Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:17 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the PureCN package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PureCN.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1461/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
PureCN 1.22.2 (landing page) Markus Riester
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: PureCN |
Version: 1.22.2 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PureCN.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings PureCN_1.22.2.tar.gz |
StartedAt: 2021-10-15 03:52:35 -0400 (Fri, 15 Oct 2021) |
EndedAt: 2021-10-15 04:26:43 -0400 (Fri, 15 Oct 2021) |
EllapsedTime: 2047.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: PureCN.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PureCN.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings PureCN_1.22.2.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/PureCN.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'PureCN/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'PureCN' version '1.22.2' * checking package namespace information ... OK * checking package dependencies ... NOTE Package which this enhances but not available for checking: 'genomicsdb' * 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 whether package 'PureCN' can be installed ... OK * checking installed package size ... NOTE installed size is 5.9Mb sub-directories of 1Mb or more: extdata 4.0Mb * 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 R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 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 ... ** running examples for arch 'i386' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed callAmplificationsInLowPurity 51.27 0.05 51.32 segmentationPSCBS 27.70 0.13 27.90 filterIntervals 25.45 0.33 25.82 runAbsoluteCN 22.97 0.04 23.02 segmentationHclust 18.89 0.03 18.93 findFocal 14.64 0.02 14.82 segmentationCBS 11.27 0.00 11.26 processMultipleSamples 6.18 0.03 6.33 annotateTargets 5.46 0.53 6.32 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed callAmplificationsInLowPurity 53.87 0.02 53.89 segmentationPSCBS 28.35 0.08 28.44 filterIntervals 24.80 0.00 24.80 segmentationHclust 20.57 0.06 20.63 runAbsoluteCN 19.89 0.04 19.94 findFocal 13.14 0.03 13.17 segmentationCBS 10.08 0.00 10.08 annotateTargets 6.44 0.16 6.59 processMultipleSamples 6.12 0.00 6.13 calculateTangentNormal 5.45 0.00 5.45 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat.R' OK ** running tests for arch 'x64' ... Running 'testthat.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/PureCN.Rcheck/00check.log' for details.
PureCN.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/PureCN_1.22.2.tar.gz && rm -rf PureCN.buildbin-libdir && mkdir PureCN.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PureCN.buildbin-libdir PureCN_1.22.2.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL PureCN_1.22.2.zip && rm PureCN_1.22.2.tar.gz PureCN_1.22.2.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 43 2906k 43 1256k 0 0 1394k 0 0:00:02 --:--:-- 0:00:02 1393k 100 2906k 100 2906k 0 0 1861k 0 0:00:01 0:00:01 --:--:-- 1863k install for i386 * installing *source* package 'PureCN' ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'PureCN' finding HTML links ... done PureCN-defunct html PureCN-deprecated html annotateTargets html bootstrapResults html calculateBamCoverageByInterval html calculateLogRatio html calculateMappingBiasGatk4 html calculateMappingBiasVcf html calculatePowerDetectSomatic html calculateTangentNormal html callAlterations html callAlterationsFromSegmentation html callAmplificationsInLowPurity html callCIN html callLOH html callMutationBurden html centromeres html correctCoverageBias html createCurationFile html createNormalDatabase html filterIntervals html filterVcfBasic html filterVcfMuTect html filterVcfMuTect2 html findFocal html getSexFromCoverage html getSexFromVcf html plotAbs html poolCoverage html predictSomatic html preprocessIntervals html processMultipleSamples html purecn.DNAcopy.bdry html purecn.example.output html readAllelicCountsFile html readCoverageFile html readCurationFile html readLogRatioFile html readSegmentationFile html runAbsoluteCN html segmentationCBS html segmentationGATK4 html segmentationHclust html segmentationPSCBS html setMappingBiasVcf html setPriorVcf html ** 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 install for x64 * installing *source* package 'PureCN' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'PureCN' as PureCN_1.22.2.zip * DONE (PureCN) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'PureCN' successfully unpacked and MD5 sums checked
PureCN.Rcheck/tests_i386/testthat.Rout R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: i386-w64-mingw32/i386 (32-bit) 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. > library(testthat) > library(PureCN) Loading required package: DNAcopy Loading required package: VariantAnnotation Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: GenomeInfoDb Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: GenomicRanges Loading required package: SummarizedExperiment Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians Loading required package: Rsamtools Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Attaching package: 'VariantAnnotation' The following object is masked from 'package:base': tabulate > > test_check("PureCN") WARN [2021-10-15 04:06:12] Attempted adding gene symbols to intervals. Heuristics have been used to pick symbols for overlapping genes. WARN [2021-10-15 04:06:12] Chromosome naming style of txdb file (UCSC) was different from interval file (Ensembl). WARN [2021-10-15 04:06:16] Attempted adding gene symbols to intervals. Heuristics have been used to pick symbols for overlapping genes. FATAL [2021-10-15 04:06:19] tumor.coverage.file and interval.file do not align. FATAL [2021-10-15 04:06:19] FATAL [2021-10-15 04:06:19] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:06:19] parameters (PureCN 1.22.2). FATAL [2021-10-15 04:06:19] Need either f or purity and ploidy. FATAL [2021-10-15 04:06:19] FATAL [2021-10-15 04:06:19] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:06:19] parameters (PureCN 1.22.2). FATAL [2021-10-15 04:06:19] f not in expected range. FATAL [2021-10-15 04:06:19] FATAL [2021-10-15 04:06:19] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:06:19] parameters (PureCN 1.22.2). FATAL [2021-10-15 04:06:19] coverage not in expected range (>=2) FATAL [2021-10-15 04:06:19] FATAL [2021-10-15 04:06:19] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:06:19] parameters (PureCN 1.22.2). FATAL [2021-10-15 04:06:19] purity not in expected range. FATAL [2021-10-15 04:06:19] FATAL [2021-10-15 04:06:19] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:06:19] parameters (PureCN 1.22.2). FATAL [2021-10-15 04:06:19] ploidy not in expected range. FATAL [2021-10-15 04:06:19] FATAL [2021-10-15 04:06:19] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:06:19] parameters (PureCN 1.22.2). FATAL [2021-10-15 04:06:19] cell.fraction not in expected range. FATAL [2021-10-15 04:06:19] FATAL [2021-10-15 04:06:19] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:06:19] parameters (PureCN 1.22.2). INFO [2021-10-15 04:06:22] 576 on-target bins with low coverage in all samples. WARN [2021-10-15 04:06:22] You are likely not using the correct baits file! WARN [2021-10-15 04:06:22] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:06:22] Allosome coverage missing, cannot determine sex. INFO [2021-10-15 04:06:22] Processing on-target regions... INFO [2021-10-15 04:06:23] Removing 930 intervals with low coverage in normalDB. INFO [2021-10-15 04:06:23] Removing 1 intervals with zero coverage in more than 3% of normalDB. INFO [2021-10-15 04:06:26] Tumor/normal noise ratio: 19.041 WARN [2021-10-15 04:06:26] Extensive noise in tumor compared to normals. INFO [2021-10-15 04:07:25] Tumor/normal noise ratio: 19.041 WARN [2021-10-15 04:07:25] Extensive noise in tumor compared to normals. INFO [2021-10-15 04:07:26] Using BiocParallel for parallel optimization. FATAL [2021-10-15 04:08:43] pvalue.cutoff not within expected range or format. FATAL [2021-10-15 04:08:43] FATAL [2021-10-15 04:08:43] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:08:43] parameters (PureCN 1.22.2). FATAL [2021-10-15 04:08:43] pvalue.cutoff not within expected range or format. FATAL [2021-10-15 04:08:43] FATAL [2021-10-15 04:08:43] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:08:43] parameters (PureCN 1.22.2). FATAL [2021-10-15 04:08:43] percentile.cutoff not in expected range (0 to 100). FATAL [2021-10-15 04:08:43] FATAL [2021-10-15 04:08:43] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:08:43] parameters (PureCN 1.22.2). FATAL [2021-10-15 04:08:43] percentile.cutoff not in expected range (0 to 100). FATAL [2021-10-15 04:08:43] FATAL [2021-10-15 04:08:43] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:08:43] parameters (PureCN 1.22.2). FATAL [2021-10-15 04:08:43] purity not within expected range or format. FATAL [2021-10-15 04:08:43] FATAL [2021-10-15 04:08:43] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:08:43] parameters (PureCN 1.22.2). FATAL [2021-10-15 04:08:43] purity not within expected range or format. FATAL [2021-10-15 04:08:43] FATAL [2021-10-15 04:08:43] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:08:43] parameters (PureCN 1.22.2). INFO [2021-10-15 04:08:45] ------------------------------------------------------------ INFO [2021-10-15 04:08:45] PureCN 1.22.2 INFO [2021-10-15 04:08:45] ------------------------------------------------------------ INFO [2021-10-15 04:08:45] Loading coverage files... INFO [2021-10-15 04:08:45] Mean target coverages: 112X (tumor) 99X (normal). WARN [2021-10-15 04:08:46] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:08:46] Allosome coverage missing, cannot determine sex. INFO [2021-10-15 04:08:46] Removing 228 intervals with missing log.ratio. INFO [2021-10-15 04:08:46] Removing 22 small (< 5bp) intervals. INFO [2021-10-15 04:08:46] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2021-10-15 04:08:46] No normalDB provided. Provide one for better results. INFO [2021-10-15 04:08:46] Removing 233 low coverage (< 15.0000X) intervals. INFO [2021-10-15 04:08:46] Removing 1497 low count (< 100 total reads) intervals. INFO [2021-10-15 04:08:46] Using 8050 intervals (8050 on-target, 0 off-target). INFO [2021-10-15 04:08:46] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2021-10-15 04:08:46] No interval.file provided. Cannot check for any GC-biases. INFO [2021-10-15 04:08:46] Loading VCF... INFO [2021-10-15 04:08:46] Found 127 variants in VCF file. INFO [2021-10-15 04:08:46] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2021-10-15 04:08:46] LIB-02240e4 is tumor in VCF file. INFO [2021-10-15 04:08:46] No homozygous variants in VCF, provide unfiltered VCF. INFO [2021-10-15 04:08:46] Removing 1 non heterozygous (in matched normal) germline SNPs. INFO [2021-10-15 04:08:47] Removing 1 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15. INFO [2021-10-15 04:08:47] Removing 0 low quality variants with BQ < 25. INFO [2021-10-15 04:08:47] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding). INFO [2021-10-15 04:08:47] 1.2% of targets contain variants. INFO [2021-10-15 04:08:47] Removing 4 variants outside intervals. INFO [2021-10-15 04:08:47] Found SOMATIC annotation in VCF. INFO [2021-10-15 04:08:47] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. INFO [2021-10-15 04:08:48] Found SOMATIC annotation in VCF. Setting mapping bias to 0.972. INFO [2021-10-15 04:08:48] Excluding 0 novel or poor quality variants from segmentation. INFO [2021-10-15 04:08:48] Sample sex: ? INFO [2021-10-15 04:08:48] Segmenting data... INFO [2021-10-15 04:08:48] Loading pre-computed boundaries for DNAcopy... INFO [2021-10-15 04:08:48] Setting undo.SD parameter to 1.000000. INFO [2021-10-15 04:08:49] Setting prune.hclust.h parameter to 0.200000. INFO [2021-10-15 04:08:49] Found 59 segments with median size of 17.67Mb. INFO [2021-10-15 04:08:50] Using 121 variants. INFO [2021-10-15 04:08:50] Mean standard deviation of log-ratios: 0.34 INFO [2021-10-15 04:08:50] 2D-grid search of purity and ploidy... INFO [2021-10-15 04:08:52] Local optima: 0.63/1.9, 0.5/2 INFO [2021-10-15 04:08:52] Testing local optimum 1/2 at purity 0.63 and total ploidy 1.90... INFO [2021-10-15 04:08:54] Testing local optimum 2/2 at purity 0.50 and total ploidy 2.00... INFO [2021-10-15 04:08:55] Skipping 1 solutions that converged to the same optima. INFO [2021-10-15 04:08:55] Fitting variants with beta model for local optimum 1/2... INFO [2021-10-15 04:08:55] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01. INFO [2021-10-15 04:08:58] Optimized purity: 0.65 INFO [2021-10-15 04:08:58] Done. INFO [2021-10-15 04:08:58] ------------------------------------------------------------ INFO [2021-10-15 04:08:59] Estimating callable regions. FATAL [2021-10-15 04:09:03] exclude not a GRanges object. FATAL [2021-10-15 04:09:03] FATAL [2021-10-15 04:09:03] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:09:03] parameters (PureCN 1.22.2). FATAL [2021-10-15 04:09:03] callable not a GRanges object. FATAL [2021-10-15 04:09:03] FATAL [2021-10-15 04:09:03] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:09:03] parameters (PureCN 1.22.2). WARN [2021-10-15 04:09:17] tumor.coverage.file and interval.file do not align. FATAL [2021-10-15 04:09:20] No gc_bias column in interval.file. FATAL [2021-10-15 04:09:20] FATAL [2021-10-15 04:09:20] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:09:20] parameters (PureCN 1.22.2). FATAL [2021-10-15 04:09:20] Provided coverage is zero, most likely due to a corrupt BAM file. FATAL [2021-10-15 04:09:20] FATAL [2021-10-15 04:09:20] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:09:20] parameters (PureCN 1.22.2). INFO [2021-10-15 04:09:29] Reading C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmp2RVCFq\fileabec57363890.rds... INFO [2021-10-15 04:09:29] Reading C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmp2RVCFq\fileabec57363890.rds... INFO [2021-10-15 04:09:29] Reading C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmp2RVCFq\fileabec57363890.rds... INFO [2021-10-15 04:09:29] Reading C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmp2RVCFq\fileabec57363890.rds... INFO [2021-10-15 04:09:30] Reading C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmp2RVCFq\fileabec57363890.rds... INFO [2021-10-15 04:09:30] Reading C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmp2RVCFq\fileabec57363890.rds... FATAL [2021-10-15 04:09:30] Purity or Ploidy not numeric or in expected range. FATAL [2021-10-15 04:09:30] FATAL [2021-10-15 04:09:30] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:09:30] parameters (PureCN 1.22.2). INFO [2021-10-15 04:09:30] Reading C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmp2RVCFq\fileabec57363890.rds... INFO [2021-10-15 04:09:30] Reading C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmp2RVCFq\fileabec57363890.rds... FATAL [2021-10-15 04:09:30] 'Failed' column in FATAL [2021-10-15 04:09:30] C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmp2RVCFq\fileabec57363890.csv FATAL [2021-10-15 04:09:30] not logical(1). FATAL [2021-10-15 04:09:30] FATAL [2021-10-15 04:09:30] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:09:30] parameters (PureCN 1.22.2). INFO [2021-10-15 04:09:30] 576 on-target bins with low coverage in all samples. WARN [2021-10-15 04:09:30] You are likely not using the correct baits file! WARN [2021-10-15 04:09:31] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:09:31] Allosome coverage missing, cannot determine sex. INFO [2021-10-15 04:09:31] Processing on-target regions... INFO [2021-10-15 04:09:31] Removing 930 intervals with low coverage in normalDB. INFO [2021-10-15 04:09:31] Removing 1 intervals with zero coverage in more than 3% of normalDB. INFO [2021-10-15 04:09:36] 576 on-target bins with low coverage in all samples. WARN [2021-10-15 04:09:36] You are likely not using the correct baits file! WARN [2021-10-15 04:09:36] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:09:36] Allosome coverage missing, cannot determine sex. INFO [2021-10-15 04:09:36] Processing on-target regions... INFO [2021-10-15 04:09:37] Removing 930 intervals with low coverage in normalDB. INFO [2021-10-15 04:09:37] Removing 1 intervals with zero coverage in more than 3% of normalDB. INFO [2021-10-15 04:09:40] 576 on-target bins with low coverage in all samples. WARN [2021-10-15 04:09:40] You are likely not using the correct baits file! WARN [2021-10-15 04:09:40] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:09:40] Allosome coverage missing, cannot determine sex. INFO [2021-10-15 04:09:40] Processing on-target regions... INFO [2021-10-15 04:09:40] Removing 930 intervals with low coverage in normalDB. INFO [2021-10-15 04:09:40] Removing 1 intervals with zero coverage in more than 3% of normalDB. WARN [2021-10-15 04:09:42] Allosome coverage missing, cannot determine sex. INFO [2021-10-15 04:09:42] Sample sex: NA WARN [2021-10-15 04:09:42] Allosome coverage missing, cannot determine sex. INFO [2021-10-15 04:09:42] Sample sex: NA INFO [2021-10-15 04:09:44] 576 on-target bins with low coverage in all samples. WARN [2021-10-15 04:09:44] You are likely not using the correct baits file! WARN [2021-10-15 04:09:44] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:09:44] Allosome coverage missing, cannot determine sex. FATAL [2021-10-15 04:09:44] Length of normal.coverage.files and sex different FATAL [2021-10-15 04:09:44] FATAL [2021-10-15 04:09:44] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:09:44] parameters (PureCN 1.22.2). WARN [2021-10-15 04:09:51] Target intervals were not sorted. INFO [2021-10-15 04:09:52] 560 on-target bins with low coverage in all samples. WARN [2021-10-15 04:09:52] You are likely not using the correct baits file! WARN [2021-10-15 04:09:52] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:09:52] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:09:52] Allosome coverage missing, cannot determine sex. INFO [2021-10-15 04:09:52] Processing on-target regions... INFO [2021-10-15 04:09:53] Removing 978 intervals with low coverage in normalDB. INFO [2021-10-15 04:09:53] Removing 11 intervals with zero coverage in more than 3% of normalDB. FATAL [2021-10-15 04:09:59] tumor.coverage.file and normalDB do not align. FATAL [2021-10-15 04:09:59] FATAL [2021-10-15 04:09:59] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:09:59] parameters (PureCN 1.22.2). FATAL [2021-10-15 04:09:59] At least 2 normal.coverage.files required. FATAL [2021-10-15 04:09:59] FATAL [2021-10-15 04:09:59] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:09:59] parameters (PureCN 1.22.2). INFO [2021-10-15 04:10:04] ------------------------------------------------------------ INFO [2021-10-15 04:10:04] PureCN 1.22.2 INFO [2021-10-15 04:10:04] ------------------------------------------------------------ INFO [2021-10-15 04:10:04] Loading coverage files... INFO [2021-10-15 04:10:05] Mean target coverages: 112X (tumor) 99X (normal). WARN [2021-10-15 04:10:05] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:10:05] Allosome coverage missing, cannot determine sex. INFO [2021-10-15 04:10:05] Removing 228 intervals with missing log.ratio. FATAL [2021-10-15 04:10:05] normalDB incompatible with this PureCN version. Please re-run FATAL [2021-10-15 04:10:05] NormalDB.R. FATAL [2021-10-15 04:10:05] FATAL [2021-10-15 04:10:05] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:10:05] parameters (PureCN 1.22.2). FATAL [2021-10-15 04:10:05] normalDB incompatible with this PureCN version. Please re-run FATAL [2021-10-15 04:10:05] NormalDB.R. FATAL [2021-10-15 04:10:05] FATAL [2021-10-15 04:10:05] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:10:05] parameters (PureCN 1.22.2). FATAL [2021-10-15 04:10:05] normal.coverage.files with _coverage.txt and _loess.txt suffix FATAL [2021-10-15 04:10:05] provided. Provide either only GC-normalized or raw coverage files! FATAL [2021-10-15 04:10:05] FATAL [2021-10-15 04:10:05] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:10:05] parameters (PureCN 1.22.2). INFO [2021-10-15 04:10:06] Removing 22 non heterozygous (in matched normal) germline SNPs. INFO [2021-10-15 04:10:07] Initial testing for significant sample cross-contamination: unlikely INFO [2021-10-15 04:10:07] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15. INFO [2021-10-15 04:10:07] Removing 16 low quality variants with BQ < 25. INFO [2021-10-15 04:10:07] Removing 22 non heterozygous (in matched normal) germline SNPs. INFO [2021-10-15 04:10:08] Initial testing for significant sample cross-contamination: unlikely INFO [2021-10-15 04:10:08] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15. INFO [2021-10-15 04:10:08] Removing 6 blacklisted variants. INFO [2021-10-15 04:10:08] Removing 16 low quality variants with BQ < 25. INFO [2021-10-15 04:10:09] Removing 22 non heterozygous (in matched normal) germline SNPs. INFO [2021-10-15 04:10:09] Initial testing for significant sample cross-contamination: unlikely INFO [2021-10-15 04:10:09] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15. INFO [2021-10-15 04:10:09] Removing 16 low quality variants with BQ < 25. WARN [2021-10-15 04:10:09] MuTect stats file lacks contig and position columns. INFO [2021-10-15 04:10:10] Removing 22 non heterozygous (in matched normal) germline SNPs. INFO [2021-10-15 04:10:10] Initial testing for significant sample cross-contamination: unlikely INFO [2021-10-15 04:10:10] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15. INFO [2021-10-15 04:10:10] Removing 16 low quality variants with BQ < 25. WARN [2021-10-15 04:10:10] MuTect stats file and VCF file do not align perfectly. Will remove 2325 unmatched variants. WARN [2021-10-15 04:10:10] MuTect stats file lacks failure_reasons column. Keeping all variants listed in stats file. INFO [2021-10-15 04:10:11] Removing 0 non heterozygous (in matched normal) germline SNPs. INFO [2021-10-15 04:10:11] Removing 0 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15. INFO [2021-10-15 04:10:11] Removing 0 low quality variants with BQ < 25. INFO [2021-10-15 04:10:11] Removing 22 non heterozygous (in matched normal) germline SNPs. INFO [2021-10-15 04:10:12] Initial testing for significant sample cross-contamination: unlikely INFO [2021-10-15 04:10:12] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15. INFO [2021-10-15 04:10:12] Removing 22 non heterozygous (in matched normal) germline SNPs. INFO [2021-10-15 04:10:13] Initial testing for significant sample cross-contamination: unlikely INFO [2021-10-15 04:10:13] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15. INFO [2021-10-15 04:10:13] Removing 22 non heterozygous (in matched normal) germline SNPs. INFO [2021-10-15 04:10:13] Initial testing for significant sample cross-contamination: unlikely INFO [2021-10-15 04:10:14] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15. FATAL [2021-10-15 04:10:14] No variants passed filter BQ. FATAL [2021-10-15 04:10:14] FATAL [2021-10-15 04:10:14] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:10:14] parameters (PureCN 1.22.2). INFO [2021-10-15 04:10:14] Found 11 variants in VCF file. WARN [2021-10-15 04:10:15] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead. INFO [2021-10-15 04:10:15] 1 (9.1%) variants annotated as likely germline (DB INFO flag). INFO [2021-10-15 04:10:18] Found 11 variants in VCF file. WARN [2021-10-15 04:10:18] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead. INFO [2021-10-15 04:10:18] 1 (9.1%) variants annotated as likely germline (DB INFO flag). INFO [2021-10-15 04:10:20] Found 11 variants in VCF file. WARN [2021-10-15 04:10:20] vcf.file has no DB or POP_AF info field for membership in germline databases. Guessing it based on available dbSNP ID. INFO [2021-10-15 04:10:21] 1 (9.1%) variants annotated as likely germline (DB INFO flag). INFO [2021-10-15 04:10:22] Found 1000 variants in VCF file. INFO [2021-10-15 04:10:22] Removing 2 triallelic sites. WARN [2021-10-15 04:10:22] Having trouble guessing SOMATIC status... WARN [2021-10-15 04:10:22] DP FORMAT field contains NAs. Removing 44 variants. INFO [2021-10-15 04:10:22] 954 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2021-10-15 04:10:26] Found 12 variants in VCF file. INFO [2021-10-15 04:10:26] Removing 1 triallelic sites. WARN [2021-10-15 04:10:26] DP FORMAT field contains NAs. Removing 1 variants. WARN [2021-10-15 04:10:27] vcf.file has no DB info field for membership in germline databases. Found and used somatic status instead. INFO [2021-10-15 04:10:27] 8 (80.0%) variants annotated as likely germline (DB INFO flag). WARN [2021-10-15 04:10:28] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:10:29] Allosome coverage missing, cannot determine sex. INFO [2021-10-15 04:10:29] Mean coverages: chrX: 108.58, chrY: 108.58, chr1-22: 104.87. INFO [2021-10-15 04:10:29] Mean coverages: chrX: 108.58, chrY: 2.17, chr1-22: 104.87. INFO [2021-10-15 04:10:29] Mean coverages: chrX: 108.58, chrY: 5.17, chr1-22: 104.87. INFO [2021-10-15 04:10:29] No homozygous variants in VCF, provide unfiltered VCF. INFO [2021-10-15 04:10:30] No germline variants in VCF. FATAL [2021-10-15 04:10:30] No solution with id hello FATAL [2021-10-15 04:10:30] FATAL [2021-10-15 04:10:30] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:10:30] parameters (PureCN 1.22.2). FATAL [2021-10-15 04:10:30] No solution with id 100 FATAL [2021-10-15 04:10:30] FATAL [2021-10-15 04:10:30] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:10:30] parameters (PureCN 1.22.2). FATAL [2021-10-15 04:10:32] all.data and w have different lengths. FATAL [2021-10-15 04:10:32] FATAL [2021-10-15 04:10:32] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:10:32] parameters (PureCN 1.22.2). WARN [2021-10-15 04:10:33] No mappability scores provided. WARN [2021-10-15 04:10:33] No reptiming scores provided. INFO [2021-10-15 04:10:33] Calculating GC-content... WARN [2021-10-15 04:10:33] No mappability scores provided. WARN [2021-10-15 04:10:34] No reptiming scores provided. INFO [2021-10-15 04:10:34] Calculating GC-content... INFO [2021-10-15 04:10:34] Removing 1 targets overlapping with exclude. WARN [2021-10-15 04:10:34] No mappability scores provided. WARN [2021-10-15 04:10:34] No reptiming scores provided. INFO [2021-10-15 04:10:34] Calculating GC-content... WARN [2021-10-15 04:10:34] Found small target regions (< 100bp). Will resize them. FATAL [2021-10-15 04:10:34] off.target.padding must be negative. FATAL [2021-10-15 04:10:34] FATAL [2021-10-15 04:10:34] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:10:34] parameters (PureCN 1.22.2). FATAL [2021-10-15 04:10:35] Interval coordinates should start at 1, not at 0 FATAL [2021-10-15 04:10:35] FATAL [2021-10-15 04:10:35] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:10:35] parameters (PureCN 1.22.2). WARN [2021-10-15 04:10:35] Found small target regions (< 100bp). Will resize them. FATAL [2021-10-15 04:10:35] No off-target regions after filtering for mappability and FATAL [2021-10-15 04:10:35] off.target.padding FATAL [2021-10-15 04:10:35] FATAL [2021-10-15 04:10:35] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:10:35] parameters (PureCN 1.22.2). WARN [2021-10-15 04:10:36] Found small target regions (< 100bp). Will resize them. WARN [2021-10-15 04:10:36] No mappability scores provided. INFO [2021-10-15 04:10:36] Calculating GC-content... WARN [2021-10-15 04:10:36] Found small target regions (< 100bp). Will resize them. INFO [2021-10-15 04:10:37] Averaging reptiming into bins of size 200... WARN [2021-10-15 04:10:37] No mappability scores provided. INFO [2021-10-15 04:10:37] Calculating GC-content... WARN [2021-10-15 04:10:37] Found small target regions (< 100bp). Will resize them. INFO [2021-10-15 04:10:38] Splitting 1 large targets to an average width of 200. WARN [2021-10-15 04:10:38] No mappability scores provided. WARN [2021-10-15 04:10:38] No reptiming scores provided. INFO [2021-10-15 04:10:38] Calculating GC-content... WARN [2021-10-15 04:10:38] Found small target regions (< 100bp). Will resize them. WARN [2021-10-15 04:10:38] No mappability scores provided. WARN [2021-10-15 04:10:38] No reptiming scores provided. INFO [2021-10-15 04:10:38] Calculating GC-content... INFO [2021-10-15 04:10:39] Tiling off-target regions to an average width of 200000. WARN [2021-10-15 04:10:39] No mappability scores provided. WARN [2021-10-15 04:10:39] No reptiming scores provided. INFO [2021-10-15 04:10:39] Calculating GC-content... WARN [2021-10-15 04:10:39] Intervals contain off-target regions. Will not change intervals. WARN [2021-10-15 04:10:39] No mappability scores provided. WARN [2021-10-15 04:10:39] No reptiming scores provided. INFO [2021-10-15 04:10:40] Calculating GC-content... WARN [2021-10-15 04:10:40] Found small target regions (< 100bp). Will resize them. WARN [2021-10-15 04:10:40] No reptiming scores provided. INFO [2021-10-15 04:10:40] Calculating GC-content... WARN [2021-10-15 04:10:41] Found small target regions (< 100bp). Will resize them. WARN [2021-10-15 04:10:42] 1 intervals without mappability score (1 on-target). INFO [2021-10-15 04:10:42] Removing 1 intervals with low mappability score (<0.60). WARN [2021-10-15 04:10:42] No reptiming scores provided. INFO [2021-10-15 04:10:42] Calculating GC-content... WARN [2021-10-15 04:10:42] Found small target regions (< 100bp). Will resize them. INFO [2021-10-15 04:10:43] Tiling off-target regions to an average width of 200000. WARN [2021-10-15 04:10:43] No reptiming scores provided. INFO [2021-10-15 04:10:43] Calculating GC-content... WARN [2021-10-15 04:10:44] No mappability scores provided. WARN [2021-10-15 04:10:44] No reptiming scores provided. INFO [2021-10-15 04:10:44] Calculating GC-content... WARN [2021-10-15 04:10:45] Chromosome naming style of interval file (Ensembl) was different from reference (UCSC). WARN [2021-10-15 04:10:45] No mappability scores provided. WARN [2021-10-15 04:10:45] No reptiming scores provided. INFO [2021-10-15 04:10:45] Calculating GC-content... FATAL [2021-10-15 04:10:45] Chromosome naming style of interval file unknown, should be UCSC. FATAL [2021-10-15 04:10:45] FATAL [2021-10-15 04:10:45] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:10:45] parameters (PureCN 1.22.2). WARN [2021-10-15 04:10:45] Chromosome naming style of interval file (Ensembl) was different from reference (UCSC). WARN [2021-10-15 04:10:46] Chromosome naming style of mappability file (Ensembl) was different from reference (UCSC). WARN [2021-10-15 04:10:46] No reptiming scores provided. INFO [2021-10-15 04:10:46] Calculating GC-content... WARN [2021-10-15 04:10:46] Found small target regions (< 60bp). Will resize them. WARN [2021-10-15 04:10:47] No mappability scores provided. WARN [2021-10-15 04:10:47] No reptiming scores provided. INFO [2021-10-15 04:10:47] Calculating GC-content... WARN [2021-10-15 04:10:47] Found small target regions (< 60bp). Will drop them. WARN [2021-10-15 04:10:47] No mappability scores provided. WARN [2021-10-15 04:10:47] No reptiming scores provided. INFO [2021-10-15 04:10:47] Calculating GC-content... WARN [2021-10-15 04:10:47] Found small target regions (< 200bp). Will resize them. WARN [2021-10-15 04:10:48] No mappability scores provided. WARN [2021-10-15 04:10:48] No reptiming scores provided. INFO [2021-10-15 04:10:48] Calculating GC-content... INFO [2021-10-15 04:10:49] 576 on-target bins with low coverage in all samples. WARN [2021-10-15 04:10:49] You are likely not using the correct baits file! WARN [2021-10-15 04:10:49] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:10:49] Allosome coverage missing, cannot determine sex. INFO [2021-10-15 04:10:49] Processing on-target regions... INFO [2021-10-15 04:10:50] Removing 930 intervals with low coverage in normalDB. INFO [2021-10-15 04:10:50] Removing 1 intervals with zero coverage in more than 3% of normalDB. INFO [2021-10-15 04:10:55] Interval weights found, but currently not supported by copynumber. Will simply exclude intervals with low weight. multipcf finished for chromosome arm 1p multipcf finished for chromosome arm 1q multipcf finished for chromosome arm 2p multipcf finished for chromosome arm 2q multipcf finished for chromosome arm 3p multipcf finished for chromosome arm 3q multipcf finished for chromosome arm 4p multipcf finished for chromosome arm 4q multipcf finished for chromosome arm 5p multipcf finished for chromosome arm 5q multipcf finished for chromosome arm 6p multipcf finished for chromosome arm 6q multipcf finished for chromosome arm 7p multipcf finished for chromosome arm 7q multipcf finished for chromosome arm 8p multipcf finished for chromosome arm 8q multipcf finished for chromosome arm 9p multipcf finished for chromosome arm 9q multipcf finished for chromosome arm 10p multipcf finished for chromosome arm 10q multipcf finished for chromosome arm 11p multipcf finished for chromosome arm 11q multipcf finished for chromosome arm 12p multipcf finished for chromosome arm 12q multipcf finished for chromosome arm 13q multipcf finished for chromosome arm 14q multipcf finished for chromosome arm 15q multipcf finished for chromosome arm 16p multipcf finished for chromosome arm 16q multipcf finished for chromosome arm 17p multipcf finished for chromosome arm 17q multipcf finished for chromosome arm 18p multipcf finished for chromosome arm 18q multipcf finished for chromosome arm 19p multipcf finished for chromosome arm 19q multipcf finished for chromosome arm 20p multipcf finished for chromosome arm 20q multipcf finished for chromosome arm 21q multipcf finished for chromosome arm 22q INFO [2021-10-15 04:11:01] Interval weights found, but currently not supported by copynumber. Will simply exclude intervals with low weight. multipcf finished for chromosome arm 1p multipcf finished for chromosome arm 1q multipcf finished for chromosome arm 2p multipcf finished for chromosome arm 2q multipcf finished for chromosome arm 3p multipcf finished for chromosome arm 3q multipcf finished for chromosome arm 4p multipcf finished for chromosome arm 4q multipcf finished for chromosome arm 5p multipcf finished for chromosome arm 5q multipcf finished for chromosome arm 6p multipcf finished for chromosome arm 6q multipcf finished for chromosome arm 7p multipcf finished for chromosome arm 7q multipcf finished for chromosome arm 8p multipcf finished for chromosome arm 8q multipcf finished for chromosome arm 9p multipcf finished for chromosome arm 9q multipcf finished for chromosome arm 10p multipcf finished for chromosome arm 10q multipcf finished for chromosome arm 11p multipcf finished for chromosome arm 11q multipcf finished for chromosome arm 12p multipcf finished for chromosome arm 12q multipcf finished for chromosome arm 13q multipcf finished for chromosome arm 14q multipcf finished for chromosome arm 15q multipcf finished for chromosome arm 16p multipcf finished for chromosome arm 16q multipcf finished for chromosome arm 17p multipcf finished for chromosome arm 17q multipcf finished for chromosome arm 18p multipcf finished for chromosome arm 18q multipcf finished for chromosome arm 19p multipcf finished for chromosome arm 19q multipcf finished for chromosome arm 20p multipcf finished for chromosome arm 20q multipcf finished for chromosome arm 21q multipcf finished for chromosome arm 22q INFO [2021-10-15 04:11:02] ------------------------------------------------------------ INFO [2021-10-15 04:11:02] PureCN 1.22.2 INFO [2021-10-15 04:11:02] ------------------------------------------------------------ INFO [2021-10-15 04:11:02] Loading coverage files... INFO [2021-10-15 04:11:03] seg.file and normal.coverage.file provided. Using both. INFO [2021-10-15 04:11:03] Mean target coverages: 112X (tumor) 105X (normal). WARN [2021-10-15 04:11:03] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:11:03] Allosome coverage missing, cannot determine sex. INFO [2021-10-15 04:11:03] Removing 199 intervals with missing log.ratio. INFO [2021-10-15 04:11:03] Using 9850 intervals (9850 on-target, 0 off-target). INFO [2021-10-15 04:11:03] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2021-10-15 04:11:03] Loading VCF... INFO [2021-10-15 04:11:04] Found 127 variants in VCF file. INFO [2021-10-15 04:11:04] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2021-10-15 04:11:04] LIB-02240e4 is tumor in VCF file. INFO [2021-10-15 04:11:04] No homozygous variants in VCF, provide unfiltered VCF. INFO [2021-10-15 04:11:04] Removing 1 non heterozygous (in matched normal) germline SNPs. INFO [2021-10-15 04:11:05] Removing 1 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15. INFO [2021-10-15 04:11:05] Removing 0 low quality variants with BQ < 25. INFO [2021-10-15 04:11:05] Total size of targeted genomic region: 1.68Mb (2.66Mb with 50bp padding). INFO [2021-10-15 04:11:05] 1.0% of targets contain variants. INFO [2021-10-15 04:11:06] Removing 0 variants outside intervals. INFO [2021-10-15 04:11:06] Found SOMATIC annotation in VCF. INFO [2021-10-15 04:11:06] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. INFO [2021-10-15 04:11:06] Found SOMATIC annotation in VCF. Setting mapping bias to 0.976. INFO [2021-10-15 04:11:07] Excluding 0 novel or poor quality variants from segmentation. INFO [2021-10-15 04:11:07] Sample sex: ? INFO [2021-10-15 04:11:07] Segmenting data... INFO [2021-10-15 04:11:07] Loaded provided segmentation file fileabec45c12688.seg (format DNAcopy). INFO [2021-10-15 04:11:07] Re-centering provided segment means (offset 0.0110). INFO [2021-10-15 04:11:07] Setting prune.hclust.h parameter to 0.200000. INFO [2021-10-15 04:11:07] Found 59 segments with median size of 30.15Mb. INFO [2021-10-15 04:11:07] Using 125 variants. INFO [2021-10-15 04:11:07] Mean standard deviation of log-ratios: 0.34 INFO [2021-10-15 04:11:07] 2D-grid search of purity and ploidy... INFO [2021-10-15 04:11:09] Local optima: 0.6/1.9 INFO [2021-10-15 04:11:09] Testing local optimum 1/1 at purity 0.60 and total ploidy 1.90... INFO [2021-10-15 04:11:11] Fitting variants with beta model for local optimum 1/1... INFO [2021-10-15 04:11:11] Fitting variants for purity 0.60, tumor ploidy 1.76 and contamination 0.01. INFO [2021-10-15 04:11:15] Fitting variants for purity 0.40, tumor ploidy 1.76 and contamination 0.01. INFO [2021-10-15 04:11:19] Fitting variants for purity 0.45, tumor ploidy 1.76 and contamination 0.01. INFO [2021-10-15 04:11:22] Fitting variants for purity 0.50, tumor ploidy 1.76 and contamination 0.01. INFO [2021-10-15 04:11:25] Fitting variants for purity 0.55, tumor ploidy 1.76 and contamination 0.01. INFO [2021-10-15 04:11:29] Fitting variants for purity 0.65, tumor ploidy 1.76 and contamination 0.01. INFO [2021-10-15 04:11:33] Fitting variants for purity 0.70, tumor ploidy 1.76 and contamination 0.01. INFO [2021-10-15 04:11:37] Optimized purity: 0.65 INFO [2021-10-15 04:11:37] Done. INFO [2021-10-15 04:11:37] ------------------------------------------------------------ INFO [2021-10-15 04:11:40] Interval weights found, but currently not supported by copynumber. Will simply exclude intervals with low weight. FATAL [2021-10-15 04:11:40] Cannot find centromeres for hg20. Provide them manually or select a FATAL [2021-10-15 04:11:40] supported genome. FATAL [2021-10-15 04:11:40] FATAL [2021-10-15 04:11:40] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:11:40] parameters (PureCN 1.22.2). INFO [2021-10-15 04:11:41] Found 20 variants in VCF file. INFO [2021-10-15 04:11:42] 20 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2021-10-15 04:11:44] Found 127 variants in VCF file. INFO [2021-10-15 04:11:44] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2021-10-15 04:11:45] ------------------------------------------------------------ INFO [2021-10-15 04:11:45] PureCN 1.22.2 INFO [2021-10-15 04:11:45] ------------------------------------------------------------ INFO [2021-10-15 04:11:45] Loading coverage files... INFO [2021-10-15 04:11:46] Mean target coverages: 112X (tumor) 99X (normal). WARN [2021-10-15 04:11:46] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:11:46] Allosome coverage missing, cannot determine sex. INFO [2021-10-15 04:11:46] Removing 228 intervals with missing log.ratio. INFO [2021-10-15 04:11:46] Removing 22 small (< 5bp) intervals. INFO [2021-10-15 04:11:46] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2021-10-15 04:11:46] No normalDB provided. Provide one for better results. INFO [2021-10-15 04:11:46] Removing 233 low coverage (< 15.0000X) intervals. INFO [2021-10-15 04:11:46] Removing 1497 low count (< 100 total reads) intervals. INFO [2021-10-15 04:11:46] Using 8050 intervals (8050 on-target, 0 off-target). INFO [2021-10-15 04:11:46] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2021-10-15 04:11:46] No interval.file provided. Cannot check for any GC-biases. INFO [2021-10-15 04:11:46] Loading VCF... INFO [2021-10-15 04:11:46] Found 127 variants in VCF file. INFO [2021-10-15 04:11:46] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2021-10-15 04:11:46] LIB-02240e4 is tumor in VCF file. INFO [2021-10-15 04:11:47] No homozygous variants in VCF, provide unfiltered VCF. INFO [2021-10-15 04:11:47] Removing 1 non heterozygous (in matched normal) germline SNPs. INFO [2021-10-15 04:11:47] Removing 1 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15. INFO [2021-10-15 04:11:47] Removing 0 low quality variants with BQ < 25. INFO [2021-10-15 04:11:47] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding). INFO [2021-10-15 04:11:47] 1.2% of targets contain variants. INFO [2021-10-15 04:11:47] Removing 4 variants outside intervals. INFO [2021-10-15 04:11:48] Found SOMATIC annotation in VCF. INFO [2021-10-15 04:11:48] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. INFO [2021-10-15 04:11:48] Found SOMATIC annotation in VCF. Setting mapping bias to 0.972. INFO [2021-10-15 04:11:48] Excluding 0 novel or poor quality variants from segmentation. INFO [2021-10-15 04:11:48] Sample sex: ? INFO [2021-10-15 04:11:48] Segmenting data... INFO [2021-10-15 04:11:48] Loading pre-computed boundaries for DNAcopy... INFO [2021-10-15 04:11:48] Setting undo.SD parameter to 1.000000. INFO [2021-10-15 04:11:50] Setting prune.hclust.h parameter to 0.200000. INFO [2021-10-15 04:11:50] Found 59 segments with median size of 17.67Mb. INFO [2021-10-15 04:11:50] Using 121 variants. INFO [2021-10-15 04:11:50] Mean standard deviation of log-ratios: 0.34 INFO [2021-10-15 04:11:50] 2D-grid search of purity and ploidy... INFO [2021-10-15 04:11:50] Local optima: 0.65/1.8, 0.52/2 INFO [2021-10-15 04:11:50] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80... INFO [2021-10-15 04:11:52] Testing local optimum 2/2 at purity 0.52 and total ploidy 2.00... INFO [2021-10-15 04:11:55] Skipping 1 solutions that converged to the same optima. INFO [2021-10-15 04:11:56] Fitting variants with beta model for local optimum 1/2... INFO [2021-10-15 04:11:56] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01. INFO [2021-10-15 04:12:01] Optimized purity: 0.65 INFO [2021-10-15 04:12:01] Done. INFO [2021-10-15 04:12:01] ------------------------------------------------------------ FATAL [2021-10-15 04:12:24] log.ratio NULL in .writeLogRatioFileGATK4 FATAL [2021-10-15 04:12:24] FATAL [2021-10-15 04:12:24] This runtime error might be caused by invalid input data or parameters. FATAL [2021-10-15 04:12:24] Please report bug (PureCN 1.22.2). INFO [2021-10-15 04:12:25] Loaded provided segmentation file example_seg.txt (format DNAcopy). INFO [2021-10-15 04:12:25] Re-centering provided segment means (offset -0.0033). INFO [2021-10-15 04:12:25] Loaded provided segmentation file example_gatk4_modelfinal.seg.gz (format GATK4). WARN [2021-10-15 04:12:25] Expecting numeric chromosome names in seg.file, assuming file is properly sorted. INFO [2021-10-15 04:12:25] Re-centering provided segment means (offset -0.0037). INFO [2021-10-15 04:12:26] 576 on-target bins with low coverage in all samples. WARN [2021-10-15 04:12:26] You are likely not using the correct baits file! WARN [2021-10-15 04:12:26] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:12:26] Allosome coverage missing, cannot determine sex. INFO [2021-10-15 04:12:26] Processing on-target regions... INFO [2021-10-15 04:12:27] Removing 930 intervals with low coverage in normalDB. INFO [2021-10-15 04:12:27] Removing 1 intervals with zero coverage in more than 3% of normalDB. INFO [2021-10-15 04:12:29] ------------------------------------------------------------ INFO [2021-10-15 04:12:29] PureCN 1.22.2 INFO [2021-10-15 04:12:29] ------------------------------------------------------------ INFO [2021-10-15 04:12:29] Using BiocParallel for parallel optimization. INFO [2021-10-15 04:12:29] Loading coverage files... INFO [2021-10-15 04:12:30] Mean target coverages: 112X (tumor) 99X (normal). WARN [2021-10-15 04:12:30] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:12:30] Allosome coverage missing, cannot determine sex. INFO [2021-10-15 04:12:30] Removing 228 intervals with missing log.ratio. INFO [2021-10-15 04:12:30] Removing 705 intervals excluded in normalDB. INFO [2021-10-15 04:12:30] normalDB provided. Setting minimum coverage for segmentation to 0.0015X. INFO [2021-10-15 04:12:30] Removing 1066 low count (< 100 total reads) intervals. INFO [2021-10-15 04:12:30] Using 8050 intervals (8050 on-target, 0 off-target). INFO [2021-10-15 04:12:30] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2021-10-15 04:12:30] No interval.file provided. Cannot check for any GC-biases. INFO [2021-10-15 04:12:31] Sample sex: ? INFO [2021-10-15 04:12:31] Segmenting data... INFO [2021-10-15 04:12:31] Interval weights found, will use weighted CBS. INFO [2021-10-15 04:12:31] Loading pre-computed boundaries for DNAcopy... INFO [2021-10-15 04:12:31] Setting undo.SD parameter to 1.000000. Setting multi-figure configuration INFO [2021-10-15 04:12:33] Found 54 segments with median size of 23.50Mb. INFO [2021-10-15 04:12:33] Mean standard deviation of log-ratios: 0.34 INFO [2021-10-15 04:12:33] 2D-grid search of purity and ploidy... INFO [2021-10-15 04:12:33] Local optima: 0.65/1.8, 0.52/2 INFO [2021-10-15 04:13:15] Skipping 1 solutions that converged to the same optima. INFO [2021-10-15 04:13:16] Done. INFO [2021-10-15 04:13:16] ------------------------------------------------------------ INFO [2021-10-15 04:13:16] Reading C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmp2RVCFq\fileabec3d4253e.rds... FATAL [2021-10-15 04:13:16] runAbsoluteCN was run without a VCF file. FATAL [2021-10-15 04:13:16] FATAL [2021-10-15 04:13:16] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:13:16] parameters (PureCN 1.22.2). FATAL [2021-10-15 04:13:16] runAbsoluteCN was run without a VCF file. FATAL [2021-10-15 04:13:16] FATAL [2021-10-15 04:13:16] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:13:16] parameters (PureCN 1.22.2). INFO [2021-10-15 04:13:16] ------------------------------------------------------------ INFO [2021-10-15 04:13:16] PureCN 1.22.2 INFO [2021-10-15 04:13:16] ------------------------------------------------------------ INFO [2021-10-15 04:13:16] Loading coverage files... FATAL [2021-10-15 04:13:16] Need a normal coverage file if log.ratio and seg.file are not provided. FATAL [2021-10-15 04:13:16] FATAL [2021-10-15 04:13:16] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:13:16] parameters (PureCN 1.22.2). INFO [2021-10-15 04:13:16] ------------------------------------------------------------ INFO [2021-10-15 04:13:16] PureCN 1.22.2 INFO [2021-10-15 04:13:16] ------------------------------------------------------------ FATAL [2021-10-15 04:13:16] min.ploidy or max.ploidy not within expected range. FATAL [2021-10-15 04:13:16] FATAL [2021-10-15 04:13:16] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:13:16] parameters (PureCN 1.22.2). INFO [2021-10-15 04:13:16] ------------------------------------------------------------ INFO [2021-10-15 04:13:16] PureCN 1.22.2 INFO [2021-10-15 04:13:16] ------------------------------------------------------------ FATAL [2021-10-15 04:13:16] min.ploidy or max.ploidy not within expected range. FATAL [2021-10-15 04:13:16] FATAL [2021-10-15 04:13:16] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:13:16] parameters (PureCN 1.22.2). INFO [2021-10-15 04:13:16] ------------------------------------------------------------ INFO [2021-10-15 04:13:16] PureCN 1.22.2 INFO [2021-10-15 04:13:16] ------------------------------------------------------------ INFO [2021-10-15 04:13:16] ------------------------------------------------------------ INFO [2021-10-15 04:13:16] PureCN 1.22.2 INFO [2021-10-15 04:13:16] ------------------------------------------------------------ INFO [2021-10-15 04:13:16] ------------------------------------------------------------ INFO [2021-10-15 04:13:16] PureCN 1.22.2 INFO [2021-10-15 04:13:16] ------------------------------------------------------------ FATAL [2021-10-15 04:13:16] test.num.copy not within expected range. FATAL [2021-10-15 04:13:16] FATAL [2021-10-15 04:13:16] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:13:16] parameters (PureCN 1.22.2). INFO [2021-10-15 04:13:16] ------------------------------------------------------------ INFO [2021-10-15 04:13:16] PureCN 1.22.2 INFO [2021-10-15 04:13:16] ------------------------------------------------------------ WARN [2021-10-15 04:13:16] test.num.copy outside recommended range. FATAL [2021-10-15 04:13:16] max.non.clonal not within expected range or format. FATAL [2021-10-15 04:13:16] FATAL [2021-10-15 04:13:16] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:13:16] parameters (PureCN 1.22.2). INFO [2021-10-15 04:13:16] ------------------------------------------------------------ INFO [2021-10-15 04:13:16] PureCN 1.22.2 INFO [2021-10-15 04:13:16] ------------------------------------------------------------ WARN [2021-10-15 04:13:16] test.num.copy outside recommended range. FATAL [2021-10-15 04:13:16] max.non.clonal not within expected range or format. FATAL [2021-10-15 04:13:16] FATAL [2021-10-15 04:13:16] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:13:16] parameters (PureCN 1.22.2). INFO [2021-10-15 04:13:16] ------------------------------------------------------------ INFO [2021-10-15 04:13:16] PureCN 1.22.2 INFO [2021-10-15 04:13:16] ------------------------------------------------------------ FATAL [2021-10-15 04:13:16] test.purity not within expected range. FATAL [2021-10-15 04:13:16] FATAL [2021-10-15 04:13:16] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:13:16] parameters (PureCN 1.22.2). INFO [2021-10-15 04:13:16] ------------------------------------------------------------ INFO [2021-10-15 04:13:16] PureCN 1.22.2 INFO [2021-10-15 04:13:16] ------------------------------------------------------------ INFO [2021-10-15 04:13:16] Loading coverage files... FATAL [2021-10-15 04:13:17] Tumor and normal are identical. This won't give any meaningful results FATAL [2021-10-15 04:13:17] and I'm stopping here. FATAL [2021-10-15 04:13:17] FATAL [2021-10-15 04:13:17] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:13:17] parameters (PureCN 1.22.2). INFO [2021-10-15 04:13:17] ------------------------------------------------------------ INFO [2021-10-15 04:13:17] PureCN 1.22.2 INFO [2021-10-15 04:13:17] ------------------------------------------------------------ INFO [2021-10-15 04:13:17] Loading coverage files... FATAL [2021-10-15 04:13:17] Length of log.ratio different from tumor coverage. FATAL [2021-10-15 04:13:17] FATAL [2021-10-15 04:13:17] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:13:17] parameters (PureCN 1.22.2). INFO [2021-10-15 04:13:18] ------------------------------------------------------------ INFO [2021-10-15 04:13:18] PureCN 1.22.2 INFO [2021-10-15 04:13:18] ------------------------------------------------------------ FATAL [2021-10-15 04:13:18] prior.purity must have the same length as test.purity. FATAL [2021-10-15 04:13:18] FATAL [2021-10-15 04:13:18] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:13:18] parameters (PureCN 1.22.2). INFO [2021-10-15 04:13:18] ------------------------------------------------------------ INFO [2021-10-15 04:13:18] PureCN 1.22.2 INFO [2021-10-15 04:13:18] ------------------------------------------------------------ FATAL [2021-10-15 04:13:18] min.gof not within expected range or format. FATAL [2021-10-15 04:13:18] FATAL [2021-10-15 04:13:18] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:13:18] parameters (PureCN 1.22.2). INFO [2021-10-15 04:13:18] ------------------------------------------------------------ INFO [2021-10-15 04:13:18] PureCN 1.22.2 INFO [2021-10-15 04:13:18] ------------------------------------------------------------ FATAL [2021-10-15 04:13:18] prior.purity not within expected range or format. FATAL [2021-10-15 04:13:18] FATAL [2021-10-15 04:13:18] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:13:18] parameters (PureCN 1.22.2). INFO [2021-10-15 04:13:18] ------------------------------------------------------------ INFO [2021-10-15 04:13:18] PureCN 1.22.2 INFO [2021-10-15 04:13:18] ------------------------------------------------------------ FATAL [2021-10-15 04:13:18] prior.purity must add to 1. Sum is 1.5 FATAL [2021-10-15 04:13:18] FATAL [2021-10-15 04:13:18] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:13:18] parameters (PureCN 1.22.2). INFO [2021-10-15 04:13:18] ------------------------------------------------------------ INFO [2021-10-15 04:13:18] PureCN 1.22.2 INFO [2021-10-15 04:13:18] ------------------------------------------------------------ FATAL [2021-10-15 04:13:18] max.homozygous.loss not within expected range or format. FATAL [2021-10-15 04:13:18] FATAL [2021-10-15 04:13:18] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:13:18] parameters (PureCN 1.22.2). INFO [2021-10-15 04:13:18] ------------------------------------------------------------ INFO [2021-10-15 04:13:18] PureCN 1.22.2 INFO [2021-10-15 04:13:18] ------------------------------------------------------------ FATAL [2021-10-15 04:13:18] prior.K not within expected range or format. FATAL [2021-10-15 04:13:18] FATAL [2021-10-15 04:13:18] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:13:18] parameters (PureCN 1.22.2). INFO [2021-10-15 04:13:18] ------------------------------------------------------------ INFO [2021-10-15 04:13:18] PureCN 1.22.2 INFO [2021-10-15 04:13:18] ------------------------------------------------------------ FATAL [2021-10-15 04:13:18] prior.contamination not within expected range or format. FATAL [2021-10-15 04:13:18] FATAL [2021-10-15 04:13:18] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:13:18] parameters (PureCN 1.22.2). INFO [2021-10-15 04:13:18] ------------------------------------------------------------ INFO [2021-10-15 04:13:18] PureCN 1.22.2 INFO [2021-10-15 04:13:18] ------------------------------------------------------------ FATAL [2021-10-15 04:13:18] Iterations not in the expected range from 10 to 250. FATAL [2021-10-15 04:13:18] FATAL [2021-10-15 04:13:18] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:13:18] parameters (PureCN 1.22.2). INFO [2021-10-15 04:13:18] ------------------------------------------------------------ INFO [2021-10-15 04:13:18] PureCN 1.22.2 INFO [2021-10-15 04:13:18] ------------------------------------------------------------ FATAL [2021-10-15 04:13:18] Iterations not in the expected range from 10 to 250. FATAL [2021-10-15 04:13:18] FATAL [2021-10-15 04:13:18] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:13:18] parameters (PureCN 1.22.2). INFO [2021-10-15 04:13:18] ------------------------------------------------------------ INFO [2021-10-15 04:13:18] PureCN 1.22.2 INFO [2021-10-15 04:13:18] ------------------------------------------------------------ INFO [2021-10-15 04:13:18] Loading coverage files... FATAL [2021-10-15 04:13:18] Missing tumor.coverage.file requires seg.file or log.ratio and FATAL [2021-10-15 04:13:18] interval.file. FATAL [2021-10-15 04:13:18] FATAL [2021-10-15 04:13:18] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:13:18] parameters (PureCN 1.22.2). INFO [2021-10-15 04:13:18] ------------------------------------------------------------ INFO [2021-10-15 04:13:18] PureCN 1.22.2 INFO [2021-10-15 04:13:18] ------------------------------------------------------------ INFO [2021-10-15 04:13:19] ------------------------------------------------------------ INFO [2021-10-15 04:13:19] PureCN 1.22.2 INFO [2021-10-15 04:13:19] ------------------------------------------------------------ INFO [2021-10-15 04:13:19] Loading coverage files... FATAL [2021-10-15 04:13:19] Interval files in normal and tumor different. FATAL [2021-10-15 04:13:19] FATAL [2021-10-15 04:13:19] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:13:19] parameters (PureCN 1.22.2). INFO [2021-10-15 04:13:19] ------------------------------------------------------------ INFO [2021-10-15 04:13:19] PureCN 1.22.2 INFO [2021-10-15 04:13:19] ------------------------------------------------------------ INFO [2021-10-15 04:13:19] Loading coverage files... INFO [2021-10-15 04:13:20] Mean target coverages: 0X (tumor) 99X (normal). WARN [2021-10-15 04:13:20] Large difference in coverage of tumor and normal. FATAL [2021-10-15 04:13:20] No finite intervals. FATAL [2021-10-15 04:13:20] FATAL [2021-10-15 04:13:20] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:13:20] parameters (PureCN 1.22.2). INFO [2021-10-15 04:13:20] ------------------------------------------------------------ INFO [2021-10-15 04:13:20] PureCN 1.22.2 INFO [2021-10-15 04:13:20] ------------------------------------------------------------ INFO [2021-10-15 04:13:20] Loading coverage files... INFO [2021-10-15 04:13:21] Mean target coverages: 112X (tumor) 99X (normal). WARN [2021-10-15 04:13:21] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:13:21] Allosome coverage missing, cannot determine sex. INFO [2021-10-15 04:13:21] Removing 228 intervals with missing log.ratio. INFO [2021-10-15 04:13:21] Removing 22 small (< 5bp) intervals. INFO [2021-10-15 04:13:21] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2021-10-15 04:13:21] No normalDB provided. Provide one for better results. INFO [2021-10-15 04:13:21] Removing 233 low coverage (< 15.0000X) intervals. INFO [2021-10-15 04:13:21] Removing 1497 low count (< 100 total reads) intervals. INFO [2021-10-15 04:13:21] Using 8050 intervals (8050 on-target, 0 off-target). INFO [2021-10-15 04:13:21] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2021-10-15 04:13:21] No interval.file provided. Cannot check for any GC-biases. INFO [2021-10-15 04:13:21] Loading VCF... INFO [2021-10-15 04:13:22] Found 127 variants in VCF file. INFO [2021-10-15 04:13:22] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2021-10-15 04:13:22] LIB-02240e4 is tumor in VCF file. INFO [2021-10-15 04:13:22] No homozygous variants in VCF, provide unfiltered VCF. INFO [2021-10-15 04:13:22] Removing 1 non heterozygous (in matched normal) germline SNPs. INFO [2021-10-15 04:13:22] Removing 1 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15. Error in h(simpleError(msg, call)) : error in evaluating the argument 'con' in selecting a method for function 'import': Format 'txt' unsupported FATAL [2021-10-15 04:13:22] Could not import snp.blacklist FATAL [2021-10-15 04:13:22] C:/Users/biocbuild/bbs-3.13-bioc/R/library/PureCN/extdata/example_normal.txt:Error FATAL [2021-10-15 04:13:22] in h(simpleError(msg, call)) : error in evaluating the argument 'con' FATAL [2021-10-15 04:13:22] in selecting a method for function 'import': Format 'txt' unsupported FATAL [2021-10-15 04:13:22] FATAL [2021-10-15 04:13:22] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:13:22] parameters (PureCN 1.22.2). INFO [2021-10-15 04:13:22] ------------------------------------------------------------ INFO [2021-10-15 04:13:22] PureCN 1.22.2 INFO [2021-10-15 04:13:22] ------------------------------------------------------------ INFO [2021-10-15 04:13:22] Loading coverage files... INFO [2021-10-15 04:13:23] Mean target coverages: 112X (tumor) 99X (normal). WARN [2021-10-15 04:13:23] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:13:23] Allosome coverage missing, cannot determine sex. INFO [2021-10-15 04:13:23] Removing 228 intervals with missing log.ratio. INFO [2021-10-15 04:13:23] Removing 22 small (< 5bp) intervals. INFO [2021-10-15 04:13:23] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2021-10-15 04:13:23] No normalDB provided. Provide one for better results. INFO [2021-10-15 04:13:23] Removing 233 low coverage (< 15.0000X) intervals. INFO [2021-10-15 04:13:23] Using 9547 intervals (9547 on-target, 0 off-target). INFO [2021-10-15 04:13:23] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2021-10-15 04:13:23] No interval.file provided. Cannot check for any GC-biases. INFO [2021-10-15 04:13:23] Loading VCF... INFO [2021-10-15 04:13:24] Found 127 variants in VCF file. INFO [2021-10-15 04:13:24] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2021-10-15 04:13:24] LIB-02240e4 is tumor in VCF file. INFO [2021-10-15 04:13:24] No homozygous variants in VCF, provide unfiltered VCF. INFO [2021-10-15 04:13:24] Removing 1 non heterozygous (in matched normal) germline SNPs. INFO [2021-10-15 04:13:25] Removing 1 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15. INFO [2021-10-15 04:13:25] Removing 0 low quality variants with BQ < 25. INFO [2021-10-15 04:13:25] Total size of targeted genomic region: 1.63Mb (2.58Mb with 50bp padding). INFO [2021-10-15 04:13:25] 1.0% of targets contain variants. INFO [2021-10-15 04:13:25] Removing 2 variants outside intervals. INFO [2021-10-15 04:13:25] Found SOMATIC annotation in VCF. INFO [2021-10-15 04:13:25] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. INFO [2021-10-15 04:13:26] Found SOMATIC annotation in VCF. Setting mapping bias to 0.973. INFO [2021-10-15 04:13:26] Excluding 0 novel or poor quality variants from segmentation. INFO [2021-10-15 04:13:26] Sample sex: ? INFO [2021-10-15 04:13:26] Segmenting data... INFO [2021-10-15 04:13:26] Loading pre-computed boundaries for DNAcopy... INFO [2021-10-15 04:13:26] Setting undo.SD parameter to 1.000000. INFO [2021-10-15 04:13:28] Setting prune.hclust.h parameter to 0.200000. INFO [2021-10-15 04:13:28] Found 54 segments with median size of 24.88Mb. INFO [2021-10-15 04:13:28] Using 123 variants. INFO [2021-10-15 04:13:28] Mean standard deviation of log-ratios: 0.37 INFO [2021-10-15 04:13:28] 2D-grid search of purity and ploidy... INFO [2021-10-15 04:13:30] Local optima: 0.62/1.9, 0.3/1.9, 0.32/2 INFO [2021-10-15 04:13:30] Testing local optimum 1/3 at purity 0.62 and total ploidy 1.90... INFO [2021-10-15 04:13:32] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90... INFO [2021-10-15 04:13:32] Recalibrating log-ratios... INFO [2021-10-15 04:13:32] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90... INFO [2021-10-15 04:13:33] Recalibrating log-ratios... INFO [2021-10-15 04:13:33] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90... INFO [2021-10-15 04:13:33] Recalibrating log-ratios... INFO [2021-10-15 04:13:33] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90... INFO [2021-10-15 04:13:34] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00... INFO [2021-10-15 04:13:34] Recalibrating log-ratios... INFO [2021-10-15 04:13:34] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00... INFO [2021-10-15 04:13:35] Recalibrating log-ratios... INFO [2021-10-15 04:13:35] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00... INFO [2021-10-15 04:13:35] Recalibrating log-ratios... INFO [2021-10-15 04:13:35] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00... INFO [2021-10-15 04:13:36] Skipping 1 solutions that converged to the same optima. INFO [2021-10-15 04:13:36] Skipping 1 solutions exceeding max.non.clonal (0.20): 0.3/1.9 (purity/tumor ploidy) INFO [2021-10-15 04:13:36] Fitting variants with beta model for local optimum 1/3... INFO [2021-10-15 04:13:36] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01. INFO [2021-10-15 04:13:39] Optimized purity: 0.65 INFO [2021-10-15 04:13:39] Done. INFO [2021-10-15 04:13:39] ------------------------------------------------------------ INFO [2021-10-15 04:13:39] ------------------------------------------------------------ INFO [2021-10-15 04:13:39] PureCN 1.22.2 INFO [2021-10-15 04:13:39] ------------------------------------------------------------ INFO [2021-10-15 04:13:39] Loading coverage files... INFO [2021-10-15 04:13:40] Mean target coverages: 112X (tumor) 99X (normal). WARN [2021-10-15 04:13:40] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:13:40] Allosome coverage missing, cannot determine sex. INFO [2021-10-15 04:13:40] Removing 228 intervals with missing log.ratio. INFO [2021-10-15 04:13:40] Removing 22 small (< 5bp) intervals. INFO [2021-10-15 04:13:40] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2021-10-15 04:13:40] No normalDB provided. Provide one for better results. INFO [2021-10-15 04:13:40] Removing 233 low coverage (< 15.0000X) intervals. INFO [2021-10-15 04:13:40] Removing 1497 low count (< 100 total reads) intervals. INFO [2021-10-15 04:13:40] Using 8050 intervals (8050 on-target, 0 off-target). INFO [2021-10-15 04:13:40] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2021-10-15 04:13:40] No interval.file provided. Cannot check for any GC-biases. INFO [2021-10-15 04:13:40] Loading VCF... INFO [2021-10-15 04:13:41] Found 127 variants in VCF file. WARN [2021-10-15 04:13:41] DP FORMAT field contains NAs. Removing 3 variants. WARN [2021-10-15 04:13:41] DB INFO flag contains NAs INFO [2021-10-15 04:13:41] 119 (96.0%) variants annotated as likely germline (DB INFO flag). INFO [2021-10-15 04:13:41] LIB-02240e4 is tumor in VCF file. INFO [2021-10-15 04:13:41] No homozygous variants in VCF, provide unfiltered VCF. INFO [2021-10-15 04:13:41] Removing 1 variants with AF < 0.030 or AF >= 0.970 or less than 4 supporting reads or depth < 15. INFO [2021-10-15 04:13:42] Removing 0 low quality variants with BQ < 25. INFO [2021-10-15 04:13:42] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding). INFO [2021-10-15 04:13:42] 1.2% of targets contain variants. INFO [2021-10-15 04:13:42] Setting somatic prior probabilities for dbSNP hits to 0.000500 or to 0.500000 otherwise. INFO [2021-10-15 04:13:42] Excluding 5 novel or poor quality variants from segmentation. INFO [2021-10-15 04:13:42] Sample sex: ? INFO [2021-10-15 04:13:42] Segmenting data... INFO [2021-10-15 04:13:43] Loading pre-computed boundaries for DNAcopy... INFO [2021-10-15 04:13:43] Setting undo.SD parameter to 1.000000. Setting multi-figure configuration INFO [2021-10-15 04:13:45] Setting prune.hclust.h parameter to 0.200000. INFO [2021-10-15 04:13:45] Found 59 segments with median size of 17.67Mb. INFO [2021-10-15 04:13:45] Using 123 variants. INFO [2021-10-15 04:13:45] Mean standard deviation of log-ratios: 0.34 INFO [2021-10-15 04:13:45] 2D-grid search of purity and ploidy... INFO [2021-10-15 04:13:47] Local optima: 0.62/1.9, 0.3/1.9, 0.32/2 INFO [2021-10-15 04:13:47] Testing local optimum 1/3 at purity 0.62 and total ploidy 1.90... INFO [2021-10-15 04:13:49] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90... INFO [2021-10-15 04:13:49] Recalibrating log-ratios... INFO [2021-10-15 04:13:49] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90... INFO [2021-10-15 04:13:50] Recalibrating log-ratios... INFO [2021-10-15 04:13:50] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90... INFO [2021-10-15 04:13:50] Recalibrating log-ratios... INFO [2021-10-15 04:13:50] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90... INFO [2021-10-15 04:13:50] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00... INFO [2021-10-15 04:13:51] Recalibrating log-ratios... INFO [2021-10-15 04:13:51] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00... INFO [2021-10-15 04:13:51] Recalibrating log-ratios... INFO [2021-10-15 04:13:51] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00... INFO [2021-10-15 04:13:52] Recalibrating log-ratios... INFO [2021-10-15 04:13:52] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00... INFO [2021-10-15 04:13:52] Skipping 2 solutions exceeding max.non.clonal (0.20): 0.3/1.9, 0.35/1.67 (purity/tumor ploidy) INFO [2021-10-15 04:13:52] Fitting variants with beta model for local optimum 1/3... INFO [2021-10-15 04:13:52] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01. INFO [2021-10-15 04:13:56] Optimized purity: 0.65 INFO [2021-10-15 04:13:56] Done. INFO [2021-10-15 04:13:56] ------------------------------------------------------------ INFO [2021-10-15 04:13:56] ------------------------------------------------------------ INFO [2021-10-15 04:13:56] PureCN 1.22.2 INFO [2021-10-15 04:13:56] ------------------------------------------------------------ INFO [2021-10-15 04:13:56] Loading coverage files... INFO [2021-10-15 04:13:57] Mean target coverages: 112X (tumor) 99X (normal). WARN [2021-10-15 04:13:57] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:13:57] Allosome coverage missing, cannot determine sex. INFO [2021-10-15 04:13:57] No Gene column in interval.file. You won't get gene-level calls. INFO [2021-10-15 04:13:58] Removing 228 intervals with missing log.ratio. INFO [2021-10-15 04:13:59] Removing 15 low/high GC targets. INFO [2021-10-15 04:13:59] Removing 21 small (< 5bp) intervals. INFO [2021-10-15 04:13:59] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2021-10-15 04:13:59] No normalDB provided. Provide one for better results. INFO [2021-10-15 04:13:59] Removing 232 low coverage (< 15.0000X) intervals. INFO [2021-10-15 04:13:59] Removing 1492 low count (< 100 total reads) intervals. INFO [2021-10-15 04:13:59] Removing 36 low mappability intervals. INFO [2021-10-15 04:13:59] Using 8006 intervals (8006 on-target, 0 off-target). INFO [2021-10-15 04:13:59] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2021-10-15 04:13:59] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio). INFO [2021-10-15 04:13:59] Loading VCF... INFO [2021-10-15 04:13:59] Found 127 variants in VCF file. INFO [2021-10-15 04:13:59] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2021-10-15 04:14:00] LIB-02240e4 is tumor in VCF file. INFO [2021-10-15 04:14:00] No homozygous variants in VCF, provide unfiltered VCF. INFO [2021-10-15 04:14:00] Removing 1 non heterozygous (in matched normal) germline SNPs. INFO [2021-10-15 04:14:00] Removing 1 variants with AF < 0.030 or AF >= Inf or less than 4 supporting reads or depth < 15. INFO [2021-10-15 04:14:00] Removing 0 low quality variants with BQ < 25. INFO [2021-10-15 04:14:00] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding). INFO [2021-10-15 04:14:01] 1.2% of targets contain variants. INFO [2021-10-15 04:14:01] Removing 11 variants outside intervals. INFO [2021-10-15 04:14:01] Found SOMATIC annotation in VCF. INFO [2021-10-15 04:14:01] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. INFO [2021-10-15 04:14:01] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970. INFO [2021-10-15 04:14:01] Excluding 0 novel or poor quality variants from segmentation. INFO [2021-10-15 04:14:01] Sample sex: ? INFO [2021-10-15 04:14:01] Segmenting data... INFO [2021-10-15 04:14:02] Using unweighted PSCBS. INFO [2021-10-15 04:14:02] Setting undo.SD parameter to 1.000000. INFO [2021-10-15 04:14:17] Setting prune.hclust.h parameter to 0.200000. INFO [2021-10-15 04:14:18] Found 72 segments with median size of 27.25Mb. INFO [2021-10-15 04:14:18] Using 114 variants. INFO [2021-10-15 04:14:18] Mean standard deviation of log-ratios: 0.34 INFO [2021-10-15 04:14:18] 2D-grid search of purity and ploidy... INFO [2021-10-15 04:14:18] Local optima: 0.65/1.8, 0.38/2.2 INFO [2021-10-15 04:14:18] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80... INFO [2021-10-15 04:14:18] Recalibrating log-ratios... INFO [2021-10-15 04:14:18] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80... INFO [2021-10-15 04:14:18] Recalibrating log-ratios... INFO [2021-10-15 04:14:18] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80... INFO [2021-10-15 04:14:19] Recalibrating log-ratios... INFO [2021-10-15 04:14:19] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80... INFO [2021-10-15 04:14:19] Testing local optimum 2/2 at purity 0.38 and total ploidy 2.20... INFO [2021-10-15 04:14:20] Skipping 1 solutions exceeding max.non.clonal (0.20): 0.65/2.06 (purity/tumor ploidy) INFO [2021-10-15 04:14:20] Fitting variants with beta model for local optimum 2/2... INFO [2021-10-15 04:14:20] Fitting variants for purity 0.40, tumor ploidy 2.55 and contamination 0.01. INFO [2021-10-15 04:14:23] Optimized purity: 0.40 INFO [2021-10-15 04:14:23] Done. INFO [2021-10-15 04:14:23] ------------------------------------------------------------ FATAL [2021-10-15 04:14:23] This function requires gene-level calls. Please add a column 'Gene' FATAL [2021-10-15 04:14:23] containing gene symbols to the interval.file. FATAL [2021-10-15 04:14:23] FATAL [2021-10-15 04:14:23] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:14:23] parameters (PureCN 1.22.2). INFO [2021-10-15 04:14:24] ------------------------------------------------------------ INFO [2021-10-15 04:14:24] PureCN 1.22.2 INFO [2021-10-15 04:14:24] ------------------------------------------------------------ INFO [2021-10-15 04:14:24] Loading coverage files... INFO [2021-10-15 04:14:25] Mean target coverages: 112X (tumor) 99X (normal). WARN [2021-10-15 04:14:25] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:14:25] Allosome coverage missing, cannot determine sex. INFO [2021-10-15 04:14:25] Removing 228 intervals with missing log.ratio. INFO [2021-10-15 04:14:25] Removing 22 small (< 5bp) intervals. INFO [2021-10-15 04:14:25] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2021-10-15 04:14:25] No normalDB provided. Provide one for better results. INFO [2021-10-15 04:14:25] Removing 233 low coverage (< 15.0000X) intervals. INFO [2021-10-15 04:14:25] Removing 1497 low count (< 100 total reads) intervals. INFO [2021-10-15 04:14:25] Using 8050 intervals (8050 on-target, 0 off-target). INFO [2021-10-15 04:14:25] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2021-10-15 04:14:25] No interval.file provided. Cannot check for any GC-biases. INFO [2021-10-15 04:14:25] Loading VCF... INFO [2021-10-15 04:14:25] Found 127 variants in VCF file. INFO [2021-10-15 04:14:25] 127 (100.0%) variants annotated as likely germline (DB INFO flag). FATAL [2021-10-15 04:14:26] Different chromosome names in coverage and VCF. FATAL [2021-10-15 04:14:26] FATAL [2021-10-15 04:14:26] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:14:26] parameters (PureCN 1.22.2). INFO [2021-10-15 04:14:26] ------------------------------------------------------------ INFO [2021-10-15 04:14:26] PureCN 1.22.2 INFO [2021-10-15 04:14:26] ------------------------------------------------------------ INFO [2021-10-15 04:14:26] Loading coverage files... INFO [2021-10-15 04:14:26] Mean target coverages: 112X (tumor) 99X (normal). WARN [2021-10-15 04:14:26] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:14:26] Allosome coverage missing, cannot determine sex. FATAL [2021-10-15 04:14:26] tumor.coverage.file and interval.file do not align. FATAL [2021-10-15 04:14:26] FATAL [2021-10-15 04:14:26] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:14:26] parameters (PureCN 1.22.2). INFO [2021-10-15 04:14:27] ------------------------------------------------------------ INFO [2021-10-15 04:14:27] PureCN 1.22.2 INFO [2021-10-15 04:14:27] ------------------------------------------------------------ INFO [2021-10-15 04:14:27] Loading coverage files... INFO [2021-10-15 04:14:27] Mean target coverages: 112X (tumor) 99X (normal). WARN [2021-10-15 04:14:27] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:14:27] Allosome coverage missing, cannot determine sex. INFO [2021-10-15 04:14:28] Removing 228 intervals with missing log.ratio. INFO [2021-10-15 04:14:28] Removing 15 low/high GC targets. INFO [2021-10-15 04:14:28] Removing 21 small (< 5bp) intervals. INFO [2021-10-15 04:14:28] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2021-10-15 04:14:28] No normalDB provided. Provide one for better results. INFO [2021-10-15 04:14:28] Removing 232 low coverage (< 15.0000X) intervals. INFO [2021-10-15 04:14:28] Removing 1492 low count (< 100 total reads) intervals. INFO [2021-10-15 04:14:28] Removing 36 low mappability intervals. INFO [2021-10-15 04:14:28] Using 8006 intervals (8006 on-target, 0 off-target). INFO [2021-10-15 04:14:28] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2021-10-15 04:14:28] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio). INFO [2021-10-15 04:14:28] Loading VCF... INFO [2021-10-15 04:14:28] Found 127 variants in VCF file. INFO [2021-10-15 04:14:28] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2021-10-15 04:14:28] LIB-02240e4 is tumor in VCF file. INFO [2021-10-15 04:14:29] No homozygous variants in VCF, provide unfiltered VCF. INFO [2021-10-15 04:14:29] Removing 1 non heterozygous (in matched normal) germline SNPs. INFO [2021-10-15 04:14:29] Removing 1 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15. INFO [2021-10-15 04:14:29] Removing 0 low quality variants with BQ < 25. INFO [2021-10-15 04:14:29] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding). INFO [2021-10-15 04:14:29] 1.2% of targets contain variants. INFO [2021-10-15 04:14:29] Removing 11 variants outside intervals. INFO [2021-10-15 04:14:29] Found SOMATIC annotation in VCF. INFO [2021-10-15 04:14:29] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. INFO [2021-10-15 04:14:30] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970. INFO [2021-10-15 04:14:30] Excluding 0 novel or poor quality variants from segmentation. INFO [2021-10-15 04:14:30] Sample sex: ? INFO [2021-10-15 04:14:30] Segmenting data... INFO [2021-10-15 04:14:30] Loading pre-computed boundaries for DNAcopy... INFO [2021-10-15 04:14:30] Setting undo.SD parameter to 1.000000. INFO [2021-10-15 04:14:31] Setting prune.hclust.h parameter to 0.200000. INFO [2021-10-15 04:14:31] Found 59 segments with median size of 17.67Mb. INFO [2021-10-15 04:14:31] Using 114 variants. INFO [2021-10-15 04:14:31] Mean standard deviation of log-ratios: 0.34 INFO [2021-10-15 04:14:31] 2D-grid search of purity and ploidy... INFO [2021-10-15 04:14:32] Local optima: 0.63/1.9 INFO [2021-10-15 04:14:32] Testing local optimum 1/1 at purity 0.63 and total ploidy 1.90... INFO [2021-10-15 04:14:33] Fitting variants with beta model for local optimum 1/1... INFO [2021-10-15 04:14:33] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01. INFO [2021-10-15 04:14:36] Optimized purity: 0.65 INFO [2021-10-15 04:14:36] Done. INFO [2021-10-15 04:14:36] ------------------------------------------------------------ INFO [2021-10-15 04:14:36] ------------------------------------------------------------ INFO [2021-10-15 04:14:36] PureCN 1.22.2 INFO [2021-10-15 04:14:36] ------------------------------------------------------------ INFO [2021-10-15 04:14:36] Loading coverage files... INFO [2021-10-15 04:14:36] Mean target coverages: 112X (tumor) 99X (normal). WARN [2021-10-15 04:14:36] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:14:36] Allosome coverage missing, cannot determine sex. INFO [2021-10-15 04:14:37] Removing 228 intervals with missing log.ratio. INFO [2021-10-15 04:14:37] Removing 15 low/high GC targets. INFO [2021-10-15 04:14:38] Removing 21 small (< 5bp) intervals. INFO [2021-10-15 04:14:38] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2021-10-15 04:14:38] No normalDB provided. Provide one for better results. INFO [2021-10-15 04:14:38] Removing 232 low coverage (< 15.0000X) intervals. INFO [2021-10-15 04:14:38] Removing 1492 low count (< 100 total reads) intervals. INFO [2021-10-15 04:14:38] Removing 36 low mappability intervals. INFO [2021-10-15 04:14:38] Using 8006 intervals (8006 on-target, 0 off-target). INFO [2021-10-15 04:14:38] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2021-10-15 04:14:38] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio). INFO [2021-10-15 04:14:38] Loading VCF... INFO [2021-10-15 04:14:38] Found 127 variants in VCF file. INFO [2021-10-15 04:14:38] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2021-10-15 04:14:38] LIB-02240e4 is tumor in VCF file. INFO [2021-10-15 04:14:38] No homozygous variants in VCF, provide unfiltered VCF. INFO [2021-10-15 04:14:38] Removing 1 non heterozygous (in matched normal) germline SNPs. INFO [2021-10-15 04:14:39] Removing 1 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15. INFO [2021-10-15 04:14:39] Removing 0 low quality variants with BQ < 25. INFO [2021-10-15 04:14:39] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding). INFO [2021-10-15 04:14:39] 1.2% of targets contain variants. INFO [2021-10-15 04:14:39] Removing 11 variants outside intervals. INFO [2021-10-15 04:14:39] Found SOMATIC annotation in VCF. INFO [2021-10-15 04:14:39] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. INFO [2021-10-15 04:14:39] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970. INFO [2021-10-15 04:14:40] Excluding 0 novel or poor quality variants from segmentation. INFO [2021-10-15 04:14:40] Sample sex: ? INFO [2021-10-15 04:14:40] Segmenting data... INFO [2021-10-15 04:14:40] Loading pre-computed boundaries for DNAcopy... INFO [2021-10-15 04:14:40] Setting undo.SD parameter to 1.000000. INFO [2021-10-15 04:14:41] Setting prune.hclust.h parameter to 0.200000. INFO [2021-10-15 04:14:41] Found 59 segments with median size of 17.67Mb. INFO [2021-10-15 04:14:41] Using 114 variants. INFO [2021-10-15 04:14:41] Mean standard deviation of log-ratios: 0.34 INFO [2021-10-15 04:14:41] 2D-grid search of purity and ploidy... INFO [2021-10-15 04:14:42] Local optima: 0.63/1.9 INFO [2021-10-15 04:14:42] Testing local optimum 1/1 at purity 0.63 and total ploidy 1.90... INFO [2021-10-15 04:14:43] Fitting variants with beta model for local optimum 1/1... INFO [2021-10-15 04:14:43] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01. INFO [2021-10-15 04:14:46] Optimized purity: 0.65 INFO [2021-10-15 04:14:46] Done. INFO [2021-10-15 04:14:46] ------------------------------------------------------------ FATAL [2021-10-15 04:14:46] chr1 not valid chromosome name(s). Valid names are: FATAL [2021-10-15 04:14:46] 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22 FATAL [2021-10-15 04:14:46] FATAL [2021-10-15 04:14:46] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:14:46] parameters (PureCN 1.22.2). INFO [2021-10-15 04:14:46] ------------------------------------------------------------ INFO [2021-10-15 04:14:46] PureCN 1.22.2 INFO [2021-10-15 04:14:46] ------------------------------------------------------------ INFO [2021-10-15 04:14:46] Loading coverage files... WARN [2021-10-15 04:14:46] Provided sampleid (Sample2) does not match Sample1 found in segmentation. WARN [2021-10-15 04:14:46] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:14:46] Allosome coverage missing, cannot determine sex. INFO [2021-10-15 04:14:46] Removing 10 intervals with missing log.ratio. INFO [2021-10-15 04:14:46] Using 10039 intervals (10039 on-target, 0 off-target). INFO [2021-10-15 04:14:46] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2021-10-15 04:14:46] Loading VCF... INFO [2021-10-15 04:14:47] Found 127 variants in VCF file. INFO [2021-10-15 04:14:47] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2021-10-15 04:14:47] LIB-02240e4 is tumor in VCF file. INFO [2021-10-15 04:14:47] No homozygous variants in VCF, provide unfiltered VCF. INFO [2021-10-15 04:14:47] Removing 1 non heterozygous (in matched normal) germline SNPs. INFO [2021-10-15 04:14:47] Removing 1 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15. INFO [2021-10-15 04:14:47] Removing 0 low quality variants with BQ < 25. INFO [2021-10-15 04:14:48] Total size of targeted genomic region: 1.71Mb (2.70Mb with 50bp padding). INFO [2021-10-15 04:14:48] 1.0% of targets contain variants. INFO [2021-10-15 04:14:48] Removing 0 variants outside intervals. INFO [2021-10-15 04:14:48] Found SOMATIC annotation in VCF. INFO [2021-10-15 04:14:48] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. INFO [2021-10-15 04:14:48] Found SOMATIC annotation in VCF. Setting mapping bias to 0.976. INFO [2021-10-15 04:14:48] Excluding 0 novel or poor quality variants from segmentation. INFO [2021-10-15 04:14:48] Sample sex: ? INFO [2021-10-15 04:14:48] Segmenting data... INFO [2021-10-15 04:14:48] Loaded provided segmentation file example_seg.txt (format DNAcopy). WARN [2021-10-15 04:14:48] Provided sampleid (Sample2) does not match Sample1 found in segmentation. INFO [2021-10-15 04:14:48] Re-centering provided segment means (offset -0.0033). INFO [2021-10-15 04:14:48] Loading pre-computed boundaries for DNAcopy... INFO [2021-10-15 04:14:48] Setting undo.SD parameter to 0.000000. Setting multi-figure configuration INFO [2021-10-15 04:14:49] Setting prune.hclust.h parameter to 0.200000. INFO [2021-10-15 04:14:49] Found 54 segments with median size of 24.88Mb. INFO [2021-10-15 04:14:49] Using 125 variants. INFO [2021-10-15 04:14:49] Mean standard deviation of log-ratios: 0.40 INFO [2021-10-15 04:14:49] 2D-grid search of purity and ploidy... INFO [2021-10-15 04:14:50] Local optima: 0.6/1.9 INFO [2021-10-15 04:14:50] Testing local optimum 1/1 at purity 0.60 and total ploidy 1.90... INFO [2021-10-15 04:14:51] Fitting variants with beta model for local optimum 1/1... INFO [2021-10-15 04:14:51] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01. INFO [2021-10-15 04:14:53] Optimized purity: 0.65 INFO [2021-10-15 04:14:53] Done. INFO [2021-10-15 04:14:53] ------------------------------------------------------------ WARN [2021-10-15 04:14:54] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:14:54] Allosome coverage missing, cannot determine sex. Setting multi-figure configuration FATAL [2021-10-15 04:15:02] Segmentation file expected with colnames ID, chrom, loc.start, loc.end, FATAL [2021-10-15 04:15:02] num.mark, seg.mean FATAL [2021-10-15 04:15:02] FATAL [2021-10-15 04:15:02] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:15:02] parameters (PureCN 1.22.2). FATAL [2021-10-15 04:15:03] seg.file contains multiple samples and sampleid missing. FATAL [2021-10-15 04:15:03] FATAL [2021-10-15 04:15:03] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:15:03] parameters (PureCN 1.22.2). FATAL [2021-10-15 04:15:03] seg.file contains multiple samples and sampleid does not match any. FATAL [2021-10-15 04:15:03] FATAL [2021-10-15 04:15:03] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:15:03] parameters (PureCN 1.22.2). WARN [2021-10-15 04:15:03] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:15:03] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:15:13] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:15:13] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:15:13] Provided sampleid (example_tumor.txt) does not match Sample1 found in segmentation. WARN [2021-10-15 04:15:16] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:15:16] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:15:18] No normalDB provided. Provide one for better results. WARN [2021-10-15 04:15:27] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:15:27] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:15:30] Provided sampleid (Sample.1) does not match Sample1 found in segmentation. Setting multi-figure configuration WARN [2021-10-15 04:15:40] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:15:40] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:15:40] No normalDB provided. Provide one for better results. WARN [2021-10-15 04:15:40] Sampleid looks like a normal in VCF, not like a tumor. WARN [2021-10-15 04:15:55] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:15:55] Allosome coverage missing, cannot determine sex. FATAL [2021-10-15 04:15:56] normalDB not a valid normalDB object. Use createNormalDatabase to FATAL [2021-10-15 04:15:56] create one. FATAL [2021-10-15 04:15:56] FATAL [2021-10-15 04:15:56] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:15:56] parameters (PureCN 1.22.2). WARN [2021-10-15 04:15:56] You are likely not using the correct baits file! WARN [2021-10-15 04:15:56] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:15:56] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:15:59] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:15:59] Allosome coverage missing, cannot determine sex. FATAL [2021-10-15 04:15:59] normalDB appears to be empty. FATAL [2021-10-15 04:15:59] FATAL [2021-10-15 04:15:59] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:15:59] parameters (PureCN 1.22.2). WARN [2021-10-15 04:16:00] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:16:00] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:16:01] Intervals in coverage and interval.file have conflicting on/off-target annotation. WARN [2021-10-15 04:16:15] Cannot find gatk binary in path. FATAL [2021-10-15 04:17:00] The normal.panel.vcf.file contains only a single sample. FATAL [2021-10-15 04:17:00] FATAL [2021-10-15 04:17:00] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:17:00] parameters (PureCN 1.22.2). FATAL [2021-10-15 04:17:00] mapping.bias.file must be a file with *.rds suffix. FATAL [2021-10-15 04:17:00] FATAL [2021-10-15 04:17:00] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:17:00] parameters (PureCN 1.22.2). Failed with error: 'there is no package called 'genomicsdb'' == Skipped tests =============================================================== * gatk binary > 4.1.7.0 required (1) * genomicsdb required (1) [ FAIL 0 | WARN 53 | SKIP 2 | PASS 367 ] > > proc.time() user system elapsed 515.32 6.70 669.93 |
PureCN.Rcheck/tests_x64/testthat.Rout R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) 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. > library(testthat) > library(PureCN) Loading required package: DNAcopy Loading required package: VariantAnnotation Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: GenomeInfoDb Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: GenomicRanges Loading required package: SummarizedExperiment Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians Loading required package: Rsamtools Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Attaching package: 'VariantAnnotation' The following object is masked from 'package:base': tabulate > > test_check("PureCN") WARN [2021-10-15 04:17:22] Attempted adding gene symbols to intervals. Heuristics have been used to pick symbols for overlapping genes. WARN [2021-10-15 04:17:22] Chromosome naming style of txdb file (UCSC) was different from interval file (Ensembl). WARN [2021-10-15 04:17:25] Attempted adding gene symbols to intervals. Heuristics have been used to pick symbols for overlapping genes. FATAL [2021-10-15 04:17:27] tumor.coverage.file and interval.file do not align. FATAL [2021-10-15 04:17:27] FATAL [2021-10-15 04:17:27] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:17:27] parameters (PureCN 1.22.2). FATAL [2021-10-15 04:17:27] Need either f or purity and ploidy. FATAL [2021-10-15 04:17:27] FATAL [2021-10-15 04:17:27] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:17:27] parameters (PureCN 1.22.2). FATAL [2021-10-15 04:17:27] f not in expected range. FATAL [2021-10-15 04:17:27] FATAL [2021-10-15 04:17:27] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:17:27] parameters (PureCN 1.22.2). FATAL [2021-10-15 04:17:27] coverage not in expected range (>=2) FATAL [2021-10-15 04:17:27] FATAL [2021-10-15 04:17:27] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:17:27] parameters (PureCN 1.22.2). FATAL [2021-10-15 04:17:27] purity not in expected range. FATAL [2021-10-15 04:17:27] FATAL [2021-10-15 04:17:27] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:17:27] parameters (PureCN 1.22.2). FATAL [2021-10-15 04:17:27] ploidy not in expected range. FATAL [2021-10-15 04:17:27] FATAL [2021-10-15 04:17:27] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:17:27] parameters (PureCN 1.22.2). FATAL [2021-10-15 04:17:27] cell.fraction not in expected range. FATAL [2021-10-15 04:17:27] FATAL [2021-10-15 04:17:27] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:17:27] parameters (PureCN 1.22.2). INFO [2021-10-15 04:17:30] 576 on-target bins with low coverage in all samples. WARN [2021-10-15 04:17:30] You are likely not using the correct baits file! WARN [2021-10-15 04:17:30] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:17:30] Allosome coverage missing, cannot determine sex. INFO [2021-10-15 04:17:30] Processing on-target regions... INFO [2021-10-15 04:17:30] Removing 930 intervals with low coverage in normalDB. INFO [2021-10-15 04:17:30] Removing 1 intervals with zero coverage in more than 3% of normalDB. INFO [2021-10-15 04:17:33] Tumor/normal noise ratio: 19.041 WARN [2021-10-15 04:17:33] Extensive noise in tumor compared to normals. INFO [2021-10-15 04:18:37] Tumor/normal noise ratio: 19.041 WARN [2021-10-15 04:18:37] Extensive noise in tumor compared to normals. INFO [2021-10-15 04:18:38] Using BiocParallel for parallel optimization. FATAL [2021-10-15 04:19:53] pvalue.cutoff not within expected range or format. FATAL [2021-10-15 04:19:53] FATAL [2021-10-15 04:19:53] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:19:53] parameters (PureCN 1.22.2). FATAL [2021-10-15 04:19:53] pvalue.cutoff not within expected range or format. FATAL [2021-10-15 04:19:53] FATAL [2021-10-15 04:19:53] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:19:53] parameters (PureCN 1.22.2). FATAL [2021-10-15 04:19:53] percentile.cutoff not in expected range (0 to 100). FATAL [2021-10-15 04:19:53] FATAL [2021-10-15 04:19:53] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:19:53] parameters (PureCN 1.22.2). FATAL [2021-10-15 04:19:53] percentile.cutoff not in expected range (0 to 100). FATAL [2021-10-15 04:19:53] FATAL [2021-10-15 04:19:53] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:19:53] parameters (PureCN 1.22.2). FATAL [2021-10-15 04:19:53] purity not within expected range or format. FATAL [2021-10-15 04:19:53] FATAL [2021-10-15 04:19:53] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:19:53] parameters (PureCN 1.22.2). FATAL [2021-10-15 04:19:53] purity not within expected range or format. FATAL [2021-10-15 04:19:53] FATAL [2021-10-15 04:19:53] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:19:53] parameters (PureCN 1.22.2). INFO [2021-10-15 04:19:56] ------------------------------------------------------------ INFO [2021-10-15 04:19:56] PureCN 1.22.2 INFO [2021-10-15 04:19:56] ------------------------------------------------------------ INFO [2021-10-15 04:19:56] Loading coverage files... INFO [2021-10-15 04:19:56] Mean target coverages: 112X (tumor) 99X (normal). WARN [2021-10-15 04:19:56] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:19:56] Allosome coverage missing, cannot determine sex. INFO [2021-10-15 04:19:56] Removing 228 intervals with missing log.ratio. INFO [2021-10-15 04:19:56] Removing 22 small (< 5bp) intervals. INFO [2021-10-15 04:19:56] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2021-10-15 04:19:56] No normalDB provided. Provide one for better results. INFO [2021-10-15 04:19:56] Removing 233 low coverage (< 15.0000X) intervals. INFO [2021-10-15 04:19:56] Removing 1497 low count (< 100 total reads) intervals. INFO [2021-10-15 04:19:56] Using 8050 intervals (8050 on-target, 0 off-target). INFO [2021-10-15 04:19:56] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2021-10-15 04:19:56] No interval.file provided. Cannot check for any GC-biases. INFO [2021-10-15 04:19:56] Loading VCF... INFO [2021-10-15 04:19:56] Found 127 variants in VCF file. INFO [2021-10-15 04:19:56] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2021-10-15 04:19:57] LIB-02240e4 is tumor in VCF file. INFO [2021-10-15 04:19:57] No homozygous variants in VCF, provide unfiltered VCF. INFO [2021-10-15 04:19:57] Removing 1 non heterozygous (in matched normal) germline SNPs. INFO [2021-10-15 04:19:57] Removing 1 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15. INFO [2021-10-15 04:19:57] Removing 0 low quality variants with BQ < 25. INFO [2021-10-15 04:19:58] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding). INFO [2021-10-15 04:19:58] 1.2% of targets contain variants. INFO [2021-10-15 04:19:58] Removing 4 variants outside intervals. INFO [2021-10-15 04:19:58] Found SOMATIC annotation in VCF. INFO [2021-10-15 04:19:58] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. INFO [2021-10-15 04:19:59] Found SOMATIC annotation in VCF. Setting mapping bias to 0.972. INFO [2021-10-15 04:19:59] Excluding 0 novel or poor quality variants from segmentation. INFO [2021-10-15 04:19:59] Sample sex: ? INFO [2021-10-15 04:19:59] Segmenting data... INFO [2021-10-15 04:19:59] Loading pre-computed boundaries for DNAcopy... INFO [2021-10-15 04:19:59] Setting undo.SD parameter to 1.000000. INFO [2021-10-15 04:20:00] Setting prune.hclust.h parameter to 0.200000. INFO [2021-10-15 04:20:01] Found 59 segments with median size of 17.67Mb. INFO [2021-10-15 04:20:01] Using 121 variants. INFO [2021-10-15 04:20:01] Mean standard deviation of log-ratios: 0.34 INFO [2021-10-15 04:20:01] 2D-grid search of purity and ploidy... INFO [2021-10-15 04:20:02] Local optima: 0.63/1.9, 0.5/2 INFO [2021-10-15 04:20:02] Testing local optimum 1/2 at purity 0.63 and total ploidy 1.90... INFO [2021-10-15 04:20:03] Testing local optimum 2/2 at purity 0.50 and total ploidy 2.00... INFO [2021-10-15 04:20:04] Skipping 1 solutions that converged to the same optima. INFO [2021-10-15 04:20:04] Fitting variants with beta model for local optimum 1/2... INFO [2021-10-15 04:20:04] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01. INFO [2021-10-15 04:20:07] Optimized purity: 0.65 INFO [2021-10-15 04:20:07] Done. INFO [2021-10-15 04:20:07] ------------------------------------------------------------ INFO [2021-10-15 04:20:08] Estimating callable regions. FATAL [2021-10-15 04:20:10] exclude not a GRanges object. FATAL [2021-10-15 04:20:10] FATAL [2021-10-15 04:20:10] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:20:10] parameters (PureCN 1.22.2). FATAL [2021-10-15 04:20:10] callable not a GRanges object. FATAL [2021-10-15 04:20:10] FATAL [2021-10-15 04:20:10] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:20:10] parameters (PureCN 1.22.2). WARN [2021-10-15 04:20:22] tumor.coverage.file and interval.file do not align. FATAL [2021-10-15 04:20:25] No gc_bias column in interval.file. FATAL [2021-10-15 04:20:25] FATAL [2021-10-15 04:20:25] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:20:25] parameters (PureCN 1.22.2). FATAL [2021-10-15 04:20:26] Provided coverage is zero, most likely due to a corrupt BAM file. FATAL [2021-10-15 04:20:26] FATAL [2021-10-15 04:20:26] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:20:26] parameters (PureCN 1.22.2). INFO [2021-10-15 04:20:32] Reading C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmpemrbp3\file9cf8292173d5.rds... INFO [2021-10-15 04:20:32] Reading C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmpemrbp3\file9cf8292173d5.rds... INFO [2021-10-15 04:20:32] Reading C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmpemrbp3\file9cf8292173d5.rds... INFO [2021-10-15 04:20:33] Reading C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmpemrbp3\file9cf8292173d5.rds... INFO [2021-10-15 04:20:33] Reading C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmpemrbp3\file9cf8292173d5.rds... INFO [2021-10-15 04:20:33] Reading C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmpemrbp3\file9cf8292173d5.rds... FATAL [2021-10-15 04:20:33] Purity or Ploidy not numeric or in expected range. FATAL [2021-10-15 04:20:33] FATAL [2021-10-15 04:20:33] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:20:33] parameters (PureCN 1.22.2). INFO [2021-10-15 04:20:33] Reading C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmpemrbp3\file9cf8292173d5.rds... INFO [2021-10-15 04:20:33] Reading C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmpemrbp3\file9cf8292173d5.rds... FATAL [2021-10-15 04:20:33] 'Failed' column in FATAL [2021-10-15 04:20:33] C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmpemrbp3\file9cf8292173d5.csv FATAL [2021-10-15 04:20:33] not logical(1). FATAL [2021-10-15 04:20:33] FATAL [2021-10-15 04:20:33] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:20:33] parameters (PureCN 1.22.2). INFO [2021-10-15 04:20:34] 576 on-target bins with low coverage in all samples. WARN [2021-10-15 04:20:34] You are likely not using the correct baits file! WARN [2021-10-15 04:20:34] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:20:34] Allosome coverage missing, cannot determine sex. INFO [2021-10-15 04:20:34] Processing on-target regions... INFO [2021-10-15 04:20:35] Removing 930 intervals with low coverage in normalDB. INFO [2021-10-15 04:20:35] Removing 1 intervals with zero coverage in more than 3% of normalDB. INFO [2021-10-15 04:20:39] 576 on-target bins with low coverage in all samples. WARN [2021-10-15 04:20:39] You are likely not using the correct baits file! WARN [2021-10-15 04:20:39] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:20:39] Allosome coverage missing, cannot determine sex. INFO [2021-10-15 04:20:39] Processing on-target regions... INFO [2021-10-15 04:20:39] Removing 930 intervals with low coverage in normalDB. INFO [2021-10-15 04:20:39] Removing 1 intervals with zero coverage in more than 3% of normalDB. INFO [2021-10-15 04:20:42] 576 on-target bins with low coverage in all samples. WARN [2021-10-15 04:20:42] You are likely not using the correct baits file! WARN [2021-10-15 04:20:42] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:20:42] Allosome coverage missing, cannot determine sex. INFO [2021-10-15 04:20:42] Processing on-target regions... INFO [2021-10-15 04:20:43] Removing 930 intervals with low coverage in normalDB. INFO [2021-10-15 04:20:43] Removing 1 intervals with zero coverage in more than 3% of normalDB. WARN [2021-10-15 04:20:44] Allosome coverage missing, cannot determine sex. INFO [2021-10-15 04:20:44] Sample sex: NA WARN [2021-10-15 04:20:44] Allosome coverage missing, cannot determine sex. INFO [2021-10-15 04:20:44] Sample sex: NA INFO [2021-10-15 04:20:46] 576 on-target bins with low coverage in all samples. WARN [2021-10-15 04:20:46] You are likely not using the correct baits file! WARN [2021-10-15 04:20:46] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:20:46] Allosome coverage missing, cannot determine sex. FATAL [2021-10-15 04:20:46] Length of normal.coverage.files and sex different FATAL [2021-10-15 04:20:46] FATAL [2021-10-15 04:20:46] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:20:46] parameters (PureCN 1.22.2). WARN [2021-10-15 04:20:51] Target intervals were not sorted. INFO [2021-10-15 04:20:51] 560 on-target bins with low coverage in all samples. WARN [2021-10-15 04:20:51] You are likely not using the correct baits file! WARN [2021-10-15 04:20:51] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:20:51] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:20:51] Allosome coverage missing, cannot determine sex. INFO [2021-10-15 04:20:51] Processing on-target regions... INFO [2021-10-15 04:20:52] Removing 978 intervals with low coverage in normalDB. INFO [2021-10-15 04:20:52] Removing 11 intervals with zero coverage in more than 3% of normalDB. FATAL [2021-10-15 04:20:55] tumor.coverage.file and normalDB do not align. FATAL [2021-10-15 04:20:55] FATAL [2021-10-15 04:20:55] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:20:55] parameters (PureCN 1.22.2). FATAL [2021-10-15 04:20:55] At least 2 normal.coverage.files required. FATAL [2021-10-15 04:20:55] FATAL [2021-10-15 04:20:55] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:20:55] parameters (PureCN 1.22.2). INFO [2021-10-15 04:20:59] ------------------------------------------------------------ INFO [2021-10-15 04:20:59] PureCN 1.22.2 INFO [2021-10-15 04:20:59] ------------------------------------------------------------ INFO [2021-10-15 04:20:59] Loading coverage files... INFO [2021-10-15 04:20:59] Mean target coverages: 112X (tumor) 99X (normal). WARN [2021-10-15 04:20:59] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:20:59] Allosome coverage missing, cannot determine sex. INFO [2021-10-15 04:20:59] Removing 228 intervals with missing log.ratio. FATAL [2021-10-15 04:20:59] normalDB incompatible with this PureCN version. Please re-run FATAL [2021-10-15 04:20:59] NormalDB.R. FATAL [2021-10-15 04:20:59] FATAL [2021-10-15 04:20:59] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:20:59] parameters (PureCN 1.22.2). FATAL [2021-10-15 04:21:00] normalDB incompatible with this PureCN version. Please re-run FATAL [2021-10-15 04:21:00] NormalDB.R. FATAL [2021-10-15 04:21:00] FATAL [2021-10-15 04:21:00] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:21:00] parameters (PureCN 1.22.2). FATAL [2021-10-15 04:21:00] normal.coverage.files with _coverage.txt and _loess.txt suffix FATAL [2021-10-15 04:21:00] provided. Provide either only GC-normalized or raw coverage files! FATAL [2021-10-15 04:21:00] FATAL [2021-10-15 04:21:00] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:21:00] parameters (PureCN 1.22.2). INFO [2021-10-15 04:21:00] Removing 22 non heterozygous (in matched normal) germline SNPs. INFO [2021-10-15 04:21:00] Initial testing for significant sample cross-contamination: unlikely INFO [2021-10-15 04:21:00] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15. INFO [2021-10-15 04:21:00] Removing 16 low quality variants with BQ < 25. INFO [2021-10-15 04:21:01] Removing 22 non heterozygous (in matched normal) germline SNPs. INFO [2021-10-15 04:21:01] Initial testing for significant sample cross-contamination: unlikely INFO [2021-10-15 04:21:01] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15. INFO [2021-10-15 04:21:01] Removing 6 blacklisted variants. INFO [2021-10-15 04:21:01] Removing 16 low quality variants with BQ < 25. INFO [2021-10-15 04:21:01] Removing 22 non heterozygous (in matched normal) germline SNPs. INFO [2021-10-15 04:21:02] Initial testing for significant sample cross-contamination: unlikely INFO [2021-10-15 04:21:02] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15. INFO [2021-10-15 04:21:02] Removing 16 low quality variants with BQ < 25. WARN [2021-10-15 04:21:02] MuTect stats file lacks contig and position columns. INFO [2021-10-15 04:21:02] Removing 22 non heterozygous (in matched normal) germline SNPs. INFO [2021-10-15 04:21:02] Initial testing for significant sample cross-contamination: unlikely INFO [2021-10-15 04:21:02] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15. INFO [2021-10-15 04:21:02] Removing 16 low quality variants with BQ < 25. WARN [2021-10-15 04:21:03] MuTect stats file and VCF file do not align perfectly. Will remove 2325 unmatched variants. WARN [2021-10-15 04:21:03] MuTect stats file lacks failure_reasons column. Keeping all variants listed in stats file. INFO [2021-10-15 04:21:03] Removing 0 non heterozygous (in matched normal) germline SNPs. INFO [2021-10-15 04:21:03] Removing 0 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15. INFO [2021-10-15 04:21:03] Removing 0 low quality variants with BQ < 25. INFO [2021-10-15 04:21:03] Removing 22 non heterozygous (in matched normal) germline SNPs. INFO [2021-10-15 04:21:03] Initial testing for significant sample cross-contamination: unlikely INFO [2021-10-15 04:21:03] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15. INFO [2021-10-15 04:21:04] Removing 22 non heterozygous (in matched normal) germline SNPs. INFO [2021-10-15 04:21:04] Initial testing for significant sample cross-contamination: unlikely INFO [2021-10-15 04:21:04] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15. INFO [2021-10-15 04:21:04] Removing 22 non heterozygous (in matched normal) germline SNPs. INFO [2021-10-15 04:21:04] Initial testing for significant sample cross-contamination: unlikely INFO [2021-10-15 04:21:05] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15. FATAL [2021-10-15 04:21:05] No variants passed filter BQ. FATAL [2021-10-15 04:21:05] FATAL [2021-10-15 04:21:05] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:21:05] parameters (PureCN 1.22.2). INFO [2021-10-15 04:21:05] Found 11 variants in VCF file. WARN [2021-10-15 04:21:05] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead. INFO [2021-10-15 04:21:05] 1 (9.1%) variants annotated as likely germline (DB INFO flag). INFO [2021-10-15 04:21:08] Found 11 variants in VCF file. WARN [2021-10-15 04:21:08] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead. INFO [2021-10-15 04:21:08] 1 (9.1%) variants annotated as likely germline (DB INFO flag). INFO [2021-10-15 04:21:09] Found 11 variants in VCF file. WARN [2021-10-15 04:21:09] vcf.file has no DB or POP_AF info field for membership in germline databases. Guessing it based on available dbSNP ID. INFO [2021-10-15 04:21:10] 1 (9.1%) variants annotated as likely germline (DB INFO flag). INFO [2021-10-15 04:21:10] Found 1000 variants in VCF file. INFO [2021-10-15 04:21:10] Removing 2 triallelic sites. WARN [2021-10-15 04:21:11] Having trouble guessing SOMATIC status... WARN [2021-10-15 04:21:11] DP FORMAT field contains NAs. Removing 44 variants. INFO [2021-10-15 04:21:11] 954 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2021-10-15 04:21:13] Found 12 variants in VCF file. INFO [2021-10-15 04:21:13] Removing 1 triallelic sites. WARN [2021-10-15 04:21:13] DP FORMAT field contains NAs. Removing 1 variants. WARN [2021-10-15 04:21:13] vcf.file has no DB info field for membership in germline databases. Found and used somatic status instead. INFO [2021-10-15 04:21:14] 8 (80.0%) variants annotated as likely germline (DB INFO flag). WARN [2021-10-15 04:21:14] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:21:15] Allosome coverage missing, cannot determine sex. INFO [2021-10-15 04:21:15] Mean coverages: chrX: 108.58, chrY: 108.58, chr1-22: 104.87. INFO [2021-10-15 04:21:15] Mean coverages: chrX: 108.58, chrY: 2.17, chr1-22: 104.87. INFO [2021-10-15 04:21:15] Mean coverages: chrX: 108.58, chrY: 5.17, chr1-22: 104.87. INFO [2021-10-15 04:21:15] No homozygous variants in VCF, provide unfiltered VCF. INFO [2021-10-15 04:21:15] No germline variants in VCF. FATAL [2021-10-15 04:21:16] No solution with id hello FATAL [2021-10-15 04:21:16] FATAL [2021-10-15 04:21:16] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:21:16] parameters (PureCN 1.22.2). FATAL [2021-10-15 04:21:16] No solution with id 100 FATAL [2021-10-15 04:21:16] FATAL [2021-10-15 04:21:16] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:21:16] parameters (PureCN 1.22.2). FATAL [2021-10-15 04:21:17] all.data and w have different lengths. FATAL [2021-10-15 04:21:17] FATAL [2021-10-15 04:21:17] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:21:17] parameters (PureCN 1.22.2). WARN [2021-10-15 04:21:18] No mappability scores provided. WARN [2021-10-15 04:21:18] No reptiming scores provided. INFO [2021-10-15 04:21:18] Calculating GC-content... WARN [2021-10-15 04:21:18] No mappability scores provided. WARN [2021-10-15 04:21:18] No reptiming scores provided. INFO [2021-10-15 04:21:18] Calculating GC-content... INFO [2021-10-15 04:21:19] Removing 1 targets overlapping with exclude. WARN [2021-10-15 04:21:19] No mappability scores provided. WARN [2021-10-15 04:21:19] No reptiming scores provided. INFO [2021-10-15 04:21:19] Calculating GC-content... WARN [2021-10-15 04:21:19] Found small target regions (< 100bp). Will resize them. FATAL [2021-10-15 04:21:19] off.target.padding must be negative. FATAL [2021-10-15 04:21:19] FATAL [2021-10-15 04:21:19] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:21:19] parameters (PureCN 1.22.2). FATAL [2021-10-15 04:21:19] Interval coordinates should start at 1, not at 0 FATAL [2021-10-15 04:21:19] FATAL [2021-10-15 04:21:19] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:21:19] parameters (PureCN 1.22.2). WARN [2021-10-15 04:21:19] Found small target regions (< 100bp). Will resize them. FATAL [2021-10-15 04:21:20] No off-target regions after filtering for mappability and FATAL [2021-10-15 04:21:20] off.target.padding FATAL [2021-10-15 04:21:20] FATAL [2021-10-15 04:21:20] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:21:20] parameters (PureCN 1.22.2). WARN [2021-10-15 04:21:20] Found small target regions (< 100bp). Will resize them. WARN [2021-10-15 04:21:21] No mappability scores provided. INFO [2021-10-15 04:21:21] Calculating GC-content... WARN [2021-10-15 04:21:21] Found small target regions (< 100bp). Will resize them. INFO [2021-10-15 04:21:21] Averaging reptiming into bins of size 200... WARN [2021-10-15 04:21:21] No mappability scores provided. INFO [2021-10-15 04:21:21] Calculating GC-content... WARN [2021-10-15 04:21:22] Found small target regions (< 100bp). Will resize them. INFO [2021-10-15 04:21:22] Splitting 1 large targets to an average width of 200. WARN [2021-10-15 04:21:22] No mappability scores provided. WARN [2021-10-15 04:21:22] No reptiming scores provided. INFO [2021-10-15 04:21:22] Calculating GC-content... WARN [2021-10-15 04:21:22] Found small target regions (< 100bp). Will resize them. WARN [2021-10-15 04:21:22] No mappability scores provided. WARN [2021-10-15 04:21:22] No reptiming scores provided. INFO [2021-10-15 04:21:22] Calculating GC-content... INFO [2021-10-15 04:21:23] Tiling off-target regions to an average width of 200000. WARN [2021-10-15 04:21:23] No mappability scores provided. WARN [2021-10-15 04:21:23] No reptiming scores provided. INFO [2021-10-15 04:21:23] Calculating GC-content... WARN [2021-10-15 04:21:23] Intervals contain off-target regions. Will not change intervals. WARN [2021-10-15 04:21:23] No mappability scores provided. WARN [2021-10-15 04:21:23] No reptiming scores provided. INFO [2021-10-15 04:21:23] Calculating GC-content... WARN [2021-10-15 04:21:24] Found small target regions (< 100bp). Will resize them. WARN [2021-10-15 04:21:24] No reptiming scores provided. INFO [2021-10-15 04:21:24] Calculating GC-content... WARN [2021-10-15 04:21:25] Found small target regions (< 100bp). Will resize them. WARN [2021-10-15 04:21:25] 1 intervals without mappability score (1 on-target). INFO [2021-10-15 04:21:26] Removing 1 intervals with low mappability score (<0.60). WARN [2021-10-15 04:21:26] No reptiming scores provided. INFO [2021-10-15 04:21:26] Calculating GC-content... WARN [2021-10-15 04:21:26] Found small target regions (< 100bp). Will resize them. INFO [2021-10-15 04:21:26] Tiling off-target regions to an average width of 200000. WARN [2021-10-15 04:21:27] No reptiming scores provided. INFO [2021-10-15 04:21:27] Calculating GC-content... WARN [2021-10-15 04:21:27] No mappability scores provided. WARN [2021-10-15 04:21:27] No reptiming scores provided. INFO [2021-10-15 04:21:27] Calculating GC-content... WARN [2021-10-15 04:21:28] Chromosome naming style of interval file (Ensembl) was different from reference (UCSC). WARN [2021-10-15 04:21:28] No mappability scores provided. WARN [2021-10-15 04:21:28] No reptiming scores provided. INFO [2021-10-15 04:21:28] Calculating GC-content... FATAL [2021-10-15 04:21:28] Chromosome naming style of interval file unknown, should be UCSC. FATAL [2021-10-15 04:21:28] FATAL [2021-10-15 04:21:28] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:21:28] parameters (PureCN 1.22.2). WARN [2021-10-15 04:21:28] Chromosome naming style of interval file (Ensembl) was different from reference (UCSC). WARN [2021-10-15 04:21:28] Chromosome naming style of mappability file (Ensembl) was different from reference (UCSC). WARN [2021-10-15 04:21:29] No reptiming scores provided. INFO [2021-10-15 04:21:29] Calculating GC-content... WARN [2021-10-15 04:21:29] Found small target regions (< 60bp). Will resize them. WARN [2021-10-15 04:21:29] No mappability scores provided. WARN [2021-10-15 04:21:29] No reptiming scores provided. INFO [2021-10-15 04:21:29] Calculating GC-content... WARN [2021-10-15 04:21:29] Found small target regions (< 60bp). Will drop them. WARN [2021-10-15 04:21:30] No mappability scores provided. WARN [2021-10-15 04:21:30] No reptiming scores provided. INFO [2021-10-15 04:21:30] Calculating GC-content... WARN [2021-10-15 04:21:30] Found small target regions (< 200bp). Will resize them. WARN [2021-10-15 04:21:30] No mappability scores provided. WARN [2021-10-15 04:21:30] No reptiming scores provided. INFO [2021-10-15 04:21:30] Calculating GC-content... INFO [2021-10-15 04:21:31] 576 on-target bins with low coverage in all samples. WARN [2021-10-15 04:21:31] You are likely not using the correct baits file! WARN [2021-10-15 04:21:31] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:21:31] Allosome coverage missing, cannot determine sex. INFO [2021-10-15 04:21:31] Processing on-target regions... INFO [2021-10-15 04:21:31] Removing 930 intervals with low coverage in normalDB. INFO [2021-10-15 04:21:31] Removing 1 intervals with zero coverage in more than 3% of normalDB. INFO [2021-10-15 04:21:36] Interval weights found, but currently not supported by copynumber. Will simply exclude intervals with low weight. multipcf finished for chromosome arm 1p multipcf finished for chromosome arm 1q multipcf finished for chromosome arm 2p multipcf finished for chromosome arm 2q multipcf finished for chromosome arm 3p multipcf finished for chromosome arm 3q multipcf finished for chromosome arm 4p multipcf finished for chromosome arm 4q multipcf finished for chromosome arm 5p multipcf finished for chromosome arm 5q multipcf finished for chromosome arm 6p multipcf finished for chromosome arm 6q multipcf finished for chromosome arm 7p multipcf finished for chromosome arm 7q multipcf finished for chromosome arm 8p multipcf finished for chromosome arm 8q multipcf finished for chromosome arm 9p multipcf finished for chromosome arm 9q multipcf finished for chromosome arm 10p multipcf finished for chromosome arm 10q multipcf finished for chromosome arm 11p multipcf finished for chromosome arm 11q multipcf finished for chromosome arm 12p multipcf finished for chromosome arm 12q multipcf finished for chromosome arm 13q multipcf finished for chromosome arm 14q multipcf finished for chromosome arm 15q multipcf finished for chromosome arm 16p multipcf finished for chromosome arm 16q multipcf finished for chromosome arm 17p multipcf finished for chromosome arm 17q multipcf finished for chromosome arm 18p multipcf finished for chromosome arm 18q multipcf finished for chromosome arm 19p multipcf finished for chromosome arm 19q multipcf finished for chromosome arm 20p multipcf finished for chromosome arm 20q multipcf finished for chromosome arm 21q multipcf finished for chromosome arm 22q INFO [2021-10-15 04:21:39] Interval weights found, but currently not supported by copynumber. Will simply exclude intervals with low weight. multipcf finished for chromosome arm 1p multipcf finished for chromosome arm 1q multipcf finished for chromosome arm 2p multipcf finished for chromosome arm 2q multipcf finished for chromosome arm 3p multipcf finished for chromosome arm 3q multipcf finished for chromosome arm 4p multipcf finished for chromosome arm 4q multipcf finished for chromosome arm 5p multipcf finished for chromosome arm 5q multipcf finished for chromosome arm 6p multipcf finished for chromosome arm 6q multipcf finished for chromosome arm 7p multipcf finished for chromosome arm 7q multipcf finished for chromosome arm 8p multipcf finished for chromosome arm 8q multipcf finished for chromosome arm 9p multipcf finished for chromosome arm 9q multipcf finished for chromosome arm 10p multipcf finished for chromosome arm 10q multipcf finished for chromosome arm 11p multipcf finished for chromosome arm 11q multipcf finished for chromosome arm 12p multipcf finished for chromosome arm 12q multipcf finished for chromosome arm 13q multipcf finished for chromosome arm 14q multipcf finished for chromosome arm 15q multipcf finished for chromosome arm 16p multipcf finished for chromosome arm 16q multipcf finished for chromosome arm 17p multipcf finished for chromosome arm 17q multipcf finished for chromosome arm 18p multipcf finished for chromosome arm 18q multipcf finished for chromosome arm 19p multipcf finished for chromosome arm 19q multipcf finished for chromosome arm 20p multipcf finished for chromosome arm 20q multipcf finished for chromosome arm 21q multipcf finished for chromosome arm 22q INFO [2021-10-15 04:21:40] ------------------------------------------------------------ INFO [2021-10-15 04:21:40] PureCN 1.22.2 INFO [2021-10-15 04:21:40] ------------------------------------------------------------ INFO [2021-10-15 04:21:40] Loading coverage files... INFO [2021-10-15 04:21:40] seg.file and normal.coverage.file provided. Using both. INFO [2021-10-15 04:21:40] Mean target coverages: 112X (tumor) 105X (normal). WARN [2021-10-15 04:21:40] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:21:40] Allosome coverage missing, cannot determine sex. INFO [2021-10-15 04:21:40] Removing 199 intervals with missing log.ratio. INFO [2021-10-15 04:21:40] Using 9850 intervals (9850 on-target, 0 off-target). INFO [2021-10-15 04:21:40] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2021-10-15 04:21:40] Loading VCF... INFO [2021-10-15 04:21:41] Found 127 variants in VCF file. INFO [2021-10-15 04:21:41] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2021-10-15 04:21:41] LIB-02240e4 is tumor in VCF file. INFO [2021-10-15 04:21:41] No homozygous variants in VCF, provide unfiltered VCF. INFO [2021-10-15 04:21:41] Removing 1 non heterozygous (in matched normal) germline SNPs. INFO [2021-10-15 04:21:41] Removing 1 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15. INFO [2021-10-15 04:21:41] Removing 0 low quality variants with BQ < 25. INFO [2021-10-15 04:21:42] Total size of targeted genomic region: 1.68Mb (2.66Mb with 50bp padding). INFO [2021-10-15 04:21:42] 1.0% of targets contain variants. INFO [2021-10-15 04:21:42] Removing 0 variants outside intervals. INFO [2021-10-15 04:21:42] Found SOMATIC annotation in VCF. INFO [2021-10-15 04:21:42] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. INFO [2021-10-15 04:21:42] Found SOMATIC annotation in VCF. Setting mapping bias to 0.976. INFO [2021-10-15 04:21:42] Excluding 0 novel or poor quality variants from segmentation. INFO [2021-10-15 04:21:42] Sample sex: ? INFO [2021-10-15 04:21:42] Segmenting data... INFO [2021-10-15 04:21:42] Loaded provided segmentation file file9cf86b0e2ac7.seg (format DNAcopy). INFO [2021-10-15 04:21:42] Re-centering provided segment means (offset 0.0110). INFO [2021-10-15 04:21:43] Setting prune.hclust.h parameter to 0.200000. INFO [2021-10-15 04:21:43] Found 59 segments with median size of 30.15Mb. INFO [2021-10-15 04:21:43] Using 125 variants. INFO [2021-10-15 04:21:43] Mean standard deviation of log-ratios: 0.34 INFO [2021-10-15 04:21:43] 2D-grid search of purity and ploidy... INFO [2021-10-15 04:21:44] Local optima: 0.6/1.9 INFO [2021-10-15 04:21:44] Testing local optimum 1/1 at purity 0.60 and total ploidy 1.90... INFO [2021-10-15 04:21:45] Fitting variants with beta model for local optimum 1/1... INFO [2021-10-15 04:21:45] Fitting variants for purity 0.60, tumor ploidy 1.76 and contamination 0.01. INFO [2021-10-15 04:21:47] Fitting variants for purity 0.40, tumor ploidy 1.76 and contamination 0.01. INFO [2021-10-15 04:21:50] Fitting variants for purity 0.45, tumor ploidy 1.76 and contamination 0.01. INFO [2021-10-15 04:21:52] Fitting variants for purity 0.50, tumor ploidy 1.76 and contamination 0.01. INFO [2021-10-15 04:21:55] Fitting variants for purity 0.55, tumor ploidy 1.76 and contamination 0.01. INFO [2021-10-15 04:21:57] Fitting variants for purity 0.65, tumor ploidy 1.76 and contamination 0.01. INFO [2021-10-15 04:22:00] Fitting variants for purity 0.70, tumor ploidy 1.76 and contamination 0.01. INFO [2021-10-15 04:22:03] Optimized purity: 0.65 INFO [2021-10-15 04:22:03] Done. INFO [2021-10-15 04:22:03] ------------------------------------------------------------ INFO [2021-10-15 04:22:05] Interval weights found, but currently not supported by copynumber. Will simply exclude intervals with low weight. FATAL [2021-10-15 04:22:05] Cannot find centromeres for hg20. Provide them manually or select a FATAL [2021-10-15 04:22:05] supported genome. FATAL [2021-10-15 04:22:05] FATAL [2021-10-15 04:22:05] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:22:05] parameters (PureCN 1.22.2). INFO [2021-10-15 04:22:06] Found 20 variants in VCF file. INFO [2021-10-15 04:22:06] 20 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2021-10-15 04:22:07] Found 127 variants in VCF file. INFO [2021-10-15 04:22:07] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2021-10-15 04:22:08] ------------------------------------------------------------ INFO [2021-10-15 04:22:08] PureCN 1.22.2 INFO [2021-10-15 04:22:08] ------------------------------------------------------------ INFO [2021-10-15 04:22:08] Loading coverage files... INFO [2021-10-15 04:22:08] Mean target coverages: 112X (tumor) 99X (normal). WARN [2021-10-15 04:22:08] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:22:08] Allosome coverage missing, cannot determine sex. INFO [2021-10-15 04:22:08] Removing 228 intervals with missing log.ratio. INFO [2021-10-15 04:22:08] Removing 22 small (< 5bp) intervals. INFO [2021-10-15 04:22:08] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2021-10-15 04:22:08] No normalDB provided. Provide one for better results. INFO [2021-10-15 04:22:08] Removing 233 low coverage (< 15.0000X) intervals. INFO [2021-10-15 04:22:08] Removing 1497 low count (< 100 total reads) intervals. INFO [2021-10-15 04:22:08] Using 8050 intervals (8050 on-target, 0 off-target). INFO [2021-10-15 04:22:08] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2021-10-15 04:22:08] No interval.file provided. Cannot check for any GC-biases. INFO [2021-10-15 04:22:08] Loading VCF... INFO [2021-10-15 04:22:08] Found 127 variants in VCF file. INFO [2021-10-15 04:22:09] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2021-10-15 04:22:09] LIB-02240e4 is tumor in VCF file. INFO [2021-10-15 04:22:09] No homozygous variants in VCF, provide unfiltered VCF. INFO [2021-10-15 04:22:09] Removing 1 non heterozygous (in matched normal) germline SNPs. INFO [2021-10-15 04:22:09] Removing 1 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15. INFO [2021-10-15 04:22:09] Removing 0 low quality variants with BQ < 25. INFO [2021-10-15 04:22:09] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding). INFO [2021-10-15 04:22:10] 1.2% of targets contain variants. INFO [2021-10-15 04:22:10] Removing 4 variants outside intervals. INFO [2021-10-15 04:22:10] Found SOMATIC annotation in VCF. INFO [2021-10-15 04:22:10] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. INFO [2021-10-15 04:22:10] Found SOMATIC annotation in VCF. Setting mapping bias to 0.972. INFO [2021-10-15 04:22:10] Excluding 0 novel or poor quality variants from segmentation. INFO [2021-10-15 04:22:10] Sample sex: ? INFO [2021-10-15 04:22:10] Segmenting data... INFO [2021-10-15 04:22:11] Loading pre-computed boundaries for DNAcopy... INFO [2021-10-15 04:22:11] Setting undo.SD parameter to 1.000000. INFO [2021-10-15 04:22:12] Setting prune.hclust.h parameter to 0.200000. INFO [2021-10-15 04:22:12] Found 59 segments with median size of 17.67Mb. INFO [2021-10-15 04:22:12] Using 121 variants. INFO [2021-10-15 04:22:12] Mean standard deviation of log-ratios: 0.34 INFO [2021-10-15 04:22:12] 2D-grid search of purity and ploidy... INFO [2021-10-15 04:22:12] Local optima: 0.65/1.8, 0.52/2 INFO [2021-10-15 04:22:12] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80... INFO [2021-10-15 04:22:13] Testing local optimum 2/2 at purity 0.52 and total ploidy 2.00... INFO [2021-10-15 04:22:14] Skipping 1 solutions that converged to the same optima. INFO [2021-10-15 04:22:14] Fitting variants with beta model for local optimum 1/2... INFO [2021-10-15 04:22:14] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01. INFO [2021-10-15 04:22:16] Optimized purity: 0.65 INFO [2021-10-15 04:22:16] Done. INFO [2021-10-15 04:22:16] ------------------------------------------------------------ FATAL [2021-10-15 04:22:20] log.ratio NULL in .writeLogRatioFileGATK4 FATAL [2021-10-15 04:22:20] FATAL [2021-10-15 04:22:20] This runtime error might be caused by invalid input data or parameters. FATAL [2021-10-15 04:22:20] Please report bug (PureCN 1.22.2). INFO [2021-10-15 04:22:20] Loaded provided segmentation file example_seg.txt (format DNAcopy). INFO [2021-10-15 04:22:20] Re-centering provided segment means (offset -0.0033). INFO [2021-10-15 04:22:20] Loaded provided segmentation file example_gatk4_modelfinal.seg.gz (format GATK4). WARN [2021-10-15 04:22:20] Expecting numeric chromosome names in seg.file, assuming file is properly sorted. INFO [2021-10-15 04:22:20] Re-centering provided segment means (offset -0.0037). INFO [2021-10-15 04:22:21] 576 on-target bins with low coverage in all samples. WARN [2021-10-15 04:22:21] You are likely not using the correct baits file! WARN [2021-10-15 04:22:21] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:22:21] Allosome coverage missing, cannot determine sex. INFO [2021-10-15 04:22:21] Processing on-target regions... INFO [2021-10-15 04:22:22] Removing 930 intervals with low coverage in normalDB. INFO [2021-10-15 04:22:22] Removing 1 intervals with zero coverage in more than 3% of normalDB. INFO [2021-10-15 04:22:24] ------------------------------------------------------------ INFO [2021-10-15 04:22:24] PureCN 1.22.2 INFO [2021-10-15 04:22:24] ------------------------------------------------------------ INFO [2021-10-15 04:22:24] Using BiocParallel for parallel optimization. INFO [2021-10-15 04:22:24] Loading coverage files... INFO [2021-10-15 04:22:24] Mean target coverages: 112X (tumor) 99X (normal). WARN [2021-10-15 04:22:24] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:22:24] Allosome coverage missing, cannot determine sex. INFO [2021-10-15 04:22:24] Removing 228 intervals with missing log.ratio. INFO [2021-10-15 04:22:24] Removing 705 intervals excluded in normalDB. INFO [2021-10-15 04:22:24] normalDB provided. Setting minimum coverage for segmentation to 0.0015X. INFO [2021-10-15 04:22:24] Removing 1066 low count (< 100 total reads) intervals. INFO [2021-10-15 04:22:24] Using 8050 intervals (8050 on-target, 0 off-target). INFO [2021-10-15 04:22:24] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2021-10-15 04:22:25] No interval.file provided. Cannot check for any GC-biases. INFO [2021-10-15 04:22:25] Sample sex: ? INFO [2021-10-15 04:22:25] Segmenting data... INFO [2021-10-15 04:22:25] Interval weights found, will use weighted CBS. INFO [2021-10-15 04:22:25] Loading pre-computed boundaries for DNAcopy... INFO [2021-10-15 04:22:25] Setting undo.SD parameter to 1.000000. Setting multi-figure configuration INFO [2021-10-15 04:22:26] Found 54 segments with median size of 23.50Mb. INFO [2021-10-15 04:22:26] Mean standard deviation of log-ratios: 0.34 INFO [2021-10-15 04:22:26] 2D-grid search of purity and ploidy... INFO [2021-10-15 04:22:26] Local optima: 0.65/1.8, 0.52/2 INFO [2021-10-15 04:22:55] Skipping 1 solutions that converged to the same optima. INFO [2021-10-15 04:22:55] Done. INFO [2021-10-15 04:22:55] ------------------------------------------------------------ INFO [2021-10-15 04:22:55] Reading C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmpemrbp3\file9cf818053865.rds... FATAL [2021-10-15 04:22:55] runAbsoluteCN was run without a VCF file. FATAL [2021-10-15 04:22:55] FATAL [2021-10-15 04:22:55] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:22:55] parameters (PureCN 1.22.2). FATAL [2021-10-15 04:22:55] runAbsoluteCN was run without a VCF file. FATAL [2021-10-15 04:22:55] FATAL [2021-10-15 04:22:55] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:22:55] parameters (PureCN 1.22.2). INFO [2021-10-15 04:22:55] ------------------------------------------------------------ INFO [2021-10-15 04:22:55] PureCN 1.22.2 INFO [2021-10-15 04:22:55] ------------------------------------------------------------ INFO [2021-10-15 04:22:55] Loading coverage files... FATAL [2021-10-15 04:22:55] Need a normal coverage file if log.ratio and seg.file are not provided. FATAL [2021-10-15 04:22:55] FATAL [2021-10-15 04:22:55] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:22:55] parameters (PureCN 1.22.2). INFO [2021-10-15 04:22:55] ------------------------------------------------------------ INFO [2021-10-15 04:22:55] PureCN 1.22.2 INFO [2021-10-15 04:22:55] ------------------------------------------------------------ FATAL [2021-10-15 04:22:55] min.ploidy or max.ploidy not within expected range. FATAL [2021-10-15 04:22:55] FATAL [2021-10-15 04:22:55] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:22:55] parameters (PureCN 1.22.2). INFO [2021-10-15 04:22:55] ------------------------------------------------------------ INFO [2021-10-15 04:22:55] PureCN 1.22.2 INFO [2021-10-15 04:22:55] ------------------------------------------------------------ FATAL [2021-10-15 04:22:55] min.ploidy or max.ploidy not within expected range. FATAL [2021-10-15 04:22:55] FATAL [2021-10-15 04:22:55] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:22:55] parameters (PureCN 1.22.2). INFO [2021-10-15 04:22:55] ------------------------------------------------------------ INFO [2021-10-15 04:22:55] PureCN 1.22.2 INFO [2021-10-15 04:22:55] ------------------------------------------------------------ INFO [2021-10-15 04:22:55] ------------------------------------------------------------ INFO [2021-10-15 04:22:55] PureCN 1.22.2 INFO [2021-10-15 04:22:55] ------------------------------------------------------------ INFO [2021-10-15 04:22:55] ------------------------------------------------------------ INFO [2021-10-15 04:22:55] PureCN 1.22.2 INFO [2021-10-15 04:22:55] ------------------------------------------------------------ FATAL [2021-10-15 04:22:55] test.num.copy not within expected range. FATAL [2021-10-15 04:22:55] FATAL [2021-10-15 04:22:55] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:22:55] parameters (PureCN 1.22.2). INFO [2021-10-15 04:22:55] ------------------------------------------------------------ INFO [2021-10-15 04:22:55] PureCN 1.22.2 INFO [2021-10-15 04:22:55] ------------------------------------------------------------ WARN [2021-10-15 04:22:55] test.num.copy outside recommended range. FATAL [2021-10-15 04:22:55] max.non.clonal not within expected range or format. FATAL [2021-10-15 04:22:55] FATAL [2021-10-15 04:22:55] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:22:55] parameters (PureCN 1.22.2). INFO [2021-10-15 04:22:55] ------------------------------------------------------------ INFO [2021-10-15 04:22:55] PureCN 1.22.2 INFO [2021-10-15 04:22:55] ------------------------------------------------------------ WARN [2021-10-15 04:22:55] test.num.copy outside recommended range. FATAL [2021-10-15 04:22:55] max.non.clonal not within expected range or format. FATAL [2021-10-15 04:22:55] FATAL [2021-10-15 04:22:55] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:22:55] parameters (PureCN 1.22.2). INFO [2021-10-15 04:22:56] ------------------------------------------------------------ INFO [2021-10-15 04:22:56] PureCN 1.22.2 INFO [2021-10-15 04:22:56] ------------------------------------------------------------ FATAL [2021-10-15 04:22:56] test.purity not within expected range. FATAL [2021-10-15 04:22:56] FATAL [2021-10-15 04:22:56] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:22:56] parameters (PureCN 1.22.2). INFO [2021-10-15 04:22:56] ------------------------------------------------------------ INFO [2021-10-15 04:22:56] PureCN 1.22.2 INFO [2021-10-15 04:22:56] ------------------------------------------------------------ INFO [2021-10-15 04:22:56] Loading coverage files... FATAL [2021-10-15 04:22:56] Tumor and normal are identical. This won't give any meaningful results FATAL [2021-10-15 04:22:56] and I'm stopping here. FATAL [2021-10-15 04:22:56] FATAL [2021-10-15 04:22:56] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:22:56] parameters (PureCN 1.22.2). INFO [2021-10-15 04:22:56] ------------------------------------------------------------ INFO [2021-10-15 04:22:56] PureCN 1.22.2 INFO [2021-10-15 04:22:56] ------------------------------------------------------------ INFO [2021-10-15 04:22:56] Loading coverage files... FATAL [2021-10-15 04:22:56] Length of log.ratio different from tumor coverage. FATAL [2021-10-15 04:22:56] FATAL [2021-10-15 04:22:56] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:22:56] parameters (PureCN 1.22.2). INFO [2021-10-15 04:22:56] ------------------------------------------------------------ INFO [2021-10-15 04:22:56] PureCN 1.22.2 INFO [2021-10-15 04:22:56] ------------------------------------------------------------ FATAL [2021-10-15 04:22:56] prior.purity must have the same length as test.purity. FATAL [2021-10-15 04:22:56] FATAL [2021-10-15 04:22:56] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:22:56] parameters (PureCN 1.22.2). INFO [2021-10-15 04:22:56] ------------------------------------------------------------ INFO [2021-10-15 04:22:56] PureCN 1.22.2 INFO [2021-10-15 04:22:56] ------------------------------------------------------------ FATAL [2021-10-15 04:22:56] min.gof not within expected range or format. FATAL [2021-10-15 04:22:56] FATAL [2021-10-15 04:22:56] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:22:56] parameters (PureCN 1.22.2). INFO [2021-10-15 04:22:56] ------------------------------------------------------------ INFO [2021-10-15 04:22:56] PureCN 1.22.2 INFO [2021-10-15 04:22:56] ------------------------------------------------------------ FATAL [2021-10-15 04:22:56] prior.purity not within expected range or format. FATAL [2021-10-15 04:22:56] FATAL [2021-10-15 04:22:56] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:22:56] parameters (PureCN 1.22.2). INFO [2021-10-15 04:22:56] ------------------------------------------------------------ INFO [2021-10-15 04:22:56] PureCN 1.22.2 INFO [2021-10-15 04:22:56] ------------------------------------------------------------ FATAL [2021-10-15 04:22:56] prior.purity must add to 1. Sum is 1.5 FATAL [2021-10-15 04:22:56] FATAL [2021-10-15 04:22:56] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:22:56] parameters (PureCN 1.22.2). INFO [2021-10-15 04:22:57] ------------------------------------------------------------ INFO [2021-10-15 04:22:57] PureCN 1.22.2 INFO [2021-10-15 04:22:57] ------------------------------------------------------------ FATAL [2021-10-15 04:22:57] max.homozygous.loss not within expected range or format. FATAL [2021-10-15 04:22:57] FATAL [2021-10-15 04:22:57] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:22:57] parameters (PureCN 1.22.2). INFO [2021-10-15 04:22:57] ------------------------------------------------------------ INFO [2021-10-15 04:22:57] PureCN 1.22.2 INFO [2021-10-15 04:22:57] ------------------------------------------------------------ FATAL [2021-10-15 04:22:57] prior.K not within expected range or format. FATAL [2021-10-15 04:22:57] FATAL [2021-10-15 04:22:57] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:22:57] parameters (PureCN 1.22.2). INFO [2021-10-15 04:22:57] ------------------------------------------------------------ INFO [2021-10-15 04:22:57] PureCN 1.22.2 INFO [2021-10-15 04:22:57] ------------------------------------------------------------ FATAL [2021-10-15 04:22:57] prior.contamination not within expected range or format. FATAL [2021-10-15 04:22:57] FATAL [2021-10-15 04:22:57] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:22:57] parameters (PureCN 1.22.2). INFO [2021-10-15 04:22:57] ------------------------------------------------------------ INFO [2021-10-15 04:22:57] PureCN 1.22.2 INFO [2021-10-15 04:22:57] ------------------------------------------------------------ FATAL [2021-10-15 04:22:57] Iterations not in the expected range from 10 to 250. FATAL [2021-10-15 04:22:57] FATAL [2021-10-15 04:22:57] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:22:57] parameters (PureCN 1.22.2). INFO [2021-10-15 04:22:57] ------------------------------------------------------------ INFO [2021-10-15 04:22:57] PureCN 1.22.2 INFO [2021-10-15 04:22:57] ------------------------------------------------------------ FATAL [2021-10-15 04:22:57] Iterations not in the expected range from 10 to 250. FATAL [2021-10-15 04:22:57] FATAL [2021-10-15 04:22:57] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:22:57] parameters (PureCN 1.22.2). INFO [2021-10-15 04:22:57] ------------------------------------------------------------ INFO [2021-10-15 04:22:57] PureCN 1.22.2 INFO [2021-10-15 04:22:57] ------------------------------------------------------------ INFO [2021-10-15 04:22:57] Loading coverage files... FATAL [2021-10-15 04:22:57] Missing tumor.coverage.file requires seg.file or log.ratio and FATAL [2021-10-15 04:22:57] interval.file. FATAL [2021-10-15 04:22:57] FATAL [2021-10-15 04:22:57] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:22:57] parameters (PureCN 1.22.2). INFO [2021-10-15 04:22:57] ------------------------------------------------------------ INFO [2021-10-15 04:22:57] PureCN 1.22.2 INFO [2021-10-15 04:22:57] ------------------------------------------------------------ INFO [2021-10-15 04:22:57] ------------------------------------------------------------ INFO [2021-10-15 04:22:57] PureCN 1.22.2 INFO [2021-10-15 04:22:57] ------------------------------------------------------------ INFO [2021-10-15 04:22:57] Loading coverage files... FATAL [2021-10-15 04:22:58] Interval files in normal and tumor different. FATAL [2021-10-15 04:22:58] FATAL [2021-10-15 04:22:58] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:22:58] parameters (PureCN 1.22.2). INFO [2021-10-15 04:22:58] ------------------------------------------------------------ INFO [2021-10-15 04:22:58] PureCN 1.22.2 INFO [2021-10-15 04:22:58] ------------------------------------------------------------ INFO [2021-10-15 04:22:58] Loading coverage files... INFO [2021-10-15 04:22:58] Mean target coverages: 0X (tumor) 99X (normal). WARN [2021-10-15 04:22:58] Large difference in coverage of tumor and normal. FATAL [2021-10-15 04:22:58] No finite intervals. FATAL [2021-10-15 04:22:58] FATAL [2021-10-15 04:22:58] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:22:58] parameters (PureCN 1.22.2). INFO [2021-10-15 04:22:58] ------------------------------------------------------------ INFO [2021-10-15 04:22:58] PureCN 1.22.2 INFO [2021-10-15 04:22:58] ------------------------------------------------------------ INFO [2021-10-15 04:22:58] Loading coverage files... INFO [2021-10-15 04:22:59] Mean target coverages: 112X (tumor) 99X (normal). WARN [2021-10-15 04:22:59] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:22:59] Allosome coverage missing, cannot determine sex. INFO [2021-10-15 04:22:59] Removing 228 intervals with missing log.ratio. INFO [2021-10-15 04:22:59] Removing 22 small (< 5bp) intervals. INFO [2021-10-15 04:22:59] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2021-10-15 04:22:59] No normalDB provided. Provide one for better results. INFO [2021-10-15 04:22:59] Removing 233 low coverage (< 15.0000X) intervals. INFO [2021-10-15 04:22:59] Removing 1497 low count (< 100 total reads) intervals. INFO [2021-10-15 04:22:59] Using 8050 intervals (8050 on-target, 0 off-target). INFO [2021-10-15 04:22:59] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2021-10-15 04:22:59] No interval.file provided. Cannot check for any GC-biases. INFO [2021-10-15 04:22:59] Loading VCF... INFO [2021-10-15 04:23:00] Found 127 variants in VCF file. INFO [2021-10-15 04:23:00] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2021-10-15 04:23:00] LIB-02240e4 is tumor in VCF file. INFO [2021-10-15 04:23:00] No homozygous variants in VCF, provide unfiltered VCF. INFO [2021-10-15 04:23:00] Removing 1 non heterozygous (in matched normal) germline SNPs. INFO [2021-10-15 04:23:01] Removing 1 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15. Error in h(simpleError(msg, call)) : error in evaluating the argument 'con' in selecting a method for function 'import': Format 'txt' unsupported FATAL [2021-10-15 04:23:01] Could not import snp.blacklist FATAL [2021-10-15 04:23:01] C:/Users/biocbuild/bbs-3.13-bioc/R/library/PureCN/extdata/example_normal.txt:Error FATAL [2021-10-15 04:23:01] in h(simpleError(msg, call)) : error in evaluating the argument 'con' FATAL [2021-10-15 04:23:01] in selecting a method for function 'import': Format 'txt' unsupported FATAL [2021-10-15 04:23:01] FATAL [2021-10-15 04:23:01] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:23:01] parameters (PureCN 1.22.2). INFO [2021-10-15 04:23:01] ------------------------------------------------------------ INFO [2021-10-15 04:23:01] PureCN 1.22.2 INFO [2021-10-15 04:23:01] ------------------------------------------------------------ INFO [2021-10-15 04:23:01] Loading coverage files... INFO [2021-10-15 04:23:01] Mean target coverages: 112X (tumor) 99X (normal). WARN [2021-10-15 04:23:01] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:23:01] Allosome coverage missing, cannot determine sex. INFO [2021-10-15 04:23:01] Removing 228 intervals with missing log.ratio. INFO [2021-10-15 04:23:01] Removing 22 small (< 5bp) intervals. INFO [2021-10-15 04:23:01] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2021-10-15 04:23:01] No normalDB provided. Provide one for better results. INFO [2021-10-15 04:23:01] Removing 233 low coverage (< 15.0000X) intervals. INFO [2021-10-15 04:23:01] Using 9547 intervals (9547 on-target, 0 off-target). INFO [2021-10-15 04:23:01] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2021-10-15 04:23:01] No interval.file provided. Cannot check for any GC-biases. INFO [2021-10-15 04:23:01] Loading VCF... INFO [2021-10-15 04:23:02] Found 127 variants in VCF file. INFO [2021-10-15 04:23:02] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2021-10-15 04:23:02] LIB-02240e4 is tumor in VCF file. INFO [2021-10-15 04:23:02] No homozygous variants in VCF, provide unfiltered VCF. INFO [2021-10-15 04:23:02] Removing 1 non heterozygous (in matched normal) germline SNPs. INFO [2021-10-15 04:23:03] Removing 1 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15. INFO [2021-10-15 04:23:03] Removing 0 low quality variants with BQ < 25. INFO [2021-10-15 04:23:03] Total size of targeted genomic region: 1.63Mb (2.58Mb with 50bp padding). INFO [2021-10-15 04:23:03] 1.0% of targets contain variants. INFO [2021-10-15 04:23:03] Removing 2 variants outside intervals. INFO [2021-10-15 04:23:04] Found SOMATIC annotation in VCF. INFO [2021-10-15 04:23:04] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. INFO [2021-10-15 04:23:04] Found SOMATIC annotation in VCF. Setting mapping bias to 0.973. INFO [2021-10-15 04:23:04] Excluding 0 novel or poor quality variants from segmentation. INFO [2021-10-15 04:23:04] Sample sex: ? INFO [2021-10-15 04:23:04] Segmenting data... INFO [2021-10-15 04:23:04] Loading pre-computed boundaries for DNAcopy... INFO [2021-10-15 04:23:04] Setting undo.SD parameter to 1.000000. INFO [2021-10-15 04:23:05] Setting prune.hclust.h parameter to 0.200000. INFO [2021-10-15 04:23:06] Found 54 segments with median size of 24.88Mb. INFO [2021-10-15 04:23:06] Using 123 variants. INFO [2021-10-15 04:23:06] Mean standard deviation of log-ratios: 0.37 INFO [2021-10-15 04:23:06] 2D-grid search of purity and ploidy... INFO [2021-10-15 04:23:07] Local optima: 0.62/1.9, 0.3/1.9, 0.32/2 INFO [2021-10-15 04:23:07] Testing local optimum 1/3 at purity 0.62 and total ploidy 1.90... INFO [2021-10-15 04:23:08] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90... INFO [2021-10-15 04:23:09] Recalibrating log-ratios... INFO [2021-10-15 04:23:09] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90... INFO [2021-10-15 04:23:09] Recalibrating log-ratios... INFO [2021-10-15 04:23:09] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90... INFO [2021-10-15 04:23:09] Recalibrating log-ratios... INFO [2021-10-15 04:23:09] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90... INFO [2021-10-15 04:23:10] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00... INFO [2021-10-15 04:23:10] Recalibrating log-ratios... INFO [2021-10-15 04:23:10] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00... INFO [2021-10-15 04:23:10] Recalibrating log-ratios... INFO [2021-10-15 04:23:10] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00... INFO [2021-10-15 04:23:11] Recalibrating log-ratios... INFO [2021-10-15 04:23:11] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00... INFO [2021-10-15 04:23:11] Skipping 1 solutions that converged to the same optima. INFO [2021-10-15 04:23:11] Skipping 1 solutions exceeding max.non.clonal (0.20): 0.3/1.9 (purity/tumor ploidy) INFO [2021-10-15 04:23:11] Fitting variants with beta model for local optimum 1/3... INFO [2021-10-15 04:23:11] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01. INFO [2021-10-15 04:23:14] Optimized purity: 0.65 INFO [2021-10-15 04:23:14] Done. INFO [2021-10-15 04:23:14] ------------------------------------------------------------ INFO [2021-10-15 04:23:14] ------------------------------------------------------------ INFO [2021-10-15 04:23:14] PureCN 1.22.2 INFO [2021-10-15 04:23:14] ------------------------------------------------------------ INFO [2021-10-15 04:23:14] Loading coverage files... INFO [2021-10-15 04:23:15] Mean target coverages: 112X (tumor) 99X (normal). WARN [2021-10-15 04:23:15] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:23:15] Allosome coverage missing, cannot determine sex. INFO [2021-10-15 04:23:15] Removing 228 intervals with missing log.ratio. INFO [2021-10-15 04:23:15] Removing 22 small (< 5bp) intervals. INFO [2021-10-15 04:23:15] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2021-10-15 04:23:15] No normalDB provided. Provide one for better results. INFO [2021-10-15 04:23:15] Removing 233 low coverage (< 15.0000X) intervals. INFO [2021-10-15 04:23:15] Removing 1497 low count (< 100 total reads) intervals. INFO [2021-10-15 04:23:15] Using 8050 intervals (8050 on-target, 0 off-target). INFO [2021-10-15 04:23:15] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2021-10-15 04:23:15] No interval.file provided. Cannot check for any GC-biases. INFO [2021-10-15 04:23:15] Loading VCF... INFO [2021-10-15 04:23:15] Found 127 variants in VCF file. WARN [2021-10-15 04:23:15] DP FORMAT field contains NAs. Removing 3 variants. WARN [2021-10-15 04:23:15] DB INFO flag contains NAs INFO [2021-10-15 04:23:15] 119 (96.0%) variants annotated as likely germline (DB INFO flag). INFO [2021-10-15 04:23:16] LIB-02240e4 is tumor in VCF file. INFO [2021-10-15 04:23:16] No homozygous variants in VCF, provide unfiltered VCF. INFO [2021-10-15 04:23:16] Removing 1 variants with AF < 0.030 or AF >= 0.970 or less than 4 supporting reads or depth < 15. INFO [2021-10-15 04:23:16] Removing 0 low quality variants with BQ < 25. INFO [2021-10-15 04:23:16] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding). INFO [2021-10-15 04:23:17] 1.2% of targets contain variants. INFO [2021-10-15 04:23:17] Setting somatic prior probabilities for dbSNP hits to 0.000500 or to 0.500000 otherwise. INFO [2021-10-15 04:23:17] Excluding 5 novel or poor quality variants from segmentation. INFO [2021-10-15 04:23:17] Sample sex: ? INFO [2021-10-15 04:23:17] Segmenting data... INFO [2021-10-15 04:23:17] Loading pre-computed boundaries for DNAcopy... INFO [2021-10-15 04:23:17] Setting undo.SD parameter to 1.000000. Setting multi-figure configuration INFO [2021-10-15 04:23:19] Setting prune.hclust.h parameter to 0.200000. INFO [2021-10-15 04:23:19] Found 59 segments with median size of 17.67Mb. INFO [2021-10-15 04:23:19] Using 123 variants. INFO [2021-10-15 04:23:19] Mean standard deviation of log-ratios: 0.34 INFO [2021-10-15 04:23:19] 2D-grid search of purity and ploidy... INFO [2021-10-15 04:23:20] Local optima: 0.62/1.9, 0.3/1.9, 0.32/2 INFO [2021-10-15 04:23:20] Testing local optimum 1/3 at purity 0.62 and total ploidy 1.90... INFO [2021-10-15 04:23:21] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90... INFO [2021-10-15 04:23:21] Recalibrating log-ratios... INFO [2021-10-15 04:23:21] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90... INFO [2021-10-15 04:23:22] Recalibrating log-ratios... INFO [2021-10-15 04:23:22] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90... INFO [2021-10-15 04:23:22] Recalibrating log-ratios... INFO [2021-10-15 04:23:22] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90... INFO [2021-10-15 04:23:22] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00... INFO [2021-10-15 04:23:23] Recalibrating log-ratios... INFO [2021-10-15 04:23:23] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00... INFO [2021-10-15 04:23:23] Recalibrating log-ratios... INFO [2021-10-15 04:23:23] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00... INFO [2021-10-15 04:23:23] Recalibrating log-ratios... INFO [2021-10-15 04:23:23] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00... INFO [2021-10-15 04:23:24] Skipping 2 solutions exceeding max.non.clonal (0.20): 0.3/1.9, 0.35/1.67 (purity/tumor ploidy) INFO [2021-10-15 04:23:24] Fitting variants with beta model for local optimum 1/3... INFO [2021-10-15 04:23:24] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01. INFO [2021-10-15 04:23:27] Optimized purity: 0.65 INFO [2021-10-15 04:23:27] Done. INFO [2021-10-15 04:23:27] ------------------------------------------------------------ INFO [2021-10-15 04:23:27] ------------------------------------------------------------ INFO [2021-10-15 04:23:27] PureCN 1.22.2 INFO [2021-10-15 04:23:27] ------------------------------------------------------------ INFO [2021-10-15 04:23:27] Loading coverage files... INFO [2021-10-15 04:23:27] Mean target coverages: 112X (tumor) 99X (normal). WARN [2021-10-15 04:23:28] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:23:28] Allosome coverage missing, cannot determine sex. INFO [2021-10-15 04:23:28] No Gene column in interval.file. You won't get gene-level calls. INFO [2021-10-15 04:23:28] Removing 228 intervals with missing log.ratio. INFO [2021-10-15 04:23:28] Removing 15 low/high GC targets. INFO [2021-10-15 04:23:28] Removing 21 small (< 5bp) intervals. INFO [2021-10-15 04:23:28] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2021-10-15 04:23:28] No normalDB provided. Provide one for better results. INFO [2021-10-15 04:23:28] Removing 232 low coverage (< 15.0000X) intervals. INFO [2021-10-15 04:23:28] Removing 1492 low count (< 100 total reads) intervals. INFO [2021-10-15 04:23:28] Removing 36 low mappability intervals. INFO [2021-10-15 04:23:28] Using 8006 intervals (8006 on-target, 0 off-target). INFO [2021-10-15 04:23:29] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2021-10-15 04:23:29] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio). INFO [2021-10-15 04:23:29] Loading VCF... INFO [2021-10-15 04:23:29] Found 127 variants in VCF file. INFO [2021-10-15 04:23:29] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2021-10-15 04:23:29] LIB-02240e4 is tumor in VCF file. INFO [2021-10-15 04:23:29] No homozygous variants in VCF, provide unfiltered VCF. INFO [2021-10-15 04:23:30] Removing 1 non heterozygous (in matched normal) germline SNPs. INFO [2021-10-15 04:23:30] Removing 1 variants with AF < 0.030 or AF >= Inf or less than 4 supporting reads or depth < 15. INFO [2021-10-15 04:23:30] Removing 0 low quality variants with BQ < 25. INFO [2021-10-15 04:23:30] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding). INFO [2021-10-15 04:23:30] 1.2% of targets contain variants. INFO [2021-10-15 04:23:31] Removing 11 variants outside intervals. INFO [2021-10-15 04:23:31] Found SOMATIC annotation in VCF. INFO [2021-10-15 04:23:31] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. INFO [2021-10-15 04:23:31] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970. INFO [2021-10-15 04:23:31] Excluding 0 novel or poor quality variants from segmentation. INFO [2021-10-15 04:23:31] Sample sex: ? INFO [2021-10-15 04:23:31] Segmenting data... INFO [2021-10-15 04:23:32] Using unweighted PSCBS. INFO [2021-10-15 04:23:32] Setting undo.SD parameter to 1.000000. INFO [2021-10-15 04:23:47] Setting prune.hclust.h parameter to 0.200000. INFO [2021-10-15 04:23:47] Found 72 segments with median size of 27.25Mb. INFO [2021-10-15 04:23:47] Using 114 variants. INFO [2021-10-15 04:23:47] Mean standard deviation of log-ratios: 0.34 INFO [2021-10-15 04:23:47] 2D-grid search of purity and ploidy... INFO [2021-10-15 04:23:47] Local optima: 0.65/1.8, 0.38/2.2 INFO [2021-10-15 04:23:47] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80... INFO [2021-10-15 04:23:47] Recalibrating log-ratios... INFO [2021-10-15 04:23:47] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80... INFO [2021-10-15 04:23:48] Recalibrating log-ratios... INFO [2021-10-15 04:23:48] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80... INFO [2021-10-15 04:23:48] Recalibrating log-ratios... INFO [2021-10-15 04:23:48] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80... INFO [2021-10-15 04:23:49] Testing local optimum 2/2 at purity 0.38 and total ploidy 2.20... INFO [2021-10-15 04:23:50] Skipping 1 solutions exceeding max.non.clonal (0.20): 0.65/2.06 (purity/tumor ploidy) INFO [2021-10-15 04:23:50] Fitting variants with beta model for local optimum 2/2... INFO [2021-10-15 04:23:50] Fitting variants for purity 0.40, tumor ploidy 2.55 and contamination 0.01. INFO [2021-10-15 04:23:53] Optimized purity: 0.40 INFO [2021-10-15 04:23:53] Done. INFO [2021-10-15 04:23:53] ------------------------------------------------------------ FATAL [2021-10-15 04:23:53] This function requires gene-level calls. Please add a column 'Gene' FATAL [2021-10-15 04:23:53] containing gene symbols to the interval.file. FATAL [2021-10-15 04:23:53] FATAL [2021-10-15 04:23:53] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:23:53] parameters (PureCN 1.22.2). INFO [2021-10-15 04:23:55] ------------------------------------------------------------ INFO [2021-10-15 04:23:55] PureCN 1.22.2 INFO [2021-10-15 04:23:55] ------------------------------------------------------------ INFO [2021-10-15 04:23:55] Loading coverage files... INFO [2021-10-15 04:23:55] Mean target coverages: 112X (tumor) 99X (normal). WARN [2021-10-15 04:23:55] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:23:55] Allosome coverage missing, cannot determine sex. INFO [2021-10-15 04:23:55] Removing 228 intervals with missing log.ratio. INFO [2021-10-15 04:23:55] Removing 22 small (< 5bp) intervals. INFO [2021-10-15 04:23:55] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2021-10-15 04:23:55] No normalDB provided. Provide one for better results. INFO [2021-10-15 04:23:55] Removing 233 low coverage (< 15.0000X) intervals. INFO [2021-10-15 04:23:55] Removing 1497 low count (< 100 total reads) intervals. INFO [2021-10-15 04:23:55] Using 8050 intervals (8050 on-target, 0 off-target). INFO [2021-10-15 04:23:55] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2021-10-15 04:23:55] No interval.file provided. Cannot check for any GC-biases. INFO [2021-10-15 04:23:55] Loading VCF... INFO [2021-10-15 04:23:55] Found 127 variants in VCF file. INFO [2021-10-15 04:23:56] 127 (100.0%) variants annotated as likely germline (DB INFO flag). FATAL [2021-10-15 04:23:56] Different chromosome names in coverage and VCF. FATAL [2021-10-15 04:23:56] FATAL [2021-10-15 04:23:56] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:23:56] parameters (PureCN 1.22.2). INFO [2021-10-15 04:23:56] ------------------------------------------------------------ INFO [2021-10-15 04:23:56] PureCN 1.22.2 INFO [2021-10-15 04:23:56] ------------------------------------------------------------ INFO [2021-10-15 04:23:56] Loading coverage files... INFO [2021-10-15 04:23:56] Mean target coverages: 112X (tumor) 99X (normal). WARN [2021-10-15 04:23:56] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:23:56] Allosome coverage missing, cannot determine sex. FATAL [2021-10-15 04:23:56] tumor.coverage.file and interval.file do not align. FATAL [2021-10-15 04:23:56] FATAL [2021-10-15 04:23:56] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:23:56] parameters (PureCN 1.22.2). INFO [2021-10-15 04:23:57] ------------------------------------------------------------ INFO [2021-10-15 04:23:57] PureCN 1.22.2 INFO [2021-10-15 04:23:57] ------------------------------------------------------------ INFO [2021-10-15 04:23:57] Loading coverage files... INFO [2021-10-15 04:23:57] Mean target coverages: 112X (tumor) 99X (normal). WARN [2021-10-15 04:23:57] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:23:57] Allosome coverage missing, cannot determine sex. INFO [2021-10-15 04:23:58] Removing 228 intervals with missing log.ratio. INFO [2021-10-15 04:23:58] Removing 15 low/high GC targets. INFO [2021-10-15 04:23:58] Removing 21 small (< 5bp) intervals. INFO [2021-10-15 04:23:58] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2021-10-15 04:23:58] No normalDB provided. Provide one for better results. INFO [2021-10-15 04:23:58] Removing 232 low coverage (< 15.0000X) intervals. INFO [2021-10-15 04:23:58] Removing 1492 low count (< 100 total reads) intervals. INFO [2021-10-15 04:23:58] Removing 36 low mappability intervals. INFO [2021-10-15 04:23:58] Using 8006 intervals (8006 on-target, 0 off-target). INFO [2021-10-15 04:23:58] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2021-10-15 04:23:58] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio). INFO [2021-10-15 04:23:58] Loading VCF... INFO [2021-10-15 04:23:59] Found 127 variants in VCF file. INFO [2021-10-15 04:23:59] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2021-10-15 04:23:59] LIB-02240e4 is tumor in VCF file. INFO [2021-10-15 04:23:59] No homozygous variants in VCF, provide unfiltered VCF. INFO [2021-10-15 04:23:59] Removing 1 non heterozygous (in matched normal) germline SNPs. INFO [2021-10-15 04:23:59] Removing 1 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15. INFO [2021-10-15 04:24:00] Removing 0 low quality variants with BQ < 25. INFO [2021-10-15 04:24:00] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding). INFO [2021-10-15 04:24:00] 1.2% of targets contain variants. INFO [2021-10-15 04:24:00] Removing 11 variants outside intervals. INFO [2021-10-15 04:24:00] Found SOMATIC annotation in VCF. INFO [2021-10-15 04:24:00] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. INFO [2021-10-15 04:24:00] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970. INFO [2021-10-15 04:24:00] Excluding 0 novel or poor quality variants from segmentation. INFO [2021-10-15 04:24:01] Sample sex: ? INFO [2021-10-15 04:24:01] Segmenting data... INFO [2021-10-15 04:24:01] Loading pre-computed boundaries for DNAcopy... INFO [2021-10-15 04:24:01] Setting undo.SD parameter to 1.000000. INFO [2021-10-15 04:24:02] Setting prune.hclust.h parameter to 0.200000. INFO [2021-10-15 04:24:02] Found 59 segments with median size of 17.67Mb. INFO [2021-10-15 04:24:02] Using 114 variants. INFO [2021-10-15 04:24:02] Mean standard deviation of log-ratios: 0.34 INFO [2021-10-15 04:24:02] 2D-grid search of purity and ploidy... INFO [2021-10-15 04:24:03] Local optima: 0.63/1.9 INFO [2021-10-15 04:24:03] Testing local optimum 1/1 at purity 0.63 and total ploidy 1.90... INFO [2021-10-15 04:24:04] Fitting variants with beta model for local optimum 1/1... INFO [2021-10-15 04:24:04] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01. INFO [2021-10-15 04:24:06] Optimized purity: 0.65 INFO [2021-10-15 04:24:06] Done. INFO [2021-10-15 04:24:06] ------------------------------------------------------------ INFO [2021-10-15 04:24:06] ------------------------------------------------------------ INFO [2021-10-15 04:24:06] PureCN 1.22.2 INFO [2021-10-15 04:24:06] ------------------------------------------------------------ INFO [2021-10-15 04:24:06] Loading coverage files... INFO [2021-10-15 04:24:06] Mean target coverages: 112X (tumor) 99X (normal). WARN [2021-10-15 04:24:07] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:24:07] Allosome coverage missing, cannot determine sex. INFO [2021-10-15 04:24:08] Removing 228 intervals with missing log.ratio. INFO [2021-10-15 04:24:08] Removing 15 low/high GC targets. INFO [2021-10-15 04:24:08] Removing 21 small (< 5bp) intervals. INFO [2021-10-15 04:24:08] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2021-10-15 04:24:08] No normalDB provided. Provide one for better results. INFO [2021-10-15 04:24:08] Removing 232 low coverage (< 15.0000X) intervals. INFO [2021-10-15 04:24:08] Removing 1492 low count (< 100 total reads) intervals. INFO [2021-10-15 04:24:08] Removing 36 low mappability intervals. INFO [2021-10-15 04:24:08] Using 8006 intervals (8006 on-target, 0 off-target). INFO [2021-10-15 04:24:08] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2021-10-15 04:24:08] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio). INFO [2021-10-15 04:24:08] Loading VCF... INFO [2021-10-15 04:24:08] Found 127 variants in VCF file. INFO [2021-10-15 04:24:08] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2021-10-15 04:24:09] LIB-02240e4 is tumor in VCF file. INFO [2021-10-15 04:24:09] No homozygous variants in VCF, provide unfiltered VCF. INFO [2021-10-15 04:24:09] Removing 1 non heterozygous (in matched normal) germline SNPs. INFO [2021-10-15 04:24:09] Removing 1 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15. INFO [2021-10-15 04:24:09] Removing 0 low quality variants with BQ < 25. INFO [2021-10-15 04:24:09] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding). INFO [2021-10-15 04:24:10] 1.2% of targets contain variants. INFO [2021-10-15 04:24:10] Removing 11 variants outside intervals. INFO [2021-10-15 04:24:10] Found SOMATIC annotation in VCF. INFO [2021-10-15 04:24:10] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. INFO [2021-10-15 04:24:10] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970. INFO [2021-10-15 04:24:10] Excluding 0 novel or poor quality variants from segmentation. INFO [2021-10-15 04:24:10] Sample sex: ? INFO [2021-10-15 04:24:10] Segmenting data... INFO [2021-10-15 04:24:10] Loading pre-computed boundaries for DNAcopy... INFO [2021-10-15 04:24:10] Setting undo.SD parameter to 1.000000. INFO [2021-10-15 04:24:11] Setting prune.hclust.h parameter to 0.200000. INFO [2021-10-15 04:24:12] Found 59 segments with median size of 17.67Mb. INFO [2021-10-15 04:24:12] Using 114 variants. INFO [2021-10-15 04:24:12] Mean standard deviation of log-ratios: 0.34 INFO [2021-10-15 04:24:12] 2D-grid search of purity and ploidy... INFO [2021-10-15 04:24:12] Local optima: 0.63/1.9 INFO [2021-10-15 04:24:12] Testing local optimum 1/1 at purity 0.63 and total ploidy 1.90... INFO [2021-10-15 04:24:13] Fitting variants with beta model for local optimum 1/1... INFO [2021-10-15 04:24:14] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01. INFO [2021-10-15 04:24:16] Optimized purity: 0.65 INFO [2021-10-15 04:24:16] Done. INFO [2021-10-15 04:24:16] ------------------------------------------------------------ FATAL [2021-10-15 04:24:16] chr1 not valid chromosome name(s). Valid names are: FATAL [2021-10-15 04:24:16] 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22 FATAL [2021-10-15 04:24:16] FATAL [2021-10-15 04:24:16] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:24:16] parameters (PureCN 1.22.2). INFO [2021-10-15 04:24:16] ------------------------------------------------------------ INFO [2021-10-15 04:24:16] PureCN 1.22.2 INFO [2021-10-15 04:24:16] ------------------------------------------------------------ INFO [2021-10-15 04:24:16] Loading coverage files... WARN [2021-10-15 04:24:17] Provided sampleid (Sample2) does not match Sample1 found in segmentation. WARN [2021-10-15 04:24:17] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:24:17] Allosome coverage missing, cannot determine sex. INFO [2021-10-15 04:24:17] Removing 10 intervals with missing log.ratio. INFO [2021-10-15 04:24:17] Using 10039 intervals (10039 on-target, 0 off-target). INFO [2021-10-15 04:24:17] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2021-10-15 04:24:17] Loading VCF... INFO [2021-10-15 04:24:17] Found 127 variants in VCF file. INFO [2021-10-15 04:24:17] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2021-10-15 04:24:18] LIB-02240e4 is tumor in VCF file. INFO [2021-10-15 04:24:18] No homozygous variants in VCF, provide unfiltered VCF. INFO [2021-10-15 04:24:18] Removing 1 non heterozygous (in matched normal) germline SNPs. INFO [2021-10-15 04:24:18] Removing 1 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15. INFO [2021-10-15 04:24:18] Removing 0 low quality variants with BQ < 25. INFO [2021-10-15 04:24:18] Total size of targeted genomic region: 1.71Mb (2.70Mb with 50bp padding). INFO [2021-10-15 04:24:19] 1.0% of targets contain variants. INFO [2021-10-15 04:24:19] Removing 0 variants outside intervals. INFO [2021-10-15 04:24:19] Found SOMATIC annotation in VCF. INFO [2021-10-15 04:24:19] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. INFO [2021-10-15 04:24:19] Found SOMATIC annotation in VCF. Setting mapping bias to 0.976. INFO [2021-10-15 04:24:19] Excluding 0 novel or poor quality variants from segmentation. INFO [2021-10-15 04:24:19] Sample sex: ? INFO [2021-10-15 04:24:19] Segmenting data... INFO [2021-10-15 04:24:19] Loaded provided segmentation file example_seg.txt (format DNAcopy). WARN [2021-10-15 04:24:19] Provided sampleid (Sample2) does not match Sample1 found in segmentation. INFO [2021-10-15 04:24:19] Re-centering provided segment means (offset -0.0033). INFO [2021-10-15 04:24:19] Loading pre-computed boundaries for DNAcopy... INFO [2021-10-15 04:24:19] Setting undo.SD parameter to 0.000000. Setting multi-figure configuration INFO [2021-10-15 04:24:20] Setting prune.hclust.h parameter to 0.200000. INFO [2021-10-15 04:24:20] Found 54 segments with median size of 24.88Mb. INFO [2021-10-15 04:24:20] Using 125 variants. INFO [2021-10-15 04:24:20] Mean standard deviation of log-ratios: 0.40 INFO [2021-10-15 04:24:20] 2D-grid search of purity and ploidy... INFO [2021-10-15 04:24:21] Local optima: 0.6/1.9 INFO [2021-10-15 04:24:21] Testing local optimum 1/1 at purity 0.60 and total ploidy 1.90... INFO [2021-10-15 04:24:22] Fitting variants with beta model for local optimum 1/1... INFO [2021-10-15 04:24:22] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01. INFO [2021-10-15 04:24:25] Optimized purity: 0.65 INFO [2021-10-15 04:24:25] Done. INFO [2021-10-15 04:24:25] ------------------------------------------------------------ WARN [2021-10-15 04:24:26] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:24:26] Allosome coverage missing, cannot determine sex. Setting multi-figure configuration FATAL [2021-10-15 04:24:35] Segmentation file expected with colnames ID, chrom, loc.start, loc.end, FATAL [2021-10-15 04:24:35] num.mark, seg.mean FATAL [2021-10-15 04:24:35] FATAL [2021-10-15 04:24:35] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:24:35] parameters (PureCN 1.22.2). FATAL [2021-10-15 04:24:36] seg.file contains multiple samples and sampleid missing. FATAL [2021-10-15 04:24:36] FATAL [2021-10-15 04:24:36] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:24:36] parameters (PureCN 1.22.2). FATAL [2021-10-15 04:24:36] seg.file contains multiple samples and sampleid does not match any. FATAL [2021-10-15 04:24:36] FATAL [2021-10-15 04:24:36] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:24:36] parameters (PureCN 1.22.2). WARN [2021-10-15 04:24:36] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:24:36] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:24:46] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:24:46] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:24:46] Provided sampleid (example_tumor.txt) does not match Sample1 found in segmentation. WARN [2021-10-15 04:24:50] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:24:50] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:24:51] No normalDB provided. Provide one for better results. WARN [2021-10-15 04:25:00] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:25:00] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:25:04] Provided sampleid (Sample.1) does not match Sample1 found in segmentation. Setting multi-figure configuration WARN [2021-10-15 04:25:13] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:25:13] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:25:13] No normalDB provided. Provide one for better results. WARN [2021-10-15 04:25:13] Sampleid looks like a normal in VCF, not like a tumor. WARN [2021-10-15 04:25:21] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:25:21] Allosome coverage missing, cannot determine sex. FATAL [2021-10-15 04:25:21] normalDB not a valid normalDB object. Use createNormalDatabase to FATAL [2021-10-15 04:25:21] create one. FATAL [2021-10-15 04:25:21] FATAL [2021-10-15 04:25:21] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:25:21] parameters (PureCN 1.22.2). WARN [2021-10-15 04:25:22] You are likely not using the correct baits file! WARN [2021-10-15 04:25:22] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:25:22] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:25:26] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:25:26] Allosome coverage missing, cannot determine sex. FATAL [2021-10-15 04:25:26] normalDB appears to be empty. FATAL [2021-10-15 04:25:26] FATAL [2021-10-15 04:25:26] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:25:26] parameters (PureCN 1.22.2). WARN [2021-10-15 04:25:26] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:25:26] Allosome coverage missing, cannot determine sex. WARN [2021-10-15 04:25:27] Intervals in coverage and interval.file have conflicting on/off-target annotation. WARN [2021-10-15 04:25:43] Cannot find gatk binary in path. FATAL [2021-10-15 04:26:30] The normal.panel.vcf.file contains only a single sample. FATAL [2021-10-15 04:26:30] FATAL [2021-10-15 04:26:30] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:26:30] parameters (PureCN 1.22.2). FATAL [2021-10-15 04:26:31] mapping.bias.file must be a file with *.rds suffix. FATAL [2021-10-15 04:26:31] FATAL [2021-10-15 04:26:31] This is most likely a user error due to invalid input data or FATAL [2021-10-15 04:26:31] parameters (PureCN 1.22.2). Failed with error: 'there is no package called 'genomicsdb'' == Skipped tests =============================================================== * gatk binary > 4.1.7.0 required (1) * genomicsdb required (1) [ FAIL 0 | WARN 54 | SKIP 2 | PASS 367 ] > > proc.time() user system elapsed 464.34 2.84 569.15 |
PureCN.Rcheck/examples_i386/PureCN-Ex.timings
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PureCN.Rcheck/examples_x64/PureCN-Ex.timings
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