Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-11 12:06 -0400 (Sat, 11 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4864 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4652 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4597 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4586 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 455/2346 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
COTAN 2.9.7 (landing page) Galfrè Silvia Giulia
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the COTAN package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/COTAN.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: COTAN |
Version: 2.9.7 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:COTAN.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings COTAN_2.9.7.tar.gz |
StartedAt: 2025-10-10 07:33:10 -0000 (Fri, 10 Oct 2025) |
EndedAt: 2025-10-10 07:53:19 -0000 (Fri, 10 Oct 2025) |
EllapsedTime: 1208.9 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: COTAN.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:COTAN.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings COTAN_2.9.7.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/COTAN.Rcheck’ * using R version 4.5.0 (2025-04-11) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘COTAN/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘COTAN’ version ‘2.9.7’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 26 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘COTAN’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed UniformClusters 58.584 0.128 58.446 CalculatingCOEX 46.040 0.308 45.822 HandlingClusterizations 41.475 1.619 43.035 HeatmapPlots 28.973 0.439 29.059 ParametersEstimations 19.581 0.135 19.764 GenesStatistics 9.548 0.019 9.421 COTAN_ObjectCreation 8.189 0.121 8.161 RawDataCleaning 5.058 0.008 5.084 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘outputTestDatasetCreation.R’ Running ‘spelling.R’ Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: [1] 0.1588375 - 0.1588393 [1] [2] 0.5920400 - 0.5920375 [2] [3] 0.5631372 - 0.5631452 [3] [4] 1.3469346 - 1.3469312 [4] [5] 0.1624305 - 0.1624447 [5] [6] 0.0980751 - 0.0980681 [6] [7] 2.0990181 - 2.0990188 [7] [8] 0.3256293 - 0.3256359 [8] [9] 0.7567358 - 0.7567377 [9] [10] 1.2053130 - 1.2053087 [10] ... ... ... and 50 more ... [ FAIL 1 | WARN 3 | SKIP 0 | PASS 572 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 ERROR See ‘/home/biocbuild/bbs-3.22-bioc/meat/COTAN.Rcheck/00check.log’ for details.
COTAN.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL COTAN ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘COTAN’ ... ** this is package ‘COTAN’ version ‘2.9.7’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (COTAN)
COTAN.Rcheck/tests/outputTestDatasetCreation.Rout
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > > # Creates the files to be reloaded by the tests for comparisons > > outputTestDatasetCreation <- + function(testsDir = file.path("tests", "testthat")) { + utils::data("test.dataset", package = "COTAN") + options(parallelly.fork.enable = TRUE) + setLoggingLevel(3L) + + obj <- COTAN(raw = test.dataset) + obj <- initializeMetaDataset(objCOTAN = obj, GEO = " ", + sequencingMethod = "artificial", + sampleCondition = "test") + + obj <- proceedToCoex(objCOTAN = obj, cores = 6L, saveObj = FALSE) + + if (FALSE) { + saveRDS(obj, file = file.path(testsDir,"test.COTAN.RDS")) + } + + cells.names.test <- + getCells(objCOTAN = obj)[c(1L:10L, 591L:610L, 991L:1000L)] + genes.names.test <- + getGenes(objCOTAN = obj)[c(131L:140L, 291L:310L, 591L: 600L)] + saveRDS(cells.names.test, file.path(testsDir, "cells.names.test.RDS")) + saveRDS(genes.names.test, file.path(testsDir, "genes.names.test.RDS")) + + pcaRaw <- runPCA(x = getRawData(objCOTAN = obj), rank = 10L, + BSPARAM = IrlbaParam(), get.rotation = FALSE)[["x"]] + + pca.raw.test <- pcaRaw[genes.names.test, ] + saveRDS(pca.raw.test, file.path(testsDir, "pca.raw.test.RDS")) + + dispersion.test <- getDispersion(objCOTAN = obj)[genes.names.test] + saveRDS(dispersion.test, file.path(testsDir, "dispersion.test.RDS")) + + raw.norm.test <- + getNuNormData(objCOTAN = obj)[genes.names.test, cells.names.test] + saveRDS(raw.norm.test, file.path(testsDir, "raw.norm.test.RDS")) + + coex.test <- + getGenesCoex(objCOTAN = obj, genes = genes.names.test, zeroDiagonal = FALSE) + saveRDS(coex.test, file.path(testsDir, "coex.test.RDS")) + + lambda.test <- getLambda(objCOTAN = obj)[genes.names.test] + saveRDS(lambda.test, file.path(testsDir, "lambda.test.RDS")) + + GDI.test <- calculateGDI(objCOTAN = obj) + GDI.test <- GDI.test[genes.names.test, ] + saveRDS(GDI.test, file.path(testsDir, "GDI.test.RDS")) + + nu.test <- getNu(objCOTAN = obj)[cells.names.test] + saveRDS(nu.test, file.path(testsDir, "nu.test.RDS")) + + pvalues.test <- calculatePValue(objCOTAN = obj, + geneSubsetCol = genes.names.test, + geneSubsetRow = genes.names.test) + saveRDS(pvalues.test, file.path(testsDir, "pvalues.test.RDS")) + + groupMarkers <- list(G1 = c("g-000010", "g-000020", "g-000138"), + G2 = c("g-000300", "g-000330", "g-000660"), + G3 = c("g-000510", "g-000530", "g-000550", + "g-000570", "g-000590")) + + gcsData <- genesCoexSpace(objCOTAN = obj, + primaryMarkers = unlist(groupMarkers), + numGenesPerMarker = 11L) + + genes.coex.space.test <- gcsData[["GCS"]] + saveRDS(genes.coex.space.test, + file.path(testsDir, "genes.coex.space.test.RDS")) + + genesClustersData <- + establishGenesClusters(objCOTAN = obj, + groupMarkers = groupMarkers, + numGenesPerMarker = 11L, + kCuts = 6L, distance = "cosine", + hclustMethod = "ward.D2") + + pca.genes.clusters.test <- genesClustersData[["pca_clusters"]] + saveRDS(pca.genes.clusters.test, + file.path(testsDir, "pca.genes.clusters.test.RDS")) + + # Make it a less strict check as it is only for testing + checker <- new("AdvancedGDIUniformityCheck") + checker <- shiftCheckerThresholds(checker, 0.1) + + initialResolution <- 1.3 + splitData <- cellsUniformClustering(objCOTAN = obj, + checker = checker, + initialResolution = initialResolution, + useCoexEigen = TRUE, + dataMethod = "LL", + numReducedComp = 50L, + cores = 6L, optimizeForSpeed = TRUE, + deviceStr = "cuda", saveObj = FALSE) + + split.clusters.test <- splitData[["clusters"]] + saveRDS(split.clusters.test, + file = file.path(testsDir, "split.clusters.test.RDS")) + + test.dataset.clusters1 <- split.clusters.test + save(test.dataset.clusters1, compress = TRUE, + file = file.path("data", "test.dataset.clusters1.rda")) + + obj <- addClusterization(objCOTAN = obj, + clName = "split", + clusters = splitData[["clusters"]], + coexDF = splitData[["coex"]]) + + coex.clusters.test <- splitData[["coex"]][genes.names.test, ] + saveRDS(coex.clusters.test, file.path(testsDir, "coex.clusters.test.RDS")) + + pvalDF <- pValueFromDEA(splitData[["coex"]], + getNumCells(objCOTAN = obj), + adjustmentMethod = "none") + + pvalues.clusters.test <- pvalDF[genes.names.test, ] + saveRDS(pvalues.clusters.test, + file.path(testsDir, "pvalues.clusters.test.RDS")) + + mergedData <- mergeUniformCellsClusters(objCOTAN = obj, + clusters = splitData[["clusters"]], + checkers = checker, + batchSize = 1L, + cores = 6L, + distance = "cosine", + hclustMethod = "ward.D2", + saveObj = FALSE) + + merge.clusters.test <- mergedData[["clusters"]] + saveRDS(merge.clusters.test, + file = file.path(testsDir, "merge.clusters.test.RDS")) + + test.dataset.clusters2 <- merge.clusters.test + save(test.dataset.clusters2, compress = TRUE, + file = file.path("data", "test.dataset.clusters2.rda")) + + obj <- addClusterization(objCOTAN = obj, + clName = "merge", + clusters = mergedData[["clusters"]], + coexDF = mergedData[["coex"]]) + } > > proc.time() user system elapsed 0.208 0.026 0.218
COTAN.Rcheck/tests/spelling.Rout
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > if (requireNamespace("spelling", quietly = TRUE)) + spelling::spell_check_test(vignettes = TRUE, error = FALSE, + skip_on_cran = TRUE) All Done! > > proc.time() user system elapsed 0.192 0.036 0.216
COTAN.Rcheck/tests/testthat.Rout.fail
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > Sys.setenv(R_TESTS = "") > library(testthat) > library(COTAN) > library(zeallot) > test_check("COTAN") Setting new log level to 4 Initializing `COTAN` meta-data Genes/cells selection done: dropped [0] genes and [0] cells Working on [10] genes and [20] cells Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 1.49975728988647 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.903596292963576 | max: 4.67949426963453 | % negative: 10 Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.08429956436157 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.000664949417114258 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00801444053649902 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.730151176452637 Total calculations elapsed time: 2.82313013076782 Calculate genes' COEX (legacy): DONE Genes/cells selection done: dropped [0] genes and [0] cells Working on [10] genes and [20] cells Estimate `dispersion`: START Effective number of cores used: 1 Executing 5 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Parallel dispersion Newton-Raphson: used up to 4 iterations Parallel dispersion Newton-Raphson: used up to 5 iterations Parallel dispersion Newton-Raphson: used up to 5 iterations Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 4.45004463195801 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.903596292963576 | max: 4.67949426963453 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 7 cells batches Total calculations elapsed time: 0.777174472808838 Estimate `nu`: DONE `nu` change (abs) | max: 1.75595238095238 | median: 1.07156808035714 | mean: 1.07156808035714 Estimate `dispersion`/`nu`: START Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 1.48697328567505 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 1.03734183779544 | max: 4.61112297272667 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Total calculations elapsed time: 0.747205257415771 Estimate `nu`: DONE `nu` change (abs) | max: 0.0295487661210321 | median: 0.016072261901129 | mean: 0.016072261901129 `nu` mean: 1.69786080481514 Marginal errors | max: 1.95799528048 | median 1.32268477389029 | mean: 1.33563364783916 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 1.44187831878662 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.0585450475968788 | max: 3.52739274166646 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Total calculations elapsed time: 0.743573427200317 Estimate `nu`: DONE `nu` change (abs) | max: 0.417150556912302 | median: 0.240156504520849 | mean: 0.240156504520849 `nu` mean: 0.823005947608547 Marginal errors | max: 0.837672524335755 | median 0.704691669139065 | mean: 0.646575831699997 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 1.478844165802 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.328845855849147 | max: 4.03031691940854 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Total calculations elapsed time: 0.745220899581909 Estimate `nu`: DONE `nu` change (abs) | max: 0.164439840041 | median: 0.0957105992188852 | mean: 0.0957105992188852 `nu` mean: 1.06872924082212 Marginal errors | max: 0.260109847946692 | median 0.21392791155499 | mean: 0.197565106613054 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 1.49529647827148 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.229469002841045 | max: 3.87206403670079 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Total calculations elapsed time: 0.701686859130859 Estimate `nu`: DONE `nu` change (abs) | max: 0.05539667181205 | median: 0.0321044921874999 | mean: 0.0321044921874999 `nu` mean: 0.97670782037545 Marginal errors | max: 0.095347789718808 | median 0.0796003827042702 | mean: 0.0725509735761708 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 1.49027228355408 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.263830434255107 | max: 3.92953043775907 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Total calculations elapsed time: 0.767932176589966 Estimate `nu`: DONE `nu` change (abs) | max: 0.0196209299693411 | median: 0.0114037947200925 | mean: 0.0114037947200925 `nu` mean: 1.00821713524925 Marginal errors | max: 0.0329495161656741 | median 0.0273479725376324 | mean: 0.025029675152131 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 1.47091269493103 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.251734659898779 | max: 3.9096133246649 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Total calculations elapsed time: 0.757766008377075 Estimate `nu`: DONE `nu` change (abs) | max: 0.0069104540740097 | median: 0.0040109538496062 | mean: 0.0040109538496062 `nu` mean: 0.997100499775596 Marginal errors | max: 0.0116950057438405 | median 0.00972280144873849 | mean: 0.00889105008777538 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 1.4984290599823 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.256009779031907 | max: 3.91667271750655 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Total calculations elapsed time: 0.810455083847046 Estimate `nu`: DONE `nu` change (abs) | max: 0.00251004753849005 | median: 0.00146484374999994 | mean: 0.00146484374999994 `nu` mean: 1.00104520378849 Marginal errors | max: 0.00430755646112857 | median 0.00358203399504298 | mean: 0.00327684342604062 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 1.5436737537384 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.254429717857093 | max: 3.91406908073254 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Total calculations elapsed time: 0.800214767456055 Estimate `nu`: DONE `nu` change (abs) | max: 0.00104629156456748 | median: 0.000592910406456731 | mean: 0.000592910406456731 `nu` mean: 0.999546618841889 Marginal errors | max: 0.00162038706091039 | median 0.00134441676098973 | mean: 0.00123030512553282 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 1.61452054977417 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.255022049769696 | max: 3.91504587939868 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Total calculations elapsed time: 0.779638528823853 Estimate `nu`: DONE `nu` change (abs) | max: 0.000418450901304768 | median: 0.000244140625000028 | mean: 0.000244140625000028 `nu` mean: 1.0001743102763 Marginal errors | max: 0.00071569233034019 | median 0.000597297218559056 | mean: 0.00054590699507937 Total calculations elapsed time: 40.6351654529572 Estimate `dispersion`/`nu`: DONE Estimate `dispersion`/`nu`: START Initializing `COTAN` meta-data Genes/cells selection done: dropped [0] genes and [0] cells Working on [10] genes and [20] cells Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 1.48804426193237 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.903596292963576 | max: 4.67949426963453 | % negative: 10 While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.34431862831116 Calculating genes' COEX normalization factor Fraction of genes' with very low expected contingency tables: 0.181818181818182 Calculate genes' normalization factor elapsed time: 0.000930070877075195 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00410223007202148 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.792829036712646 Total calculations elapsed time: 3.1421799659729 Calculate genes' COEX (legacy): DONE Calculate cells' COEX (legacy): START Retrieving expected cells' contingency table calculating NN.. done calculating YN..NY..YY..t().. done Expected cells' contingency table elapsed time: 2.32803511619568 Calculating cells' COEX normalization factor Fraction of cells' with very low expected contingency tables: 0 Calculate cells' normalization factor elapsed time: 0.000946998596191406 Retrieving observed cells' yes/yes contingency table calculating YY.. done Observed cells' contingency table elapsed time: 0.00280976295471191 Estimating cells' COEX Calculate cells' COEX elapsed time: 0.780176639556885 Total calculations elapsed time: 3.11196851730347 Calculate cells' COEX (legacy): DONE Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.0132935047149658 Calculate `GDI`: DONE Total calculations elapsed time: 2.44823622703552 Calculate GDI dataframe: DONE Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.00423717498779297 Calculate `GDI`: DONE Total calculations elapsed time: 2.32143211364746 Calculate GDI dataframe: DONE Included 1 genes with GDI below 1.3 Selected 10 genes using HGDI selector Running genes' selection: DONE Running genes' selection: START Included 1 genes with GDI below 1.3 Selected 10 genes using HGDI selector Running genes' selection: DONE Running genes' selection: START Included 1 genes with GDI below 1.3 Selected 10 genes using HGDI selector Running genes' selection: DONE Running genes' selection: START Selected 5 genes using HGDI selector Running genes' selection: DONE Running genes' selection: START Normalizing layer: counts Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Finding variable features for layer counts Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Selected 5 genes using HVG_Seurat selector Running genes' selection: DONE Running genes' selection: START Normalizing layer: counts Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Finding variable features for layer data Calculating gene means 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating gene variance to mean ratios 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Running genes' selection: START Given 5 genes as input Running genes' selection: DONE Elaborating Reduced dimensionality Data Matrix - START Running genes' selection: START Included 1 genes with GDI below 1.3 Selected 10 genes using HGDI selector Running genes' selection: DONE Elaborating PCA - START Elaborating PCA - DONE Total calculations elapsed time: 1.50982069969177 Elaborating Reduced dimensionality Data Matrix - DONE Elaborating Reduced dimensionality Data Matrix - START Running genes' selection: START Included 1 genes with GDI below 1.3 Selected 10 genes using HGDI selector Running genes' selection: DONE Elaborating PCA - START Elaborating PCA - DONE Total calculations elapsed time: 1.56280994415283 Elaborating Reduced dimensionality Data Matrix - DONE Elaborating Reduced dimensionality Data Matrix - START Running genes' selection: START Selected 8 genes using HGDI selector Running genes' selection: DONE Elaborating PCA - START Elaborating PCA - DONE Total calculations elapsed time: 1.55171275138855 Elaborating Reduced dimensionality Data Matrix - DONE Elaborating Reduced dimensionality Data Matrix - START Running genes' selection: START Normalizing layer: counts Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Finding variable features for layer counts Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Selected 8 genes using HVG_Seurat selector Running genes' selection: DONE Elaborating PCA - START Elaborating PCA - DONE Total calculations elapsed time: 2.41883206367493 Elaborating Reduced dimensionality Data Matrix - DONE Elaborating Reduced dimensionality Data Matrix - START Elaborating COEX Eigen Vectors - START Elaborating COEX Eigen Vectors - DONE Total calculations elapsed time: 2.31196641921997 Elaborating Reduced dimensionality Data Matrix - DONE Elaborating Reduced dimensionality Data Matrix - START Elaborating COEX Eigen Vectors - START Elaborating COEX Eigen Vectors - DONE Total calculations elapsed time: 2.28414964675903 Elaborating Reduced dimensionality Data Matrix - DONE Initializing `COTAN` meta-data Initializing `COTAN` meta-data Genes/cells selection done: dropped [0] genes and [0] cells Working on [10] genes and [20] cells Estimate `dispersion`/`nu`: START Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 1.65676760673523 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.903596292963576 | max: 4.67949426963453 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Total calculations elapsed time: 0.738468647003174 Estimate `nu`: DONE `nu` change (abs) | max: 1.75719246031746 | median: 1.07229953342014 | mean: 1.07229953342014 `nu` mean: 1.68489292689732 Marginal errors | max: 1.735699617106 | median 1.37997441333659 | mean: 1.32181397451301 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 1.45202422142029 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.0655494303592343 | max: 3.54400580804152 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Total calculations elapsed time: 0.791946172714233 Estimate `nu`: DONE `nu` change (abs) | max: 0.402649984216273 | median: 0.231868788425666 | mean: 0.231868788425666 `nu` mean: 0.829218804209393 Marginal errors | max: 0.803248939260364 | median 0.677504196374571 | mean: 0.619386446933351 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 1.61246776580811 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.326019058449519 | max: 4.02612397202046 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Total calculations elapsed time: 0.740196704864502 Estimate `nu`: DONE `nu` change (abs) | max: 0.158004893526231 | median: 0.0919692884670312 | mean: 0.0919692884670312 `nu` mean: 1.0660356050592 Marginal errors | max: 0.25067700287536 | median 0.206241644985115 | mean: 0.190402167377958 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 1.48224997520447 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.230397316576369 | max: 3.87365659194104 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Total calculations elapsed time: 0.777741193771362 Estimate `nu`: DONE `nu` change (abs) | max: 0.0532774732102337 | median: 0.0308837890624999 | mean: 0.0308837890624999 `nu` mean: 0.977606315852266 Marginal errors | max: 0.0916920322976189 | median 0.0765360853958175 | mean: 0.0697673030094085 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 1.53116011619568 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.263457616228195 | max: 3.928924407347 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Total calculations elapsed time: 0.772555828094482 Estimate `nu`: DONE `nu` change (abs) | max: 0.0187878665732679 | median: 0.0109155550210726 | mean: 0.0109155550210726 `nu` mean: 1.0078723115522 Marginal errors | max: 0.0315207323253404 | median 0.0261635598193228 | mean: 0.0239435763640456 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 1.47863245010376 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.251890641847533 | max: 3.90987172241566 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Total calculations elapsed time: 0.702098369598389 Estimate `nu`: DONE `nu` change (abs) | max: 0.00649137083358098 | median: 0.00376680890457393 | mean: 0.00376680890457393 `nu` mean: 0.997275438070993 Marginal errors | max: 0.0109748802265024 | median 0.00912386940474796 | mean: 0.00834350038184244 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 1.49526214599609 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.255902752363649 | max: 3.91649655995187 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Total calculations elapsed time: 0.787474393844604 Estimate `nu`: DONE `nu` change (abs) | max: 0.00230094227000666 | median: 0.00132529141000018 | mean: 0.00132529141000018 `nu` mean: 1.00097565086001 Marginal errors | max: 0.00376864912836616 | median 0.00313421412286008 | mean: 0.00286709489297579 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 1.55592966079712 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.254520292119112 | max: 3.91421850264948 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Total calculations elapsed time: 0.776451826095581 Estimate `nu`: DONE `nu` change (abs) | max: 0.000837013154366462 | median: 0.000488281250000028 | mean: 0.000488281250000028 `nu` mean: 0.999651268095634 Marginal errors | max: 0.00144055320514802 | median 0.00119489364392944 | mean: 0.00109355439757213 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 1.57266998291016 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.255046800817986 | max: 3.9150866760965 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Total calculations elapsed time: 0.794625282287598 Estimate `nu`: DONE `nu` change (abs) | max: 0.000418448154490214 | median: 0.000244140624999917 | mean: 0.000244140624999917 `nu` mean: 1.00017430752949 Marginal errors | max: 0.000715683388516908 | median 0.0005972847342397 | mean: 0.00054589991652243 Total calculations elapsed time: 41.3173639774323 Estimate `dispersion`/`nu`: DONE While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.44574546813965 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.000757932662963867 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00202584266662598 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.805728673934937 Total calculations elapsed time: 3.25425791740417 Calculate genes' COEX (legacy): DONE Calculate cells' COEX (legacy): START Retrieving expected cells' contingency table calculating NN.. done calculating YN..NY..YY..t().. done Expected cells' contingency table elapsed time: 2.4592924118042 Calculating cells' COEX normalization factor Calculate cells' normalization factor elapsed time: 0.000761747360229492 Retrieving observed cells' yes/yes contingency table calculating YY.. done Observed cells' contingency table elapsed time: 0.00209283828735352 Estimating cells' COEX Calculate cells' COEX elapsed time: 0.827409267425537 Total calculations elapsed time: 3.28955626487732 Calculate cells' COEX (legacy): DONE Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.00415420532226562 Calculate `GDI`: DONE Total calculations elapsed time: 2.38329339027405 Calculate GDI dataframe: DONE Calculate genes' partial COEX: START Retrieving expected genes' partial contingency table calculating partial NN.. done calculating partial NY..YN..YY.. done Calculating genes' partial COEX normalization factor Fraction of genes with very low expected contingency tables: 0.325 Retrieving observed genes' yes/yes partial contingency table calculating partial YY.. done Estimating genes' partial COEX Total calculations elapsed time: 6.17999935150146 Calculate genes' partial COEX: DONE Calculate cells' partial COEX: START Retrieving expected cells' partial contingency table calculating partial NN.. done calculating partial YN..NY..YY.. done Calculating cells' partial COEX normalization factor Fraction of genes with very low expected contingency tables: 0 Retrieving observed cells' yes/yes partial contingency table calculating partial YY.. done Estimating cells' partial COEX Total calculations elapsed time: 6.33288836479187 Calculate cells' partial COEX: DONE Asked to drop 2 genes and 0 cells Asked to drop 0 genes and 4 cells Asked to drop 2 genes and 2 cells Attaching package: 'rlang' The following objects are masked from 'package:testthat': is_false, is_null, is_true Genes/cells selection done: dropped [0] genes and [0] cells Working on [10] genes and [20] cells calculating YY.. done calculating YY.. done calculating YN..NY..NN..t().. done Estimate `dispersion`: START Effective number of cores used: 1 Executing 3 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Parallel dispersion Newton-Raphson: used up to 5 iterations Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 3.12017416954041 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.903596292963576 | max: 4.67949426963453 | % negative: 10 calculating NN.. done calculating NN.. done calculating NY..YN..YY..t().. done Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.25240278244019 Calculating genes' COEX normalization factor Fraction of genes' with very low expected contingency tables: 0.181818181818182 Calculate genes' normalization factor elapsed time: 0.000993251800537109 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00187206268310547 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.769450664520264 Total calculations elapsed time: 3.02471876144409 Calculate genes' COEX (legacy): DONE While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.24706745147705 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.000732660293579102 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00198650360107422 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.802281618118286 Total calculations elapsed time: 3.05206823348999 Calculate genes' COEX (legacy): DONE Calculate genes' partial COEX: START Retrieving expected genes' partial contingency table calculating partial NN.. done calculating partial NY..YN..YY.. done Calculating genes' partial COEX normalization factor Fraction of genes with very low expected contingency tables: 0.1 Retrieving observed genes' yes/yes partial contingency table calculating partial YY.. done Estimating genes' partial COEX Total calculations elapsed time: 6.40530562400818 Calculate genes' partial COEX: DONE Calculate genes' partial COEX: START Retrieving expected genes' partial contingency table calculating partial NN.. done calculating partial NY..YN..YY.. done Calculating genes' partial COEX normalization factor Fraction of genes with very low expected contingency tables: 0.4 Retrieving observed genes' yes/yes partial contingency table calculating partial YY.. done Estimating genes' partial COEX Total calculations elapsed time: 6.53454637527466 Calculate genes' partial COEX: DONE Genes/cells selection done: dropped [0] genes and [0] cells Working on [10] genes and [20] cells calculating YY.. done calculating YY.. done calculating NY..YN..NN..t().. done Estimate `dispersion`/`nu`: START Estimate `dispersion`: START Effective number of cores used: 1 Executing 3 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Parallel dispersion Newton-Raphson: used up to 5 iterations Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 3.03671193122864 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.903596292963576 | max: 4.67949426963453 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 5 cells batches Total calculations elapsed time: 0.764187574386597 Estimate `nu`: DONE `nu` change (abs) | max: 1.75719246031746 | median: 1.07229953342014 | mean: 1.07229953342014 `nu` mean: 1.68489292689732 Marginal errors | max: 0.255290533439036 | median 0.080731376500534 | mean: 0.101968565509112 Estimate `dispersion`: START Effective number of cores used: 1 Executing 3 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Parallel dispersion Newton-Raphson: used up to 5 iterations Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 3.06801819801331 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 1.03709166563768 | max: 4.61069655774133 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 5 cells batches Total calculations elapsed time: 0.787486553192139 Estimate `nu`: DONE `nu` change (abs) | max: 0.0273438105507502 | median: 0.0148852611818011 | mean: 0.0148852611818011 `nu` mean: 1.69735147626627 Marginal errors | max: 0.00330148418741594 | median 0.00111713187082163 | mean: 0.00132007186542964 Estimate `dispersion`: START Effective number of cores used: 1 Executing 3 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Parallel dispersion Newton-Raphson: used up to 5 iterations Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 3.02341032028198 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 1.03887279473672 | max: 4.60974134092906 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 5 cells batches Total calculations elapsed time: 0.742886543273926 Estimate `nu`: DONE `nu` change (abs) | max: 0 | median: 0 | mean: 0 `nu` mean: 1.69735147626627 Marginal errors | max: 5.14174422185931e-05 | median 1.6818224857218e-07 | mean: 5.57649710835051e-06 Total calculations elapsed time: 18.2489669322968 Estimate `dispersion`/`nu`: DONE calculating NN.. done calculating NN.. done calculating YN..NY..YY..t().. done Calculate cells' COEX (legacy): START Retrieving expected cells' contingency table calculating NN.. done calculating YN..NY..YY..t().. done Expected cells' contingency table elapsed time: 2.37293314933777 Calculating cells' COEX normalization factor Fraction of cells' with very low expected contingency tables: 0 Calculate cells' normalization factor elapsed time: 0.000943422317504883 Retrieving observed cells' yes/yes contingency table calculating YY.. done Observed cells' contingency table elapsed time: 0.0019073486328125 Estimating cells' COEX Calculate cells' COEX elapsed time: 0.769304752349854 Total calculations elapsed time: 3.14508867263794 Calculate cells' COEX (legacy): DONE Calculate cells' partial COEX: START Retrieving expected cells' partial contingency table calculating partial NN.. done calculating partial YN..NY..YY.. done Calculating cells' partial COEX normalization factor Fraction of genes with very low expected contingency tables: 0 Retrieving observed cells' yes/yes partial contingency table calculating partial YY.. done Estimating cells' partial COEX Total calculations elapsed time: 5.89147996902466 Calculate cells' partial COEX: DONE Calculate cells' partial COEX: START Retrieving expected cells' partial contingency table calculating partial NN.. done calculating partial YN..NY..YY.. done Calculating cells' partial COEX normalization factor Fraction of genes with very low expected contingency tables: 0 Retrieving observed cells' yes/yes partial contingency table calculating partial YY.. done Estimating cells' partial COEX Total calculations elapsed time: 5.98868632316589 Calculate cells' partial COEX: DONE Genes/cells selection done: dropped [0] genes and [0] cells Working on [10] genes and [20] cells Estimate `dispersion`/`nu`: START Estimate `dispersion`: START Effective number of cores used: 1 Executing 3 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Parallel dispersion Newton-Raphson: used up to 5 iterations Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 3.10156941413879 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.903596292963576 | max: 4.67949426963453 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 5 cells batches Total calculations elapsed time: 0.833273887634277 Estimate `nu`: DONE `nu` change (abs) | max: 1.75719246031746 | median: 1.07229953342014 | mean: 1.07229953342014 `nu` mean: 1.68489292689732 Marginal errors | max: 0.255290533439036 | median 0.080731376500534 | mean: 0.101968565509112 Estimate `dispersion`: START Effective number of cores used: 1 Executing 3 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Parallel dispersion Newton-Raphson: used up to 5 iterations Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 3.06711435317993 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 1.03709166563768 | max: 4.61069655774133 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 5 cells batches Total calculations elapsed time: 0.741283178329468 Estimate `nu`: DONE `nu` change (abs) | max: 0.0273438105507502 | median: 0.0148852611818011 | mean: 0.0148852611818011 `nu` mean: 1.69735147626627 Marginal errors | max: 0.00330148418741594 | median 0.00111713187082163 | mean: 0.00132007186542964 Estimate `dispersion`: START Effective number of cores used: 1 Executing 3 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Parallel dispersion Newton-Raphson: used up to 5 iterations Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 2.96291017532349 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 1.03887279473672 | max: 4.60974134092906 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 5 cells batches Total calculations elapsed time: 0.793923616409302 Estimate `nu`: DONE `nu` change (abs) | max: 0 | median: 0 | mean: 0 `nu` mean: 1.69735147626627 Marginal errors | max: 5.14174422185931e-05 | median 1.6818224857218e-07 | mean: 5.57649710835051e-06 Total calculations elapsed time: 18.2578806877136 Estimate `dispersion`/`nu`: DONE Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.2881600856781 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.000689268112182617 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00185823440551758 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.770939588546753 Total calculations elapsed time: 3.06164717674255 Calculate genes' COEX (legacy): DONE Calculating S: START Calculating S: DONE Calculating G: START calculating YY.. done calculating YN..NY..NN..t().. done calculating NN.. done calculating NY..YN..YY..t().. done Estimating G Total calculations elapsed time: 5.32271075248718 Calculating G: DONE Using S Calculating S: START Calculating S: DONE calculating PValues: START Get p-values genome wide on columns and genome wide on rows Total calculations elapsed time: 0.00306439399719238 calculating PValues: DONE Using G Calculating G: START calculating YY.. done calculating YN..NY..NN..t().. done calculating NN.. done calculating NY..YN..YY..t().. done Estimating G Total calculations elapsed time: 5.41368889808655 Calculating G: DONE calculating PValues: START Get p-values on a set of genes on columns and on a set of genes on rows Total calculations elapsed time: 5.41532015800476 calculating PValues: DONE Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.00407910346984863 Calculate `GDI`: DONE Total calculations elapsed time: 2.29773426055908 Calculate GDI dataframe: DONE Calculate GDI dataframe: START Using G Calculating G: START calculating YY.. done calculating YN..NY..NN..t().. done calculating NN.. done calculating NY..YN..YY..t().. done Estimating G Total calculations elapsed time: 5.42421197891235 Calculating G: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.00440669059753418 Calculate `GDI`: DONE Total calculations elapsed time: 7.81561493873596 Calculate GDI dataframe: DONE Calculate `GDI`: START Calculating S: START Calculating S: DONE Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.00607562065124512 Calculate `GDI`: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.00497865676879883 Calculate `GDI`: DONE Initializing `COTAN` meta-data COTAN dataset analysis: START Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1000] cells Dataset cleaning elapsed time: 0.762699365615845 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 7 iterations Total calculations elapsed time: 1.80236077308655 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333 Model parameter estimation elapsed time: 2.56738758087158 COTAN genes' COEX estimation: START While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.41323256492615 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.0133016109466553 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0640289783477783 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.708489418029785 Total calculations elapsed time: 3.19905257225037 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 3.91187572479248 Dataset analysis elapsed time: 7.24196267127991 COTAN dataset analysis: DONE Initializing `COTAN` meta-data Condition test n cells 1000 COTAN dataset analysis: START Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1000] cells Dataset cleaning elapsed time: 0.733115673065186 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 7 iterations Total calculations elapsed time: 1.70601773262024 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333 Model parameter estimation elapsed time: 2.44895219802856 COTAN genes' COEX estimation: START While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.48853993415833 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.0130667686462402 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0655531883239746 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.765835523605347 Total calculations elapsed time: 3.33299541473389 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 4.05501413345337 Dataset analysis elapsed time: 7.23708200454712 COTAN dataset analysis: DONE Using S Calculating S: START Calculating S: DONE calculating PValues: START Get p-values on a set of genes on columns and on a set of genes on rows Total calculations elapsed time: 0.0215120315551758 calculating PValues: DONE Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.0317356586456299 Calculate `GDI`: DONE Total calculations elapsed time: 2.16425228118896 Calculate GDI dataframe: DONE Initializing `COTAN` meta-data Condition test n cells 1000 COTAN dataset analysis: START Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1000] cells Dataset cleaning elapsed time: 0.708115816116333 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 7 iterations Total calculations elapsed time: 1.67148327827454 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333 Model parameter estimation elapsed time: 2.40498423576355 COTAN genes' COEX estimation: START While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.4334180355072 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.0127770900726318 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0633149147033691 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.726704359054565 Total calculations elapsed time: 3.23621439933777 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 3.97565102577209 Dataset analysis elapsed time: 7.08875107765198 COTAN dataset analysis: DONE Using S Calculating S: START Calculating S: DONE calculating PValues: START Get p-values on a set of genes on columns and genome wide on rows Total calculations elapsed time: 0.0199174880981445 calculating PValues: DONE Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.0315053462982178 Calculate `GDI`: DONE Total calculations elapsed time: 2.27776122093201 Calculate GDI dataframe: DONE Initializing `COTAN` meta-data Condition test n cells 1000 COTAN dataset analysis: START Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1000] cells Dataset cleaning elapsed time: 0.734123229980469 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 7 iterations Total calculations elapsed time: 1.68414950370789 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333 Model parameter estimation elapsed time: 2.47339296340942 COTAN genes' COEX estimation: START While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.69379043579102 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.0144834518432617 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.06740403175354 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.853117704391479 Total calculations elapsed time: 3.6287956237793 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 4.50345420837402 Dataset analysis elapsed time: 7.71097040176392 COTAN dataset analysis: DONE Using S Calculating S: START Calculating S: DONE calculating PValues: START Get p-values on a set of genes on columns and on a set of genes on rows Total calculations elapsed time: 0.00773358345031738 calculating PValues: DONE Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.0324490070343018 Calculate `GDI`: DONE Total calculations elapsed time: 2.30578351020813 Calculate GDI dataframe: DONE Initializing `COTAN` meta-data Asked to drop 0 genes and 960 cells COTAN dataset analysis: START Asked to drop 83 genes and 0 cells Genes/cells selection done: dropped [83] genes and [0] cells Working on [517] genes and [40] cells Dataset cleaning elapsed time: 0.80724573135376 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 7 iterations Total calculations elapsed time: 1.56832432746887 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.267567793681876 | max: 101.923257389521 | % negative: 52.6112185686654 Model parameter estimation elapsed time: 2.34314680099487 COTAN genes' COEX estimation not requested Only genes' COEX elapsed time: 0.767343759536743 Dataset analysis elapsed time: 3.91773629188538 COTAN dataset analysis: DONE Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.3165647983551 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.0103344917297363 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0128133296966553 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.807830810546875 Total calculations elapsed time: 3.14754343032837 Calculate genes' COEX (legacy): DONE While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.26841521263123 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.010606050491333 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.012836217880249 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.752063512802124 Total calculations elapsed time: 3.04392099380493 Calculate genes' COEX (legacy): DONE While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.28821444511414 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00993800163269043 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0118041038513184 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.734480857849121 Total calculations elapsed time: 3.04443740844727 Calculate genes' COEX (legacy): DONE Hangling COTAN object with condition: test Using S Calculating S: START Calculating S: DONE calculating PValues: START Get p-values on a set of genes on columns and on a set of genes on rows Total calculations elapsed time: 0.00728678703308105 calculating PValues: DONE Handling genes type: G2 Handling genes type: G3 Initializing `COTAN` meta-data COTAN dataset analysis: START Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1000] cells Clean plots: START PCA: START PCA: DONE Hierarchical clustering: START Hierarchical clustering: DONE Total calculations elapsed time: 1.79146718978882 Clean plots: DONE Dataset cleaning elapsed time: 4.26249361038208 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 7 iterations Total calculations elapsed time: 1.83365416526794 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333 Model parameter estimation elapsed time: 2.58603930473328 COTAN genes' COEX estimation: START While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.57836008071899 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.0129354000091553 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0655527114868164 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.76366114616394 Total calculations elapsed time: 3.42050933837891 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 4.2359311580658 Dataset analysis elapsed time: 11.0844640731812 COTAN dataset analysis: DONE Saving elaborated data locally at: /home/biocbuild/tmp/RtmpLiGDCF/test.cotan.RDS Creating new clusterization: START Elaborating Reduced dimensionality Data Matrix - START Elaborating COEX Eigen Vectors - START Elaborating COEX Eigen Vectors - DONE Total calculations elapsed time: 2.5680992603302 Elaborating Reduced dimensionality Data Matrix - DONE Computing nearest neighbor graph Computing SNN Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck Number of nodes: 1000 Number of edges: 44886 Running Louvain algorithm with multilevel refinement... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: 0.4008 Number of communities: 4 Elapsed time: 0 seconds Used resolution for Seurat clusterization is: 1.3 Total calculations elapsed time: 3.75101041793823 Creating new clusterization: DONE Creating cells' uniform clustering: START In iteration 1 the number of cells to re-cluster is 1000 cells belonging to 0 clusters Asked to drop no genes or cells Creating new clusterization: START Elaborating Reduced dimensionality Data Matrix - START Elaborating COEX Eigen Vectors - START Elaborating COEX Eigen Vectors - DONE Total calculations elapsed time: 2.70998811721802 Elaborating Reduced dimensionality Data Matrix - DONE Computing nearest neighbor graph Computing SNN Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck Number of nodes: 1000 Number of edges: 36652 Running Louvain algorithm with multilevel refinement... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: 0.3743 Number of communities: 4 Elapsed time: 0 seconds Used resolution for Seurat clusterization is: 1.3 Total calculations elapsed time: 3.78556704521179 Creating new clusterization: DONE Creating PDF UMAP in file: /home/biocbuild/tmp/RtmpLiGDCF/test/reclustering/pdf_umap_1.pdf UMAP plot: START Calculating UMAP: START 07:48:55 UMAP embedding parameters a = 0.9922 b = 1.112 07:48:55 Read 1000 rows and found 65 numeric columns 07:48:55 Using Annoy for neighbor search, n_neighbors = 30 07:48:55 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 07:48:55 Writing NN index file to temp file /home/biocbuild/tmp/RtmpLiGDCF/file4998f496515f9 07:48:55 Searching Annoy index using 1 thread, search_k = 3000 07:48:56 Annoy recall = 100% 07:48:56 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30 07:48:58 Initializing from normalized Laplacian + noise (using RSpectra) 07:48:58 Commencing optimization for 500 epochs, with 39044 positive edges 07:48:58 Using rng type: pcg Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 07:49:01 Optimization finished Calculating UMAP: DONE Total calculations elapsed time: 5.83986377716064 UMAP plot: DONE UMAP plot: START Calculating UMAP: START 07:49:01 UMAP embedding parameters a = 0.9922 b = 1.112 07:49:01 Read 1000 rows and found 65 numeric columns 07:49:01 Using Annoy for neighbor search, n_neighbors = 30 07:49:01 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 07:49:01 Writing NN index file to temp file /home/biocbuild/tmp/RtmpLiGDCF/file4998f7e1154a6 07:49:01 Searching Annoy index using 1 thread, search_k = 3000 07:49:02 Annoy recall = 100% 07:49:03 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30 07:49:04 Initializing from normalized Laplacian + noise (using RSpectra) 07:49:04 Commencing optimization for 500 epochs, with 39044 positive edges 07:49:04 Using rng type: pcg Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 07:49:07 Optimization finished Calculating UMAP: DONE Total calculations elapsed time: 5.79358386993408 UMAP plot: DONE * checking uniformity of cluster '0' of 4 clusters Asked to drop 0 genes and 687 cells COTAN dataset analysis: START Asked to drop 43 genes and 0 cells Genes/cells selection done: dropped [43] genes and [0] cells Working on [557] genes and [313] cells Dataset cleaning elapsed time: 0.822511196136475 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 11 iterations Total calculations elapsed time: 1.70666670799255 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.126565269702225 | max: 788.372048308528 | % negative: 38.5996409335727 Model parameter estimation elapsed time: 2.51063537597656 COTAN genes' COEX estimation: START While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.44228601455688 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.012244701385498 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0303313732147217 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.833991050720215 Total calculations elapsed time: 3.31885313987732 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 4.13932013511658 Dataset analysis elapsed time: 7.47246670722961 COTAN dataset analysis: DONE Checking uniformity for the cluster '01_0000' with 313 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.0303421020507812 Calculate `GDI`: DONE Total calculations elapsed time: 2.56337714195251 Calculate GDI dataframe: DONE Clean plots: START Total calculations elapsed time: 0.0515058040618896 Clean plots: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 01_0000, with size 313, is uniform Cluster 01_0000's shift to uniformity: -0.0175178017151116 class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.0412926391382406, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.37948219828489, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.0323159784560144, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.43089123341142, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.00179533213644524, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.44383613651627, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 1, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.47612588512219, isUniform = TRUE, clusterSize = 313 cluster 01_0000 is uniform * checking uniformity of cluster '1' of 4 clusters Asked to drop 0 genes and 743 cells COTAN dataset analysis: START Asked to drop 51 genes and 0 cells Genes/cells selection done: dropped [51] genes and [0] cells Working on [549] genes and [257] cells Dataset cleaning elapsed time: 0.859102249145508 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 10 iterations Total calculations elapsed time: 1.6527853012085 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.112503099391263 | max: 646.681464270838 | % negative: 40.8014571948998 Model parameter estimation elapsed time: 2.48427033424377 COTAN genes' COEX estimation: START While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.58022308349609 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.0109238624572754 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0258018970489502 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.855251789093018 Total calculations elapsed time: 3.47220063209534 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 4.30274248123169 Dataset analysis elapsed time: 7.64611506462097 COTAN dataset analysis: DONE Checking uniformity for the cluster '01_0001' with 257 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.0291049480438232 Calculate `GDI`: DONE Total calculations elapsed time: 2.37652063369751 Calculate GDI dataframe: DONE Clean plots: START Total calculations elapsed time: 0.0515494346618652 Clean plots: DONE GDI plot Removed 1 low GDI genes (such as the fully-expressed) in GDI plot Cluster 01_0001, with size 257, is uniform Cluster 01_0001's shift to uniformity: -0.0466523594846466 class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.00910746812386157, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.35034764051535, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.00728597449908925, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.37278730407695, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.38664163146848, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 0, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.45240567481125, isUniform = TRUE, clusterSize = 257 cluster 01_0001 is uniform * checking uniformity of cluster '2' of 4 clusters Asked to drop 0 genes and 758 cells COTAN dataset analysis: START Asked to drop 77 genes and 0 cells Genes/cells selection done: dropped [77] genes and [0] cells Working on [523] genes and [242] cells Dataset cleaning elapsed time: 0.800464391708374 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 7 iterations Total calculations elapsed time: 1.61498212814331 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.166254045792573 | max: 224.924342782861 | % negative: 42.6386233269598 Model parameter estimation elapsed time: 2.46072030067444 COTAN genes' COEX estimation: START While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.44227290153503 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.0100181102752686 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0251011848449707 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.803223133087158 Total calculations elapsed time: 3.28061532974243 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 4.11303043365479 Dataset analysis elapsed time: 7.3742151260376 COTAN dataset analysis: DONE Checking uniformity for the cluster '01_0002' with 242 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.0273580551147461 Calculate `GDI`: DONE Total calculations elapsed time: 2.48013210296631 Calculate GDI dataframe: DONE Clean plots: START Total calculations elapsed time: 0.0526669025421143 Clean plots: DONE GDI plot Removed 2 low GDI genes (such as the fully-expressed) in GDI plot Cluster 01_0002, with size 242, is uniform Cluster 01_0002's shift to uniformity: -0.0473527936300073 class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.00764818355640535, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.34964720636999, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.00764818355640535, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.37472946305403, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.38771313919655, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 0, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.43097703442028, isUniform = TRUE, clusterSize = 242 cluster 01_0002 is uniform * checking uniformity of cluster '3' of 4 clusters Asked to drop 0 genes and 812 cells COTAN dataset analysis: START Asked to drop 79 genes and 0 cells Genes/cells selection done: dropped [79] genes and [0] cells Working on [521] genes and [188] cells Dataset cleaning elapsed time: 0.795925140380859 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 6 iterations Total calculations elapsed time: 1.61792826652527 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.210007411487223 | max: 67.8701314818728 | % negative: 45.6813819577735 Model parameter estimation elapsed time: 2.40830254554749 COTAN genes' COEX estimation: START While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.56759715080261 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00937247276306152 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0208227634429932 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.846875190734863 Total calculations elapsed time: 3.44466757774353 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 4.276522397995 Dataset analysis elapsed time: 7.48075008392334 COTAN dataset analysis: DONE Checking uniformity for the cluster '01_0003' with 188 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.0265138149261475 Calculate `GDI`: DONE Total calculations elapsed time: 2.46877384185791 Calculate GDI dataframe: DONE Clean plots: START Total calculations elapsed time: 0.0523719787597656 Clean plots: DONE GDI plot Removed 4 low GDI genes (such as the fully-expressed) in GDI plot Cluster 01_0003, with size 188, is uniform Cluster 01_0003's shift to uniformity: -0.0672912272436044 class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.00383877159309021, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.3297087727564, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.00191938579654511, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.35752445041521, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.37495297633957, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 0, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.4014884302523, isUniform = TRUE, clusterSize = 188 cluster 01_0003 is uniform Found 4 uniform and 0 non-uniform clusters Stopping: too few cells left to cluster Unclustered cell left: 0 The final raw clusterization contains [ 4 ] different clusters: 01_0000, 01_0001, 01_0002, 01_0003 Differential Expression Analysis - START * DEA on cluster '1' with 313 cells * DEA on cluster '2' with 257 cells * DEA on cluster '3' with 242 cells * DEA on cluster '4' with 188 cells Total calculations elapsed time: 0.0500547885894775 Differential Expression Analysis - DONE Applied reordering to clusterization is: 1 -> 3, 2 -> 1, 3 -> 2, 4 -> 4 Total calculations elapsed time: 71.9528288841248 Creating cells' uniform clustering: DONE Applied reordering to clusterization is: 1 -> 1, 2 -> 2, 3 -> 3, 4 -> 4 Asked to drop 0 genes and 812 cells COTAN dataset analysis: START Asked to drop 79 genes and 0 cells Genes/cells selection done: dropped [79] genes and [0] cells Working on [521] genes and [188] cells Dataset cleaning elapsed time: 0.861881494522095 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 6 iterations Total calculations elapsed time: 1.68620991706848 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.210007411487223 | max: 67.8701314818728 | % negative: 45.6813819577735 Model parameter estimation elapsed time: 2.5238561630249 COTAN genes' COEX estimation: START While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.4938497543335 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00985360145568848 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.021834135055542 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.824799537658691 Total calculations elapsed time: 3.35033702850342 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 4.17639327049255 Dataset analysis elapsed time: 7.56213092803955 COTAN dataset analysis: DONE Checking uniformity for the cluster 'Cluster_4' with 188 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.0278384685516357 Calculate `GDI`: DONE Total calculations elapsed time: 2.45471286773682 Calculate GDI dataframe: DONE Clean plots: START Total calculations elapsed time: 0.0546829700469971 Clean plots: DONE GDI plot Removed 4 low GDI genes (such as the fully-expressed) in GDI plot Cluster Cluster_4, with size 188, is uniform Cluster Cluster_4's shift to uniformity: -0.0672912272436044 class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.00383877159309021, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.3297087727564, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.00191938579654511, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.35752445041521, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.37495297633957, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 0, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.4014884302523, isUniform = TRUE, clusterSize = 188 Differential Expression Analysis - START * DEA on cluster '-1' with 50 cells * DEA on cluster '1' with 257 cells * DEA on cluster '2' with 242 cells * DEA on cluster '3' with 280 cells * DEA on cluster '4' with 171 cells Total calculations elapsed time: 0.0443270206451416 Differential Expression Analysis - DONE Applied reordering to clusterization is: 1 -> 4, 2 -> 3, 3 -> 2, 4 -> 1, -1 -> -1 Applied reordering to clusterization is: 1 -> 1, 2 -> 2, 3 -> 3, 4 -> 4, -1 -> -1 Creating cells' uniform clustering: START In iteration 1 the number of cells to re-cluster is 1000 cells belonging to 0 clusters Asked to drop no genes or cells Creating new clusterization: START Elaborating Reduced dimensionality Data Matrix - START Running genes' selection: START Normalizing layer: counts Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Finding variable features for layer counts Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Selected 600 genes using HVG_Seurat selector Running genes' selection: DONE Elaborating PCA - START Elaborating PCA - DONE Total calculations elapsed time: 3.06681394577026 Elaborating Reduced dimensionality Data Matrix - DONE Computing nearest neighbor graph Computing SNN Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck Number of nodes: 1000 Number of edges: 67288 Running Louvain algorithm with multilevel refinement... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: 0.3650 Number of communities: 5 Elapsed time: 0 seconds Used resolution for Seurat clusterization is: 1.3 Total calculations elapsed time: 4.15575456619263 Creating new clusterization: DONE Using passed in clusterization Creating PDF UMAP in file: /home/biocbuild/tmp/RtmpLiGDCF/test/reclustering/pdf_umap_1.pdf UMAP plot: START Calculating UMAP: START 07:50:21 UMAP embedding parameters a = 0.9922 b = 1.112 07:50:21 Read 1000 rows and found 40 numeric columns 07:50:21 Using Annoy for neighbor search, n_neighbors = 30 07:50:21 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 07:50:22 Writing NN index file to temp file /home/biocbuild/tmp/RtmpLiGDCF/file4998f190e2627 07:50:22 Searching Annoy index using 1 thread, search_k = 3000 07:50:22 Annoy recall = 100% 07:50:23 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30 07:50:24 Found 2 connected components, falling back to 'spca' initialization with init_sdev = 1 07:50:24 Using 'irlba' for PCA 07:50:24 PCA: 2 components explained 36.15% variance 07:50:24 Scaling init to sdev = 1 07:50:24 Commencing optimization for 500 epochs, with 41630 positive edges 07:50:24 Using rng type: pcg Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 07:50:27 Optimization finished Calculating UMAP: DONE Total calculations elapsed time: 5.62691259384155 UMAP plot: DONE UMAP plot: START Calculating UMAP: START 07:50:27 UMAP embedding parameters a = 0.9922 b = 1.112 07:50:27 Read 1000 rows and found 40 numeric columns 07:50:27 Using Annoy for neighbor search, n_neighbors = 30 07:50:27 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 07:50:28 Writing NN index file to temp file /home/biocbuild/tmp/RtmpLiGDCF/file4998f7bb6e739 07:50:28 Searching Annoy index using 1 thread, search_k = 3000 07:50:28 Annoy recall = 100% 07:50:29 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30 07:50:30 Found 2 connected components, falling back to 'spca' initialization with init_sdev = 1 07:50:30 Using 'irlba' for PCA 07:50:30 PCA: 2 components explained 36.15% variance 07:50:30 Scaling init to sdev = 1 07:50:30 Commencing optimization for 500 epochs, with 41630 positive edges 07:50:30 Using rng type: pcg Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 07:50:33 Optimization finished Calculating UMAP: DONE Total calculations elapsed time: 5.72977471351624 UMAP plot: DONE * checking uniformity of cluster '1' of 2 clusters Asked to drop 0 genes and 500 cells COTAN dataset analysis: START Asked to drop 38 genes and 0 cells Genes/cells selection done: dropped [38] genes and [0] cells Working on [562] genes and [500] cells Dataset cleaning elapsed time: 0.869023084640503 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 7 iterations Total calculations elapsed time: 1.76828980445862 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.108871643378045 | max: 295.971778839086 | % negative: 35.0533807829181 Model parameter estimation elapsed time: 2.5938937664032 COTAN genes' COEX estimation: START While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.59081363677979 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.0120139122009277 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0376436710357666 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.810770273208618 Total calculations elapsed time: 3.4512414932251 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 4.28995704650879 Dataset analysis elapsed time: 7.75287389755249 COTAN dataset analysis: DONE Checking uniformity for the cluster '01_0001' with 500 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.0301897525787354 Calculate `GDI`: DONE Total calculations elapsed time: 2.50762534141541 Calculate GDI dataframe: DONE Clean plots: START Total calculations elapsed time: 0.054678201675415 Clean plots: DONE GDI plot Removed 2 low GDI genes (such as the fully-expressed) in GDI plot Cluster 01_0001, with size 500, is uniform Cluster 01_0001's shift to uniformity: -0.0417301990664185 class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.0124555160142349, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.35526980093358, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.00889679715302491, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.38536328181495, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.40346106115496, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 0, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.42565794715039, isUniform = TRUE, clusterSize = 500 cluster 01_0001 is uniform * checking uniformity of cluster '2' of 2 clusters Asked to drop 0 genes and 500 cells COTAN dataset analysis: START Asked to drop 44 genes and 0 cells Genes/cells selection done: dropped [44] genes and [0] cells Working on [556] genes and [500] cells Dataset cleaning elapsed time: 0.847472190856934 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 7 iterations Total calculations elapsed time: 1.76241517066956 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0636486786621688 | max: 141.389145035675 | % negative: 36.1510791366906 Model parameter estimation elapsed time: 2.60381984710693 COTAN genes' COEX estimation: START While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.53586292266846 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.01076340675354 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0364408493041992 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.811734437942505 Total calculations elapsed time: 3.3948016166687 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 4.24663758277893 Dataset analysis elapsed time: 7.6979296207428 COTAN dataset analysis: DONE Checking uniformity for the cluster '01_0002' with 500 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.0299022197723389 Calculate `GDI`: DONE Total calculations elapsed time: 2.41718006134033 Calculate GDI dataframe: DONE Clean plots: START Total calculations elapsed time: 0.0557703971862793 Clean plots: DONE GDI plot Removed 2 low GDI genes (such as the fully-expressed) in GDI plot Cluster 01_0002, with size 500, is uniform Cluster 01_0002's shift to uniformity: -0.0413872276843519 class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.00719424460431655, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.35561277231565, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.00359712230215827, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.37204026755189, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.38757136821537, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 0, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.40876953414112, isUniform = TRUE, clusterSize = 500 cluster 01_0002 is uniform Found 2 uniform and 0 non-uniform clusters Stopping: too few cells left to cluster Unclustered cell left: 0 The final raw clusterization contains [ 2 ] different clusters: 01_0001, 01_0002 Differential Expression Analysis - START * DEA on cluster '1' with 500 cells * DEA on cluster '2' with 500 cells Total calculations elapsed time: 0.0370995998382568 Differential Expression Analysis - DONE Applied reordering to clusterization is: 1 -> 1, 2 -> 2 Total calculations elapsed time: 45.0000007152557 Creating cells' uniform clustering: DONE findClustersMarkers - START Log Fold Change Analysis - START * Analysis of cluster: '1' * Analysis of cluster: '2' * Analysis of cluster: '3' * Analysis of cluster: '4' Total calculations elapsed time: 3.26560568809509 Log Fold Change Analysis - DONE Total calculations elapsed time: 3.28097200393677 findClustersMarkers - DONE findClustersMarkers - START Log Fold Change Analysis - START * Analysis of cluster: '1' * Analysis of cluster: '2' * Analysis of cluster: '3' * Analysis of cluster: '4' Total calculations elapsed time: 3.30766606330872 Log Fold Change Analysis - DONE Total calculations elapsed time: 3.32273268699646 findClustersMarkers - DONE findClustersMarkers - START Differential Expression Analysis - START * DEA on cluster '1' with 257 cells * DEA on cluster '2' with 242 cells * DEA on cluster '3' with 313 cells * DEA on cluster '4' with 188 cells Total calculations elapsed time: 0.0431900024414062 Differential Expression Analysis - DONE Log Fold Change Analysis - START * Analysis of cluster: '1' * Analysis of cluster: '2' * Analysis of cluster: '3' * Analysis of cluster: '4' Total calculations elapsed time: 3.24558305740356 Log Fold Change Analysis - DONE Total calculations elapsed time: 3.3023316860199 findClustersMarkers - DONE [1] "Tested cluster: 1" Asked to drop 0 genes and 743 cells COTAN dataset analysis: START Asked to drop 51 genes and 0 cells Genes/cells selection done: dropped [51] genes and [0] cells Working on [549] genes and [257] cells Dataset cleaning elapsed time: 0.820304155349731 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 10 iterations Total calculations elapsed time: 1.61657953262329 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.112503099391263 | max: 646.681464270838 | % negative: 40.8014571948998 Model parameter estimation elapsed time: 2.41879653930664 COTAN genes' COEX estimation: START While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.45873832702637 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.0109236240386963 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0266416072845459 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.836469650268555 Total calculations elapsed time: 3.33277320861816 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 4.14633512496948 Dataset analysis elapsed time: 7.38543581962585 COTAN dataset analysis: DONE Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.0288405418395996 Calculate `GDI`: DONE Total calculations elapsed time: 2.49067831039429 Calculate GDI dataframe: DONE Genes/cells selection done: dropped [0] genes and [0] cells Working on [10] genes and [20] cells Initializing `COTAN` meta-data Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1000] cells Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 7 iterations Total calculations elapsed time: 1.85823106765747 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333 Initializing `COTAN` meta-data COTAN dataset analysis: START Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1000] cells Dataset cleaning elapsed time: 0.876241683959961 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 7 iterations Total calculations elapsed time: 1.81821632385254 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333 Model parameter estimation elapsed time: 2.63565564155579 COTAN genes' COEX estimation not requested Only genes' COEX elapsed time: 0.848463773727417 Dataset analysis elapsed time: 4.36036109924316 COTAN dataset analysis: DONE Normalizing layer: counts Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Finding variable features for layer counts Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Centering and scaling data matrix | | | 0% | |======================================================================| 100% PC_ 1 Positive: g-000397, g-000525, g-000460, g-000458, g-000535, g-000217, g-000194, g-000497, g-000432, g-000383 g-000318, g-000486, g-000464, g-000588, g-000549, g-000368, g-000252, g-000151, g-000209, g-000538 g-000325, g-000514, g-000524, g-000244, g-000320, g-000201, g-000499, g-000309, g-000290, g-000483 Negative: g-000415, g-000506, g-000496, g-000579, g-000572, g-000421, g-000455, g-000328, g-000178, g-000567 g-000405, g-000296, g-000387, g-000501, g-000493, g-000481, g-000343, g-000528, g-000551, g-000414 g-000367, g-000594, g-000159, g-000517, g-000574, g-000229, g-000222, g-000533, g-000243, g-000306 PC_ 2 Positive: g-000141, g-000093, g-000089, g-000033, g-000123, g-000557, g-000330, g-000156, g-000142, g-000095 g-000061, g-000235, g-000032, g-000186, g-000056, g-000259, g-000027, g-000041, g-000333, g-000386 g-000009, g-000395, g-000048, g-000116, g-000340, g-000418, g-000035, g-000332, g-000086, g-000040 Negative: g-000088, g-000158, g-000255, g-000115, g-000054, g-000472, g-000554, g-000391, g-000253, g-000226 g-000051, g-000147, g-000541, g-000077, g-000224, g-000194, g-000290, g-000293, g-000313, g-000118 g-000121, g-000220, g-000467, g-000500, g-000341, g-000039, g-000091, g-000249, g-000426, g-000288 PC_ 3 Positive: g-000126, g-000083, g-000086, g-000117, g-000130, g-000010, g-000498, g-000333, g-000047, g-000179 g-000340, g-000035, g-000531, g-000140, g-000527, g-000049, g-000316, g-000031, g-000014, g-000073 g-000218, g-000445, g-000129, g-000175, g-000105, g-000581, g-000404, g-000025, g-000266, g-000354 Negative: g-000096, g-000575, g-000370, g-000337, g-000319, g-000364, g-000308, g-000293, g-000147, g-000307 g-000038, g-000492, g-000541, g-000185, g-000008, g-000482, g-000562, g-000097, g-000222, g-000084 g-000141, g-000377, g-000224, g-000223, g-000136, g-000434, g-000277, g-000426, g-000139, g-000093 PC_ 4 Positive: g-000006, g-000043, g-000462, g-000279, g-000180, g-000576, g-000087, g-000584, g-000498, g-000333 g-000189, g-000088, g-000451, g-000059, g-000135, g-000281, g-000106, g-000429, g-000316, g-000578 g-000303, g-000031, g-000581, g-000026, g-000122, g-000561, g-000546, g-000164, g-000353, g-000300 Negative: g-000072, g-000012, g-000129, g-000052, g-000097, g-000262, g-000080, g-000056, g-000025, g-000092 g-000354, g-000334, g-000423, g-000228, g-000002, g-000010, g-000086, g-000147, g-000185, g-000172 g-000124, g-000009, g-000077, g-000476, g-000126, g-000145, g-000065, g-000268, g-000152, g-000348 PC_ 5 Positive: g-000051, g-000150, g-000088, g-000476, g-000344, g-000116, g-000428, g-000012, g-000523, g-000394 g-000101, g-000127, g-000069, g-000214, g-000049, g-000357, g-000075, g-000081, g-000576, g-000342 g-000439, g-000018, g-000070, g-000079, g-000015, g-000550, g-000600, g-000247, g-000218, g-000331 Negative: g-000105, g-000037, g-000110, g-000054, g-000090, g-000389, g-000022, g-000578, g-000289, g-000147 g-000547, g-000011, g-000477, g-000433, g-000200, g-000348, g-000404, g-000003, g-000250, g-000109 g-000402, g-000241, g-000595, g-000341, g-000560, g-000385, g-000413, g-000352, g-000573, g-000265 Computing nearest neighbor graph Computing SNN Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck Number of nodes: 1000 Number of edges: 67836 Running Louvain algorithm with multilevel refinement... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: 0.5999 Number of communities: 2 Elapsed time: 0 seconds Clusterizations found: RNA_snn_res.0.8, seurat_clusters Conditions found: orig.ident COTAN dataset analysis: START Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1000] cells Dataset cleaning elapsed time: 0.853104829788208 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 7 iterations Total calculations elapsed time: 1.85687112808228 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333 Model parameter estimation elapsed time: 2.70984697341919 COTAN genes' COEX estimation not requested Only genes' COEX elapsed time: 0.846550464630127 Dataset analysis elapsed time: 4.40950226783752 COTAN dataset analysis: DONE COTAN dataset analysis: START Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1000] cells Dataset cleaning elapsed time: 0.877962827682495 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 7 iterations Total calculations elapsed time: 1.94790697097778 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333 Model parameter estimation elapsed time: 2.79142904281616 COTAN genes' COEX estimation: START While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.77713251113892 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.0132589340209961 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0668735504150391 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.891450166702271 Total calculations elapsed time: 3.74871516227722 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 4.64240336418152 Dataset analysis elapsed time: 8.31179523468018 COTAN dataset analysis: DONE Calculating gene co-expression space - START Using S Calculating S: START Calculating S: DONE calculating PValues: START Get p-values on a set of genes on columns and genome wide on rows Total calculations elapsed time: 0.00663447380065918 calculating PValues: DONE Number of selected secondary markers: 6 Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.0101251602172852 Calculate `GDI`: DONE Number of columns (V set - secondary markers): 6 Number of rows (U set): 60 Total calculations elapsed time: 0.876377820968628 Calculating gene co-expression space - DONE Calculating gene co-expression space - START Using S Calculating S: START Calculating S: DONE calculating PValues: START Get p-values on a set of genes on columns and genome wide on rows Total calculations elapsed time: 0.00928211212158203 calculating PValues: DONE Number of selected secondary markers: 98 Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.00983762741088867 Calculate `GDI`: DONE Number of columns (V set - secondary markers): 98 Number of rows (U set): 60 Total calculations elapsed time: 0.932630062103271 Calculating gene co-expression space - DONE Establishing gene clusters - START Calculating gene co-expression space - START Using S Calculating S: START Calculating S: DONE calculating PValues: START Get p-values on a set of genes on columns and genome wide on rows Total calculations elapsed time: 0.00910711288452148 calculating PValues: DONE Number of selected secondary markers: 98 Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.0100767612457275 Calculate `GDI`: DONE Number of columns (V set - secondary markers): 98 Number of rows (U set): 60 Total calculations elapsed time: 0.893374681472778 Calculating gene co-expression space - DONE Total calculations elapsed time: 0.989068984985352 Establishing gene clusters - DONE Initializing `COTAN` meta-data COTAN dataset analysis: START Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1000] cells Dataset cleaning elapsed time: 0.867350101470947 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 7 iterations Total calculations elapsed time: 1.91983246803284 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333 Model parameter estimation elapsed time: 2.79571199417114 COTAN genes' COEX estimation not requested Only genes' COEX elapsed time: 0.821666479110718 Dataset analysis elapsed time: 4.48472857475281 COTAN dataset analysis: DONE Differential Expression Analysis - START * DEA on cluster '1' with 257 cells * DEA on cluster '2' with 242 cells * DEA on cluster '3' with 313 cells * DEA on cluster '4' with 188 cells Total calculations elapsed time: 0.0430817604064941 Differential Expression Analysis - DONE Log Fold Change Analysis - START * Analysis of cluster: '1' * Analysis of cluster: '2' * Analysis of cluster: '3' * Analysis of cluster: '4' Total calculations elapsed time: 3.32191252708435 Log Fold Change Analysis - DONE clustersDeltaExpression - START Handling cluster '1' with mean UDE 1.10997640736885 Handling cluster '2' with mean UDE 1.00770245700749 Handling cluster '3' with mean UDE 0.95940682189354 Handling cluster '4' with mean UDE 0.907328369455933 clustersDeltaExpression - DONE In group G1 there are 3 detected over 3 genes In group G2 there are 2 detected over 3 genes In group G3 there are 5 detected over 5 genes Merging cells' uniform clustering: START The merge algorithm will use 2 passes Start merging nearest clusters - the main threshold is: 1.297 Start merging nearest clusters: iteration 1 Differential Expression Analysis - START * DEA on cluster '1' with 257 cells * DEA on cluster '2' with 242 cells * DEA on cluster '3' with 313 cells * DEA on cluster '4' with 188 cells Total calculations elapsed time: 0.0446438789367676 Differential Expression Analysis - DONE Updating check results for the 0 already tested pairs to align to new checker 1 new clusters pairs to be tested for merging: c("1", "2") *1_2-merge Asked to drop 0 genes and 501 cells COTAN dataset analysis: START Asked to drop 16 genes and 0 cells Genes/cells selection done: dropped [16] genes and [0] cells Working on [584] genes and [499] cells Dataset cleaning elapsed time: 0.849193572998047 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 10 iterations Total calculations elapsed time: 1.73512172698975 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0608154544840047 | max: 1260.06995351592 | % negative: 35.6164383561644 Model parameter estimation elapsed time: 2.57048439979553 COTAN genes' COEX estimation: START While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.6050660610199 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.0120735168457031 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0390920639038086 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.826178789138794 Total calculations elapsed time: 3.4824104309082 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 4.327965259552 Dataset analysis elapsed time: 7.74764323234558 COTAN dataset analysis: DONE Checking uniformity for the cluster '1_2-merge' with 499 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.0325033664703369 Calculate `GDI`: DONE Total calculations elapsed time: 2.52381157875061 Calculate GDI dataframe: DONE Clean plots: START Total calculations elapsed time: 0.0528817176818848 Clean plots: DONE GDI plot Removed 1 low GDI genes (such as the fully-expressed) in GDI plot Cluster 1_2-merge, with size 499, is not uniform Cluster 1_2-merge's shift to uniformity: 0.0566581136434268 class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.297, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.178082191780822, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.35365811364343, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.307, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.148972602739726, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.37149326865969, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.4, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.00513698630136986, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.38256306292787, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.4, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 3, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.42111642638122, isUniform = FALSE, clusterSize = 499 Clusters 1 and 2 cannot be merged Finished the first batch - no merges were executed Loop calculations elapsed time: 15.0076994895935 Start merging nearest clusters: iteration 2 Differential Expression Analysis - START * DEA on cluster '1' with 257 cells * DEA on cluster '2' with 242 cells * DEA on cluster '3' with 313 cells * DEA on cluster '4' with 188 cells Total calculations elapsed time: 0.0426783561706543 Differential Expression Analysis - DONE Updating check results for the 1 already tested pairs to align to new checker 1 new clusters pairs to be tested for merging: c("3", "4") *3_4-merge Asked to drop 0 genes and 499 cells COTAN dataset analysis: START Asked to drop 37 genes and 0 cells Genes/cells selection done: dropped [37] genes and [0] cells Working on [563] genes and [501] cells Dataset cleaning elapsed time: 0.847573280334473 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 11 iterations Total calculations elapsed time: 1.72829747200012 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.107568326617881 | max: 698.639334552754 | % negative: 32.1492007104796 Model parameter estimation elapsed time: 2.55084609985352 COTAN genes' COEX estimation: START While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.67061638832092 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.0113236904144287 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0375421047210693 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.848589658737183 Total calculations elapsed time: 3.5680718421936 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 4.40889549255371 Dataset analysis elapsed time: 7.8073148727417 COTAN dataset analysis: DONE Checking uniformity for the cluster '3_4-merge' with 501 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.0301544666290283 Calculate `GDI`: DONE Total calculations elapsed time: 2.47793364524841 Calculate GDI dataframe: DONE Clean plots: START Total calculations elapsed time: 0.0528242588043213 Clean plots: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 3_4-merge, with size 501, is not uniform Cluster 3_4-merge's shift to uniformity: 0.0813107504723543 class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.297, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.259325044404973, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.37831075047235, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.307, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.216696269982238, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.41473792188167, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.4, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.0301953818827709, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.43341610223243, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.4, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 17, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.46173948790285, isUniform = FALSE, clusterSize = 501 Clusters 3 and 4 cannot be merged No clusters will be merged None of the remaining tested cluster pairs could be merged Executed all merges for threshold 1.297 out of 2 checks Start merging nearest clusters - the main threshold is: 1.397 Start merging nearest clusters: iteration 3 Differential Expression Analysis - START * DEA on cluster '1' with 257 cells * DEA on cluster '2' with 242 cells * DEA on cluster '3' with 313 cells * DEA on cluster '4' with 188 cells Total calculations elapsed time: 0.0435600280761719 Differential Expression Analysis - DONE Updating check results for the 2 already tested pairs to align to new checker 1 new clusters pairs to be tested for merging: c("2", "4") *2_4-merge Asked to drop 0 genes and 570 cells COTAN dataset analysis: START Asked to drop 9 genes and 0 cells Genes/cells selection done: dropped [9] genes and [0] cells Working on [591] genes and [430] cells Dataset cleaning elapsed time: 0.878965377807617 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 7 iterations Total calculations elapsed time: 1.85126876831055 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0739592351622374 | max: 400.051960722894 | % negative: 25.7191201353638 Model parameter estimation elapsed time: 2.68003797531128 COTAN genes' COEX estimation: START While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.58617877960205 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.0135796070098877 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0380542278289795 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.830939054489136 Total calculations elapsed time: 3.46875166893005 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 4.31147885322571 Dataset analysis elapsed time: 7.8704822063446 COTAN dataset analysis: DONE Checking uniformity for the cluster '2_4-merge' with 430 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.0311422348022461 Calculate `GDI`: DONE Total calculations elapsed time: 2.58421587944031 Calculate GDI dataframe: DONE Clean plots: START Total calculations elapsed time: 0.053095817565918 Clean plots: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 2_4-merge, with size 430, is not uniform Cluster 2_4-merge's shift to uniformity: 3.07228472969514 class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.583756345177665, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 3.7954982715656, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.576988155668359, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 4.08354952912925, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.524534686971235, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 4.42722016730736, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 310, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 4.57228472969514, isUniform = FALSE, clusterSize = 430 Clusters 2 and 4 cannot be merged Clusters 1 and 2 will be merged Clusters 4 and 3 will be merged Executed 2 merges Loop calculations elapsed time: 15.2303638458252 Start merging nearest clusters: iteration 4 Differential Expression Analysis - START * DEA on cluster '1_2-merge' with 499 cells * DEA on cluster '3_4-merge' with 501 cells Total calculations elapsed time: 0.038820743560791 Differential Expression Analysis - DONE Updating check results for the 3 already tested pairs to align to new checker 1 new clusters pairs to be tested for merging: c("1_2-merge", "3_4-merge") *1_2-merge_3_4-merge-merge Asked to drop no genes or cells COTAN dataset analysis: START Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1000] cells Dataset cleaning elapsed time: 0.826256275177002 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 7 iterations Total calculations elapsed time: 1.91038703918457 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333 Model parameter estimation elapsed time: 2.77250480651855 COTAN genes' COEX estimation: START While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.72128558158875 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.013535737991333 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0667252540588379 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.863584280014038 Total calculations elapsed time: 3.66513085365295 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 4.50782918930054 Dataset analysis elapsed time: 8.10659027099609 COTAN dataset analysis: DONE Checking uniformity for the cluster '1_2-merge_3_4-merge-merge' with 1000 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.0313220024108887 Calculate `GDI`: DONE Total calculations elapsed time: 2.48795104026794 Calculate GDI dataframe: DONE Clean plots: START Total calculations elapsed time: 0.0537769794464111 Clean plots: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 1_2-merge_3_4-merge-merge, with size 1000, is not uniform Cluster 1_2-merge_3_4-merge-merge's shift to uniformity: 3.8698838512041 class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.69, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 4.54596809454194, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.678333333333333, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 4.93144728766684, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.593333333333333, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 5.25322968524779, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 356, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 5.3698838512041, isUniform = FALSE, clusterSize = 1000 Clusters 1_2-merge and 3_4-merge cannot be merged No clusters will be merged None of the remaining tested cluster pairs could be merged Executed all merges for threshold 1.397 out of 4 checks The final merged clusterization contains [2] different clusters: 1_2-merge, 3_4-merge Differential Expression Analysis - START * DEA on cluster '1' with 499 cells * DEA on cluster '2' with 501 cells Total calculations elapsed time: 0.039515495300293 Differential Expression Analysis - DONE Applied reordering to clusterization is: 1 -> 1, 2 -> 2 Total calculations elapsed time: 60.7533757686615 Merging cells' uniform clustering: DONE Applied reordering to clusterization is: 1 -> 1, 2 -> 2 Log Fold Change Analysis - START * Analysis of cluster: '1' * Analysis of cluster: '2' Total calculations elapsed time: 1.66883683204651 Log Fold Change Analysis - DONE [1] "Tested cluster: 1" Asked to drop 0 genes and 501 cells COTAN dataset analysis: START Asked to drop 16 genes and 0 cells Genes/cells selection done: dropped [16] genes and [0] cells Working on [584] genes and [499] cells Dataset cleaning elapsed time: 0.871537446975708 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 10 iterations Total calculations elapsed time: 1.79941391944885 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0608154544840047 | max: 1260.06995351592 | % negative: 35.6164383561644 Model parameter estimation elapsed time: 2.70188307762146 COTAN genes' COEX estimation: START While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.59931421279907 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.0124282836914062 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0374267101287842 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.866321325302124 Total calculations elapsed time: 3.51549053192139 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 4.37774062156677 Dataset analysis elapsed time: 7.95116114616394 COTAN dataset analysis: DONE Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.0325624942779541 Calculate `GDI`: DONE Total calculations elapsed time: 2.52888011932373 Calculate GDI dataframe: DONE Dispersion bisection: straddling used 2 iterations Dispersion bisection: used 8 iterations Dispersion bisection: straddling used 1 iterations Dispersion bisection: used 9 iterations Dispersion Newton-Raphson: used up to 4 iterations Dispersion Newton-Raphson: used up to 4 iterations parallel dispersion bisection: straddling used up to 2 iterations Parallel dispersion bisection: used up to 9 iterations Parallel dispersion Newton-Raphson: used up to 4 iterations [ FAIL 1 | WARN 3 | SKIP 0 | PASS 572 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-establishGenesClusters.R:70:5'): Establish genes clusters ──── abs(pcaClusters[, 1L:4L]) (`actual`) not equal to abs(pcaClustersExp[, 1L:4L]) (`expected`). actual vs expected PC3 PC4 - actual[1, ] 0.658895212 0.15883750 + expected[1, ] 0.658892533 0.15883934 - actual[2, ] 0.079564425 0.59203995 + expected[2, ] 0.079567203 0.59203753 - actual[3, ] 0.918532721 0.56313722 + expected[3, ] 0.918529216 0.56314516 - actual[4, ] 0.702531238 1.34693455 + expected[4, ] 0.702534262 1.34693118 - actual[5, ] 1.794575928 0.16243050 + expected[5, ] 1.794578322 0.16244473 - actual[6, ] 1.945309666 0.09807515 + expected[6, ] 1.945313360 0.09806812 - actual[7, ] 0.928430613 2.09901814 + expected[7, ] 0.928419834 2.09901875 - actual[8, ] 1.245356622 0.32562932 + expected[8, ] 1.245358368 0.32563594 - actual[9, ] 0.101983190 0.75673576 + expected[9, ] 0.101974678 0.75673771 - actual[10, ] 0.068781346 1.20531303 + expected[10, ] 0.068787701 1.20530874 and 50 more ... actual$PC3 | expected$PC3 [1] 0.6588952 - 0.6588925 [1] [2] 0.0795644 - 0.0795672 [2] [3] 0.9185327 - 0.9185292 [3] [4] 0.7025312 - 0.7025343 [4] [5] 1.7945759 - 1.7945783 [5] [6] 1.9453097 - 1.9453134 [6] [7] 0.9284306 - 0.9284198 [7] [8] 1.2453566 - 1.2453584 [8] [9] 0.1019832 - 0.1019747 [9] [10] 0.0687813 - 0.0687877 [10] ... ... ... and 50 more ... actual$PC4 | expected$PC4 [1] 0.1588375 - 0.1588393 [1] [2] 0.5920400 - 0.5920375 [2] [3] 0.5631372 - 0.5631452 [3] [4] 1.3469346 - 1.3469312 [4] [5] 0.1624305 - 0.1624447 [5] [6] 0.0980751 - 0.0980681 [6] [7] 2.0990181 - 2.0990188 [7] [8] 0.3256293 - 0.3256359 [8] [9] 0.7567358 - 0.7567377 [9] [10] 1.2053130 - 1.2053087 [10] ... ... ... and 50 more ... [ FAIL 1 | WARN 3 | SKIP 0 | PASS 572 ] Error: Test failures Execution halted
COTAN.Rcheck/COTAN-Ex.timings
name | user | system | elapsed | |
COTAN_Legacy | 0.002 | 0.000 | 0.002 | |
COTAN_ObjectCreation | 8.189 | 0.121 | 8.161 | |
CalculatingCOEX | 46.040 | 0.308 | 45.822 | |
ClustersList | 0.012 | 0.000 | 0.012 | |
Conversions | 4.379 | 0.032 | 4.418 | |
GenesStatistics | 9.548 | 0.019 | 9.421 | |
HandleMetaData | 0.043 | 0.001 | 0.043 | |
HandlingClusterizations | 41.475 | 1.619 | 43.035 | |
HandlingConditions | 0.091 | 0.004 | 0.095 | |
HeatmapPlots | 28.973 | 0.439 | 29.059 | |
Installing_torch | 0.001 | 0.000 | 0.001 | |
LoggingFunctions | 0.003 | 0.000 | 0.003 | |
ParametersEstimations | 19.581 | 0.135 | 19.764 | |
RawDataCleaning | 5.058 | 0.008 | 5.084 | |
RawDataGetters | 0.043 | 0.000 | 0.043 | |
UniformClusters | 58.584 | 0.128 | 58.446 | |
getColorsVector | 0.001 | 0.000 | 0.001 | |