Adding GeneScoreMatrix to scATAC_PBMC_R1 for Chr (7 of 23)!, 0.883 mins elapsed.
2024-09-28 21:22:12.871827 : Creating Temp GeneScoreMatrix for scATAC_BMMC_R1, Chr (10 of 23)!, 0.316 mins elapsed.
2024-09-28 21:22:12.921237 : Adding GeneScoreMatrix to scATAC_PBMC_R1 for Chr (8 of 23)!, 0.899 mins elapsed.
2024-09-28 21:22:13.045879 : Creating Temp GeneScoreMatrix for scATAC_BMMC_R1, Chr (11 of 23)!, 0.319 mins elapsed.

2024-09-28 21:22:13.117809 : scATAC_CD34_BMMC_R1 .addGeneScoreMat FeatureDF, Class = data.frame
scATAC_CD34_BMMC_R1 .addGeneScoreMat FeatureDF: nRows = 23127, nCols = 6
  seqnames  start    end strand         name idx
1     chr1  11874  14409      1      DDX11L1   1
2     chr1  29961  14362      2       WASH7P   2
3     chr1  69091  70008      1        OR4F5   3
4     chr1 140566 134773      2    LOC729737   4
5     chr1 714068 700245      2 LOC100288069   5
6     chr1 762971 794826      1    LINC01128   6

2024-09-28 21:22:13.448822 : Creating Temp GeneScoreMatrix for scATAC_BMMC_R1, Chr (12 of 23)!, 0.325 mins elapsed.
2024-09-28 21:22:13.780502 : Adding GeneScoreMatrix to scATAC_PBMC_R1 for Chr (9 of 23)!, 0.913 mins elapsed.
2024-09-28 21:22:14.439366 : Adding GeneScoreMatrix to scATAC_CD34_BMMC_R1 for Chr (1 of 23)!, 0.776 mins elapsed.
2024-09-28 21:22:15.236556 : Adding GeneScoreMatrix to scATAC_PBMC_R1 for Chr (10 of 23)!, 0.937 mins elapsed.
2024-09-28 21:22:15.612723 : Adding GeneScoreMatrix to scATAC_CD34_BMMC_R1 for Chr (2 of 23)!, 0.795 mins elapsed.
2024-09-28 21:22:16.153454 : Adding GeneScoreMatrix to scATAC_PBMC_R1 for Chr (11 of 23)!, 0.953 mins elapsed.
2024-09-28 21:22:16.685695 : Adding GeneScoreMatrix to scATAC_CD34_BMMC_R1 for Chr (3 of 23)!, 0.813 mins elapsed.
2024-09-28 21:22:17.221939 : Adding GeneScoreMatrix to scATAC_PBMC_R1 for Chr (12 of 23)!, 0.971 mins elapsed.
2024-09-28 21:22:17.860287 : Creating Temp GeneScoreMatrix for scATAC_BMMC_R1, Chr (13 of 23)!, 0.399 mins elapsed.
2024-09-28 21:22:18.267208 : Creating Temp GeneScoreMatrix for scATAC_BMMC_R1, Chr (14 of 23)!, 0.406 mins elapsed.
2024-09-28 21:22:18.478322 : Adding GeneScoreMatrix to scATAC_CD34_BMMC_R1 for Chr (4 of 23)!, 0.843 mins elapsed.
2024-09-28 21:22:18.616184 : Creating Temp GeneScoreMatrix for scATAC_BMMC_R1, Chr (15 of 23)!, 0.411 mins elapsed.
2024-09-28 21:22:18.944703 : Adding GeneScoreMatrix to scATAC_PBMC_R1 for Chr (13 of 23)!, 0.999 mins elapsed.
2024-09-28 21:22:19.334833 : Adding GeneScoreMatrix to scATAC_CD34_BMMC_R1 for Chr (5 of 23)!, 0.858 mins elapsed.
2024-09-28 21:22:19.708251 : Adding GeneScoreMatrix to scATAC_PBMC_R1 for Chr (14 of 23)!, 1.012 mins elapsed.
2024-09-28 21:22:20.250512 : Adding GeneScoreMatrix to scATAC_CD34_BMMC_R1 for Chr (6 of 23)!, 0.873 mins elapsed.
2024-09-28 21:22:20.586571 : Adding GeneScoreMatrix to scATAC_PBMC_R1 for Chr (15 of 23)!, 1.027 mins elapsed.
2024-09-28 21:22:22.033247 : Adding GeneScoreMatrix to scATAC_CD34_BMMC_R1 for Chr (7 of 23)!, 0.902 mins elapsed.
2024-09-28 21:22:22.336797 : Adding GeneScoreMatrix to scATAC_PBMC_R1 for Chr (16 of 23)!, 1.056 mins elapsed.
2024-09-28 21:22:22.436664 : Creating Temp GeneScoreMatrix for scATAC_BMMC_R1, Chr (16 of 23)!, 0.475 mins elapsed.
2024-09-28 21:22:23.014881 : Creating Temp GeneScoreMatrix for scATAC_BMMC_R1, Chr (17 of 23)!, 0.485 mins elapsed.
2024-09-28 21:22:23.115469 : Adding GeneScoreMatrix to scATAC_CD34_BMMC_R1 for Chr (8 of 23)!, 0.921 mins elapsed.
2024-09-28 21:22:23.29365 : Creating Temp GeneScoreMatrix for scATAC_BMMC_R1, Chr (18 of 23)!, 0.489 mins elapsed.
2024-09-28 21:22:23.347442 : Adding GeneScoreMatrix to scATAC_PBMC_R1 for Chr (17 of 23)!, 1.073 mins elapsed.
2024-09-28 21:22:23.941003 : Adding GeneScoreMatrix to scATAC_CD34_BMMC_R1 for Chr (9 of 23)!, 0.934 mins elapsed.
2024-09-28 21:22:24.183393 : Adding GeneScoreMatrix to scATAC_PBMC_R1 for Chr (18 of 23)!, 1.087 mins elapsed.
2024-09-28 21:22:25.454645 : Adding GeneScoreMatrix to scATAC_CD34_BMMC_R1 for Chr (10 of 23)!, 0.96 mins elapsed.
2024-09-28 21:22:25.757102 : Adding GeneScoreMatrix to scATAC_PBMC_R1 for Chr (19 of 23)!, 1.113 mins elapsed.
2024-09-28 21:22:26.41485 : Adding GeneScoreMatrix to scATAC_CD34_BMMC_R1 for Chr (11 of 23)!, 0.976 mins elapsed.
2024-09-28 21:22:26.810773 : Adding GeneScoreMatrix to scATAC_PBMC_R1 for Chr (20 of 23)!, 1.13 mins elapsed.
2024-09-28 21:22:27.212894 : Creating Temp GeneScoreMatrix for scATAC_BMMC_R1, Chr (19 of 23)!, 0.555 mins elapsed.
2024-09-28 21:22:27.545388 : Adding GeneScoreMatrix to scATAC_CD34_BMMC_R1 for Chr (12 of 23)!, 0.994 mins elapsed.
2024-09-28 21:22:27.715158 : Creating Temp GeneScoreMatrix for scATAC_BMMC_R1, Chr (20 of 23)!, 0.563 mins elapsed.
2024-09-28 21:22:27.77736 : Adding GeneScoreMatrix to scATAC_PBMC_R1 for Chr (21 of 23)!, 1.146 mins elapsed.
2024-09-28 21:22:28.25431 : Creating Temp GeneScoreMatrix for scATAC_BMMC_R1, Chr (21 of 23)!, 0.572 mins elapsed.
2024-09-28 21:22:29.013598 : Adding GeneScoreMatrix to scATAC_CD34_BMMC_R1 for Chr (13 of 23)!, 1.019 mins elapsed.
2024-09-28 21:22:29.13852 : Adding GeneScoreMatrix to scATAC_PBMC_R1 for Chr (22 of 23)!, 1.169 mins elapsed.
2024-09-28 21:22:29.914549 : Adding GeneScoreMatrix to scATAC_CD34_BMMC_R1 for Chr (14 of 23)!, 1.034 mins elapsed.
2024-09-28 21:22:30.0538 : Adding GeneScoreMatrix to scATAC_PBMC_R1 for Chr (23 of 23)!, 1.184 mins elapsed.
2024-09-28 21:22:30.993005 : Adding GeneScoreMatrix to scATAC_CD34_BMMC_R1 for Chr (15 of 23)!, 1.052 mins elapsed.
2024-09-28 21:22:32.597301 : Creating Temp GeneScoreMatrix for scATAC_BMMC_R1, Chr (22 of 23)!, 0.644 mins elapsed.
2024-09-28 21:22:32.648695 : (scATAC_PBMC_R1 : 3 of 3) Finished Adding GeneScoreMatrix!, 8.044 mins elapsed.
2024-09-28 21:22:32.653593 : (scATAC_PBMC_R1 : 3 of 3) Finished Creating Arrow File, 8.044 mins elapsed.
2024-09-28 21:22:32.762561 : Creating Temp GeneScoreMatrix for scATAC_BMMC_R1, Chr (23 of 23)!, 0.647 mins elapsed.
2024-09-28 21:22:32.856508 : Adding GeneScoreMatrix to scATAC_CD34_BMMC_R1 for Chr (16 of 23)!, 1.083 mins elapsed.
2024-09-28 21:22:33.580387 : Adding GeneScoreMatrix to scATAC_CD34_BMMC_R1 for Chr (17 of 23)!, 1.095 mins elapsed.
2024-09-28 21:22:34.399141 : Adding GeneScoreMatrix to scATAC_CD34_BMMC_R1 for Chr (18 of 23)!, 1.109 mins elapsed.
2024-09-28 21:22:35.785104 : Adding GeneScoreMatrix to scATAC_CD34_BMMC_R1 for Chr (19 of 23)!, 1.132 mins elapsed.
2024-09-28 21:22:36.663957 : Adding GeneScoreMatrix to scATAC_CD34_BMMC_R1 for Chr (20 of 23)!, 1.146 mins elapsed.
2024-09-28 21:22:37.438979 : Adding GeneScoreMatrix to scATAC_CD34_BMMC_R1 for Chr (21 of 23)!, 1.159 mins elapsed.

2024-09-28 21:22:37.44899 : scATAC_BMMC_R1 .addGeneScoreMat FeatureDF, Class = data.frame
scATAC_BMMC_R1 .addGeneScoreMat FeatureDF: nRows = 23127, nCols = 6
  seqnames  start    end strand         name idx
1     chr1  11874  14409      1      DDX11L1   1
2     chr1  29961  14362      2       WASH7P   2
3     chr1  69091  70008      1        OR4F5   3
4     chr1 140566 134773      2    LOC729737   4
5     chr1 714068 700245      2 LOC100288069   5
6     chr1 762971 794826      1    LINC01128   6

2024-09-28 21:22:38.618597 : Adding GeneScoreMatrix to scATAC_CD34_BMMC_R1 for Chr (22 of 23)!, 1.179 mins elapsed.
2024-09-28 21:22:38.635199 : Adding GeneScoreMatrix to scATAC_BMMC_R1 for Chr (1 of 23)!, 0.745 mins elapsed.
2024-09-28 21:22:39.317501 : Adding GeneScoreMatrix to scATAC_CD34_BMMC_R1 for Chr (23 of 23)!, 1.191 mins elapsed.
2024-09-28 21:22:39.683691 : Adding GeneScoreMatrix to scATAC_BMMC_R1 for Chr (2 of 23)!, 0.762 mins elapsed.
2024-09-28 21:22:40.581784 : Adding GeneScoreMatrix to scATAC_BMMC_R1 for Chr (3 of 23)!, 0.777 mins elapsed.
2024-09-28 21:22:41.000546 : (scATAC_CD34_BMMC_R1 : 2 of 3) Finished Adding GeneScoreMatrix!, 8.183 mins elapsed.
2024-09-28 21:22:41.00783 : (scATAC_CD34_BMMC_R1 : 2 of 3) Finished Creating Arrow File, 8.183 mins elapsed.
2024-09-28 21:22:41.866963 : Adding GeneScoreMatrix to scATAC_BMMC_R1 for Chr (4 of 23)!, 0.799 mins elapsed.
2024-09-28 21:22:42.591931 : Adding GeneScoreMatrix to scATAC_BMMC_R1 for Chr (5 of 23)!, 0.811 mins elapsed.
2024-09-28 21:22:43.310373 : Adding GeneScoreMatrix to scATAC_BMMC_R1 for Chr (6 of 23)!, 0.823 mins elapsed.
2024-09-28 21:22:44.499218 : Adding GeneScoreMatrix to scATAC_BMMC_R1 for Chr (7 of 23)!, 0.843 mins elapsed.
2024-09-28 21:22:45.239315 : Adding GeneScoreMatrix to scATAC_BMMC_R1 for Chr (8 of 23)!, 0.855 mins elapsed.
2024-09-28 21:22:46.086942 : Adding GeneScoreMatrix to scATAC_BMMC_R1 for Chr (9 of 23)!, 0.869 mins elapsed.
2024-09-28 21:22:47.293004 : Adding GeneScoreMatrix to scATAC_BMMC_R1 for Chr (10 of 23)!, 0.889 mins elapsed.
2024-09-28 21:22:48.120879 : Adding GeneScoreMatrix to scATAC_BMMC_R1 for Chr (11 of 23)!, 0.903 mins elapsed.
2024-09-28 21:22:48.970482 : Adding GeneScoreMatrix to scATAC_BMMC_R1 for Chr (12 of 23)!, 0.917 mins elapsed.
2024-09-28 21:22:50.302697 : Adding GeneScoreMatrix to scATAC_BMMC_R1 for Chr (13 of 23)!, 0.939 mins elapsed.
2024-09-28 21:22:51.002847 : Adding GeneScoreMatrix to scATAC_BMMC_R1 for Chr (14 of 23)!, 0.951 mins elapsed.
2024-09-28 21:22:51.73419 : Adding GeneScoreMatrix to scATAC_BMMC_R1 for Chr (15 of 23)!, 0.963 mins elapsed.
2024-09-28 21:22:52.951781 : Adding GeneScoreMatrix to scATAC_BMMC_R1 for Chr (16 of 23)!, 0.984 mins elapsed.
2024-09-28 21:22:53.688723 : Adding GeneScoreMatrix to scATAC_BMMC_R1 for Chr (17 of 23)!, 0.996 mins elapsed.
2024-09-28 21:22:54.443211 : Adding GeneScoreMatrix to scATAC_BMMC_R1 for Chr (18 of 23)!, 1.008 mins elapsed.
2024-09-28 21:22:55.599115 : Adding GeneScoreMatrix to scATAC_BMMC_R1 for Chr (19 of 23)!, 1.028 mins elapsed.
2024-09-28 21:22:56.463166 : Adding GeneScoreMatrix to scATAC_BMMC_R1 for Chr (20 of 23)!, 1.042 mins elapsed.
2024-09-28 21:22:57.156293 : Adding GeneScoreMatrix to scATAC_BMMC_R1 for Chr (21 of 23)!, 1.054 mins elapsed.
2024-09-28 21:22:58.300989 : Adding GeneScoreMatrix to scATAC_BMMC_R1 for Chr (22 of 23)!, 1.073 mins elapsed.
2024-09-28 21:22:59.000495 : Adding GeneScoreMatrix to scATAC_BMMC_R1 for Chr (23 of 23)!, 1.084 mins elapsed.
2024-09-28 21:23:00.619336 : (scATAC_BMMC_R1 : 1 of 3) Finished Adding GeneScoreMatrix!, 8.51 mins elapsed.
2024-09-28 21:23:00.623774 : (scATAC_BMMC_R1 : 1 of 3) Finished Creating Arrow File, 8.51 mins elapsed.

------- Completed

End Time : 2024-09-28 21:23:00.672318
Elapsed Time Minutes = 8.51245918273926
Elapsed Time Hours = 0.141874507599407

-------

How should I solve this problem?

Thanks a lot

[rcorces]

Hi @danli349! 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.

[Erfan1369]

Hello, I use ArchR on a Unix-based R system, and the exact same issue happened to me. However, it is not a problem with ArchR itself, but rather with the compatibility of the different packages that ArchR relies on. After using the following packages, the plots were created successfully. This issue has already been discussed as well.

Here is my sessionInfo(). I hope this will be useful.

R version 4.2.2 (2022-10-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Rocky Linux 8.9 (Green Obsidian)

Matrix products: default BLAS/LAPACK: /cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/flexiblas/3.0.4/lib64/libflexiblas.so.3.0

Random number generation: RNG: L'Ecuyer-CMRG Normal: Inversion Sample: Rejection

locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 [5] LC_MONETARY=en_US.utf8 LC_MESSAGES=en_US.utf8 [7] LC_PAPER=en_US.utf8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C

attached base packages: [1] parallel grid stats4 stats graphics grDevices utils [8] datasets methods base

other attached packages: [1] nabor_0.5.0 BSgenome.Hsapiens.UCSC.hg38_1.4.5 [3] Seurat_5.1.0 SeuratObject_5.0.2 [5] sp_2.1-4 DirichletMultinomial_1.40.0 [7] ggrastr_1.0.2 Cairo_1.6-2 [9] rhdf5_2.42.1 SummarizedExperiment_1.28.0 [11] Biobase_2.58.0 MatrixGenerics_1.10.0 [13] Rcpp_1.0.13 matrixStats_1.4.1 [15] data.table_1.16.0 stringr_1.5.1 [17] plyr_1.8.9 magrittr_2.0.3 [19] ggplot2_3.4.0 gtable_0.3.5 [21] gtools_3.9.5 gridExtra_2.3 [23] ArchR_1.0.2 BSgenome_1.66.3 [25] rtracklayer_1.58.0 Biostrings_2.66.0 [27] XVector_0.38.0 GenomicRanges_1.50.2 [29] GenomeInfoDb_1.34.9 IRanges_2.32.0 [31] S4Vectors_0.36.2 BiocGenerics_0.44.0 [33] RSpectra_0.16-2 irlba_2.3.5.1 [35] Matrix_1.6-4

loaded via a namespace (and not attached): [1] spatstat.univar_3.0-1 spam_2.10-0 igraph_2.0.3 [4] lazyeval_0.2.2 splines_4.2.2 RcppHNSW_0.6.0 [7] BiocParallel_1.32.6 listenv_0.9.1 scattermore_1.2 [10] digest_0.6.37 htmltools_0.5.8.1 fansi_1.0.6 [13] tensor_1.5 cluster_2.1.4 ROCR_1.0-11 [16] globals_0.16.3 spatstat.sparse_3.1-0 colorspace_2.1-1 [19] ggrepel_0.9.6 dplyr_1.1.4 tcltk_4.2.2 [22] crayon_1.5.3 RCurl_1.98-1.16 jsonlite_1.8.9 [25] progressr_0.14.0 spatstat.data_3.1-2 survival_3.4-0 [28] zoo_1.8-12 glue_1.7.0 polyclip_1.10-7 [31] zlibbioc_1.44.0 leiden_0.4.3.1 DelayedArray_0.24.0 [34] Rhdf5lib_1.20.0 future.apply_1.11.2 abind_1.4-8 [37] scales_1.3.0 spatstat.random_3.3-2 miniUI_0.1.1.1 [40] viridisLite_0.4.2 xtable_1.8-4 reticulate_1.39.0 [43] dotCall64_1.1-1 htmlwidgets_1.6.4 httr_1.4.7 [46] RColorBrewer_1.1-3 ica_1.0-3 pkgconfig_2.0.3 [49] XML_3.99-0.17 farver_2.1.2 uwot_0.2.2 [52] deldir_2.0-4 utf8_1.2.4 labeling_0.4.3 [55] tidyselect_1.2.1 rlang_1.1.4 reshape2_1.4.4 [58] later_1.3.2 munsell_0.5.1 tools_4.2.2 [61] cli_3.6.3 generics_0.1.3 ggridges_0.5.6 [64] fastmap_1.2.0 goftest_1.2-3 yaml_2.3.10 [67] fitdistrplus_1.2-1 purrr_1.0.2 RANN_2.6.2 [70] nlme_3.1-160 pbapply_1.7-2 future_1.34.0 [73] mime_0.12 compiler_4.2.2 beeswarm_0.4.0 [76] plotly_4.10.4 png_0.1-8 spatstat.utils_3.1-0 [79] tibble_3.2.1 stringi_1.8.4 lattice_0.20-45 [82] vctrs_0.6.5 pillar_1.9.0 lifecycle_1.0.4 [85] rhdf5filters_1.10.1 spatstat.geom_3.3-3 lmtest_0.9-40 [88] RcppAnnoy_0.0.22 cowplot_1.1.3 bitops_1.0-8 [91] httpuv_1.6.15 patchwork_1.3.0 R6_2.5.1 [94] BiocIO_1.8.0 promises_1.3.0 KernSmooth_2.23-20 [97] vipor_0.4.7 parallelly_1.38.0 codetools_0.2-18 [100] fastDummies_1.7.4 MASS_7.3-58.1 rjson_0.2.23 [103] withr_3.0.1 GenomicAlignments_1.34.1 sctransform_0.4.1 [106] Rsamtools_2.14.0 GenomeInfoDbData_1.2.9 tidyr_1.3.1 [109] Rtsne_0.17 spatstat.explore_3.3-2 shiny_1.9.1 [112] ggbeeswarm_0.7.2 restfulr_0.0.15