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Published
20 hours ago •
GreenleafLab
GreenleafLab
`createArrowFiles` can't generate "QualityControl" plots
trafficstars
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
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.
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
