Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-08 12:53 -0400 (Wed, 08 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4854 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4641 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4586 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4584 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 1650/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
PureCN 2.15.4 (landing page) Markus Riester
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the PureCN package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: PureCN |
Version: 2.15.4 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PureCN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PureCN_2.15.4.tar.gz |
StartedAt: 2025-10-07 21:12:54 -0400 (Tue, 07 Oct 2025) |
EndedAt: 2025-10-07 21:18:29 -0400 (Tue, 07 Oct 2025) |
EllapsedTime: 334.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: PureCN.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PureCN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PureCN_2.15.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/PureCN.Rcheck’ * using R version 4.5.1 Patched (2025-09-10 r88807) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘PureCN/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘PureCN’ version ‘2.15.4’ * checking package namespace information ... OK * checking package dependencies ... INFO Package which this enhances but not available for checking: ‘genomicsdb’ Imports includes 21 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘PureCN’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed callAmplificationsInLowPurity 13.863 0.171 14.049 segmentationPSCBS 12.960 0.166 13.143 filterIntervals 7.235 0.184 7.430 runAbsoluteCN 6.056 0.122 6.233 segmentationHclust 5.873 0.110 5.989 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK
PureCN.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PureCN ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘PureCN’ ... ** this is package ‘PureCN’ version ‘2.15.4’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (PureCN)
PureCN.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union Attaching package: 'BiocGenerics' 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, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, 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: Seqinfo Loading required package: GenomicRanges Loading required package: stats4 Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges 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 [2025-10-07 21:16:13] Attempted adding gene symbols to intervals. Heuristics have been used to pick symbols for overlapping genes. WARN [2025-10-07 21:16:14] Chromosome naming style of txdb file (UCSC) was different from interval file (Ensembl). WARN [2025-10-07 21:16:15] Attempted adding gene symbols to intervals. Heuristics have been used to pick symbols for overlapping genes. FATAL [2025-10-07 21:16:16] tumor.coverage.file and interval.file do not align. FATAL [2025-10-07 21:16:16] FATAL [2025-10-07 21:16:16] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:16:16] parameters (PureCN 2.15.4). WARN [2025-10-07 21:16:16] Cannot find all contig lengths while exporting interval file. INFO [2025-10-07 21:16:16] Processing seq1:1-21 (1/3)... INFO [2025-10-07 21:16:17] Processing seq1:1227-1247 (2/3)... INFO [2025-10-07 21:16:17] Processing seq2:594-614 (3/3)... WARN [2025-10-07 21:16:17] Large potential mis-calibration of on- and off-target log2 ratios: 0.26 FATAL [2025-10-07 21:16:17] Need either f or purity and ploidy. FATAL [2025-10-07 21:16:17] FATAL [2025-10-07 21:16:17] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:16:17] parameters (PureCN 2.15.4). FATAL [2025-10-07 21:16:17] f not in expected range. FATAL [2025-10-07 21:16:17] FATAL [2025-10-07 21:16:17] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:16:17] parameters (PureCN 2.15.4). FATAL [2025-10-07 21:16:17] coverage not in expected range (>=2) FATAL [2025-10-07 21:16:17] FATAL [2025-10-07 21:16:17] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:16:17] parameters (PureCN 2.15.4). FATAL [2025-10-07 21:16:17] purity not in expected range. FATAL [2025-10-07 21:16:17] FATAL [2025-10-07 21:16:17] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:16:17] parameters (PureCN 2.15.4). FATAL [2025-10-07 21:16:17] ploidy not in expected range. FATAL [2025-10-07 21:16:17] FATAL [2025-10-07 21:16:17] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:16:17] parameters (PureCN 2.15.4). FATAL [2025-10-07 21:16:17] cell.fraction not in expected range. FATAL [2025-10-07 21:16:17] FATAL [2025-10-07 21:16:17] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:16:17] parameters (PureCN 2.15.4). INFO [2025-10-07 21:16:18] 576 on-target bins with low coverage in all samples. WARN [2025-10-07 21:16:18] You are likely not using the correct baits file! WARN [2025-10-07 21:16:18] Allosome coverage missing, cannot determine sex. WARN [2025-10-07 21:16:18] Allosome coverage missing, cannot determine sex. INFO [2025-10-07 21:16:18] Processing on-target regions... INFO [2025-10-07 21:16:18] Removing 930 intervals with low coverage in normalDB. INFO [2025-10-07 21:16:18] Removing 1 intervals with zero coverage in more than 3% of normalDB. INFO [2025-10-07 21:16:19] Tumor/normal noise ratio: 19.041 WARN [2025-10-07 21:16:19] Extensive noise in tumor compared to normals. INFO [2025-10-07 21:16:34] Tumor/normal noise ratio: 19.041 WARN [2025-10-07 21:16:34] Extensive noise in tumor compared to normals. INFO [2025-10-07 21:16:36] Using BiocParallel for parallel optimization. FATAL [2025-10-07 21:16:40] pvalue.cutoff not within expected range or format. FATAL [2025-10-07 21:16:40] FATAL [2025-10-07 21:16:40] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:16:40] parameters (PureCN 2.15.4). FATAL [2025-10-07 21:16:40] pvalue.cutoff not within expected range or format. FATAL [2025-10-07 21:16:40] FATAL [2025-10-07 21:16:40] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:16:40] parameters (PureCN 2.15.4). FATAL [2025-10-07 21:16:40] percentile.cutoff not in expected range (0 to 100). FATAL [2025-10-07 21:16:40] FATAL [2025-10-07 21:16:40] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:16:40] parameters (PureCN 2.15.4). FATAL [2025-10-07 21:16:40] percentile.cutoff not in expected range (0 to 100). FATAL [2025-10-07 21:16:40] FATAL [2025-10-07 21:16:40] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:16:40] parameters (PureCN 2.15.4). FATAL [2025-10-07 21:16:40] purity not within expected range or format. FATAL [2025-10-07 21:16:40] FATAL [2025-10-07 21:16:40] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:16:40] parameters (PureCN 2.15.4). FATAL [2025-10-07 21:16:40] purity not within expected range or format. FATAL [2025-10-07 21:16:40] FATAL [2025-10-07 21:16:40] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:16:40] parameters (PureCN 2.15.4). INFO [2025-10-07 21:16:41] ------------------------------------------------------------ INFO [2025-10-07 21:16:41] PureCN 2.15.4 INFO [2025-10-07 21:16:41] ------------------------------------------------------------ INFO [2025-10-07 21:16:41] Loading coverage files... INFO [2025-10-07 21:16:41] Mean target coverages: 112X (tumor) 99X (normal). WARN [2025-10-07 21:16:41] Allosome coverage missing, cannot determine sex. WARN [2025-10-07 21:16:41] Allosome coverage missing, cannot determine sex. INFO [2025-10-07 21:16:41] Removing 228 intervals with missing log.ratio. INFO [2025-10-07 21:16:41] Removing 22 small (< 5bp) intervals. INFO [2025-10-07 21:16:41] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2025-10-07 21:16:41] No normalDB provided. Provide one for better results. INFO [2025-10-07 21:16:41] Removing 1724 low count (< 100 total reads) intervals. INFO [2025-10-07 21:16:41] Removing 6 low coverage (< 15.0000X) intervals. INFO [2025-10-07 21:16:41] Using 8050 intervals (8050 on-target, 0 off-target). INFO [2025-10-07 21:16:41] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2025-10-07 21:16:41] No interval.file provided. Cannot check for any GC-biases. INFO [2025-10-07 21:16:41] Loading VCF... INFO [2025-10-07 21:16:41] Found 127 variants in VCF file. INFO [2025-10-07 21:16:41] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2025-10-07 21:16:41] LIB-02240e4 is tumor in VCF file. INFO [2025-10-07 21:16:41] No homozygous variants in VCF, provide unfiltered VCF. INFO [2025-10-07 21:16:41] Removing 1 non heterozygous (in matched normal) germline SNPs. INFO [2025-10-07 21:16:41] Removing 0 low quality variants with non-offset BQ < 25. INFO [2025-10-07 21:16:41] Base quality scores range from 29 to 35 (offset by 1) INFO [2025-10-07 21:16:41] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS. INFO [2025-10-07 21:16:41] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. INFO [2025-10-07 21:16:41] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding). INFO [2025-10-07 21:16:41] 1.2% of targets contain variants. INFO [2025-10-07 21:16:41] Removing 4 variants outside intervals. INFO [2025-10-07 21:16:41] Found SOMATIC annotation in VCF. INFO [2025-10-07 21:16:41] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. INFO [2025-10-07 21:16:41] Found SOMATIC annotation in VCF. Setting mapping bias to 0.972. INFO [2025-10-07 21:16:41] Excluding 0 novel or poor quality variants from segmentation. INFO [2025-10-07 21:16:41] Sample sex: ? INFO [2025-10-07 21:16:41] Segmenting data... INFO [2025-10-07 21:16:41] Loading pre-computed boundaries for DNAcopy... INFO [2025-10-07 21:16:41] Setting undo.SD parameter to 1.000000. INFO [2025-10-07 21:16:42] Setting prune.hclust.h parameter to 0.200000. INFO [2025-10-07 21:16:42] Found 59 segments with median size of 17.67Mb. INFO [2025-10-07 21:16:42] Using 121 variants. INFO [2025-10-07 21:16:42] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30) INFO [2025-10-07 21:16:42] 2D-grid search of purity and ploidy... INFO [2025-10-07 21:16:42] Local optima: 0.63/1.9, 0.5/2 INFO [2025-10-07 21:16:42] Testing local optimum 1/2 at purity 0.63 and total ploidy 1.90... INFO [2025-10-07 21:16:43] Testing local optimum 2/2 at purity 0.50 and total ploidy 2.00... INFO [2025-10-07 21:16:43] Skipping 1 solutions that converged to the same optima. INFO [2025-10-07 21:16:43] Fitting variants with beta model for local optimum 1/2... INFO [2025-10-07 21:16:43] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01. INFO [2025-10-07 21:16:44] Optimized purity: 0.65 INFO [2025-10-07 21:16:44] Done. INFO [2025-10-07 21:16:44] ------------------------------------------------------------ INFO [2025-10-07 21:16:44] Estimating callable regions. FATAL [2025-10-07 21:16:45] exclude not a GRanges object. FATAL [2025-10-07 21:16:45] FATAL [2025-10-07 21:16:45] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:16:45] parameters (PureCN 2.15.4). FATAL [2025-10-07 21:16:45] callable not a GRanges object. FATAL [2025-10-07 21:16:45] FATAL [2025-10-07 21:16:45] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:16:45] parameters (PureCN 2.15.4). WARN [2025-10-07 21:16:48] tumor.coverage.file and interval.file do not align. INFO [2025-10-07 21:16:48] No Gene column in interval.file. You won't get gene-level calls. FATAL [2025-10-07 21:16:49] No gc_bias column in interval.file. FATAL [2025-10-07 21:16:49] FATAL [2025-10-07 21:16:49] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:16:49] parameters (PureCN 2.15.4). FATAL [2025-10-07 21:16:49] Provided coverage is zero, most likely due to a corrupt BAM file. FATAL [2025-10-07 21:16:49] FATAL [2025-10-07 21:16:49] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:16:49] parameters (PureCN 2.15.4). INFO [2025-10-07 21:16:50] No reptiming column in interval.file. INFO [2025-10-07 21:16:51] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp0PSuPi/file1819f5aeb99e.rds... INFO [2025-10-07 21:16:51] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp0PSuPi/file1819f5aeb99e.rds... INFO [2025-10-07 21:16:51] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp0PSuPi/file1819f5aeb99e.rds... INFO [2025-10-07 21:16:51] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp0PSuPi/file1819f5aeb99e.rds... INFO [2025-10-07 21:16:51] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp0PSuPi/file1819f5aeb99e.rds... INFO [2025-10-07 21:16:51] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp0PSuPi/file1819f5aeb99e.rds... FATAL [2025-10-07 21:16:51] Purity or Ploidy not numeric or in expected range. FATAL [2025-10-07 21:16:51] FATAL [2025-10-07 21:16:51] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:16:51] parameters (PureCN 2.15.4). INFO [2025-10-07 21:16:51] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp0PSuPi/file1819f5aeb99e.rds... INFO [2025-10-07 21:16:51] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp0PSuPi/file1819f5aeb99e.rds... FATAL [2025-10-07 21:16:51] 'Failed' column in FATAL [2025-10-07 21:16:51] /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp0PSuPi/file1819f5aeb99e.csv FATAL [2025-10-07 21:16:51] not logical(1). FATAL [2025-10-07 21:16:51] FATAL [2025-10-07 21:16:51] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:16:51] parameters (PureCN 2.15.4). INFO [2025-10-07 21:16:52] 576 on-target bins with low coverage in all samples. WARN [2025-10-07 21:16:52] You are likely not using the correct baits file! WARN [2025-10-07 21:16:52] Allosome coverage missing, cannot determine sex. WARN [2025-10-07 21:16:52] Allosome coverage missing, cannot determine sex. INFO [2025-10-07 21:16:52] Processing on-target regions... INFO [2025-10-07 21:16:52] Removing 930 intervals with low coverage in normalDB. INFO [2025-10-07 21:16:52] Removing 1 intervals with zero coverage in more than 3% of normalDB. INFO [2025-10-07 21:16:53] 576 on-target bins with low coverage in all samples. WARN [2025-10-07 21:16:53] You are likely not using the correct baits file! WARN [2025-10-07 21:16:53] Allosome coverage missing, cannot determine sex. WARN [2025-10-07 21:16:53] Allosome coverage missing, cannot determine sex. INFO [2025-10-07 21:16:53] Processing on-target regions... INFO [2025-10-07 21:16:53] Removing 930 intervals with low coverage in normalDB. INFO [2025-10-07 21:16:53] Removing 1 intervals with zero coverage in more than 3% of normalDB. INFO [2025-10-07 21:16:54] 576 on-target bins with low coverage in all samples. WARN [2025-10-07 21:16:54] You are likely not using the correct baits file! WARN [2025-10-07 21:16:54] Allosome coverage missing, cannot determine sex. WARN [2025-10-07 21:16:54] Allosome coverage missing, cannot determine sex. INFO [2025-10-07 21:16:54] Processing on-target regions... INFO [2025-10-07 21:16:54] Removing 930 intervals with low coverage in normalDB. INFO [2025-10-07 21:16:54] Removing 1 intervals with zero coverage in more than 3% of normalDB. WARN [2025-10-07 21:16:54] Allosome coverage missing, cannot determine sex. INFO [2025-10-07 21:16:54] Sample sex: NA WARN [2025-10-07 21:16:54] Allosome coverage missing, cannot determine sex. INFO [2025-10-07 21:16:54] Sample sex: NA INFO [2025-10-07 21:16:55] 576 on-target bins with low coverage in all samples. WARN [2025-10-07 21:16:55] You are likely not using the correct baits file! WARN [2025-10-07 21:16:55] Allosome coverage missing, cannot determine sex. WARN [2025-10-07 21:16:55] Allosome coverage missing, cannot determine sex. FATAL [2025-10-07 21:16:55] Length of normal.coverage.files and sex different FATAL [2025-10-07 21:16:55] FATAL [2025-10-07 21:16:55] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:16:55] parameters (PureCN 2.15.4). WARN [2025-10-07 21:16:56] Target intervals were not sorted. INFO [2025-10-07 21:16:56] 560 on-target bins with low coverage in all samples. WARN [2025-10-07 21:16:56] You are likely not using the correct baits file! WARN [2025-10-07 21:16:56] Allosome coverage missing, cannot determine sex. WARN [2025-10-07 21:16:56] Allosome coverage missing, cannot determine sex. WARN [2025-10-07 21:16:56] Allosome coverage missing, cannot determine sex. INFO [2025-10-07 21:16:56] Processing on-target regions... INFO [2025-10-07 21:16:56] Removing 978 intervals with low coverage in normalDB. INFO [2025-10-07 21:16:56] Removing 11 intervals with zero coverage in more than 3% of normalDB. FATAL [2025-10-07 21:16:57] tumor.coverage.file and normalDB do not align. FATAL [2025-10-07 21:16:57] FATAL [2025-10-07 21:16:57] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:16:57] parameters (PureCN 2.15.4). FATAL [2025-10-07 21:16:57] At least 2 normal.coverage.files required. FATAL [2025-10-07 21:16:57] FATAL [2025-10-07 21:16:57] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:16:57] parameters (PureCN 2.15.4). INFO [2025-10-07 21:16:58] ------------------------------------------------------------ INFO [2025-10-07 21:16:58] PureCN 2.15.4 INFO [2025-10-07 21:16:58] ------------------------------------------------------------ INFO [2025-10-07 21:16:58] Loading coverage files... INFO [2025-10-07 21:16:58] Mean target coverages: 112X (tumor) 99X (normal). WARN [2025-10-07 21:16:58] Allosome coverage missing, cannot determine sex. WARN [2025-10-07 21:16:58] Allosome coverage missing, cannot determine sex. INFO [2025-10-07 21:16:58] Removing 228 intervals with missing log.ratio. FATAL [2025-10-07 21:16:58] normalDB incompatible with this PureCN version. Please re-run FATAL [2025-10-07 21:16:58] NormalDB.R. FATAL [2025-10-07 21:16:58] FATAL [2025-10-07 21:16:58] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:16:58] parameters (PureCN 2.15.4). FATAL [2025-10-07 21:16:58] normalDB incompatible with this PureCN version. Please re-run FATAL [2025-10-07 21:16:58] NormalDB.R. FATAL [2025-10-07 21:16:58] FATAL [2025-10-07 21:16:58] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:16:58] parameters (PureCN 2.15.4). FATAL [2025-10-07 21:16:58] normal.coverage.files with _coverage.txt and _loess.txt suffix FATAL [2025-10-07 21:16:58] provided. Provide either only GC-normalized or raw coverage files! FATAL [2025-10-07 21:16:58] FATAL [2025-10-07 21:16:58] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:16:58] parameters (PureCN 2.15.4). INFO [2025-10-07 21:16:58] Removing 22 non heterozygous (in matched normal) germline SNPs. INFO [2025-10-07 21:16:59] Removing 19 low quality variants with non-offset BQ < 25. INFO [2025-10-07 21:16:59] Base quality scores range from 24 to 35 (offset by 1) INFO [2025-10-07 21:16:59] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS. INFO [2025-10-07 21:16:59] Initial testing for significant sample cross-contamination: unlikely INFO [2025-10-07 21:16:59] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. INFO [2025-10-07 21:16:59] Removing 22 non heterozygous (in matched normal) germline SNPs. INFO [2025-10-07 21:16:59] Removing 19 low quality variants with non-offset BQ < 25. INFO [2025-10-07 21:16:59] Base quality scores range from 24 to 35 (offset by 1) INFO [2025-10-07 21:16:59] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS. INFO [2025-10-07 21:16:59] Initial testing for significant sample cross-contamination: unlikely INFO [2025-10-07 21:16:59] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. INFO [2025-10-07 21:16:59] Removing 6 blacklisted variants. INFO [2025-10-07 21:16:59] Removing 22 non heterozygous (in matched normal) germline SNPs. INFO [2025-10-07 21:16:59] Removing 19 low quality variants with non-offset BQ < 25. INFO [2025-10-07 21:16:59] Base quality scores range from 24 to 35 (offset by 1) INFO [2025-10-07 21:16:59] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS. INFO [2025-10-07 21:16:59] Initial testing for significant sample cross-contamination: unlikely INFO [2025-10-07 21:16:59] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. WARN [2025-10-07 21:16:59] MuTect stats file lacks contig and position columns. INFO [2025-10-07 21:16:59] Removing 22 non heterozygous (in matched normal) germline SNPs. INFO [2025-10-07 21:16:59] Removing 19 low quality variants with non-offset BQ < 25. INFO [2025-10-07 21:16:59] Base quality scores range from 24 to 35 (offset by 1) INFO [2025-10-07 21:16:59] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS. INFO [2025-10-07 21:17:00] Initial testing for significant sample cross-contamination: unlikely INFO [2025-10-07 21:17:00] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. WARN [2025-10-07 21:17:00] MuTect stats file and VCF file do not align perfectly. Will remove 2325 unmatched variants. WARN [2025-10-07 21:17:00] MuTect stats file lacks failure_reasons column. Keeping all variants listed in stats file. INFO [2025-10-07 21:17:00] Removing 0 non heterozygous (in matched normal) germline SNPs. INFO [2025-10-07 21:17:00] Removing 0 low quality variants with non-offset BQ < 25. INFO [2025-10-07 21:17:00] Base quality scores range from 31 to 33 (offset by 1) INFO [2025-10-07 21:17:00] Minimum number of supporting reads ranges from 3 to 4, depending on coverage and BQS. INFO [2025-10-07 21:17:00] Removing 0 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. INFO [2025-10-07 21:17:00] Removing 22 non heterozygous (in matched normal) germline SNPs. INFO [2025-10-07 21:17:00] Base quality scores range from 7 to 35 (offset by 1) INFO [2025-10-07 21:17:00] Minimum number of supporting reads ranges from 1 to 41, depending on coverage and BQS. INFO [2025-10-07 21:17:00] Initial testing for significant sample cross-contamination: unlikely INFO [2025-10-07 21:17:00] Removing 49 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. INFO [2025-10-07 21:17:00] Removing 22 non heterozygous (in matched normal) germline SNPs. INFO [2025-10-07 21:17:00] Base quality scores range from 7 to 35 (offset by 1) INFO [2025-10-07 21:17:00] Minimum number of supporting reads ranges from 1 to 41, depending on coverage and BQS. INFO [2025-10-07 21:17:00] Initial testing for significant sample cross-contamination: unlikely INFO [2025-10-07 21:17:00] Removing 49 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. INFO [2025-10-07 21:17:00] Removing 22 non heterozygous (in matched normal) germline SNPs. WARN [2025-10-07 21:17:00] Many variants removed by min.base.quality (50) filter. You might want to lower the cutoff. FATAL [2025-10-07 21:17:00] No variants passed filter BQ. FATAL [2025-10-07 21:17:00] FATAL [2025-10-07 21:17:00] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:17:00] parameters (PureCN 2.15.4). INFO [2025-10-07 21:17:00] Found 11 variants in VCF file. WARN [2025-10-07 21:17:00] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead. INFO [2025-10-07 21:17:00] 1 (9.1%) variants annotated as likely germline (DB INFO flag). INFO [2025-10-07 21:17:01] Found 11 variants in VCF file. WARN [2025-10-07 21:17:01] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead. INFO [2025-10-07 21:17:01] 1 (9.1%) variants annotated as likely germline (DB INFO flag). INFO [2025-10-07 21:17:01] Found 11 variants in VCF file. WARN [2025-10-07 21:17:01] vcf.file has no DB or POP_AF info field for membership in germline databases. Guessing it based on available dbSNP ID. INFO [2025-10-07 21:17:01] 1 (9.1%) variants annotated as likely germline (DB INFO flag). INFO [2025-10-07 21:17:02] Found 1000 variants in VCF file. INFO [2025-10-07 21:17:02] Removing 2 triallelic sites. WARN [2025-10-07 21:17:02] Having trouble guessing SOMATIC status... WARN [2025-10-07 21:17:02] DP FORMAT field contains NAs. Removing 44 variants. INFO [2025-10-07 21:17:02] 954 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2025-10-07 21:17:02] Found 12 variants in VCF file. INFO [2025-10-07 21:17:02] Removing 1 triallelic sites. WARN [2025-10-07 21:17:02] DP FORMAT field contains NAs. Removing 1 variants. WARN [2025-10-07 21:17:02] vcf.file has no DB info field for membership in germline databases. Found and used somatic status instead. INFO [2025-10-07 21:17:02] 8 (80.0%) variants annotated as likely germline (DB INFO flag). WARN [2025-10-07 21:17:02] BQ FORMAT field contains NAs. INFO [2025-10-07 21:17:02] Found 2331 variants in VCF file. INFO [2025-10-07 21:17:03] 2282 (97.9%) variants annotated as likely germline (DB INFO flag). INFO [2025-10-07 21:17:03] Found 2331 variants in VCF file. INFO [2025-10-07 21:17:03] 2282 (97.9%) variants annotated as likely germline (DB INFO flag). WARN [2025-10-07 21:17:03] Did not find base quality scores, will use global error rate of 0.0010 instead. INFO [2025-10-07 21:17:03] Removing 21 low quality variants with non-offset BQ < 25. INFO [2025-10-07 21:17:03] Base quality scores range from 24 to 35 (offset by 1) INFO [2025-10-07 21:17:03] Initial testing for significant sample cross-contamination: unlikely INFO [2025-10-07 21:17:03] Removing 89 variants with AF < 0.030 or AF >= 0.970 or insufficient supporting reads or depth < 15. INFO [2025-10-07 21:17:03] Found 2331 variants in VCF file. INFO [2025-10-07 21:17:03] 2282 (97.9%) variants annotated as likely germline (DB INFO flag). WARN [2025-10-07 21:17:03] BQ FORMAT field contains NAs. WARN [2025-10-07 21:17:03] Allosome coverage missing, cannot determine sex. WARN [2025-10-07 21:17:04] Allosome coverage missing, cannot determine sex. INFO [2025-10-07 21:17:04] Mean coverages: chrX: 108.58, chrY: 108.58, chr1-22: 104.87. INFO [2025-10-07 21:17:04] Mean coverages: chrX: 108.58, chrY: 2.17, chr1-22: 104.87. INFO [2025-10-07 21:17:04] Mean coverages: chrX: 108.58, chrY: 5.17, chr1-22: 104.87. INFO [2025-10-07 21:17:04] No homozygous variants in VCF, provide unfiltered VCF. INFO [2025-10-07 21:17:04] No germline variants in VCF. FATAL [2025-10-07 21:17:04] No solution with id hello FATAL [2025-10-07 21:17:04] FATAL [2025-10-07 21:17:04] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:17:04] parameters (PureCN 2.15.4). FATAL [2025-10-07 21:17:04] No solution with id 100 FATAL [2025-10-07 21:17:04] FATAL [2025-10-07 21:17:04] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:17:04] parameters (PureCN 2.15.4). FATAL [2025-10-07 21:17:04] all.data and w have different lengths. FATAL [2025-10-07 21:17:04] FATAL [2025-10-07 21:17:04] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:17:04] parameters (PureCN 2.15.4). INFO [2025-10-07 21:17:05] Splitting 5 large targets to an average width of 400. WARN [2025-10-07 21:17:05] No mappability scores provided. WARN [2025-10-07 21:17:05] No reptiming scores provided. INFO [2025-10-07 21:17:05] Calculating GC-content... INFO [2025-10-07 21:17:05] Splitting 5 large targets to an average width of 400. WARN [2025-10-07 21:17:05] No mappability scores provided. WARN [2025-10-07 21:17:05] No reptiming scores provided. INFO [2025-10-07 21:17:05] Calculating GC-content... INFO [2025-10-07 21:17:05] Splitting 5 large targets to an average width of 400. INFO [2025-10-07 21:17:05] Removing 1 targets overlapping with exclude. WARN [2025-10-07 21:17:05] No mappability scores provided. WARN [2025-10-07 21:17:05] No reptiming scores provided. INFO [2025-10-07 21:17:05] Calculating GC-content... WARN [2025-10-07 21:17:05] Found small target regions (< 100bp). Will resize them. INFO [2025-10-07 21:17:05] Splitting 5 large targets to an average width of 400. FATAL [2025-10-07 21:17:05] off.target.padding must be negative. FATAL [2025-10-07 21:17:05] FATAL [2025-10-07 21:17:05] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:17:05] parameters (PureCN 2.15.4). FATAL [2025-10-07 21:17:05] Interval coordinates should start at 1, not at 0 FATAL [2025-10-07 21:17:05] FATAL [2025-10-07 21:17:05] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:17:05] parameters (PureCN 2.15.4). WARN [2025-10-07 21:17:05] Found small target regions (< 100bp). Will resize them. INFO [2025-10-07 21:17:05] Splitting 5 large targets to an average width of 400. FATAL [2025-10-07 21:17:05] No off-target regions after filtering for mappability and FATAL [2025-10-07 21:17:05] off.target.padding FATAL [2025-10-07 21:17:05] FATAL [2025-10-07 21:17:05] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:17:05] parameters (PureCN 2.15.4). WARN [2025-10-07 21:17:05] Found small target regions (< 100bp). Will resize them. INFO [2025-10-07 21:17:05] Splitting 5 large targets to an average width of 400. WARN [2025-10-07 21:17:05] No mappability scores provided. INFO [2025-10-07 21:17:05] Calculating GC-content... WARN [2025-10-07 21:17:05] Found small target regions (< 100bp). Will resize them. INFO [2025-10-07 21:17:05] Averaging reptiming into bins of size 200... INFO [2025-10-07 21:17:05] Splitting 5 large targets to an average width of 400. WARN [2025-10-07 21:17:05] No mappability scores provided. INFO [2025-10-07 21:17:05] Calculating GC-content... WARN [2025-10-07 21:17:05] Found small target regions (< 100bp). Will resize them. INFO [2025-10-07 21:17:05] Splitting 6 large targets to an average width of 200. WARN [2025-10-07 21:17:05] No mappability scores provided. WARN [2025-10-07 21:17:05] No reptiming scores provided. INFO [2025-10-07 21:17:05] Calculating GC-content... WARN [2025-10-07 21:17:06] Found small target regions (< 100bp). Will resize them. INFO [2025-10-07 21:17:06] Splitting 5 large targets to an average width of 400. WARN [2025-10-07 21:17:06] No mappability scores provided. WARN [2025-10-07 21:17:06] No reptiming scores provided. INFO [2025-10-07 21:17:06] Calculating GC-content... INFO [2025-10-07 21:17:06] Splitting 5 large targets to an average width of 400. INFO [2025-10-07 21:17:06] Tiling off-target regions to an average width of 200000. WARN [2025-10-07 21:17:06] No mappability scores provided. WARN [2025-10-07 21:17:06] No reptiming scores provided. INFO [2025-10-07 21:17:06] Calculating GC-content... WARN [2025-10-07 21:17:06] Intervals contain off-target regions. Will not change intervals. WARN [2025-10-07 21:17:06] No mappability scores provided. WARN [2025-10-07 21:17:06] No reptiming scores provided. INFO [2025-10-07 21:17:06] Calculating GC-content... INFO [2025-10-07 21:17:06] Splitting 5 large targets to an average width of 400. WARN [2025-10-07 21:17:06] No reptiming scores provided. INFO [2025-10-07 21:17:06] Calculating GC-content... WARN [2025-10-07 21:17:06] Found small target regions (< 100bp). Will resize them. INFO [2025-10-07 21:17:06] Splitting 5 large targets to an average width of 400. WARN [2025-10-07 21:17:06] No reptiming scores provided. INFO [2025-10-07 21:17:06] Calculating GC-content... WARN [2025-10-07 21:17:06] Found small target regions (< 100bp). Will resize them. INFO [2025-10-07 21:17:06] Splitting 5 large targets to an average width of 400. WARN [2025-10-07 21:17:06] 1 intervals without mappability score (1 on-target). INFO [2025-10-07 21:17:06] Removing 1 intervals with low mappability score (<0.60). WARN [2025-10-07 21:17:06] No reptiming scores provided. INFO [2025-10-07 21:17:06] Calculating GC-content... WARN [2025-10-07 21:17:06] Found small target regions (< 100bp). Will resize them. INFO [2025-10-07 21:17:07] Splitting 5 large targets to an average width of 400. INFO [2025-10-07 21:17:07] Tiling off-target regions to an average width of 200000. WARN [2025-10-07 21:17:07] No reptiming scores provided. INFO [2025-10-07 21:17:07] Calculating GC-content... INFO [2025-10-07 21:17:07] Splitting 5 large targets to an average width of 400. WARN [2025-10-07 21:17:07] No mappability scores provided. WARN [2025-10-07 21:17:07] No reptiming scores provided. INFO [2025-10-07 21:17:07] Calculating GC-content... WARN [2025-10-07 21:17:07] Chromosome naming style of interval file (Ensembl) was different from reference (UCSC). INFO [2025-10-07 21:17:07] Splitting 5 large targets to an average width of 400. WARN [2025-10-07 21:17:07] No mappability scores provided. WARN [2025-10-07 21:17:07] No reptiming scores provided. INFO [2025-10-07 21:17:07] Calculating GC-content... FATAL [2025-10-07 21:17:07] Chromosome naming style of interval file unknown, should be UCSC. FATAL [2025-10-07 21:17:07] FATAL [2025-10-07 21:17:07] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:17:07] parameters (PureCN 2.15.4). WARN [2025-10-07 21:17:07] Chromosome naming style of interval file (Ensembl) was different from reference (UCSC). WARN [2025-10-07 21:17:07] Chromosome naming style of mappability file (Ensembl) was different from reference (UCSC). INFO [2025-10-07 21:17:07] Splitting 5 large targets to an average width of 400. WARN [2025-10-07 21:17:07] No reptiming scores provided. INFO [2025-10-07 21:17:07] Calculating GC-content... WARN [2025-10-07 21:17:07] Found small target regions (< 60bp). Will resize them. INFO [2025-10-07 21:17:07] Splitting 5 large targets to an average width of 400. WARN [2025-10-07 21:17:07] No mappability scores provided. WARN [2025-10-07 21:17:07] No reptiming scores provided. INFO [2025-10-07 21:17:07] Calculating GC-content... WARN [2025-10-07 21:17:07] Found small target regions (< 60bp). Will drop them. INFO [2025-10-07 21:17:07] Splitting 4 large targets to an average width of 400. WARN [2025-10-07 21:17:07] No mappability scores provided. WARN [2025-10-07 21:17:07] No reptiming scores provided. INFO [2025-10-07 21:17:07] Calculating GC-content... WARN [2025-10-07 21:17:07] Found small target regions (< 200bp). Will resize them. INFO [2025-10-07 21:17:08] Splitting 5 large targets to an average width of 400. WARN [2025-10-07 21:17:08] No mappability scores provided. WARN [2025-10-07 21:17:08] No reptiming scores provided. INFO [2025-10-07 21:17:08] Calculating GC-content... INFO [2025-10-07 21:17:08] Found 20 variants in VCF file. INFO [2025-10-07 21:17:08] 20 (100.0%) variants annotated as likely germline (DB INFO flag). WARN [2025-10-07 21:17:08] Did not find base quality scores, will use global error rate of 0.0010 instead. Error in read.table(file = file, header = header, sep = sep, quote = quote, : no lines available in input FATAL [2025-10-07 21:17:08] Error reading AllelicCountsFile FATAL [2025-10-07 21:17:08] /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/PureCN/extdata/example_allelic_counts_empty.tsv FATAL [2025-10-07 21:17:08] FATAL [2025-10-07 21:17:08] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:17:08] parameters (PureCN 2.15.4). INFO [2025-10-07 21:17:08] Found 127 variants in VCF file. INFO [2025-10-07 21:17:08] 127 (100.0%) variants annotated as likely germline (DB INFO flag). WARN [2025-10-07 21:17:08] Did not find base quality scores, will use global error rate of 0.0010 instead. INFO [2025-10-07 21:17:08] ------------------------------------------------------------ INFO [2025-10-07 21:17:08] PureCN 2.15.4 INFO [2025-10-07 21:17:08] ------------------------------------------------------------ INFO [2025-10-07 21:17:08] Loading coverage files... INFO [2025-10-07 21:17:08] Mean target coverages: 112X (tumor) 99X (normal). WARN [2025-10-07 21:17:08] Allosome coverage missing, cannot determine sex. WARN [2025-10-07 21:17:08] Allosome coverage missing, cannot determine sex. INFO [2025-10-07 21:17:08] Removing 228 intervals with missing log.ratio. INFO [2025-10-07 21:17:08] Removing 22 small (< 5bp) intervals. INFO [2025-10-07 21:17:08] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2025-10-07 21:17:08] No normalDB provided. Provide one for better results. INFO [2025-10-07 21:17:08] Removing 1724 low count (< 100 total reads) intervals. INFO [2025-10-07 21:17:08] Removing 6 low coverage (< 15.0000X) intervals. INFO [2025-10-07 21:17:08] Using 8050 intervals (8050 on-target, 0 off-target). INFO [2025-10-07 21:17:08] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2025-10-07 21:17:08] No interval.file provided. Cannot check for any GC-biases. INFO [2025-10-07 21:17:08] Loading VCF... INFO [2025-10-07 21:17:08] Found 127 variants in VCF file. INFO [2025-10-07 21:17:09] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2025-10-07 21:17:09] LIB-02240e4 is tumor in VCF file. INFO [2025-10-07 21:17:09] No homozygous variants in VCF, provide unfiltered VCF. INFO [2025-10-07 21:17:09] Removing 1 non heterozygous (in matched normal) germline SNPs. INFO [2025-10-07 21:17:09] Removing 0 low quality variants with non-offset BQ < 25. INFO [2025-10-07 21:17:09] Base quality scores range from 29 to 35 (offset by 1) INFO [2025-10-07 21:17:09] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS. INFO [2025-10-07 21:17:09] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. INFO [2025-10-07 21:17:09] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding). INFO [2025-10-07 21:17:09] 1.2% of targets contain variants. INFO [2025-10-07 21:17:09] Removing 4 variants outside intervals. INFO [2025-10-07 21:17:09] Found SOMATIC annotation in VCF. INFO [2025-10-07 21:17:09] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. INFO [2025-10-07 21:17:09] Found SOMATIC annotation in VCF. Setting mapping bias to 0.972. INFO [2025-10-07 21:17:09] Excluding 0 novel or poor quality variants from segmentation. INFO [2025-10-07 21:17:09] Sample sex: ? INFO [2025-10-07 21:17:09] Segmenting data... INFO [2025-10-07 21:17:09] Loading pre-computed boundaries for DNAcopy... INFO [2025-10-07 21:17:09] Setting undo.SD parameter to 1.000000. INFO [2025-10-07 21:17:09] Setting prune.hclust.h parameter to 0.200000. INFO [2025-10-07 21:17:09] Found 59 segments with median size of 17.67Mb. INFO [2025-10-07 21:17:09] Using 121 variants. INFO [2025-10-07 21:17:09] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30) INFO [2025-10-07 21:17:09] 2D-grid search of purity and ploidy... INFO [2025-10-07 21:17:09] Local optima: 0.65/1.8, 0.52/2 INFO [2025-10-07 21:17:09] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80... INFO [2025-10-07 21:17:10] Testing local optimum 2/2 at purity 0.52 and total ploidy 2.00... INFO [2025-10-07 21:17:10] Skipping 1 solutions that converged to the same optima. INFO [2025-10-07 21:17:10] Fitting variants with beta model for local optimum 1/2... INFO [2025-10-07 21:17:10] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01. INFO [2025-10-07 21:17:11] Optimized purity: 0.65 INFO [2025-10-07 21:17:11] Done. INFO [2025-10-07 21:17:11] ------------------------------------------------------------ FATAL [2025-10-07 21:17:12] log.ratio NULL in .writeLogRatioFileGATK4 FATAL [2025-10-07 21:17:12] FATAL [2025-10-07 21:17:12] This runtime error might be caused by invalid input data or parameters. FATAL [2025-10-07 21:17:12] Please report bug (PureCN 2.15.4). INFO [2025-10-07 21:17:12] Loaded provided segmentation file example_seg.txt (format DNAcopy). INFO [2025-10-07 21:17:12] Re-centering provided segment means (offset -0.0033). INFO [2025-10-07 21:17:12] Loaded provided segmentation file example_gatk4_modelfinal.seg.gz (format GATK4). WARN [2025-10-07 21:17:12] Expecting numeric chromosome names in seg.file, assuming file is properly sorted. INFO [2025-10-07 21:17:12] Re-centering provided segment means (offset -0.0037). INFO [2025-10-07 21:17:12] 576 on-target bins with low coverage in all samples. WARN [2025-10-07 21:17:12] You are likely not using the correct baits file! WARN [2025-10-07 21:17:12] Allosome coverage missing, cannot determine sex. WARN [2025-10-07 21:17:12] Allosome coverage missing, cannot determine sex. INFO [2025-10-07 21:17:12] Processing on-target regions... INFO [2025-10-07 21:17:12] Removing 930 intervals with low coverage in normalDB. INFO [2025-10-07 21:17:12] Removing 1 intervals with zero coverage in more than 3% of normalDB. INFO [2025-10-07 21:17:13] ------------------------------------------------------------ INFO [2025-10-07 21:17:13] PureCN 2.15.4 INFO [2025-10-07 21:17:13] ------------------------------------------------------------ INFO [2025-10-07 21:17:13] Using BiocParallel for parallel optimization. INFO [2025-10-07 21:17:13] Loading coverage files... INFO [2025-10-07 21:17:13] Mean target coverages: 112X (tumor) 99X (normal). WARN [2025-10-07 21:17:13] Allosome coverage missing, cannot determine sex. WARN [2025-10-07 21:17:13] Allosome coverage missing, cannot determine sex. INFO [2025-10-07 21:17:13] Removing 228 intervals with missing log.ratio. INFO [2025-10-07 21:17:13] Removing 705 intervals excluded in normalDB. INFO [2025-10-07 21:17:13] normalDB provided. Setting minimum coverage for segmentation to 0.0015X. INFO [2025-10-07 21:17:13] Removing 1066 low count (< 100 total reads) intervals. INFO [2025-10-07 21:17:13] Using 8050 intervals (8050 on-target, 0 off-target). INFO [2025-10-07 21:17:13] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2025-10-07 21:17:13] No interval.file provided. Cannot check for any GC-biases. INFO [2025-10-07 21:17:13] Sample sex: ? INFO [2025-10-07 21:17:13] Segmenting data... INFO [2025-10-07 21:17:13] Interval weights found, will use weighted CBS. INFO [2025-10-07 21:17:13] Loading pre-computed boundaries for DNAcopy... INFO [2025-10-07 21:17:13] Setting undo.SD parameter to 1.000000. Setting multi-figure configuration INFO [2025-10-07 21:17:14] Found 52 segments with median size of 29.35Mb. INFO [2025-10-07 21:17:14] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30) INFO [2025-10-07 21:17:14] 2D-grid search of purity and ploidy... INFO [2025-10-07 21:17:14] Local optima: 0.65/1.8, 0.52/2 INFO [2025-10-07 21:17:15] Skipping 1 solutions that converged to the same optima. INFO [2025-10-07 21:17:15] Done. INFO [2025-10-07 21:17:15] ------------------------------------------------------------ INFO [2025-10-07 21:17:15] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp0PSuPi/file1819f5d7066d7.rds... FATAL [2025-10-07 21:17:15] runAbsoluteCN was run without a VCF file. FATAL [2025-10-07 21:17:15] FATAL [2025-10-07 21:17:15] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:17:15] parameters (PureCN 2.15.4). FATAL [2025-10-07 21:17:15] runAbsoluteCN was run without a VCF file. FATAL [2025-10-07 21:17:15] FATAL [2025-10-07 21:17:15] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:17:15] parameters (PureCN 2.15.4). INFO [2025-10-07 21:17:15] ------------------------------------------------------------ INFO [2025-10-07 21:17:15] PureCN 2.15.4 INFO [2025-10-07 21:17:15] ------------------------------------------------------------ INFO [2025-10-07 21:17:15] Loading coverage files... INFO [2025-10-07 21:17:15] Mean target coverages: 112X (tumor) 99X (normal). WARN [2025-10-07 21:17:15] Allosome coverage missing, cannot determine sex. WARN [2025-10-07 21:17:15] Allosome coverage missing, cannot determine sex. INFO [2025-10-07 21:17:15] Removing 228 intervals with missing log.ratio. INFO [2025-10-07 21:17:15] Removing 705 intervals excluded in normalDB. INFO [2025-10-07 21:17:15] normalDB provided. Setting minimum coverage for segmentation to 0.0015X. INFO [2025-10-07 21:17:15] Removing 1066 low count (< 100 total reads) intervals. INFO [2025-10-07 21:17:15] Using 8050 intervals (8050 on-target, 0 off-target). INFO [2025-10-07 21:17:15] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2025-10-07 21:17:15] No interval.file provided. Cannot check for any GC-biases. INFO [2025-10-07 21:17:15] Sample sex: ? INFO [2025-10-07 21:17:15] Segmenting data... INFO [2025-10-07 21:17:15] Interval weights found, will use weighted PSCBS. FATAL [2025-10-07 21:17:15] segmentationPSCBS requires VCF file. FATAL [2025-10-07 21:17:15] FATAL [2025-10-07 21:17:15] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:17:15] parameters (PureCN 2.15.4). INFO [2025-10-07 21:17:17] ------------------------------------------------------------ INFO [2025-10-07 21:17:17] PureCN 2.15.4 INFO [2025-10-07 21:17:17] ------------------------------------------------------------ INFO [2025-10-07 21:17:17] Loading coverage files... FATAL [2025-10-07 21:17:17] Need a normal coverage file if log.ratio and seg.file are not provided. FATAL [2025-10-07 21:17:17] FATAL [2025-10-07 21:17:17] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:17:17] parameters (PureCN 2.15.4). INFO [2025-10-07 21:17:17] ------------------------------------------------------------ INFO [2025-10-07 21:17:17] PureCN 2.15.4 INFO [2025-10-07 21:17:17] ------------------------------------------------------------ FATAL [2025-10-07 21:17:17] min.ploidy or max.ploidy not within expected range. FATAL [2025-10-07 21:17:17] FATAL [2025-10-07 21:17:17] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:17:17] parameters (PureCN 2.15.4). INFO [2025-10-07 21:17:17] ------------------------------------------------------------ INFO [2025-10-07 21:17:17] PureCN 2.15.4 INFO [2025-10-07 21:17:17] ------------------------------------------------------------ FATAL [2025-10-07 21:17:17] min.ploidy or max.ploidy not within expected range. FATAL [2025-10-07 21:17:17] FATAL [2025-10-07 21:17:17] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:17:17] parameters (PureCN 2.15.4). INFO [2025-10-07 21:17:17] ------------------------------------------------------------ INFO [2025-10-07 21:17:17] PureCN 2.15.4 INFO [2025-10-07 21:17:17] ------------------------------------------------------------ INFO [2025-10-07 21:17:17] ------------------------------------------------------------ INFO [2025-10-07 21:17:17] PureCN 2.15.4 INFO [2025-10-07 21:17:17] ------------------------------------------------------------ INFO [2025-10-07 21:17:17] ------------------------------------------------------------ INFO [2025-10-07 21:17:17] PureCN 2.15.4 INFO [2025-10-07 21:17:17] ------------------------------------------------------------ FATAL [2025-10-07 21:17:17] test.num.copy not within expected range. FATAL [2025-10-07 21:17:17] FATAL [2025-10-07 21:17:17] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:17:17] parameters (PureCN 2.15.4). INFO [2025-10-07 21:17:17] ------------------------------------------------------------ INFO [2025-10-07 21:17:17] PureCN 2.15.4 INFO [2025-10-07 21:17:17] ------------------------------------------------------------ WARN [2025-10-07 21:17:17] test.num.copy outside recommended range. FATAL [2025-10-07 21:17:17] max.non.clonal not within expected range or format. FATAL [2025-10-07 21:17:17] FATAL [2025-10-07 21:17:17] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:17:17] parameters (PureCN 2.15.4). INFO [2025-10-07 21:17:17] ------------------------------------------------------------ INFO [2025-10-07 21:17:17] PureCN 2.15.4 INFO [2025-10-07 21:17:17] ------------------------------------------------------------ WARN [2025-10-07 21:17:17] test.num.copy outside recommended range. FATAL [2025-10-07 21:17:17] max.non.clonal not within expected range or format. FATAL [2025-10-07 21:17:17] FATAL [2025-10-07 21:17:17] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:17:17] parameters (PureCN 2.15.4). INFO [2025-10-07 21:17:17] ------------------------------------------------------------ INFO [2025-10-07 21:17:17] PureCN 2.15.4 INFO [2025-10-07 21:17:17] ------------------------------------------------------------ FATAL [2025-10-07 21:17:17] test.purity not within expected range. FATAL [2025-10-07 21:17:17] FATAL [2025-10-07 21:17:17] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:17:17] parameters (PureCN 2.15.4). INFO [2025-10-07 21:17:17] ------------------------------------------------------------ INFO [2025-10-07 21:17:17] PureCN 2.15.4 INFO [2025-10-07 21:17:17] ------------------------------------------------------------ INFO [2025-10-07 21:17:17] Loading coverage files... FATAL [2025-10-07 21:17:18] Tumor and normal are identical. This won't give any meaningful results FATAL [2025-10-07 21:17:18] and I'm stopping here. FATAL [2025-10-07 21:17:18] FATAL [2025-10-07 21:17:18] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:17:18] parameters (PureCN 2.15.4). INFO [2025-10-07 21:17:18] ------------------------------------------------------------ INFO [2025-10-07 21:17:18] PureCN 2.15.4 INFO [2025-10-07 21:17:18] ------------------------------------------------------------ INFO [2025-10-07 21:17:18] Loading coverage files... FATAL [2025-10-07 21:17:18] Length of log.ratio different from tumor coverage. FATAL [2025-10-07 21:17:18] FATAL [2025-10-07 21:17:18] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:17:18] parameters (PureCN 2.15.4). INFO [2025-10-07 21:17:18] ------------------------------------------------------------ INFO [2025-10-07 21:17:18] PureCN 2.15.4 INFO [2025-10-07 21:17:18] ------------------------------------------------------------ FATAL [2025-10-07 21:17:18] prior.purity must have the same length as test.purity. FATAL [2025-10-07 21:17:18] FATAL [2025-10-07 21:17:18] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:17:18] parameters (PureCN 2.15.4). INFO [2025-10-07 21:17:18] ------------------------------------------------------------ INFO [2025-10-07 21:17:18] PureCN 2.15.4 INFO [2025-10-07 21:17:18] ------------------------------------------------------------ FATAL [2025-10-07 21:17:18] min.gof not within expected range or format. FATAL [2025-10-07 21:17:18] FATAL [2025-10-07 21:17:18] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:17:18] parameters (PureCN 2.15.4). INFO [2025-10-07 21:17:18] ------------------------------------------------------------ INFO [2025-10-07 21:17:18] PureCN 2.15.4 INFO [2025-10-07 21:17:18] ------------------------------------------------------------ FATAL [2025-10-07 21:17:18] prior.purity not within expected range or format. FATAL [2025-10-07 21:17:18] FATAL [2025-10-07 21:17:18] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:17:18] parameters (PureCN 2.15.4). INFO [2025-10-07 21:17:18] ------------------------------------------------------------ INFO [2025-10-07 21:17:18] PureCN 2.15.4 INFO [2025-10-07 21:17:18] ------------------------------------------------------------ FATAL [2025-10-07 21:17:18] prior.purity must add to 1. Sum is 1.5 FATAL [2025-10-07 21:17:18] FATAL [2025-10-07 21:17:18] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:17:18] parameters (PureCN 2.15.4). INFO [2025-10-07 21:17:18] ------------------------------------------------------------ INFO [2025-10-07 21:17:18] PureCN 2.15.4 INFO [2025-10-07 21:17:18] ------------------------------------------------------------ FATAL [2025-10-07 21:17:18] max.homozygous.loss not within expected range or format. FATAL [2025-10-07 21:17:18] FATAL [2025-10-07 21:17:18] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:17:18] parameters (PureCN 2.15.4). INFO [2025-10-07 21:17:18] ------------------------------------------------------------ INFO [2025-10-07 21:17:18] PureCN 2.15.4 INFO [2025-10-07 21:17:18] ------------------------------------------------------------ FATAL [2025-10-07 21:17:18] prior.K not within expected range or format. FATAL [2025-10-07 21:17:18] FATAL [2025-10-07 21:17:18] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:17:18] parameters (PureCN 2.15.4). INFO [2025-10-07 21:17:18] ------------------------------------------------------------ INFO [2025-10-07 21:17:18] PureCN 2.15.4 INFO [2025-10-07 21:17:18] ------------------------------------------------------------ FATAL [2025-10-07 21:17:18] prior.contamination not within expected range or format. FATAL [2025-10-07 21:17:18] FATAL [2025-10-07 21:17:18] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:17:18] parameters (PureCN 2.15.4). INFO [2025-10-07 21:17:18] ------------------------------------------------------------ INFO [2025-10-07 21:17:18] PureCN 2.15.4 INFO [2025-10-07 21:17:18] ------------------------------------------------------------ FATAL [2025-10-07 21:17:18] Iterations not in the expected range from 10 to 250. FATAL [2025-10-07 21:17:18] FATAL [2025-10-07 21:17:18] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:17:18] parameters (PureCN 2.15.4). INFO [2025-10-07 21:17:18] ------------------------------------------------------------ INFO [2025-10-07 21:17:18] PureCN 2.15.4 INFO [2025-10-07 21:17:18] ------------------------------------------------------------ FATAL [2025-10-07 21:17:18] Iterations not in the expected range from 10 to 250. FATAL [2025-10-07 21:17:18] FATAL [2025-10-07 21:17:18] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:17:18] parameters (PureCN 2.15.4). INFO [2025-10-07 21:17:18] ------------------------------------------------------------ INFO [2025-10-07 21:17:18] PureCN 2.15.4 INFO [2025-10-07 21:17:18] ------------------------------------------------------------ INFO [2025-10-07 21:17:18] Loading coverage files... FATAL [2025-10-07 21:17:18] Missing tumor.coverage.file requires seg.file or log.ratio and FATAL [2025-10-07 21:17:18] interval.file. FATAL [2025-10-07 21:17:18] FATAL [2025-10-07 21:17:18] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:17:18] parameters (PureCN 2.15.4). INFO [2025-10-07 21:17:18] ------------------------------------------------------------ INFO [2025-10-07 21:17:18] PureCN 2.15.4 INFO [2025-10-07 21:17:18] ------------------------------------------------------------ INFO [2025-10-07 21:17:18] ------------------------------------------------------------ INFO [2025-10-07 21:17:18] PureCN 2.15.4 INFO [2025-10-07 21:17:18] ------------------------------------------------------------ INFO [2025-10-07 21:17:18] Loading coverage files... FATAL [2025-10-07 21:17:18] Interval files in normal and tumor different. FATAL [2025-10-07 21:17:18] FATAL [2025-10-07 21:17:18] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:17:18] parameters (PureCN 2.15.4). INFO [2025-10-07 21:17:18] ------------------------------------------------------------ INFO [2025-10-07 21:17:18] PureCN 2.15.4 INFO [2025-10-07 21:17:18] ------------------------------------------------------------ INFO [2025-10-07 21:17:18] Loading coverage files... INFO [2025-10-07 21:17:19] Mean target coverages: 0X (tumor) 99X (normal). WARN [2025-10-07 21:17:19] Large difference in coverage of tumor and normal. FATAL [2025-10-07 21:17:19] No finite intervals. FATAL [2025-10-07 21:17:19] FATAL [2025-10-07 21:17:19] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:17:19] parameters (PureCN 2.15.4). INFO [2025-10-07 21:17:19] ------------------------------------------------------------ INFO [2025-10-07 21:17:19] PureCN 2.15.4 INFO [2025-10-07 21:17:19] ------------------------------------------------------------ INFO [2025-10-07 21:17:19] Loading coverage files... INFO [2025-10-07 21:17:19] Mean target coverages: 112X (tumor) 99X (normal). WARN [2025-10-07 21:17:19] Allosome coverage missing, cannot determine sex. WARN [2025-10-07 21:17:19] Allosome coverage missing, cannot determine sex. INFO [2025-10-07 21:17:19] Removing 228 intervals with missing log.ratio. INFO [2025-10-07 21:17:19] Removing 22 small (< 5bp) intervals. INFO [2025-10-07 21:17:19] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2025-10-07 21:17:19] No normalDB provided. Provide one for better results. INFO [2025-10-07 21:17:19] Removing 1724 low count (< 100 total reads) intervals. INFO [2025-10-07 21:17:19] Removing 6 low coverage (< 15.0000X) intervals. INFO [2025-10-07 21:17:19] Using 8050 intervals (8050 on-target, 0 off-target). INFO [2025-10-07 21:17:19] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2025-10-07 21:17:19] No interval.file provided. Cannot check for any GC-biases. INFO [2025-10-07 21:17:19] Loading VCF... INFO [2025-10-07 21:17:19] Found 127 variants in VCF file. INFO [2025-10-07 21:17:19] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2025-10-07 21:17:19] LIB-02240e4 is tumor in VCF file. INFO [2025-10-07 21:17:19] No homozygous variants in VCF, provide unfiltered VCF. INFO [2025-10-07 21:17:19] Removing 1 non heterozygous (in matched normal) germline SNPs. INFO [2025-10-07 21:17:19] Removing 0 low quality variants with non-offset BQ < 25. INFO [2025-10-07 21:17:19] Base quality scores range from 29 to 35 (offset by 1) INFO [2025-10-07 21:17:19] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS. INFO [2025-10-07 21:17:19] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. Error in FileForFormat(resource(con), fileFormat(con)) : Format 'txt' unsupported In addition: Warning messages: 1: In for (i in seq_len(n)) { : closing unused connection 4 (/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/PureCN/extdata/example_allelic_counts_empty.tsv) 2: In list(...) : closing unused connection 5 (/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp0PSuPi/file1819f25178ead.tsv) 3: In list(...) : closing unused connection 4 (/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/PureCN/extdata/example_gatk4_denoised_cr.tsv.gz) FATAL [2025-10-07 21:17:19] Could not import snp.blacklist FATAL [2025-10-07 21:17:19] /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/PureCN/extdata/example_normal.txt.gz:Error FATAL [2025-10-07 21:17:19] in FileForFormat(resource(con), fileFormat(con)) : Format 'txt' FATAL [2025-10-07 21:17:19] unsupported FATAL [2025-10-07 21:17:19] FATAL [2025-10-07 21:17:19] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:17:19] parameters (PureCN 2.15.4). INFO [2025-10-07 21:17:19] ------------------------------------------------------------ INFO [2025-10-07 21:17:19] PureCN 2.15.4 INFO [2025-10-07 21:17:19] ------------------------------------------------------------ INFO [2025-10-07 21:17:19] Loading coverage files... INFO [2025-10-07 21:17:20] Mean target coverages: 112X (tumor) 99X (normal). WARN [2025-10-07 21:17:20] Allosome coverage missing, cannot determine sex. WARN [2025-10-07 21:17:20] Allosome coverage missing, cannot determine sex. INFO [2025-10-07 21:17:20] Removing 228 intervals with missing log.ratio. INFO [2025-10-07 21:17:20] Removing 22 small (< 5bp) intervals. INFO [2025-10-07 21:17:20] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2025-10-07 21:17:20] No normalDB provided. Provide one for better results. INFO [2025-10-07 21:17:20] Removing 233 low coverage (< 15.0000X) intervals. INFO [2025-10-07 21:17:20] Using 9547 intervals (9547 on-target, 0 off-target). INFO [2025-10-07 21:17:20] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2025-10-07 21:17:20] No interval.file provided. Cannot check for any GC-biases. INFO [2025-10-07 21:17:20] Loading VCF... INFO [2025-10-07 21:17:20] Found 127 variants in VCF file. INFO [2025-10-07 21:17:20] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2025-10-07 21:17:20] LIB-02240e4 is tumor in VCF file. INFO [2025-10-07 21:17:20] No homozygous variants in VCF, provide unfiltered VCF. INFO [2025-10-07 21:17:20] Removing 1 non heterozygous (in matched normal) germline SNPs. INFO [2025-10-07 21:17:20] Removing 0 low quality variants with non-offset BQ < 25. INFO [2025-10-07 21:17:20] Base quality scores range from 29 to 35 (offset by 1) INFO [2025-10-07 21:17:20] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS. INFO [2025-10-07 21:17:21] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. INFO [2025-10-07 21:17:21] Total size of targeted genomic region: 1.63Mb (2.58Mb with 50bp padding). INFO [2025-10-07 21:17:21] 1.0% of targets contain variants. INFO [2025-10-07 21:17:21] Removing 2 variants outside intervals. INFO [2025-10-07 21:17:21] Found SOMATIC annotation in VCF. INFO [2025-10-07 21:17:21] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. INFO [2025-10-07 21:17:21] Found SOMATIC annotation in VCF. Setting mapping bias to 0.973. INFO [2025-10-07 21:17:21] Excluding 0 novel or poor quality variants from segmentation. INFO [2025-10-07 21:17:21] Sample sex: ? INFO [2025-10-07 21:17:21] Segmenting data... INFO [2025-10-07 21:17:21] Loading pre-computed boundaries for DNAcopy... INFO [2025-10-07 21:17:21] Setting undo.SD parameter to 1.000000. INFO [2025-10-07 21:17:21] Setting prune.hclust.h parameter to 0.200000. INFO [2025-10-07 21:17:21] Found 54 segments with median size of 24.88Mb. INFO [2025-10-07 21:17:21] Using 123 variants. INFO [2025-10-07 21:17:21] Mean standard deviation of log-ratios: 0.37 (MAPD: 0.32) INFO [2025-10-07 21:17:21] 2D-grid search of purity and ploidy... INFO [2025-10-07 21:17:22] Local optima: 0.62/1.9, 0.3/1.9, 0.32/2 INFO [2025-10-07 21:17:22] Testing local optimum 1/3 at purity 0.62 and total ploidy 1.90... INFO [2025-10-07 21:17:22] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90... INFO [2025-10-07 21:17:22] Recalibrating log-ratios... INFO [2025-10-07 21:17:22] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90... INFO [2025-10-07 21:17:22] Recalibrating log-ratios... INFO [2025-10-07 21:17:22] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90... INFO [2025-10-07 21:17:22] Recalibrating log-ratios... INFO [2025-10-07 21:17:22] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90... INFO [2025-10-07 21:17:22] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00... INFO [2025-10-07 21:17:22] Recalibrating log-ratios... INFO [2025-10-07 21:17:22] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00... INFO [2025-10-07 21:17:23] Recalibrating log-ratios... INFO [2025-10-07 21:17:23] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00... INFO [2025-10-07 21:17:23] Recalibrating log-ratios... INFO [2025-10-07 21:17:23] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00... INFO [2025-10-07 21:17:23] Skipping 1 solutions that converged to the same optima. INFO [2025-10-07 21:17:23] Skipping 1 solutions exceeding max.non.clonal (0.20): 0.3/1.9 (purity/tumor ploidy) INFO [2025-10-07 21:17:23] Fitting variants with beta model for local optimum 1/3... INFO [2025-10-07 21:17:23] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01. INFO [2025-10-07 21:17:24] Optimized purity: 0.65 INFO [2025-10-07 21:17:24] Done. INFO [2025-10-07 21:17:24] ------------------------------------------------------------ INFO [2025-10-07 21:17:24] ------------------------------------------------------------ INFO [2025-10-07 21:17:24] PureCN 2.15.4 INFO [2025-10-07 21:17:24] ------------------------------------------------------------ INFO [2025-10-07 21:17:24] Loading coverage files... INFO [2025-10-07 21:17:24] Mean target coverages: 112X (tumor) 99X (normal). WARN [2025-10-07 21:17:24] Allosome coverage missing, cannot determine sex. WARN [2025-10-07 21:17:24] Allosome coverage missing, cannot determine sex. INFO [2025-10-07 21:17:24] Removing 228 intervals with missing log.ratio. INFO [2025-10-07 21:17:24] Removing 22 small (< 5bp) intervals. INFO [2025-10-07 21:17:24] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2025-10-07 21:17:24] No normalDB provided. Provide one for better results. INFO [2025-10-07 21:17:24] Removing 1724 low count (< 100 total reads) intervals. INFO [2025-10-07 21:17:24] Removing 6 low coverage (< 15.0000X) intervals. INFO [2025-10-07 21:17:24] Using 8050 intervals (8050 on-target, 0 off-target). INFO [2025-10-07 21:17:24] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2025-10-07 21:17:24] No interval.file provided. Cannot check for any GC-biases. INFO [2025-10-07 21:17:24] Loading VCF... INFO [2025-10-07 21:17:24] Found 127 variants in VCF file. WARN [2025-10-07 21:17:24] DP FORMAT field contains NAs. Removing 3 variants. WARN [2025-10-07 21:17:24] DB INFO flag contains NAs INFO [2025-10-07 21:17:24] 119 (96.0%) variants annotated as likely germline (DB INFO flag). INFO [2025-10-07 21:17:24] LIB-02240e4 is tumor in VCF file. INFO [2025-10-07 21:17:24] No homozygous variants in VCF, provide unfiltered VCF. INFO [2025-10-07 21:17:24] Removing 0 low quality variants with non-offset BQ < 25. INFO [2025-10-07 21:17:24] Base quality scores range from 29 to 35 (offset by 1) INFO [2025-10-07 21:17:24] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS. INFO [2025-10-07 21:17:24] Removing 1 variants with AF < 0.030 or AF >= 0.970 or insufficient supporting reads or depth < 15. INFO [2025-10-07 21:17:24] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding). INFO [2025-10-07 21:17:24] 1.2% of targets contain variants. INFO [2025-10-07 21:17:24] Setting somatic prior probabilities for likely germline hits to 0.000500 or to 0.500000 otherwise. INFO [2025-10-07 21:17:24] Excluding 5 novel or poor quality variants from segmentation. INFO [2025-10-07 21:17:24] Sample sex: ? INFO [2025-10-07 21:17:24] Segmenting data... INFO [2025-10-07 21:17:24] Loading pre-computed boundaries for DNAcopy... INFO [2025-10-07 21:17:24] Setting undo.SD parameter to 1.000000. Setting multi-figure configuration INFO [2025-10-07 21:17:25] Setting prune.hclust.h parameter to 0.200000. INFO [2025-10-07 21:17:25] Found 59 segments with median size of 17.67Mb. INFO [2025-10-07 21:17:25] Using 123 variants. INFO [2025-10-07 21:17:25] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30) INFO [2025-10-07 21:17:25] 2D-grid search of purity and ploidy... INFO [2025-10-07 21:17:25] Local optima: 0.62/1.9, 0.3/1.9, 0.32/2 INFO [2025-10-07 21:17:25] Testing local optimum 1/3 at purity 0.62 and total ploidy 1.90... INFO [2025-10-07 21:17:26] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90... INFO [2025-10-07 21:17:26] Recalibrating log-ratios... INFO [2025-10-07 21:17:26] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90... INFO [2025-10-07 21:17:26] Recalibrating log-ratios... INFO [2025-10-07 21:17:26] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90... INFO [2025-10-07 21:17:26] Recalibrating log-ratios... INFO [2025-10-07 21:17:26] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90... INFO [2025-10-07 21:17:26] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00... INFO [2025-10-07 21:17:26] Recalibrating log-ratios... INFO [2025-10-07 21:17:26] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00... INFO [2025-10-07 21:17:26] Recalibrating log-ratios... INFO [2025-10-07 21:17:26] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00... INFO [2025-10-07 21:17:26] Recalibrating log-ratios... INFO [2025-10-07 21:17:26] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00... INFO [2025-10-07 21:17:26] Skipping 2 solutions exceeding max.non.clonal (0.20): 0.3/1.9, 0.35/1.61 (purity/tumor ploidy) INFO [2025-10-07 21:17:26] Fitting variants with beta model for local optimum 1/3... INFO [2025-10-07 21:17:26] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01. INFO [2025-10-07 21:17:27] Optimized purity: 0.65 INFO [2025-10-07 21:17:27] Done. INFO [2025-10-07 21:17:27] ------------------------------------------------------------ INFO [2025-10-07 21:17:27] ------------------------------------------------------------ INFO [2025-10-07 21:17:27] PureCN 2.15.4 INFO [2025-10-07 21:17:27] ------------------------------------------------------------ INFO [2025-10-07 21:17:27] Loading coverage files... INFO [2025-10-07 21:17:28] Mean target coverages: 112X (tumor) 99X (normal). WARN [2025-10-07 21:17:28] Allosome coverage missing, cannot determine sex. WARN [2025-10-07 21:17:28] Allosome coverage missing, cannot determine sex. INFO [2025-10-07 21:17:28] No Gene column in interval.file. You won't get gene-level calls. INFO [2025-10-07 21:17:28] Removing 228 intervals with missing log.ratio. INFO [2025-10-07 21:17:28] Removing 15 low/high GC targets. INFO [2025-10-07 21:17:28] Removing 21 small (< 5bp) intervals. INFO [2025-10-07 21:17:28] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2025-10-07 21:17:28] No normalDB provided. Provide one for better results. INFO [2025-10-07 21:17:28] Removing 1718 low count (< 100 total reads) intervals. INFO [2025-10-07 21:17:28] Removing 6 low coverage (< 15.0000X) intervals. INFO [2025-10-07 21:17:28] Removing 36 low mappability intervals. INFO [2025-10-07 21:17:28] Using 8006 intervals (8006 on-target, 0 off-target). INFO [2025-10-07 21:17:28] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2025-10-07 21:17:28] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio). INFO [2025-10-07 21:17:28] Loading VCF... INFO [2025-10-07 21:17:28] Found 127 variants in VCF file. INFO [2025-10-07 21:17:28] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2025-10-07 21:17:28] LIB-02240e4 is tumor in VCF file. INFO [2025-10-07 21:17:28] No homozygous variants in VCF, provide unfiltered VCF. INFO [2025-10-07 21:17:28] Removing 1 non heterozygous (in matched normal) germline SNPs. INFO [2025-10-07 21:17:28] Removing 0 low quality variants with non-offset BQ < 25. INFO [2025-10-07 21:17:28] Base quality scores range from 29 to 35 (offset by 1) INFO [2025-10-07 21:17:28] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS. INFO [2025-10-07 21:17:28] Removing 1 variants with AF < 0.030 or AF >= Inf or insufficient supporting reads or depth < 15. INFO [2025-10-07 21:17:28] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding). INFO [2025-10-07 21:17:28] 1.2% of targets contain variants. INFO [2025-10-07 21:17:28] Removing 11 variants outside intervals. INFO [2025-10-07 21:17:28] Found SOMATIC annotation in VCF. INFO [2025-10-07 21:17:28] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. INFO [2025-10-07 21:17:28] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970. INFO [2025-10-07 21:17:28] Excluding 0 novel or poor quality variants from segmentation. INFO [2025-10-07 21:17:28] Sample sex: ? INFO [2025-10-07 21:17:28] Segmenting data... INFO [2025-10-07 21:17:28] MAPD of 114 allelic fractions: 0.14 (0.15 adjusted). INFO [2025-10-07 21:17:29] Using unweighted PSCBS. INFO [2025-10-07 21:17:29] Setting undo.SD parameter to 1.000000. INFO [2025-10-07 21:17:39] Setting prune.hclust.h parameter to 0.200000. INFO [2025-10-07 21:17:39] Found 72 segments with median size of 27.25Mb. INFO [2025-10-07 21:17:39] Using 114 variants. INFO [2025-10-07 21:17:39] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30) INFO [2025-10-07 21:17:39] 2D-grid search of purity and ploidy... INFO [2025-10-07 21:17:39] Local optima: 0.65/1.8, 0.38/2.2 INFO [2025-10-07 21:17:39] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80... INFO [2025-10-07 21:17:39] Recalibrating log-ratios... INFO [2025-10-07 21:17:39] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80... INFO [2025-10-07 21:17:39] Recalibrating log-ratios... INFO [2025-10-07 21:17:39] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80... INFO [2025-10-07 21:17:39] Recalibrating log-ratios... INFO [2025-10-07 21:17:39] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80... INFO [2025-10-07 21:17:39] Testing local optimum 2/2 at purity 0.38 and total ploidy 2.20... INFO [2025-10-07 21:17:40] Skipping 1 solutions exceeding max.non.clonal (0.20): 0.65/2.05 (purity/tumor ploidy) INFO [2025-10-07 21:17:40] Fitting variants with beta model for local optimum 2/2... INFO [2025-10-07 21:17:40] Fitting variants for purity 0.40, tumor ploidy 2.55 and contamination 0.01. INFO [2025-10-07 21:17:41] Optimized purity: 0.40 INFO [2025-10-07 21:17:41] Done. INFO [2025-10-07 21:17:41] ------------------------------------------------------------ FATAL [2025-10-07 21:17:41] This function requires gene-level calls. Please add a column 'Gene' FATAL [2025-10-07 21:17:41] containing gene symbols to the interval.file. FATAL [2025-10-07 21:17:41] FATAL [2025-10-07 21:17:41] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:17:41] parameters (PureCN 2.15.4). INFO [2025-10-07 21:17:41] ------------------------------------------------------------ INFO [2025-10-07 21:17:41] PureCN 2.15.4 INFO [2025-10-07 21:17:41] ------------------------------------------------------------ INFO [2025-10-07 21:17:41] Loading coverage files... INFO [2025-10-07 21:17:41] Mean target coverages: 112X (tumor) 99X (normal). WARN [2025-10-07 21:17:41] Allosome coverage missing, cannot determine sex. WARN [2025-10-07 21:17:41] Allosome coverage missing, cannot determine sex. INFO [2025-10-07 21:17:41] Removing 228 intervals with missing log.ratio. INFO [2025-10-07 21:17:41] Removing 22 small (< 5bp) intervals. INFO [2025-10-07 21:17:41] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2025-10-07 21:17:41] No normalDB provided. Provide one for better results. INFO [2025-10-07 21:17:41] Removing 1724 low count (< 100 total reads) intervals. INFO [2025-10-07 21:17:41] Removing 6 low coverage (< 15.0000X) intervals. INFO [2025-10-07 21:17:41] Using 8050 intervals (8050 on-target, 0 off-target). INFO [2025-10-07 21:17:41] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2025-10-07 21:17:41] No interval.file provided. Cannot check for any GC-biases. INFO [2025-10-07 21:17:41] Loading VCF... INFO [2025-10-07 21:17:41] Found 127 variants in VCF file. INFO [2025-10-07 21:17:42] 127 (100.0%) variants annotated as likely germline (DB INFO flag). FATAL [2025-10-07 21:17:42] Different chromosome names in coverage and VCF. FATAL [2025-10-07 21:17:42] FATAL [2025-10-07 21:17:42] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:17:42] parameters (PureCN 2.15.4). INFO [2025-10-07 21:17:42] ------------------------------------------------------------ INFO [2025-10-07 21:17:42] PureCN 2.15.4 INFO [2025-10-07 21:17:42] ------------------------------------------------------------ INFO [2025-10-07 21:17:42] Loading coverage files... INFO [2025-10-07 21:17:42] Mean target coverages: 112X (tumor) 99X (normal). WARN [2025-10-07 21:17:42] Allosome coverage missing, cannot determine sex. WARN [2025-10-07 21:17:42] Allosome coverage missing, cannot determine sex. FATAL [2025-10-07 21:17:42] tumor.coverage.file and interval.file do not align. FATAL [2025-10-07 21:17:42] FATAL [2025-10-07 21:17:42] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:17:42] parameters (PureCN 2.15.4). INFO [2025-10-07 21:17:42] ------------------------------------------------------------ INFO [2025-10-07 21:17:42] PureCN 2.15.4 INFO [2025-10-07 21:17:42] ------------------------------------------------------------ INFO [2025-10-07 21:17:42] Loading coverage files... INFO [2025-10-07 21:17:42] Mean target coverages: 112X (tumor) 99X (normal). WARN [2025-10-07 21:17:42] Allosome coverage missing, cannot determine sex. WARN [2025-10-07 21:17:42] Allosome coverage missing, cannot determine sex. INFO [2025-10-07 21:17:42] Removing 228 intervals with missing log.ratio. INFO [2025-10-07 21:17:42] Removing 15 low/high GC targets. INFO [2025-10-07 21:17:42] Removing 21 small (< 5bp) intervals. INFO [2025-10-07 21:17:42] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2025-10-07 21:17:42] No normalDB provided. Provide one for better results. INFO [2025-10-07 21:17:42] Removing 1718 low count (< 100 total reads) intervals. INFO [2025-10-07 21:17:42] Removing 6 low coverage (< 15.0000X) intervals. INFO [2025-10-07 21:17:42] Removing 36 low mappability intervals. INFO [2025-10-07 21:17:42] Using 8006 intervals (8006 on-target, 0 off-target). INFO [2025-10-07 21:17:42] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2025-10-07 21:17:42] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio). INFO [2025-10-07 21:17:42] Loading VCF... INFO [2025-10-07 21:17:42] Found 127 variants in VCF file. INFO [2025-10-07 21:17:42] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2025-10-07 21:17:42] LIB-02240e4 is tumor in VCF file. INFO [2025-10-07 21:17:42] No homozygous variants in VCF, provide unfiltered VCF. INFO [2025-10-07 21:17:42] Removing 1 non heterozygous (in matched normal) germline SNPs. INFO [2025-10-07 21:17:42] Removing 0 low quality variants with non-offset BQ < 25. INFO [2025-10-07 21:17:42] Base quality scores range from 29 to 35 (offset by 1) INFO [2025-10-07 21:17:42] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS. INFO [2025-10-07 21:17:43] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. INFO [2025-10-07 21:17:43] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding). INFO [2025-10-07 21:17:43] 1.2% of targets contain variants. INFO [2025-10-07 21:17:43] Removing 11 variants outside intervals. INFO [2025-10-07 21:17:43] Found SOMATIC annotation in VCF. INFO [2025-10-07 21:17:43] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. INFO [2025-10-07 21:17:43] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970. INFO [2025-10-07 21:17:43] Excluding 0 novel or poor quality variants from segmentation. INFO [2025-10-07 21:17:43] Sample sex: ? INFO [2025-10-07 21:17:43] Segmenting data... INFO [2025-10-07 21:17:43] Loading pre-computed boundaries for DNAcopy... INFO [2025-10-07 21:17:43] Setting undo.SD parameter to 1.000000. INFO [2025-10-07 21:17:43] Setting prune.hclust.h parameter to 0.200000. INFO [2025-10-07 21:17:43] Found 59 segments with median size of 17.67Mb. INFO [2025-10-07 21:17:43] Using 114 variants. INFO [2025-10-07 21:17:43] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30) INFO [2025-10-07 21:17:43] 2D-grid search of purity and ploidy... INFO [2025-10-07 21:17:43] Local optima: 0.63/1.9 INFO [2025-10-07 21:17:43] Testing local optimum 1/1 at purity 0.63 and total ploidy 1.90... INFO [2025-10-07 21:17:44] Fitting variants with beta model for local optimum 1/1... INFO [2025-10-07 21:17:44] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01. INFO [2025-10-07 21:17:45] Optimized purity: 0.65 INFO [2025-10-07 21:17:45] Done. INFO [2025-10-07 21:17:45] ------------------------------------------------------------ INFO [2025-10-07 21:17:45] ------------------------------------------------------------ INFO [2025-10-07 21:17:45] PureCN 2.15.4 INFO [2025-10-07 21:17:45] ------------------------------------------------------------ INFO [2025-10-07 21:17:45] Loading coverage files... INFO [2025-10-07 21:17:45] Mean target coverages: 112X (tumor) 99X (normal). WARN [2025-10-07 21:17:45] Allosome coverage missing, cannot determine sex. WARN [2025-10-07 21:17:45] Allosome coverage missing, cannot determine sex. INFO [2025-10-07 21:17:45] Removing 228 intervals with missing log.ratio. INFO [2025-10-07 21:17:45] Removing 15 low/high GC targets. INFO [2025-10-07 21:17:45] Removing 21 small (< 5bp) intervals. INFO [2025-10-07 21:17:45] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2025-10-07 21:17:45] No normalDB provided. Provide one for better results. INFO [2025-10-07 21:17:45] Removing 1718 low count (< 100 total reads) intervals. INFO [2025-10-07 21:17:45] Removing 6 low coverage (< 15.0000X) intervals. INFO [2025-10-07 21:17:45] Removing 36 low mappability intervals. INFO [2025-10-07 21:17:45] Using 8006 intervals (8006 on-target, 0 off-target). INFO [2025-10-07 21:17:45] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2025-10-07 21:17:45] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio). INFO [2025-10-07 21:17:45] Loading VCF... INFO [2025-10-07 21:17:45] Found 127 variants in VCF file. INFO [2025-10-07 21:17:45] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2025-10-07 21:17:45] LIB-02240e4 is tumor in VCF file. INFO [2025-10-07 21:17:45] No homozygous variants in VCF, provide unfiltered VCF. INFO [2025-10-07 21:17:45] Removing 1 non heterozygous (in matched normal) germline SNPs. INFO [2025-10-07 21:17:45] Removing 0 low quality variants with non-offset BQ < 25. INFO [2025-10-07 21:17:45] Base quality scores range from 29 to 35 (offset by 1) INFO [2025-10-07 21:17:45] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS. INFO [2025-10-07 21:17:45] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. INFO [2025-10-07 21:17:45] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding). INFO [2025-10-07 21:17:45] 1.2% of targets contain variants. INFO [2025-10-07 21:17:45] Removing 11 variants outside intervals. INFO [2025-10-07 21:17:45] Found SOMATIC annotation in VCF. INFO [2025-10-07 21:17:45] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. INFO [2025-10-07 21:17:46] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970. INFO [2025-10-07 21:17:46] Excluding 0 novel or poor quality variants from segmentation. INFO [2025-10-07 21:17:46] Sample sex: ? INFO [2025-10-07 21:17:46] Segmenting data... INFO [2025-10-07 21:17:46] Loading pre-computed boundaries for DNAcopy... INFO [2025-10-07 21:17:46] Setting undo.SD parameter to 1.000000. INFO [2025-10-07 21:17:46] Setting prune.hclust.h parameter to 0.200000. INFO [2025-10-07 21:17:46] Found 59 segments with median size of 17.67Mb. INFO [2025-10-07 21:17:46] Using 114 variants. INFO [2025-10-07 21:17:46] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30) INFO [2025-10-07 21:17:46] 2D-grid search of purity and ploidy... INFO [2025-10-07 21:17:46] Local optima: 0.63/1.9 INFO [2025-10-07 21:17:46] Testing local optimum 1/1 at purity 0.63 and total ploidy 1.90... INFO [2025-10-07 21:17:47] Fitting variants with beta model for local optimum 1/1... WARN [2025-10-07 21:17:47] Some gene symbols found on multiple chromosomes. Use of approved symbols suggested. INFO [2025-10-07 21:17:47] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01. INFO [2025-10-07 21:17:48] Optimized purity: 0.65 INFO [2025-10-07 21:17:48] Done. INFO [2025-10-07 21:17:48] ------------------------------------------------------------ FATAL [2025-10-07 21:17:48] chr1 not valid chromosome name(s). Valid names are: FATAL [2025-10-07 21:17:48] 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22 FATAL [2025-10-07 21:17:48] FATAL [2025-10-07 21:17:48] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:17:48] parameters (PureCN 2.15.4). INFO [2025-10-07 21:17:48] ------------------------------------------------------------ INFO [2025-10-07 21:17:48] PureCN 2.15.4 INFO [2025-10-07 21:17:48] ------------------------------------------------------------ INFO [2025-10-07 21:17:48] Loading coverage files... WARN [2025-10-07 21:17:48] Provided sampleid (Sample2) does not match Sample1 found in segmentation. WARN [2025-10-07 21:17:48] Allosome coverage missing, cannot determine sex. WARN [2025-10-07 21:17:48] Allosome coverage missing, cannot determine sex. INFO [2025-10-07 21:17:48] Removing 10 intervals with missing log.ratio. INFO [2025-10-07 21:17:48] Using 10039 intervals (10039 on-target, 0 off-target). INFO [2025-10-07 21:17:48] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2025-10-07 21:17:48] Loading VCF... INFO [2025-10-07 21:17:48] Found 127 variants in VCF file. INFO [2025-10-07 21:17:48] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2025-10-07 21:17:48] LIB-02240e4 is tumor in VCF file. INFO [2025-10-07 21:17:48] No homozygous variants in VCF, provide unfiltered VCF. INFO [2025-10-07 21:17:48] Removing 1 non heterozygous (in matched normal) germline SNPs. INFO [2025-10-07 21:17:48] Removing 0 low quality variants with non-offset BQ < 25. INFO [2025-10-07 21:17:48] Base quality scores range from 29 to 35 (offset by 1) INFO [2025-10-07 21:17:48] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS. INFO [2025-10-07 21:17:48] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. INFO [2025-10-07 21:17:48] Total size of targeted genomic region: 1.71Mb (2.70Mb with 50bp padding). INFO [2025-10-07 21:17:48] 1.0% of targets contain variants. INFO [2025-10-07 21:17:48] Removing 0 variants outside intervals. INFO [2025-10-07 21:17:48] Found SOMATIC annotation in VCF. INFO [2025-10-07 21:17:48] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. INFO [2025-10-07 21:17:48] Found SOMATIC annotation in VCF. Setting mapping bias to 0.976. INFO [2025-10-07 21:17:48] Excluding 0 novel or poor quality variants from segmentation. INFO [2025-10-07 21:17:48] Sample sex: ? INFO [2025-10-07 21:17:48] Segmenting data... INFO [2025-10-07 21:17:48] Loaded provided segmentation file example_seg.txt (format DNAcopy). WARN [2025-10-07 21:17:48] Provided sampleid (Sample2) does not match Sample1 found in segmentation. INFO [2025-10-07 21:17:48] Re-centering provided segment means (offset -0.0033). INFO [2025-10-07 21:17:48] Loading pre-computed boundaries for DNAcopy... INFO [2025-10-07 21:17:48] Setting undo.SD parameter to 0.000000. Setting multi-figure configuration INFO [2025-10-07 21:17:48] Setting prune.hclust.h parameter to 0.200000. INFO [2025-10-07 21:17:48] Found 54 segments with median size of 24.88Mb. INFO [2025-10-07 21:17:48] Using 125 variants. INFO [2025-10-07 21:17:48] Mean standard deviation of log-ratios: 0.40 (MAPD: 0.00) INFO [2025-10-07 21:17:48] 2D-grid search of purity and ploidy... INFO [2025-10-07 21:17:49] Local optima: 0.6/1.9 INFO [2025-10-07 21:17:49] Testing local optimum 1/1 at purity 0.60 and total ploidy 1.90... INFO [2025-10-07 21:17:49] Fitting variants with beta model for local optimum 1/1... INFO [2025-10-07 21:17:49] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01. INFO [2025-10-07 21:17:50] Optimized purity: 0.65 INFO [2025-10-07 21:17:50] Done. INFO [2025-10-07 21:17:50] ------------------------------------------------------------ WARN [2025-10-07 21:17:50] Allosome coverage missing, cannot determine sex. WARN [2025-10-07 21:17:50] Allosome coverage missing, cannot determine sex. Setting multi-figure configuration FATAL [2025-10-07 21:17:53] Segmentation file expected with colnames ID, chrom, loc.start, loc.end, FATAL [2025-10-07 21:17:53] num.mark, seg.mean FATAL [2025-10-07 21:17:53] FATAL [2025-10-07 21:17:53] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:17:53] parameters (PureCN 2.15.4). FATAL [2025-10-07 21:17:53] seg.file contains multiple samples and sampleid missing. FATAL [2025-10-07 21:17:53] FATAL [2025-10-07 21:17:53] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:17:53] parameters (PureCN 2.15.4). FATAL [2025-10-07 21:17:53] seg.file contains multiple samples and sampleid does not match any. FATAL [2025-10-07 21:17:53] FATAL [2025-10-07 21:17:53] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:17:53] parameters (PureCN 2.15.4). WARN [2025-10-07 21:17:53] Allosome coverage missing, cannot determine sex. WARN [2025-10-07 21:17:53] Allosome coverage missing, cannot determine sex. WARN [2025-10-07 21:17:56] Allosome coverage missing, cannot determine sex. WARN [2025-10-07 21:17:56] Allosome coverage missing, cannot determine sex. WARN [2025-10-07 21:17:56] Provided sampleid (example_tumor.txt.gz) does not match Sample1 found in segmentation. WARN [2025-10-07 21:17:57] Allosome coverage missing, cannot determine sex. WARN [2025-10-07 21:17:57] Allosome coverage missing, cannot determine sex. WARN [2025-10-07 21:17:57] No normalDB provided. Provide one for better results. WARN [2025-10-07 21:18:00] Allosome coverage missing, cannot determine sex. WARN [2025-10-07 21:18:00] Allosome coverage missing, cannot determine sex. WARN [2025-10-07 21:18:00] Provided sampleid (Sample.1) does not match Sample1 found in segmentation. Setting multi-figure configuration WARN [2025-10-07 21:18:03] Allosome coverage missing, cannot determine sex. WARN [2025-10-07 21:18:03] Allosome coverage missing, cannot determine sex. WARN [2025-10-07 21:18:03] No normalDB provided. Provide one for better results. WARN [2025-10-07 21:18:03] Sampleid looks like a normal in VCF, not like a tumor. WARN [2025-10-07 21:18:05] Allosome coverage missing, cannot determine sex. WARN [2025-10-07 21:18:05] Allosome coverage missing, cannot determine sex. FATAL [2025-10-07 21:18:05] normalDB not a valid normalDB object. Use createNormalDatabase to FATAL [2025-10-07 21:18:05] create one. FATAL [2025-10-07 21:18:05] FATAL [2025-10-07 21:18:05] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:18:05] parameters (PureCN 2.15.4). WARN [2025-10-07 21:18:06] You are likely not using the correct baits file! WARN [2025-10-07 21:18:06] Allosome coverage missing, cannot determine sex. WARN [2025-10-07 21:18:06] Allosome coverage missing, cannot determine sex. WARN [2025-10-07 21:18:07] Allosome coverage missing, cannot determine sex. WARN [2025-10-07 21:18:07] Allosome coverage missing, cannot determine sex. FATAL [2025-10-07 21:18:07] normalDB appears to be empty. FATAL [2025-10-07 21:18:07] FATAL [2025-10-07 21:18:07] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:18:07] parameters (PureCN 2.15.4). WARN [2025-10-07 21:18:07] Allosome coverage missing, cannot determine sex. WARN [2025-10-07 21:18:07] Allosome coverage missing, cannot determine sex. WARN [2025-10-07 21:18:07] Intervals in coverage and interval.file have conflicting on/off-target annotation. WARN [2025-10-07 21:18:11] Allosome coverage missing, cannot determine sex. WARN [2025-10-07 21:18:11] Allosome coverage missing, cannot determine sex. FATAL [2025-10-07 21:18:11] Seqlevels missing in provided segmentation: 6 FATAL [2025-10-07 21:18:11] FATAL [2025-10-07 21:18:11] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:18:11] parameters (PureCN 2.15.4). sh: gatk: command not found WARN [2025-10-07 21:18:12] Cannot find gatk binary in path. WARN [2025-10-07 21:18:12] Allosome coverage missing, cannot determine sex. WARN [2025-10-07 21:18:12] Allosome coverage missing, cannot determine sex. WARN [2025-10-07 21:18:12] No normalDB provided. Provide one for better results. FATAL [2025-10-07 21:18:12] segmentationHclust requires an input segmentation. FATAL [2025-10-07 21:18:12] FATAL [2025-10-07 21:18:12] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:18:12] parameters (PureCN 2.15.4). WARN [2025-10-07 21:18:12] Allosome coverage missing, cannot determine sex. WARN [2025-10-07 21:18:12] Allosome coverage missing, cannot determine sex. WARN [2025-10-07 21:18:12] No normalDB provided. Provide one for better results. FATAL [2025-10-07 21:18:22] The normal.panel.vcf.file contains only a single sample. FATAL [2025-10-07 21:18:22] FATAL [2025-10-07 21:18:22] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:18:22] parameters (PureCN 2.15.4). FATAL [2025-10-07 21:18:22] mapping.bias.file must be a file with *.rds suffix. FATAL [2025-10-07 21:18:22] FATAL [2025-10-07 21:18:22] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:18:22] parameters (PureCN 2.15.4). Failed with error: 'there is no package called 'genomicsdb'' FATAL [2025-10-07 21:18:22] min.normals (0) must be >= 1. FATAL [2025-10-07 21:18:22] FATAL [2025-10-07 21:18:22] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:18:22] parameters (PureCN 2.15.4). FATAL [2025-10-07 21:18:22] min.normals (10) cannot be larger than min.normals.assign.betafit (3). FATAL [2025-10-07 21:18:22] FATAL [2025-10-07 21:18:22] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:18:22] parameters (PureCN 2.15.4). FATAL [2025-10-07 21:18:22] min.normals.assign.betafit (10) cannot be larger than FATAL [2025-10-07 21:18:22] min.normals.betafit (7). FATAL [2025-10-07 21:18:22] FATAL [2025-10-07 21:18:22] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:18:22] parameters (PureCN 2.15.4). FATAL [2025-10-07 21:18:22] min.normals.betafit (20) cannot be larger than FATAL [2025-10-07 21:18:22] min.normals.position.specific.fit (10). FATAL [2025-10-07 21:18:22] FATAL [2025-10-07 21:18:22] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:18:22] parameters (PureCN 2.15.4). FATAL [2025-10-07 21:18:22] min.betafit.rho not within expected range or format. FATAL [2025-10-07 21:18:22] FATAL [2025-10-07 21:18:22] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:18:22] parameters (PureCN 2.15.4). FATAL [2025-10-07 21:18:23] max.betafit.rho not within expected range or format. FATAL [2025-10-07 21:18:23] FATAL [2025-10-07 21:18:23] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:18:23] parameters (PureCN 2.15.4). FATAL [2025-10-07 21:18:23] min.betafit.rho (0.9) cannot be larger than max.betafit.rho (0.2). FATAL [2025-10-07 21:18:23] FATAL [2025-10-07 21:18:23] This is most likely a user error due to invalid input data or FATAL [2025-10-07 21:18:23] parameters (PureCN 2.15.4). [ FAIL 0 | WARN 12 | SKIP 2 | PASS 405 ] ══ Skipped tests (2) ═══════════════════════════════════════════════════════════ • gatk binary > 4.1.7.0 required (1): 'test_segmentation.R:25:4' • genomicsdb required (1): 'test_setMappingBiasVcf.R:45:5' [ FAIL 0 | WARN 12 | SKIP 2 | PASS 405 ] > > proc.time() user system elapsed 144.783 4.657 138.797
PureCN.Rcheck/PureCN-Ex.timings
name | user | system | elapsed | |
adjustLogRatio | 0.850 | 0.014 | 0.889 | |
annotateTargets | 2.655 | 0.103 | 2.856 | |
bootstrapResults | 0.243 | 0.020 | 0.280 | |
calculateBamCoverageByInterval | 0.081 | 0.003 | 0.090 | |
calculateLogRatio | 0.243 | 0.014 | 0.269 | |
calculateMappingBiasGatk4 | 0 | 0 | 0 | |
calculateMappingBiasVcf | 0.668 | 0.019 | 0.748 | |
calculatePowerDetectSomatic | 0.494 | 0.007 | 0.515 | |
calculateTangentNormal | 1.031 | 0.019 | 1.064 | |
callAlterations | 0.054 | 0.002 | 0.057 | |
callAlterationsFromSegmentation | 0.556 | 0.015 | 0.572 | |
callAmplificationsInLowPurity | 13.863 | 0.171 | 14.049 | |
callCIN | 0.084 | 0.002 | 0.086 | |
callLOH | 0.073 | 0.001 | 0.075 | |
callMutationBurden | 0.565 | 0.011 | 0.578 | |
centromeres | 0.001 | 0.001 | 0.001 | |
correctCoverageBias | 0.587 | 0.016 | 0.603 | |
createCurationFile | 0.150 | 0.004 | 0.156 | |
createNormalDatabase | 0.844 | 0.012 | 0.856 | |
filterIntervals | 7.235 | 0.184 | 7.430 | |
filterVcfBasic | 0.249 | 0.003 | 0.252 | |
filterVcfMuTect | 0.241 | 0.002 | 0.243 | |
filterVcfMuTect2 | 0.213 | 0.003 | 0.216 | |
findFocal | 3.700 | 0.024 | 3.760 | |
findHighQualitySNPs | 0.574 | 0.012 | 0.584 | |
getSexFromCoverage | 0.092 | 0.005 | 0.097 | |
getSexFromVcf | 0.093 | 0.002 | 0.095 | |
plotAbs | 0.088 | 0.004 | 0.093 | |
poolCoverage | 0.235 | 0.012 | 0.247 | |
predictSomatic | 0.165 | 0.002 | 0.167 | |
preprocessIntervals | 0.264 | 0.005 | 0.276 | |
processMultipleSamples | 0.940 | 0.016 | 0.964 | |
readAllelicCountsFile | 0.207 | 0.001 | 0.210 | |
readCoverageFile | 0.090 | 0.005 | 0.094 | |
readCurationFile | 0.090 | 0.003 | 0.094 | |
readIntervalFile | 0.063 | 0.003 | 0.066 | |
readLogRatioFile | 0.026 | 0.001 | 0.027 | |
readSegmentationFile | 0.003 | 0.001 | 0.004 | |
runAbsoluteCN | 6.056 | 0.122 | 6.233 | |
segmentationCBS | 2.926 | 0.023 | 2.961 | |
segmentationGATK4 | 0.001 | 0.000 | 0.001 | |
segmentationHclust | 5.873 | 0.110 | 5.989 | |
segmentationPSCBS | 12.960 | 0.166 | 13.143 | |
setMappingBiasVcf | 0.120 | 0.004 | 0.123 | |
setPriorVcf | 0.096 | 0.003 | 0.099 | |