___ .______ ______ __ __ .______ / \ | _ \ / || | | | | _ \ / ^ \ | |_) | | ,----'| |__| | | |_) | / /_\ \ | / | | | __ | | / / _____ \ | |\ \\___ | `----.| | | | | |\ \\___. /__/ \__\ | _| `._____| \______||__| |__| | _| `._____| Logging With ArchR! Start Time : 2023-12-05 13:32:05.807482 ------- ArchR Info ArchRThreads = 16 ArchRGenome = Hg38 ------- System Info Computer OS = unix ------- Session Info R version 4.3.1 (2023-06-16) Platform: x86_64-conda-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) Matrix products: default BLAS/LAPACK: /net/bmc-lab5/data/kellis/group/Benjamin/software/miniconda3/envs/scorch/lib/libopenblasp-r0.3.25.so; LAPACK version 3.11.0 Random number generation: RNG: L'Ecuyer-CMRG Normal: Inversion Sample: Rejection locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C time zone: America/New_York tzcode source: system (glibc) attached base packages: [1] stats4 grid stats graphics grDevices utils datasets [8] methods base other attached packages: [1] BSgenome.Hsapiens.UCSC.hg38_1.4.5 BSgenome_1.68.0 [3] rtracklayer_1.60.0 Biostrings_2.68.1 [5] XVector_0.40.0 rhdf5_2.44.0 [7] SummarizedExperiment_1.30.2 Biobase_2.60.0 [9] MatrixGenerics_1.12.2 Rcpp_1.0.11 [11] Matrix_1.6-3 GenomicRanges_1.52.0 [13] GenomeInfoDb_1.36.1 IRanges_2.34.1 [15] S4Vectors_0.38.1 BiocGenerics_0.46.0 [17] matrixStats_1.1.0 data.table_1.14.8 [19] stringr_1.5.1 plyr_1.8.9 [21] magrittr_2.0.3 ggplot2_3.4.4 [23] gtable_0.3.4 gtools_3.9.5 [25] gridExtra_2.3 ArchR_1.0.2 loaded via a namespace (and not attached): [1] rjson_0.2.21 lattice_0.22-5 rhdf5filters_1.12.1 [4] vctrs_0.6.5 tools_4.3.1 bitops_1.0-7 [7] generics_0.1.3 parallel_4.3.1 getopt_1.20.4 [10] tibble_3.2.1 fansi_1.0.5 pkgconfig_2.0.3 [13] lifecycle_1.0.4 GenomeInfoDbData_1.2.10 compiler_4.3.1 [16] Rsamtools_2.16.0 munsell_0.5.0 codetools_0.2-19 [19] RCurl_1.98-1.13 yaml_2.3.7 pillar_1.9.0 [22] crayon_1.5.2 BiocParallel_1.34.2 DelayedArray_0.26.6 [25] abind_1.4-5 tidyselect_1.2.0 stringi_1.8.2 [28] dplyr_1.1.4 restfulr_0.0.15 colorspace_2.1-0 [31] cli_3.6.1 S4Arrays_1.2.0 XML_3.99-0.15 [34] utf8_1.2.4 withr_2.5.2 scales_1.3.0 [37] BiocIO_1.10.0 rlang_1.1.2 glue_1.6.2 [40] optparse_1.7.3 R6_2.5.1 Rhdf5lib_1.22.0 [43] GenomicAlignments_1.36.0 zlibbioc_1.46.0 ------- Log Info 2023-12-05 13:32:05.831172 : createArrowFiles Input-Parameters, Class = list createArrowFiles Input-Parameters$inputFiles: length = 1 pbmc_granulocyte_sorted_10k "/net/bmc-lab4/data/kellis/users/benjames/10X/pbmc_granulocyte_sorted_10k/outs/atac_fragments.tsv.gz" createArrowFiles Input-Parameters$sampleNames: length = 1 [1] "pbmc_granulocyte_sorted_10k" createArrowFiles Input-Parameters$outputNames: length = 1 [1] "pbmc_granulocyte_sorted_10k" createArrowFiles Input-Parameters$validBarcodes: length = 0 NULL createArrowFiles Input-Parameters$minTSS: length = 1 [1] 1 createArrowFiles Input-Parameters$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] TRUE createArrowFiles Input-Parameters$threads: length = 1 [1] 16 createArrowFiles Input-Parameters$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-d08b67b633b1-Date-2023-12-05_Time-13-32-05.792144.log" createArrowFiles Input-Parameters$filterFrags: length = 1 [1] 1000 createArrowFiles Input-Parameters$filterTSS: length = 1 [1] 1 2023-12-05 13:32:05.893286 : Cleaning Temporary Files 2023-12-05 13:32:05.896692 : Batch Execution w/ safelapply!, 0 mins elapsed. ########### 2023-12-05 13:32:05.897801 : Creating Arrow File pbmc_granulocyte_sorted_10k.arrow (pbmc_granulocyte_sorted_10k : 1 of 1) ########### 2023-12-05 13:32:05.898437 : validBC, Class = NULL validBC: length = 0 NULL 2023-12-05 13:32:05.930456 : (pbmc_granulocyte_sorted_10k : 1 of 1) Determining Arrow Method to use! 2023-12-05 13:32:05.935734 : (pbmc_granulocyte_sorted_10k : 1 of 1) Reading In Fragments from inputFiles (readMethod = tabix), 0.001 mins elapsed. 2023-12-05 13:32:05.940548 : (pbmc_granulocyte_sorted_10k : 1 of 1) Tabix Bed To Temporary File, 0.001 mins elapsed. 2023-12-05 13:32:06.030509 : tileChromSizes, Class = GRanges GRanges object with 120 ranges and 1 metadata column: seqnames ranges strand | chunkName | [1] chr1 1-49791284 * | chr1#chunk1 [2] chr1 49791285-99582568 * | chr1#chunk2 [3] chr1 99582569-149373853 * | chr1#chunk3 [4] chr1 149373854-199165137 * | chr1#chunk4 [5] chr1 199165138-248956422 * | chr1#chunk5 ... ... ... ... . ... [116] chrY 1-11445483 * | chrY#chunk116 [117] chrY 11445484-22890966 * | chrY#chunk117 [118] chrY 22890967-34336449 * | chrY#chunk118 [119] chrY 34336450-45781932 * | chrY#chunk119 [120] chrY 45781933-57227415 * | chrY#chunk120 ------- seqinfo: 24 sequences from an unspecified genome; no seqlengths 2023-12-05 13:32:58.421621 : (pbmc_granulocyte_sorted_10k : 1 of 1) Reading TabixFile 28 Percent, 0.875 mins elapsed. 2023-12-05 13:33:01.600949 : (pbmc_granulocyte_sorted_10k : 1 of 1) .tabixToTmp Fragments-Chunk-(1 of 120)-chr1:1-49791284, Class = data.table 2023-12-05 13:33:01.600949 : (pbmc_granulocyte_sorted_10k : 1 of 1) .tabixToTmp Fragments-Chunk-(1 of 120)-chr1:1-49791284, Class = data.frame (pbmc_granulocyte_sorted_10k : 1 of 1) .tabixToTmp Fragments-Chunk-(1 of 120)-chr1:1-49791284: nRows = 8282850, nCols = 3 V2 V3 V4 1: 10013 10013 TTTGCGACACCCACAG-1 2: 10067 10198 ACGAATCTCATTTGCT-1 3: 10067 10478 TCAAGAACAGTAATAG-1 4: 10073 10191 AACCCGCAGGTAGCTT-1 5: 10073 10203 GGTTGCTCACTTCATC-1 6: 10074 10340 CGCATATAGGTTACGT-1 2023-12-05 13:33:01.655705 : (pbmc_granulocyte_sorted_10k : 1 of 1) .tabixToTmp Barcodes-Chunk-(1 of 120)-chr1:1-49791284, Class = character (pbmc_granulocyte_sorted_10k : 1 of 1) .tabixToTmp Barcodes-Chunk-(1 of 120)-chr1:1-49791284: length = 209642 [1] "TTTGCGACACCCACAG-1" "ACGAATCTCATTTGCT-1" "TCAAGAACAGTAATAG-1" [4] "AACCCGCAGGTAGCTT-1" "GGTTGCTCACTTCATC-1" "CGCATATAGGTTACGT-1" 2023-12-05 13:33:51.182684 : (pbmc_granulocyte_sorted_10k : 1 of 1) Reading TabixFile 55 Percent, 1.755 mins elapsed. 2023-12-05 13:34:40.543261 : (pbmc_granulocyte_sorted_10k : 1 of 1) Reading TabixFile 82 Percent, 2.577 mins elapsed. 2023-12-05 13:35:23.038125 : (pbmc_granulocyte_sorted_10k : 1 of 1) Parallel Hdf5 Linkage Temporary File, 3.286 mins elapsed. 2023-12-05 13:35:24.222564 : (pbmc_granulocyte_sorted_10k : 1 of 1) Successful creation of Temporary File, 3.305 mins elapsed. 2023-12-05 13:35:24.225661 : (pbmc_granulocyte_sorted_10k : 1 of 1) Creating ArrowFile From Temporary File, 3.305 mins elapsed. 2023-12-05 13:35:24.536439 : (pbmc_granulocyte_sorted_10k : 1 of 1) chunkChrNames, Class = data.frame (pbmc_granulocyte_sorted_10k : 1 of 1) chunkChrNames: nRows = 118, nCols = 1 chunkNames 1 chr1#chunk1 2 chr1#chunk2 3 chr1#chunk3 4 chr1#chunk4 5 chr1#chunk5 6 chr10#chunk46 2023-12-05 13:35:24.541859 : (pbmc_granulocyte_sorted_10k : 1 of 1) Counting Unique Barcodes From Temporary File, 3.311 mins elapsed. 2023-12-05 13:35:57.27979 : (pbmc_granulocyte_sorted_10k : 1 of 1) BarcodeFrequencyTable, Class = data.table 2023-12-05 13:35:57.27979 : (pbmc_granulocyte_sorted_10k : 1 of 1) BarcodeFrequencyTable, Class = data.frame (pbmc_granulocyte_sorted_10k : 1 of 1) BarcodeFrequencyTable: nRows = 669442, nCols = 2 values.V1 V1 1: CGTTAAATCCACCCTG-1 784328 2: TCTAACCGTATTGTCC-1 617735 3: TTGCGTCTCGCCTAAG-1 360648 4: ATGGCTTAGGCTACAT-1 348864 5: TAGTAAGCAAGGTAAC-1 327886 6: TACCCGGCATAATCCG-1 313165 2023-12-05 13:35:57.305336 : (pbmc_granulocyte_sorted_10k : 1 of 1) BarcodesMinMaxFrags, Class = data.frame (pbmc_granulocyte_sorted_10k : 1 of 1) BarcodesMinMaxFrags: nRows = 12222, nCols = 1 bc 1 GGAGTCTGTGAGCAAG-1 2 TTCATTCAGCCGCTTT-1 3 CAGCAAGCAGTAGGTG-1 4 TAGCTAGGTTTGGGTA-1 5 ACGAACAAGACACTTA-1 6 ATTTGCAAGCCGCAAC-1 2023-12-05 13:35:58.153137 : (pbmc_granulocyte_sorted_10k : 1 of 1) Unique Chromosomes, Class = data.frame (pbmc_granulocyte_sorted_10k : 1 of 1) Unique Chromosomes: nRows = 24, nCols = 1 chr 1 chr1 2 chr2 3 chr3 4 chr4 5 chr5 6 chr6 2023-12-05 13:35:58.194671 : (pbmc_granulocyte_sorted_10k : 1 of 1) Adding Chromosome 1 of 24, 3.872 mins elapsed. 2023-12-05 13:35:58.217362 : (pbmc_granulocyte_sorted_10k : 1 of 1) Adding Chromosome 2 of 24, 3.872 mins elapsed. 2023-12-05 13:35:58.240004 : (pbmc_granulocyte_sorted_10k : 1 of 1) Adding Chromosome 3 of 24, 3.872 mins elapsed. 2023-12-05 13:35:58.259976 : (pbmc_granulocyte_sorted_10k : 1 of 1) Adding Chromosome 4 of 24, 3.873 mins elapsed. 2023-12-05 13:35:58.284227 : (pbmc_granulocyte_sorted_10k : 1 of 1) Adding Chromosome 5 of 24, 3.873 mins elapsed. 2023-12-05 13:35:58.306157 : (pbmc_granulocyte_sorted_10k : 1 of 1) Adding Chromosome 6 of 24, 3.873 mins elapsed. 2023-12-05 13:35:58.329579 : (pbmc_granulocyte_sorted_10k : 1 of 1) Adding Chromosome 7 of 24, 3.874 mins elapsed. 2023-12-05 13:35:58.352852 : (pbmc_granulocyte_sorted_10k : 1 of 1) Adding Chromosome 8 of 24, 3.874 mins elapsed. 2023-12-05 13:35:58.376663 : (pbmc_granulocyte_sorted_10k : 1 of 1) Adding Chromosome 9 of 24, 3.875 mins elapsed. 2023-12-05 13:35:58.398957 : (pbmc_granulocyte_sorted_10k : 1 of 1) Adding Chromosome 10 of 24, 3.875 mins elapsed. 2023-12-05 13:35:58.42399 : (pbmc_granulocyte_sorted_10k : 1 of 1) Adding Chromosome 11 of 24, 3.875 mins elapsed. 2023-12-05 13:35:58.4512 : (pbmc_granulocyte_sorted_10k : 1 of 1) Adding Chromosome 12 of 24, 3.876 mins elapsed. 2023-12-05 13:35:58.47771 : (pbmc_granulocyte_sorted_10k : 1 of 1) Adding Chromosome 13 of 24, 3.876 mins elapsed. 2023-12-05 13:35:58.501891 : (pbmc_granulocyte_sorted_10k : 1 of 1) Adding Chromosome 14 of 24, 3.877 mins elapsed. 2023-12-05 13:35:58.528361 : (pbmc_granulocyte_sorted_10k : 1 of 1) Adding Chromosome 15 of 24, 3.877 mins elapsed. 2023-12-05 13:35:58.551632 : (pbmc_granulocyte_sorted_10k : 1 of 1) Adding Chromosome 16 of 24, 3.878 mins elapsed. 2023-12-05 13:37:10.768448 : (pbmc_granulocyte_sorted_10k : 1 of 1) Adding Chromosome 17 of 24, 5.081 mins elapsed. 2023-12-05 13:38:01.872911 : (pbmc_granulocyte_sorted_10k : 1 of 1) Adding Chromosome 18 of 24, 5.933 mins elapsed. 2023-12-05 13:38:19.383728 : (pbmc_granulocyte_sorted_10k : 1 of 1) Adding Chromosome 19 of 24, 6.225 mins elapsed. 2023-12-05 13:38:24.253521 : (pbmc_granulocyte_sorted_10k : 1 of 1) Adding Chromosome 20 of 24, 6.306 mins elapsed. 2023-12-05 13:38:25.994834 : (pbmc_granulocyte_sorted_10k : 1 of 1) Adding Chromosome 21 of 24, 6.335 mins elapsed. 2023-12-05 13:38:27.133784 : (pbmc_granulocyte_sorted_10k : 1 of 1) Adding Chromosome 22 of 24, 6.354 mins elapsed. 2023-12-05 13:38:31.676188 : (pbmc_granulocyte_sorted_10k : 1 of 1) Adding Chromosome 23 of 24, 6.43 mins elapsed. 2023-12-05 13:38:34.346307 : (pbmc_granulocyte_sorted_10k : 1 of 1) Adding Chromosome 24 of 24, 6.474 mins elapsed. 2023-12-05 13:39:40.241651 : (pbmc_granulocyte_sorted_10k : 1 of 1) .tmpToArrow Fragments-Chr-(1 of 24)-chr1, Class = IRanges (pbmc_granulocyte_sorted_10k : 1 of 1) .tmpToArrow Fragments-Chr-(1 of 24)-chr1: length = 20886882 IRanges object with 6 ranges and 1 metadata column: start end width | RG | [1] 10158 10210 53 | GGAGTCTGTGAGCAAG-1 [2] 66133 66173 41 | GGAGTCTGTGAGCAAG-1 [3] 181362 181521 160 | GGAGTCTGTGAGCAAG-1 [4] 191451 191542 92 | GGAGTCTGTGAGCAAG-1 [5] 607329 607361 33 | GGAGTCTGTGAGCAAG-1 [6] 778248 778403 156 | GGAGTCTGTGAGCAAG-1 2023-12-05 13:39:40.2554 : (pbmc_granulocyte_sorted_10k : 1 of 1) .tmpToArrow Barcodes-Chr-(1 of 24)-chr1, Class = data.frame (pbmc_granulocyte_sorted_10k : 1 of 1) .tmpToArrow Barcodes-Chr-(1 of 24)-chr1: nRows = 12222, nCols = 1 bc 1 GGAGTCTGTGAGCAAG-1 2 TTCATTCAGCCGCTTT-1 3 CAGCAAGCAGTAGGTG-1 4 TAGCTAGGTTTGGGTA-1 5 ACGAACAAGACACTTA-1 6 ATTTGCAAGCCGCAAC-1 2023-12-05 13:39:45.927237 : (pbmc_granulocyte_sorted_10k : 1 of 1) Parallel Hdf5 Linkage Arrow File, 7.667 mins elapsed. 2023-12-05 13:39:46.786072 : (pbmc_granulocyte_sorted_10k : 1 of 1) Successful creation of Arrow File, 7.681 mins elapsed. 2023-12-05 13:39:47.737497 : (pbmc_granulocyte_sorted_10k : 1 of 1) Adding Fragment Summary, 7.697 mins elapsed. 2023-12-05 13:40:28.073031 : (pbmc_granulocyte_sorted_10k : 1 of 1) Plotting Fragment Size Distribution, 8.37 mins elapsed. 2023-12-05 13:40:29.197483 : (pbmc_granulocyte_sorted_10k : 1 of 1) Computing TSS Enrichment Scores, 8.388 mins elapsed. 2023-12-05 13:41:44.437854 : (pbmc_granulocyte_sorted_10k : 1 of 1) Computed TSS Scores!, 1.254 mins elapsed. 2023-12-05 13:41:44.45009 : (pbmc_granulocyte_sorted_10k : 1 of 1) CellStats : Number of Cells Pass Filter = 12222 , 9.643 mins elapsed. 2023-12-05 13:41:44.453616 : (pbmc_granulocyte_sorted_10k : 1 of 1) CellStats : Median Frags = 17109.5 , 9.643 mins elapsed. 2023-12-05 13:41:44.457131 : (pbmc_granulocyte_sorted_10k : 1 of 1) CellStats : Median TSS Enrichment = 18.919 , 9.643 mins elapsed. 2023-12-05 13:41:44.458059 : (pbmc_granulocyte_sorted_10k : 1 of 1) Plotting TSS Enrichment Scores, 9.643 mins elapsed. 2023-12-05 13:41:47.198503 : (pbmc_granulocyte_sorted_10k : 1 of 1) Adding Metadata to Fragments, 9.688 mins elapsed. 2023-12-05 13:41:48.336677 : (pbmc_granulocyte_sorted_10k : 1 of 1) Adding Additional Feature Counts!, 9.707 mins elapsed. 2023-12-05 13:42:58.325676 : (pbmc_granulocyte_sorted_10k : 1 of 1) Finished Adding Additional Feature Counts!, 10.874 mins elapsed. 2023-12-05 13:42:58.327223 : (pbmc_granulocyte_sorted_10k : 1 of 1) Metadata, Class = DFrame DataFrame with 12222 rows and 12 columns cellNames nFrags nMonoFrags nDiFrags nMultiFrags 1 pbmc_granulocyte_sor.. 95883 49886 30010 15987 2 pbmc_granulocyte_sor.. 94243 44906 33503 15834 3 pbmc_granulocyte_sor.. 93795 16369 56565 20861 4 pbmc_granulocyte_sor.. 93604 26965 48758 17881 5 pbmc_granulocyte_sor.. 92975 44353 33374 15248 ... ... ... ... ... ... 12218 pbmc_granulocyte_sor.. 1004 451 456 97 12219 pbmc_granulocyte_sor.. 1002 538 321 143 12220 pbmc_granulocyte_sor.. 1002 649 290 63 12221 pbmc_granulocyte_sor.. 1001 388 521 92 12222 pbmc_granulocyte_sor.. 1000 603 276 121 TSSEnrichment ReadsInTSS Keep ReadsInPromoter PromoterRatio 1 8.053 26524 1 34042 0.1775184 2 3.162 7962 1 15518 0.0823297 3 4.517 3805 1 6487 0.0345807 4 16.052 28964 1 29908 0.1597581 5 19.853 79165 1 79340 0.4266738 ... ... ... ... ... ... 12218 6.566 189 1 283 0.140936 12219 21.308 764 1 803 0.400699 12220 10.458 338 1 442 0.220559 12221 7.096 172 1 213 0.106394 12222 18.201 864 1 997 0.498500 ReadsInBlacklist BlacklistRatio 1 1204 0.00627849 2 1056 0.00560254 3 1564 0.00833733 4 1073 0.00573159 5 1315 0.00707179 ... ... ... 12218 4 0.00199203 12219 22 0.01097804 12220 20 0.00998004 12221 20 0.00999001 12222 10 0.00500000 2023-12-05 13:42:58.699226 : (pbmc_granulocyte_sorted_10k : 1 of 1) Removing Fragments from Filtered Cells, 10.88 mins elapsed. 2023-12-05 13:42:58.706773 : (pbmc_granulocyte_sorted_10k : 1 of 1) Creating Filtered Arrow File, 10.88 mins elapsed. 2023-12-05 13:43:06.099275 : (pbmc_granulocyte_sorted_10k : 1 of 1) .filterCellsFromArrow Fragments-Chr-(1 of 24)-chr1, Class = GRanges GRanges object with 20886882 ranges and 1 metadata column: seqnames ranges strand | RG | [1] chr1 10158-10210 * | pbmc_granulocyte_sor.. [2] chr1 66133-66173 * | pbmc_granulocyte_sor.. [3] chr1 181362-181521 * | pbmc_granulocyte_sor.. [4] chr1 191451-191542 * | pbmc_granulocyte_sor.. [5] chr1 607329-607361 * | pbmc_granulocyte_sor.. ... ... ... ... . ... [20886878] chr1 234610075-234610115 * | pbmc_granulocyte_sor.. [20886879] chr1 243255949-243256025 * | pbmc_granulocyte_sor.. [20886880] chr1 246506542-246506588 * | pbmc_granulocyte_sor.. [20886881] chr1 247103924-247103949 * | pbmc_granulocyte_sor.. [20886882] chr1 247373785-247373817 * | pbmc_granulocyte_sor.. ------- seqinfo: 1 sequence from an unspecified genome; no seqlengths 2023-12-05 13:43:06.112862 : (pbmc_granulocyte_sorted_10k : 1 of 1) .filterCellsFromArrow Barcodes-Chr-(1 of 24)-chr1, Class = data.frame (pbmc_granulocyte_sorted_10k : 1 of 1) .filterCellsFromArrow Barcodes-Chr-(1 of 24)-chr1: nRows = 12222, nCols = 1 bc 1 pbmc_granulocyte_sorted_10k#GGAGTCTGTGAGCAAG-1 2 pbmc_granulocyte_sorted_10k#TTCATTCAGCCGCTTT-1 3 pbmc_granulocyte_sorted_10k#CAGCAAGCAGTAGGTG-1 4 pbmc_granulocyte_sorted_10k#TAGCTAGGTTTGGGTA-1 5 pbmc_granulocyte_sorted_10k#ACGAACAAGACACTTA-1 6 pbmc_granulocyte_sorted_10k#ATTTGCAAGCCGCAAC-1 2023-12-05 13:44:23.683357 : (pbmc_granulocyte_sorted_10k : 1 of 1) Finished Constructing Filtered Arrow File!, 12.296 mins elapsed. 2023-12-05 13:44:23.896972 : (pbmc_granulocyte_sorted_10k : 1 of 1) Adding TileMatrix!, 12.3 mins elapsed. 2023-12-05 13:44:25.218025 : pbmc_granulocyte_sorted_10k .addTileMat FeatureDF, Class = DFrame DataFrame with 6062095 rows and 3 columns seqnames idx start 1 chr1 1 0 2 chr1 2 500 3 chr1 3 1000 4 chr1 4 1500 5 chr1 5 2000 ... ... ... ... 6062091 chrX 312078 156038500 6062092 chrX 312079 156039000 6062093 chrX 312080 156039500 6062094 chrX 312081 156040000 6062095 chrX 312082 156040500 2023-12-05 13:44:32.991082 : Adding TileMatrix to pbmc_granulocyte_sorted_10k for Chr (1 of 23)!, 0.151 mins elapsed. 2023-12-05 13:44:38.600613 : NTiles_TileMatrix_1_chr1, Class = numeric NTiles_TileMatrix_1_chr1: length = 1 chr1 497913 2023-12-05 13:44:38.605243 : NCells_TileMatrix_1_chr1, Class = integer NCells_TileMatrix_1_chr1: length = 1 [1] 12222 2023-12-05 13:44:38.608594 : MinTile_TileMatrix_1_chr1, Class = numeric MinTile_TileMatrix_1_chr1: length = 1 [1] 21 2023-12-05 13:44:38.633464 : MaxTile_TileMatrix_1_chr1, Class = numeric MaxTile_TileMatrix_1_chr1: length = 1 [1] 497893 2023-12-05 13:44:38.75367 : MinCell_TileMatrix_1_chr1, Class = integer MinCell_TileMatrix_1_chr1: length = 1 [1] 1 2023-12-05 13:44:38.758002 : MaxCell_TileMatrix_1_chr1, Class = integer MaxCell_TileMatrix_1_chr1: length = 1 [1] 12222 2023-12-05 13:45:26.024234 : Adding TileMatrix to pbmc_granulocyte_sorted_10k for Chr (2 of 23)!, 1.035 mins elapsed. 2023-12-05 13:45:27.952905 : NTiles_TileMatrix_2_chr2, Class = numeric NTiles_TileMatrix_2_chr2: length = 1 chr2 484388 2023-12-05 13:45:27.956619 : NCells_TileMatrix_2_chr2, Class = integer NCells_TileMatrix_2_chr2: length = 1 [1] 12222 2023-12-05 13:45:27.960287 : MinTile_TileMatrix_2_chr2, Class = numeric MinTile_TileMatrix_2_chr2: length = 1 [1] 21 2023-12-05 13:45:27.979048 : MaxTile_TileMatrix_2_chr2, Class = numeric MaxTile_TileMatrix_2_chr2: length = 1 [1] 484367 2023-12-05 13:45:28.079391 : MinCell_TileMatrix_2_chr2, Class = integer MinCell_TileMatrix_2_chr2: length = 1 [1] 1 2023-12-05 13:45:28.082792 : MaxCell_TileMatrix_2_chr2, Class = integer MaxCell_TileMatrix_2_chr2: length = 1 [1] 12222 2023-12-05 13:46:04.903979 : Adding TileMatrix to pbmc_granulocyte_sorted_10k for Chr (3 of 23)!, 1.683 mins elapsed. 2023-12-05 13:46:06.632293 : NTiles_TileMatrix_3_chr3, Class = numeric NTiles_TileMatrix_3_chr3: length = 1 chr3 396592 2023-12-05 13:46:06.635638 : NCells_TileMatrix_3_chr3, Class = integer NCells_TileMatrix_3_chr3: length = 1 [1] 12222 2023-12-05 13:46:06.638554 : MinTile_TileMatrix_3_chr3, Class = numeric MinTile_TileMatrix_3_chr3: length = 1 [1] 21 2023-12-05 13:46:06.655552 : MaxTile_TileMatrix_3_chr3, Class = numeric MaxTile_TileMatrix_3_chr3: length = 1 [1] 396441 2023-12-05 13:46:06.735731 : MinCell_TileMatrix_3_chr3, Class = integer MinCell_TileMatrix_3_chr3: length = 1 [1] 1 2023-12-05 13:46:06.738776 : MaxCell_TileMatrix_3_chr3, Class = integer MaxCell_TileMatrix_3_chr3: length = 1 [1] 12222 2023-12-05 13:46:33.054225 : Adding TileMatrix to pbmc_granulocyte_sorted_10k for Chr (4 of 23)!, 2.152 mins elapsed. 2023-12-05 13:46:34.129755 : NTiles_TileMatrix_4_chr4, Class = numeric NTiles_TileMatrix_4_chr4: length = 1 chr4 380430 2023-12-05 13:46:34.136991 : NCells_TileMatrix_4_chr4, Class = integer NCells_TileMatrix_4_chr4: length = 1 [1] 12222 2023-12-05 13:46:34.139967 : MinTile_TileMatrix_4_chr4, Class = numeric MinTile_TileMatrix_4_chr4: length = 1 [1] 21 2023-12-05 13:46:34.152117 : MaxTile_TileMatrix_4_chr4, Class = numeric MaxTile_TileMatrix_4_chr4: length = 1 [1] 380410 2023-12-05 13:46:34.206724 : MinCell_TileMatrix_4_chr4, Class = integer MinCell_TileMatrix_4_chr4: length = 1 [1] 1 2023-12-05 13:46:34.210289 : MaxCell_TileMatrix_4_chr4, Class = integer MaxCell_TileMatrix_4_chr4: length = 1 [1] 12222 2023-12-05 13:46:51.279448 : Adding TileMatrix to pbmc_granulocyte_sorted_10k for Chr (5 of 23)!, 2.456 mins elapsed. 2023-12-05 13:46:52.578226 : NTiles_TileMatrix_5_chr5, Class = numeric NTiles_TileMatrix_5_chr5: length = 1 chr5 363077 2023-12-05 13:46:52.582139 : NCells_TileMatrix_5_chr5, Class = integer NCells_TileMatrix_5_chr5: length = 1 [1] 12222 2023-12-05 13:46:52.585959 : MinTile_TileMatrix_5_chr5, Class = numeric MinTile_TileMatrix_5_chr5: length = 1 [1] 21 2023-12-05 13:46:52.598268 : MaxTile_TileMatrix_5_chr5, Class = numeric MaxTile_TileMatrix_5_chr5: length = 1 [1] 362956 2023-12-05 13:46:52.666503 : MinCell_TileMatrix_5_chr5, Class = integer MinCell_TileMatrix_5_chr5: length = 1 [1] 1 2023-12-05 13:46:52.669673 : MaxCell_TileMatrix_5_chr5, Class = integer MaxCell_TileMatrix_5_chr5: length = 1 [1] 12222 2023-12-05 13:47:15.524925 : Adding TileMatrix to pbmc_granulocyte_sorted_10k for Chr (6 of 23)!, 2.86 mins elapsed. 2023-12-05 13:47:17.439008 : NTiles_TileMatrix_6_chr6, Class = numeric NTiles_TileMatrix_6_chr6: length = 1 chr6 341612 2023-12-05 13:47:17.442917 : NCells_TileMatrix_6_chr6, Class = integer NCells_TileMatrix_6_chr6: length = 1 [1] 12222 2023-12-05 13:47:17.446609 : MinTile_TileMatrix_6_chr6, Class = numeric MinTile_TileMatrix_6_chr6: length = 1 [1] 128 2023-12-05 13:47:17.463344 : MaxTile_TileMatrix_6_chr6, Class = numeric MaxTile_TileMatrix_6_chr6: length = 1 [1] 341480 2023-12-05 13:47:17.545163 : MinCell_TileMatrix_6_chr6, Class = integer MinCell_TileMatrix_6_chr6: length = 1 [1] 1 2023-12-05 13:47:17.549091 : MaxCell_TileMatrix_6_chr6, Class = integer MaxCell_TileMatrix_6_chr6: length = 1 [1] 12222 2023-12-05 13:47:38.48866 : Adding TileMatrix to pbmc_granulocyte_sorted_10k for Chr (7 of 23)!, 3.242 mins elapsed. 2023-12-05 13:47:39.859153 : NTiles_TileMatrix_7_chr7, Class = numeric NTiles_TileMatrix_7_chr7: length = 1 chr7 318692 2023-12-05 13:47:39.863148 : NCells_TileMatrix_7_chr7, Class = integer NCells_TileMatrix_7_chr7: length = 1 [1] 12222 2023-12-05 13:47:39.86697 : MinTile_TileMatrix_7_chr7, Class = numeric MinTile_TileMatrix_7_chr7: length = 1 [1] 21 2023-12-05 13:47:39.879969 : MaxTile_TileMatrix_7_chr7, Class = numeric MaxTile_TileMatrix_7_chr7: length = 1 [1] 318672 2023-12-05 13:47:39.953974 : MinCell_TileMatrix_7_chr7, Class = integer MinCell_TileMatrix_7_chr7: length = 1 [1] 1 2023-12-05 13:47:39.957989 : MaxCell_TileMatrix_7_chr7, Class = integer MaxCell_TileMatrix_7_chr7: length = 1 [1] 12222 2023-12-05 13:47:56.760548 : Adding TileMatrix to pbmc_granulocyte_sorted_10k for Chr (8 of 23)!, 3.547 mins elapsed. 2023-12-05 13:47:57.695621 : NTiles_TileMatrix_8_chr8, Class = numeric NTiles_TileMatrix_8_chr8: length = 1 chr8 290278 2023-12-05 13:47:57.699497 : NCells_TileMatrix_8_chr8, Class = integer NCells_TileMatrix_8_chr8: length = 1 [1] 12222 2023-12-05 13:47:57.703043 : MinTile_TileMatrix_8_chr8, Class = numeric MinTile_TileMatrix_8_chr8: length = 1 [1] 143 2023-12-05 13:47:57.715481 : MaxTile_TileMatrix_8_chr8, Class = numeric MaxTile_TileMatrix_8_chr8: length = 1 [1] 290153 2023-12-05 13:47:57.766256 : MinCell_TileMatrix_8_chr8, Class = integer MinCell_TileMatrix_8_chr8: length = 1 [1] 1 2023-12-05 13:47:57.769445 : MaxCell_TileMatrix_8_chr8, Class = integer MaxCell_TileMatrix_8_chr8: length = 1 [1] 12222 2023-12-05 13:48:10.880502 : Adding TileMatrix to pbmc_granulocyte_sorted_10k for Chr (9 of 23)!, 3.782 mins elapsed. 2023-12-05 13:48:12.137314 : NTiles_TileMatrix_9_chr9, Class = numeric NTiles_TileMatrix_9_chr9: length = 1 chr9 276790 2023-12-05 13:48:12.141313 : NCells_TileMatrix_9_chr9, Class = integer NCells_TileMatrix_9_chr9: length = 1 [1] 12222 2023-12-05 13:48:12.145252 : MinTile_TileMatrix_9_chr9, Class = numeric MinTile_TileMatrix_9_chr9: length = 1 [1] 21 2023-12-05 13:48:12.171901 : MaxTile_TileMatrix_9_chr9, Class = numeric MaxTile_TileMatrix_9_chr9: length = 1 [1] 276457 2023-12-05 13:48:12.230853 : MinCell_TileMatrix_9_chr9, Class = integer MinCell_TileMatrix_9_chr9: length = 1 [1] 1 2023-12-05 13:48:12.234835 : MaxCell_TileMatrix_9_chr9, Class = integer MaxCell_TileMatrix_9_chr9: length = 1 [1] 12222 2023-12-05 13:48:26.827644 : Adding TileMatrix to pbmc_granulocyte_sorted_10k for Chr (10 of 23)!, 4.048 mins elapsed. 2023-12-05 13:48:28.189362 : NTiles_TileMatrix_10_chr10, Class = numeric NTiles_TileMatrix_10_chr10: length = 1 chr10 267595 2023-12-05 13:48:28.202459 : NCells_TileMatrix_10_chr10, Class = integer NCells_TileMatrix_10_chr10: length = 1 [1] 12222 2023-12-05 13:48:28.212155 : MinTile_TileMatrix_10_chr10, Class = numeric MinTile_TileMatrix_10_chr10: length = 1 [1] 21 2023-12-05 13:48:28.225862 : MaxTile_TileMatrix_10_chr10, Class = numeric MaxTile_TileMatrix_10_chr10: length = 1 [1] 267575 2023-12-05 13:48:28.286517 : MinCell_TileMatrix_10_chr10, Class = integer MinCell_TileMatrix_10_chr10: length = 1 [1] 1 2023-12-05 13:48:28.289782 : MaxCell_TileMatrix_10_chr10, Class = integer MaxCell_TileMatrix_10_chr10: length = 1 [1] 12222 2023-12-05 13:48:44.335867 : Adding TileMatrix to pbmc_granulocyte_sorted_10k for Chr (11 of 23)!, 4.34 mins elapsed. 2023-12-05 13:48:46.035167 : NTiles_TileMatrix_11_chr11, Class = numeric NTiles_TileMatrix_11_chr11: length = 1 chr11 270174 2023-12-05 13:48:46.038834 : NCells_TileMatrix_11_chr11, Class = integer NCells_TileMatrix_11_chr11: length = 1 [1] 12222 2023-12-05 13:48:46.04196 : MinTile_TileMatrix_11_chr11, Class = numeric MinTile_TileMatrix_11_chr11: length = 1 [1] 227 2023-12-05 13:48:46.05691 : MaxTile_TileMatrix_11_chr11, Class = numeric MaxTile_TileMatrix_11_chr11: length = 1 [1] 270154 2023-12-05 13:48:46.127346 : MinCell_TileMatrix_11_chr11, Class = integer MinCell_TileMatrix_11_chr11: length = 1 [1] 1 2023-12-05 13:48:46.130532 : MaxCell_TileMatrix_11_chr11, Class = integer MaxCell_TileMatrix_11_chr11: length = 1 [1] 12222 2023-12-05 13:49:05.233485 : Adding TileMatrix to pbmc_granulocyte_sorted_10k for Chr (12 of 23)!, 4.688 mins elapsed. 2023-12-05 13:49:07.258749 : NTiles_TileMatrix_12_chr12, Class = numeric NTiles_TileMatrix_12_chr12: length = 1 chr12 266551 2023-12-05 13:49:07.270297 : NCells_TileMatrix_12_chr12, Class = integer NCells_TileMatrix_12_chr12: length = 1 [1] 12222 2023-12-05 13:49:07.283999 : MinTile_TileMatrix_12_chr12, Class = numeric MinTile_TileMatrix_12_chr12: length = 1 [1] 21 2023-12-05 13:49:07.321213 : MaxTile_TileMatrix_12_chr12, Class = numeric MaxTile_TileMatrix_12_chr12: length = 1 [1] 266531 2023-12-05 13:49:07.431887 : MinCell_TileMatrix_12_chr12, Class = integer MinCell_TileMatrix_12_chr12: length = 1 [1] 1 2023-12-05 13:49:07.435592 : MaxCell_TileMatrix_12_chr12, Class = integer MaxCell_TileMatrix_12_chr12: length = 1 [1] 12222 2023-12-05 13:49:26.443981 : Adding TileMatrix to pbmc_granulocyte_sorted_10k for Chr (13 of 23)!, 5.042 mins elapsed. 2023-12-05 13:49:27.325598 : NTiles_TileMatrix_13_chr13, Class = numeric NTiles_TileMatrix_13_chr13: length = 1 chr13 228729 2023-12-05 13:49:27.329822 : NCells_TileMatrix_13_chr13, Class = integer NCells_TileMatrix_13_chr13: length = 1 [1] 12222 2023-12-05 13:49:27.333455 : MinTile_TileMatrix_13_chr13, Class = numeric MinTile_TileMatrix_13_chr13: length = 1 [1] 34839 2023-12-05 13:49:27.344371 : MaxTile_TileMatrix_13_chr13, Class = numeric MaxTile_TileMatrix_13_chr13: length = 1 [1] 228709 2023-12-05 13:49:27.3907 : MinCell_TileMatrix_13_chr13, Class = integer MinCell_TileMatrix_13_chr13: length = 1 [1] 1 2023-12-05 13:49:27.394326 : MaxCell_TileMatrix_13_chr13, Class = integer MaxCell_TileMatrix_13_chr13: length = 1 [1] 12222 2023-12-05 13:49:35.007217 : Adding TileMatrix to pbmc_granulocyte_sorted_10k for Chr (14 of 23)!, 5.184 mins elapsed. 2023-12-05 13:49:35.847039 : NTiles_TileMatrix_14_chr14, Class = numeric NTiles_TileMatrix_14_chr14: length = 1 chr14 214088 2023-12-05 13:49:35.850877 : NCells_TileMatrix_14_chr14, Class = integer NCells_TileMatrix_14_chr14: length = 1 [1] 12222 2023-12-05 13:49:35.854324 : MinTile_TileMatrix_14_chr14, Class = numeric MinTile_TileMatrix_14_chr14: length = 1 [1] 32071 2023-12-05 13:49:35.865768 : MaxTile_TileMatrix_14_chr14, Class = numeric MaxTile_TileMatrix_14_chr14: length = 1 [1] 213768 2023-12-05 13:49:35.918722 : MinCell_TileMatrix_14_chr14, Class = integer MinCell_TileMatrix_14_chr14: length = 1 [1] 1 2023-12-05 13:49:35.922514 : MaxCell_TileMatrix_14_chr14, Class = integer MaxCell_TileMatrix_14_chr14: length = 1 [1] 12222 2023-12-05 13:49:46.245967 : Adding TileMatrix to pbmc_granulocyte_sorted_10k for Chr (15 of 23)!, 5.372 mins elapsed. 2023-12-05 13:49:47.029165 : NTiles_TileMatrix_15_chr15, Class = numeric NTiles_TileMatrix_15_chr15: length = 1 chr15 203983 2023-12-05 13:49:47.033455 : NCells_TileMatrix_15_chr15, Class = integer NCells_TileMatrix_15_chr15: length = 1 [1] 12222 2023-12-05 13:49:47.037467 : MinTile_TileMatrix_15_chr15, Class = numeric MinTile_TileMatrix_15_chr15: length = 1 [1] 34020 2023-12-05 13:49:47.047864 : MaxTile_TileMatrix_15_chr15, Class = numeric MaxTile_TileMatrix_15_chr15: length = 1 [1] 203963 2023-12-05 13:49:47.094172 : MinCell_TileMatrix_15_chr15, Class = integer MinCell_TileMatrix_15_chr15: length = 1 [1] 1 2023-12-05 13:49:47.097938 : MaxCell_TileMatrix_15_chr15, Class = integer MaxCell_TileMatrix_15_chr15: length = 1 [1] 12222 2023-12-05 13:49:55.27784 : Adding TileMatrix to pbmc_granulocyte_sorted_10k for Chr (16 of 23)!, 5.522 mins elapsed. 2023-12-05 13:49:56.32908 : NTiles_TileMatrix_16_chr16, Class = numeric NTiles_TileMatrix_16_chr16: length = 1 chr16 180677 2023-12-05 13:49:56.333372 : NCells_TileMatrix_16_chr16, Class = integer NCells_TileMatrix_16_chr16: length = 1 [1] 12222 2023-12-05 13:49:56.337568 : MinTile_TileMatrix_16_chr16, Class = numeric MinTile_TileMatrix_16_chr16: length = 1 [1] 21 2023-12-05 13:49:56.351405 : MaxTile_TileMatrix_16_chr16, Class = numeric MaxTile_TileMatrix_16_chr16: length = 1 [1] 180450 2023-12-05 13:49:56.414824 : MinCell_TileMatrix_16_chr16, Class = integer MinCell_TileMatrix_16_chr16: length = 1 [1] 1 2023-12-05 13:49:56.420217 : MaxCell_TileMatrix_16_chr16, Class = integer MaxCell_TileMatrix_16_chr16: length = 1 [1] 12222 2023-12-05 13:50:08.386351 : Adding TileMatrix to pbmc_granulocyte_sorted_10k for Chr (17 of 23)!, 5.741 mins elapsed. 2023-12-05 13:50:10.37279 : NTiles_TileMatrix_17_chr17, Class = numeric NTiles_TileMatrix_17_chr17: length = 1 chr17 166515 2023-12-05 13:50:10.37725 : NCells_TileMatrix_17_chr17, Class = integer NCells_TileMatrix_17_chr17: length = 1 [1] 12222 2023-12-05 13:50:10.381322 : MinTile_TileMatrix_17_chr17, Class = numeric MinTile_TileMatrix_17_chr17: length = 1 [1] 156 2023-12-05 13:50:10.411813 : MaxTile_TileMatrix_17_chr17, Class = numeric MaxTile_TileMatrix_17_chr17: length = 1 [1] 166495 2023-12-05 13:50:10.512895 : MinCell_TileMatrix_17_chr17, Class = integer MinCell_TileMatrix_17_chr17: length = 1 [1] 1 2023-12-05 13:50:10.51632 : MaxCell_TileMatrix_17_chr17, Class = integer MaxCell_TileMatrix_17_chr17: length = 1 [1] 12222 2023-12-05 13:50:27.598988 : Adding TileMatrix to pbmc_granulocyte_sorted_10k for Chr (18 of 23)!, 6.061 mins elapsed. 2023-12-05 13:50:28.003895 : NTiles_TileMatrix_18_chr18, Class = numeric NTiles_TileMatrix_18_chr18: length = 1 chr18 160747 2023-12-05 13:50:28.007297 : NCells_TileMatrix_18_chr18, Class = integer NCells_TileMatrix_18_chr18: length = 1 [1] 12222 2023-12-05 13:50:28.010814 : MinTile_TileMatrix_18_chr18, Class = numeric MinTile_TileMatrix_18_chr18: length = 1 [1] 21 2023-12-05 13:50:28.017231 : MaxTile_TileMatrix_18_chr18, Class = numeric MaxTile_TileMatrix_18_chr18: length = 1 [1] 160527 2023-12-05 13:50:28.039028 : MinCell_TileMatrix_18_chr18, Class = integer MinCell_TileMatrix_18_chr18: length = 1 [1] 1 2023-12-05 13:50:28.042221 : MaxCell_TileMatrix_18_chr18, Class = integer MaxCell_TileMatrix_18_chr18: length = 1 [1] 12222 2023-12-05 13:50:32.918997 : Adding TileMatrix to pbmc_granulocyte_sorted_10k for Chr (19 of 23)!, 6.15 mins elapsed. 2023-12-05 13:50:34.654134 : NTiles_TileMatrix_19_chr19, Class = numeric NTiles_TileMatrix_19_chr19: length = 1 chr19 117236 2023-12-05 13:50:34.658009 : NCells_TileMatrix_19_chr19, Class = integer NCells_TileMatrix_19_chr19: length = 1 [1] 12222 2023-12-05 13:50:34.661415 : MinTile_TileMatrix_19_chr19, Class = numeric MinTile_TileMatrix_19_chr19: length = 1 [1] 179 2023-12-05 13:50:34.67882 : MaxTile_TileMatrix_19_chr19, Class = numeric MaxTile_TileMatrix_19_chr19: length = 1 [1] 117216 2023-12-05 13:50:34.768134 : MinCell_TileMatrix_19_chr19, Class = integer MinCell_TileMatrix_19_chr19: length = 1 [1] 1 2023-12-05 13:50:34.77254 : MaxCell_TileMatrix_19_chr19, Class = integer MaxCell_TileMatrix_19_chr19: length = 1 [1] 12222 2023-12-05 13:50:51.985544 : Adding TileMatrix to pbmc_granulocyte_sorted_10k for Chr (20 of 23)!, 6.467 mins elapsed. 2023-12-05 13:50:52.848001 : NTiles_TileMatrix_20_chr20, Class = numeric NTiles_TileMatrix_20_chr20: length = 1 chr20 128889 2023-12-05 13:50:52.852301 : NCells_TileMatrix_20_chr20, Class = integer NCells_TileMatrix_20_chr20: length = 1 [1] 12222 2023-12-05 13:50:52.85602 : MinTile_TileMatrix_20_chr20, Class = numeric MinTile_TileMatrix_20_chr20: length = 1 [1] 121 2023-12-05 13:50:52.865861 : MaxTile_TileMatrix_20_chr20, Class = numeric MaxTile_TileMatrix_20_chr20: length = 1 [1] 128667 2023-12-05 13:50:52.908795 : MinCell_TileMatrix_20_chr20, Class = integer MinCell_TileMatrix_20_chr20: length = 1 [1] 1 2023-12-05 13:50:52.912282 : MaxCell_TileMatrix_20_chr20, Class = integer MaxCell_TileMatrix_20_chr20: length = 1 [1] 12222 2023-12-05 13:50:59.723061 : Adding TileMatrix to pbmc_granulocyte_sorted_10k for Chr (21 of 23)!, 6.596 mins elapsed. 2023-12-05 13:51:00.017607 : NTiles_TileMatrix_21_chr21, Class = numeric NTiles_TileMatrix_21_chr21: length = 1 chr21 93420 2023-12-05 13:51:00.021194 : NCells_TileMatrix_21_chr21, Class = integer NCells_TileMatrix_21_chr21: length = 1 [1] 12222 2023-12-05 13:51:00.024437 : MinTile_TileMatrix_21_chr21, Class = numeric MinTile_TileMatrix_21_chr21: length = 1 [1] 10062 2023-12-05 13:51:00.030499 : MaxTile_TileMatrix_21_chr21, Class = numeric MaxTile_TileMatrix_21_chr21: length = 1 [1] 93400 2023-12-05 13:51:00.04389 : MinCell_TileMatrix_21_chr21, Class = integer MinCell_TileMatrix_21_chr21: length = 1 [1] 1 2023-12-05 13:51:00.046829 : MaxCell_TileMatrix_21_chr21, Class = integer MaxCell_TileMatrix_21_chr21: length = 1 [1] 12222 2023-12-05 13:51:03.684627 : Adding TileMatrix to pbmc_granulocyte_sorted_10k for Chr (22 of 23)!, 6.662 mins elapsed. 2023-12-05 13:51:04.319207 : NTiles_TileMatrix_22_chr22, Class = numeric NTiles_TileMatrix_22_chr22: length = 1 chr22 101637 2023-12-05 13:51:04.32261 : NCells_TileMatrix_22_chr22, Class = integer NCells_TileMatrix_22_chr22: length = 1 [1] 12222 2023-12-05 13:51:04.325613 : MinTile_TileMatrix_22_chr22, Class = numeric MinTile_TileMatrix_22_chr22: length = 1 [1] 21052 2023-12-05 13:51:04.333811 : MaxTile_TileMatrix_22_chr22, Class = numeric MaxTile_TileMatrix_22_chr22: length = 1 [1] 101617 2023-12-05 13:51:04.367343 : MinCell_TileMatrix_22_chr22, Class = integer MinCell_TileMatrix_22_chr22: length = 1 [1] 1 2023-12-05 13:51:04.370613 : MaxCell_TileMatrix_22_chr22, Class = integer MaxCell_TileMatrix_22_chr22: length = 1 [1] 12222 2023-12-05 13:51:09.667479 : Adding TileMatrix to pbmc_granulocyte_sorted_10k for Chr (23 of 23)!, 6.762 mins elapsed. 2023-12-05 13:51:10.103939 : NTiles_TileMatrix_23_chrX, Class = numeric NTiles_TileMatrix_23_chrX: length = 1 chrX 312082 2023-12-05 13:51:10.107513 : NCells_TileMatrix_23_chrX, Class = integer NCells_TileMatrix_23_chrX: length = 1 [1] 12222 2023-12-05 13:51:10.110856 : MinTile_TileMatrix_23_chrX, Class = numeric MinTile_TileMatrix_23_chrX: length = 1 [1] 21 2023-12-05 13:51:10.119286 : MaxTile_TileMatrix_23_chrX, Class = numeric MaxTile_TileMatrix_23_chrX: length = 1 [1] 312062 2023-12-05 13:51:10.151519 : MinCell_TileMatrix_23_chrX, Class = integer MinCell_TileMatrix_23_chrX: length = 1 [1] 1 2023-12-05 13:51:10.154811 : MaxCell_TileMatrix_23_chrX, Class = integer MaxCell_TileMatrix_23_chrX: length = 1 [1] 12222 2023-12-05 13:51:19.432418 : (pbmc_granulocyte_sorted_10k : 1 of 1) Finished Adding TileMatrix!, 19.226 mins elapsed. 2023-12-05 13:51:19.434102 : (pbmc_granulocyte_sorted_10k : 1 of 1) Adding GeneScoreMatrix!, 19.226 mins elapsed. 2023-12-05 13:51:19.667711 : pbmc_granulocyte_sorted_10k .addGeneScoreMat geneRegions, Class = GRanges GRanges object with 36448 ranges and 5 metadata columns: seqnames ranges strand | gene_id symbol | [1] chr1 24554-31109 + | ENSG00000243485 MIR1302-2HG [2] chr1 34554-41081 - | ENSG00000237613 FAM138A [3] chr1 60419-71585 + | ENSG00000186092 OR4F5 [4] chr1 89295-138723 - | ENSG00000238009 AL627309.1 [5] chr1 89551-96105 - | ENSG00000239945 AL627309.3 ... ... ... ... . ... ... [36444] chrX 155489011-155674944 - | ENSG00000185973 TMLHE [36445] chrX 155762812-155782459 + | ENSG00000168939 SPRY3 [36446] chrX 155876345-155943769 + | ENSG00000124333 VAMP7 [36447] chrX 155992581-156010817 + | ENSG00000124334 IL9R [36448] chrX 156014623-156021837 - | ENSG00000185203 WASIR1 geneStart geneEnd geneWeight [1] 29554 31109 4.06171 [2] 36081 34554 4.07484 [3] 65419 71585 2.79749 [4] 133723 89295 1.40609 [5] 91105 89551 4.06218 ... ... ... ... [36444] 155669944 155489011 1.10796 [36445] 155767812 155782459 2.02161 [36446] 155881345 155943769 1.29770 [36447] 155997581 156010817 2.10065 [36448] 156016837 156014623 3.78206 ------- seqinfo: 23 sequences from an unspecified genome; no seqlengths 2023-12-05 13:51:19.862401 : Creating Temp GeneScoreMatrix for pbmc_granulocyte_sorted_10k, Chr (1 of 23)!, 0.001 mins elapsed. 2023-12-05 13:51:19.880762 : Creating Temp GeneScoreMatrix for pbmc_granulocyte_sorted_10k, Chr (2 of 23)!, 0.001 mins elapsed. 2023-12-05 13:51:19.906975 : Creating Temp GeneScoreMatrix for pbmc_granulocyte_sorted_10k, Chr (3 of 23)!, 0.001 mins elapsed. 2023-12-05 13:51:19.933279 : Creating Temp GeneScoreMatrix for pbmc_granulocyte_sorted_10k, Chr (4 of 23)!, 0.002 mins elapsed. 2023-12-05 13:51:19.956463 : Creating Temp GeneScoreMatrix for pbmc_granulocyte_sorted_10k, Chr (5 of 23)!, 0.002 mins elapsed. 2023-12-05 13:51:19.991323 : Creating Temp GeneScoreMatrix for pbmc_granulocyte_sorted_10k, Chr (6 of 23)!, 0.003 mins elapsed. 2023-12-05 13:51:20.009303 : Creating Temp GeneScoreMatrix for pbmc_granulocyte_sorted_10k, Chr (7 of 23)!, 0.003 mins elapsed. 2023-12-05 13:51:20.037412 : Creating Temp GeneScoreMatrix for pbmc_granulocyte_sorted_10k, Chr (8 of 23)!, 0.004 mins elapsed. 2023-12-05 13:51:20.068399 : Creating Temp GeneScoreMatrix for pbmc_granulocyte_sorted_10k, Chr (9 of 23)!, 0.004 mins elapsed. 2023-12-05 13:51:20.089008 : Creating Temp GeneScoreMatrix for pbmc_granulocyte_sorted_10k, Chr (10 of 23)!, 0.005 mins elapsed. 2023-12-05 13:51:20.114393 : Creating Temp GeneScoreMatrix for pbmc_granulocyte_sorted_10k, Chr (11 of 23)!, 0.005 mins elapsed. 2023-12-05 13:51:20.135761 : Creating Temp GeneScoreMatrix for pbmc_granulocyte_sorted_10k, Chr (12 of 23)!, 0.005 mins elapsed. 2023-12-05 13:51:20.190792 : Creating Temp GeneScoreMatrix for pbmc_granulocyte_sorted_10k, Chr (13 of 23)!, 0.006 mins elapsed. 2023-12-05 13:51:20.192722 : Creating Temp GeneScoreMatrix for pbmc_granulocyte_sorted_10k, Chr (14 of 23)!, 0.006 mins elapsed. 2023-12-05 13:51:20.216534 : Creating Temp GeneScoreMatrix for pbmc_granulocyte_sorted_10k, Chr (15 of 23)!, 0.007 mins elapsed. 2023-12-05 13:51:20.243137 : Creating Temp GeneScoreMatrix for pbmc_granulocyte_sorted_10k, Chr (16 of 23)!, 0.007 mins elapsed. 2023-12-05 13:51:30.430385 : Creating Temp GeneScoreMatrix for pbmc_granulocyte_sorted_10k, Chr (17 of 23)!, 0.177 mins elapsed. 2023-12-05 13:51:33.106321 : Creating Temp GeneScoreMatrix for pbmc_granulocyte_sorted_10k, Chr (18 of 23)!, 0.221 mins elapsed. 2023-12-05 13:51:39.453454 : Creating Temp GeneScoreMatrix for pbmc_granulocyte_sorted_10k, Chr (19 of 23)!, 0.327 mins elapsed. 2023-12-05 13:51:42.852352 : Creating Temp GeneScoreMatrix for pbmc_granulocyte_sorted_10k, Chr (20 of 23)!, 0.384 mins elapsed. 2023-12-05 13:51:44.376249 : Creating Temp GeneScoreMatrix for pbmc_granulocyte_sorted_10k, Chr (21 of 23)!, 0.409 mins elapsed. 2023-12-05 13:51:47.704632 : Creating Temp GeneScoreMatrix for pbmc_granulocyte_sorted_10k, Chr (22 of 23)!, 0.465 mins elapsed. 2023-12-05 13:51:48.658496 : Creating Temp GeneScoreMatrix for pbmc_granulocyte_sorted_10k, Chr (23 of 23)!, 0.481 mins elapsed. 2023-12-05 13:52:05.285729 : pbmc_granulocyte_sorted_10k .addGeneScoreMat FeatureDF, Class = data.frame pbmc_granulocyte_sorted_10k .addGeneScoreMat FeatureDF: nRows = 36448, nCols = 6 seqnames start end strand name idx 1 chr1 29554 31109 1 MIR1302-2HG 1 2 chr1 36081 34554 2 FAM138A 2 3 chr1 65419 71585 1 OR4F5 3 4 chr1 133723 89295 2 AL627309.1 4 5 chr1 91105 89551 2 AL627309.3 5 6 chr1 140339 139790 2 AL627309.2 6 2023-12-05 13:52:06.66356 : Adding GeneScoreMatrix to pbmc_granulocyte_sorted_10k for Chr (1 of 23)!, 0.781 mins elapsed. 2023-12-05 13:52:12.438981 : Adding GeneScoreMatrix to pbmc_granulocyte_sorted_10k for Chr (2 of 23)!, 0.877 mins elapsed. 2023-12-05 13:52:17.788286 : Adding GeneScoreMatrix to pbmc_granulocyte_sorted_10k for Chr (3 of 23)!, 0.966 mins elapsed. 2023-12-05 13:52:23.203854 : Adding GeneScoreMatrix to pbmc_granulocyte_sorted_10k for Chr (4 of 23)!, 1.056 mins elapsed. 2023-12-05 13:52:25.773653 : Adding GeneScoreMatrix to pbmc_granulocyte_sorted_10k for Chr (5 of 23)!, 1.099 mins elapsed. 2023-12-05 13:52:28.654166 : Adding GeneScoreMatrix to pbmc_granulocyte_sorted_10k for Chr (6 of 23)!, 1.147 mins elapsed. 2023-12-05 13:52:33.364333 : Adding GeneScoreMatrix to pbmc_granulocyte_sorted_10k for Chr (7 of 23)!, 1.226 mins elapsed. 2023-12-05 13:52:36.817135 : Adding GeneScoreMatrix to pbmc_granulocyte_sorted_10k for Chr (8 of 23)!, 1.283 mins elapsed. 2023-12-05 13:52:39.511589 : Adding GeneScoreMatrix to pbmc_granulocyte_sorted_10k for Chr (9 of 23)!, 1.328 mins elapsed. 2023-12-05 13:52:43.484842 : Adding GeneScoreMatrix to pbmc_granulocyte_sorted_10k for Chr (10 of 23)!, 1.394 mins elapsed. 2023-12-05 13:52:46.694981 : Adding GeneScoreMatrix to pbmc_granulocyte_sorted_10k for Chr (11 of 23)!, 1.448 mins elapsed. 2023-12-05 13:52:50.758853 : Adding GeneScoreMatrix to pbmc_granulocyte_sorted_10k for Chr (12 of 23)!, 1.516 mins elapsed. 2023-12-05 13:52:55.508766 : Adding GeneScoreMatrix to pbmc_granulocyte_sorted_10k for Chr (13 of 23)!, 1.595 mins elapsed. 2023-12-05 13:52:57.533229 : Adding GeneScoreMatrix to pbmc_granulocyte_sorted_10k for Chr (14 of 23)!, 1.629 mins elapsed. 2023-12-05 13:53:00.359771 : Adding GeneScoreMatrix to pbmc_granulocyte_sorted_10k for Chr (15 of 23)!, 1.676 mins elapsed. 2023-12-05 13:53:03.905438 : Adding GeneScoreMatrix to pbmc_granulocyte_sorted_10k for Chr (16 of 23)!, 1.735 mins elapsed. 2023-12-05 13:53:07.262301 : Adding GeneScoreMatrix to pbmc_granulocyte_sorted_10k for Chr (17 of 23)!, 1.791 mins elapsed. 2023-12-05 13:53:12.021613 : Adding GeneScoreMatrix to pbmc_granulocyte_sorted_10k for Chr (18 of 23)!, 1.87 mins elapsed. 2023-12-05 13:53:15.255023 : Adding GeneScoreMatrix to pbmc_granulocyte_sorted_10k for Chr (19 of 23)!, 1.924 mins elapsed. 2023-12-05 13:53:21.61198 : Adding GeneScoreMatrix to pbmc_granulocyte_sorted_10k for Chr (20 of 23)!, 2.03 mins elapsed. 2023-12-05 13:53:24.211043 : Adding GeneScoreMatrix to pbmc_granulocyte_sorted_10k for Chr (21 of 23)!, 2.073 mins elapsed. 2023-12-05 13:53:27.077377 : Adding GeneScoreMatrix to pbmc_granulocyte_sorted_10k for Chr (22 of 23)!, 2.121 mins elapsed. 2023-12-05 13:53:29.214585 : Adding GeneScoreMatrix to pbmc_granulocyte_sorted_10k for Chr (23 of 23)!, 2.157 mins elapsed. 2023-12-05 13:53:32.449044 : (pbmc_granulocyte_sorted_10k : 1 of 1) Finished Adding GeneScoreMatrix!, 21.443 mins elapsed. 2023-12-05 13:53:32.451228 : (pbmc_granulocyte_sorted_10k : 1 of 1) Finished Creating Arrow File, 21.443 mins elapsed. ------- Completed End Time : 2023-12-05 13:53:32.481457 Elapsed Time Minutes = 21.4445306261381 Elapsed Time Hours = 0.357409020927217 -------