Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-25 12:07 -0400 (Thu, 25 Sep 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" | 4831 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4618 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4562 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4560 |
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 1645/2334 | 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: 2025-09-24 21:07:05 -0400 (Wed, 24 Sep 2025) |
EndedAt: 2025-09-24 21:12:43 -0400 (Wed, 24 Sep 2025) |
EllapsedTime: 338.1 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 13.631 0.154 14.617 segmentationPSCBS 13.521 0.153 13.791 filterIntervals 7.441 0.146 7.654 runAbsoluteCN 5.818 0.118 6.005 segmentationHclust 5.396 0.097 5.544 * 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 [2025-09-24 21:10:28] Attempted adding gene symbols to intervals. Heuristics have been used to pick symbols for overlapping genes. WARN [2025-09-24 21:10:28] Chromosome naming style of txdb file (UCSC) was different from interval file (Ensembl). WARN [2025-09-24 21:10:30] Attempted adding gene symbols to intervals. Heuristics have been used to pick symbols for overlapping genes. FATAL [2025-09-24 21:10:31] tumor.coverage.file and interval.file do not align. FATAL [2025-09-24 21:10:31] FATAL [2025-09-24 21:10:31] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:10:31] parameters (PureCN 2.15.4). WARN [2025-09-24 21:10:31] Cannot find all contig lengths while exporting interval file. INFO [2025-09-24 21:10:31] Processing seq1:1-21 (1/3)... INFO [2025-09-24 21:10:31] Processing seq1:1227-1247 (2/3)... INFO [2025-09-24 21:10:32] Processing seq2:594-614 (3/3)... WARN [2025-09-24 21:10:32] Large potential mis-calibration of on- and off-target log2 ratios: 0.26 FATAL [2025-09-24 21:10:32] Need either f or purity and ploidy. FATAL [2025-09-24 21:10:32] FATAL [2025-09-24 21:10:32] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:10:32] parameters (PureCN 2.15.4). FATAL [2025-09-24 21:10:32] f not in expected range. FATAL [2025-09-24 21:10:32] FATAL [2025-09-24 21:10:32] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:10:32] parameters (PureCN 2.15.4). FATAL [2025-09-24 21:10:32] coverage not in expected range (>=2) FATAL [2025-09-24 21:10:32] FATAL [2025-09-24 21:10:32] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:10:32] parameters (PureCN 2.15.4). FATAL [2025-09-24 21:10:32] purity not in expected range. FATAL [2025-09-24 21:10:32] FATAL [2025-09-24 21:10:32] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:10:32] parameters (PureCN 2.15.4). FATAL [2025-09-24 21:10:32] ploidy not in expected range. FATAL [2025-09-24 21:10:32] FATAL [2025-09-24 21:10:32] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:10:32] parameters (PureCN 2.15.4). FATAL [2025-09-24 21:10:32] cell.fraction not in expected range. FATAL [2025-09-24 21:10:32] FATAL [2025-09-24 21:10:32] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:10:32] parameters (PureCN 2.15.4). INFO [2025-09-24 21:10:33] 576 on-target bins with low coverage in all samples. WARN [2025-09-24 21:10:33] You are likely not using the correct baits file! WARN [2025-09-24 21:10:33] Allosome coverage missing, cannot determine sex. WARN [2025-09-24 21:10:33] Allosome coverage missing, cannot determine sex. INFO [2025-09-24 21:10:33] Processing on-target regions... INFO [2025-09-24 21:10:33] Removing 930 intervals with low coverage in normalDB. INFO [2025-09-24 21:10:33] Removing 1 intervals with zero coverage in more than 3% of normalDB. INFO [2025-09-24 21:10:34] Tumor/normal noise ratio: 19.041 WARN [2025-09-24 21:10:34] Extensive noise in tumor compared to normals. INFO [2025-09-24 21:10:49] Tumor/normal noise ratio: 19.041 WARN [2025-09-24 21:10:49] Extensive noise in tumor compared to normals. INFO [2025-09-24 21:10:51] Using BiocParallel for parallel optimization. FATAL [2025-09-24 21:10:55] pvalue.cutoff not within expected range or format. FATAL [2025-09-24 21:10:55] FATAL [2025-09-24 21:10:55] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:10:55] parameters (PureCN 2.15.4). FATAL [2025-09-24 21:10:55] pvalue.cutoff not within expected range or format. FATAL [2025-09-24 21:10:55] FATAL [2025-09-24 21:10:55] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:10:55] parameters (PureCN 2.15.4). FATAL [2025-09-24 21:10:55] percentile.cutoff not in expected range (0 to 100). FATAL [2025-09-24 21:10:55] FATAL [2025-09-24 21:10:55] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:10:55] parameters (PureCN 2.15.4). FATAL [2025-09-24 21:10:55] percentile.cutoff not in expected range (0 to 100). FATAL [2025-09-24 21:10:55] FATAL [2025-09-24 21:10:55] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:10:55] parameters (PureCN 2.15.4). FATAL [2025-09-24 21:10:55] purity not within expected range or format. FATAL [2025-09-24 21:10:55] FATAL [2025-09-24 21:10:55] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:10:55] parameters (PureCN 2.15.4). FATAL [2025-09-24 21:10:55] purity not within expected range or format. FATAL [2025-09-24 21:10:55] FATAL [2025-09-24 21:10:55] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:10:55] parameters (PureCN 2.15.4). INFO [2025-09-24 21:10:56] ------------------------------------------------------------ INFO [2025-09-24 21:10:56] PureCN 2.15.4 INFO [2025-09-24 21:10:56] ------------------------------------------------------------ INFO [2025-09-24 21:10:56] Loading coverage files... INFO [2025-09-24 21:10:56] Mean target coverages: 112X (tumor) 99X (normal). WARN [2025-09-24 21:10:56] Allosome coverage missing, cannot determine sex. WARN [2025-09-24 21:10:56] Allosome coverage missing, cannot determine sex. INFO [2025-09-24 21:10:56] Removing 228 intervals with missing log.ratio. INFO [2025-09-24 21:10:56] Removing 22 small (< 5bp) intervals. INFO [2025-09-24 21:10:56] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2025-09-24 21:10:56] No normalDB provided. Provide one for better results. INFO [2025-09-24 21:10:56] Removing 1724 low count (< 100 total reads) intervals. INFO [2025-09-24 21:10:56] Removing 6 low coverage (< 15.0000X) intervals. INFO [2025-09-24 21:10:56] Using 8050 intervals (8050 on-target, 0 off-target). INFO [2025-09-24 21:10:56] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2025-09-24 21:10:56] No interval.file provided. Cannot check for any GC-biases. INFO [2025-09-24 21:10:56] Loading VCF... INFO [2025-09-24 21:10:56] Found 127 variants in VCF file. INFO [2025-09-24 21:10:56] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2025-09-24 21:10:56] LIB-02240e4 is tumor in VCF file. INFO [2025-09-24 21:10:56] No homozygous variants in VCF, provide unfiltered VCF. INFO [2025-09-24 21:10:56] Removing 1 non heterozygous (in matched normal) germline SNPs. INFO [2025-09-24 21:10:56] Removing 0 low quality variants with non-offset BQ < 25. INFO [2025-09-24 21:10:57] Base quality scores range from 29 to 35 (offset by 1) INFO [2025-09-24 21:10:57] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS. INFO [2025-09-24 21:10:57] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. INFO [2025-09-24 21:10:57] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding). INFO [2025-09-24 21:10:57] 1.2% of targets contain variants. INFO [2025-09-24 21:10:57] Removing 4 variants outside intervals. INFO [2025-09-24 21:10:57] Found SOMATIC annotation in VCF. INFO [2025-09-24 21:10:57] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. INFO [2025-09-24 21:10:57] Found SOMATIC annotation in VCF. Setting mapping bias to 0.972. INFO [2025-09-24 21:10:57] Excluding 0 novel or poor quality variants from segmentation. INFO [2025-09-24 21:10:57] Sample sex: ? INFO [2025-09-24 21:10:57] Segmenting data... INFO [2025-09-24 21:10:57] Loading pre-computed boundaries for DNAcopy... INFO [2025-09-24 21:10:57] Setting undo.SD parameter to 1.000000. INFO [2025-09-24 21:10:57] Setting prune.hclust.h parameter to 0.200000. INFO [2025-09-24 21:10:57] Found 59 segments with median size of 17.67Mb. INFO [2025-09-24 21:10:57] Using 121 variants. INFO [2025-09-24 21:10:57] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30) INFO [2025-09-24 21:10:57] 2D-grid search of purity and ploidy... INFO [2025-09-24 21:10:58] Local optima: 0.63/1.9, 0.5/2 INFO [2025-09-24 21:10:58] Testing local optimum 1/2 at purity 0.63 and total ploidy 1.90... INFO [2025-09-24 21:10:58] Testing local optimum 2/2 at purity 0.50 and total ploidy 2.00... INFO [2025-09-24 21:10:58] Skipping 1 solutions that converged to the same optima. INFO [2025-09-24 21:10:58] Fitting variants with beta model for local optimum 1/2... INFO [2025-09-24 21:10:58] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01. INFO [2025-09-24 21:10:59] Optimized purity: 0.65 INFO [2025-09-24 21:10:59] Done. INFO [2025-09-24 21:10:59] ------------------------------------------------------------ INFO [2025-09-24 21:11:00] Estimating callable regions. FATAL [2025-09-24 21:11:00] exclude not a GRanges object. FATAL [2025-09-24 21:11:00] FATAL [2025-09-24 21:11:00] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:11:00] parameters (PureCN 2.15.4). FATAL [2025-09-24 21:11:00] callable not a GRanges object. FATAL [2025-09-24 21:11:00] FATAL [2025-09-24 21:11:00] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:11:00] parameters (PureCN 2.15.4). WARN [2025-09-24 21:11:03] tumor.coverage.file and interval.file do not align. INFO [2025-09-24 21:11:04] No Gene column in interval.file. You won't get gene-level calls. FATAL [2025-09-24 21:11:04] No gc_bias column in interval.file. FATAL [2025-09-24 21:11:04] FATAL [2025-09-24 21:11:04] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:11:04] parameters (PureCN 2.15.4). FATAL [2025-09-24 21:11:04] Provided coverage is zero, most likely due to a corrupt BAM file. FATAL [2025-09-24 21:11:04] FATAL [2025-09-24 21:11:04] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:11:04] parameters (PureCN 2.15.4). INFO [2025-09-24 21:11:05] No reptiming column in interval.file. INFO [2025-09-24 21:11:06] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpM1a86W/file157cd404a9872.rds... INFO [2025-09-24 21:11:06] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpM1a86W/file157cd404a9872.rds... INFO [2025-09-24 21:11:06] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpM1a86W/file157cd404a9872.rds... INFO [2025-09-24 21:11:06] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpM1a86W/file157cd404a9872.rds... INFO [2025-09-24 21:11:07] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpM1a86W/file157cd404a9872.rds... INFO [2025-09-24 21:11:07] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpM1a86W/file157cd404a9872.rds... FATAL [2025-09-24 21:11:07] Purity or Ploidy not numeric or in expected range. FATAL [2025-09-24 21:11:07] FATAL [2025-09-24 21:11:07] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:11:07] parameters (PureCN 2.15.4). INFO [2025-09-24 21:11:07] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpM1a86W/file157cd404a9872.rds... INFO [2025-09-24 21:11:07] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpM1a86W/file157cd404a9872.rds... FATAL [2025-09-24 21:11:07] 'Failed' column in FATAL [2025-09-24 21:11:07] /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpM1a86W/file157cd404a9872.csv FATAL [2025-09-24 21:11:07] not logical(1). FATAL [2025-09-24 21:11:07] FATAL [2025-09-24 21:11:07] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:11:07] parameters (PureCN 2.15.4). INFO [2025-09-24 21:11:07] 576 on-target bins with low coverage in all samples. WARN [2025-09-24 21:11:07] You are likely not using the correct baits file! WARN [2025-09-24 21:11:07] Allosome coverage missing, cannot determine sex. WARN [2025-09-24 21:11:07] Allosome coverage missing, cannot determine sex. INFO [2025-09-24 21:11:07] Processing on-target regions... INFO [2025-09-24 21:11:07] Removing 930 intervals with low coverage in normalDB. INFO [2025-09-24 21:11:07] Removing 1 intervals with zero coverage in more than 3% of normalDB. INFO [2025-09-24 21:11:08] 576 on-target bins with low coverage in all samples. WARN [2025-09-24 21:11:08] You are likely not using the correct baits file! WARN [2025-09-24 21:11:08] Allosome coverage missing, cannot determine sex. WARN [2025-09-24 21:11:08] Allosome coverage missing, cannot determine sex. INFO [2025-09-24 21:11:08] Processing on-target regions... INFO [2025-09-24 21:11:09] Removing 930 intervals with low coverage in normalDB. INFO [2025-09-24 21:11:09] Removing 1 intervals with zero coverage in more than 3% of normalDB. INFO [2025-09-24 21:11:09] 576 on-target bins with low coverage in all samples. WARN [2025-09-24 21:11:09] You are likely not using the correct baits file! WARN [2025-09-24 21:11:09] Allosome coverage missing, cannot determine sex. WARN [2025-09-24 21:11:09] Allosome coverage missing, cannot determine sex. INFO [2025-09-24 21:11:09] Processing on-target regions... INFO [2025-09-24 21:11:10] Removing 930 intervals with low coverage in normalDB. INFO [2025-09-24 21:11:10] Removing 1 intervals with zero coverage in more than 3% of normalDB. WARN [2025-09-24 21:11:10] Allosome coverage missing, cannot determine sex. INFO [2025-09-24 21:11:10] Sample sex: NA WARN [2025-09-24 21:11:10] Allosome coverage missing, cannot determine sex. INFO [2025-09-24 21:11:10] Sample sex: NA INFO [2025-09-24 21:11:10] 576 on-target bins with low coverage in all samples. WARN [2025-09-24 21:11:10] You are likely not using the correct baits file! WARN [2025-09-24 21:11:10] Allosome coverage missing, cannot determine sex. WARN [2025-09-24 21:11:10] Allosome coverage missing, cannot determine sex. FATAL [2025-09-24 21:11:10] Length of normal.coverage.files and sex different FATAL [2025-09-24 21:11:10] FATAL [2025-09-24 21:11:10] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:11:10] parameters (PureCN 2.15.4). WARN [2025-09-24 21:11:12] Target intervals were not sorted. INFO [2025-09-24 21:11:12] 560 on-target bins with low coverage in all samples. WARN [2025-09-24 21:11:12] You are likely not using the correct baits file! WARN [2025-09-24 21:11:12] Allosome coverage missing, cannot determine sex. WARN [2025-09-24 21:11:12] Allosome coverage missing, cannot determine sex. WARN [2025-09-24 21:11:12] Allosome coverage missing, cannot determine sex. INFO [2025-09-24 21:11:12] Processing on-target regions... INFO [2025-09-24 21:11:12] Removing 978 intervals with low coverage in normalDB. INFO [2025-09-24 21:11:12] Removing 11 intervals with zero coverage in more than 3% of normalDB. FATAL [2025-09-24 21:11:13] tumor.coverage.file and normalDB do not align. FATAL [2025-09-24 21:11:13] FATAL [2025-09-24 21:11:13] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:11:13] parameters (PureCN 2.15.4). FATAL [2025-09-24 21:11:13] At least 2 normal.coverage.files required. FATAL [2025-09-24 21:11:13] FATAL [2025-09-24 21:11:13] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:11:13] parameters (PureCN 2.15.4). INFO [2025-09-24 21:11:14] ------------------------------------------------------------ INFO [2025-09-24 21:11:14] PureCN 2.15.4 INFO [2025-09-24 21:11:14] ------------------------------------------------------------ INFO [2025-09-24 21:11:14] Loading coverage files... INFO [2025-09-24 21:11:14] Mean target coverages: 112X (tumor) 99X (normal). WARN [2025-09-24 21:11:14] Allosome coverage missing, cannot determine sex. WARN [2025-09-24 21:11:14] Allosome coverage missing, cannot determine sex. INFO [2025-09-24 21:11:14] Removing 228 intervals with missing log.ratio. FATAL [2025-09-24 21:11:14] normalDB incompatible with this PureCN version. Please re-run FATAL [2025-09-24 21:11:14] NormalDB.R. FATAL [2025-09-24 21:11:14] FATAL [2025-09-24 21:11:14] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:11:14] parameters (PureCN 2.15.4). FATAL [2025-09-24 21:11:15] normalDB incompatible with this PureCN version. Please re-run FATAL [2025-09-24 21:11:15] NormalDB.R. FATAL [2025-09-24 21:11:15] FATAL [2025-09-24 21:11:15] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:11:15] parameters (PureCN 2.15.4). FATAL [2025-09-24 21:11:15] normal.coverage.files with _coverage.txt and _loess.txt suffix FATAL [2025-09-24 21:11:15] provided. Provide either only GC-normalized or raw coverage files! FATAL [2025-09-24 21:11:15] FATAL [2025-09-24 21:11:15] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:11:15] parameters (PureCN 2.15.4). INFO [2025-09-24 21:11:15] Removing 22 non heterozygous (in matched normal) germline SNPs. INFO [2025-09-24 21:11:15] Removing 19 low quality variants with non-offset BQ < 25. INFO [2025-09-24 21:11:15] Base quality scores range from 24 to 35 (offset by 1) INFO [2025-09-24 21:11:15] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS. INFO [2025-09-24 21:11:15] Initial testing for significant sample cross-contamination: unlikely INFO [2025-09-24 21:11:15] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. INFO [2025-09-24 21:11:15] Removing 22 non heterozygous (in matched normal) germline SNPs. INFO [2025-09-24 21:11:15] Removing 19 low quality variants with non-offset BQ < 25. INFO [2025-09-24 21:11:15] Base quality scores range from 24 to 35 (offset by 1) INFO [2025-09-24 21:11:15] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS. INFO [2025-09-24 21:11:15] Initial testing for significant sample cross-contamination: unlikely INFO [2025-09-24 21:11:15] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. INFO [2025-09-24 21:11:15] Removing 6 blacklisted variants. INFO [2025-09-24 21:11:15] Removing 22 non heterozygous (in matched normal) germline SNPs. INFO [2025-09-24 21:11:15] Removing 19 low quality variants with non-offset BQ < 25. INFO [2025-09-24 21:11:15] Base quality scores range from 24 to 35 (offset by 1) INFO [2025-09-24 21:11:15] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS. INFO [2025-09-24 21:11:15] Initial testing for significant sample cross-contamination: unlikely INFO [2025-09-24 21:11:15] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. WARN [2025-09-24 21:11:15] MuTect stats file lacks contig and position columns. INFO [2025-09-24 21:11:15] Removing 22 non heterozygous (in matched normal) germline SNPs. INFO [2025-09-24 21:11:15] Removing 19 low quality variants with non-offset BQ < 25. INFO [2025-09-24 21:11:15] Base quality scores range from 24 to 35 (offset by 1) INFO [2025-09-24 21:11:16] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS. INFO [2025-09-24 21:11:16] Initial testing for significant sample cross-contamination: unlikely INFO [2025-09-24 21:11:16] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. WARN [2025-09-24 21:11:16] MuTect stats file and VCF file do not align perfectly. Will remove 2325 unmatched variants. WARN [2025-09-24 21:11:16] MuTect stats file lacks failure_reasons column. Keeping all variants listed in stats file. INFO [2025-09-24 21:11:16] Removing 0 non heterozygous (in matched normal) germline SNPs. INFO [2025-09-24 21:11:16] Removing 0 low quality variants with non-offset BQ < 25. INFO [2025-09-24 21:11:16] Base quality scores range from 31 to 33 (offset by 1) INFO [2025-09-24 21:11:16] Minimum number of supporting reads ranges from 3 to 4, depending on coverage and BQS. INFO [2025-09-24 21:11:16] Removing 0 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. INFO [2025-09-24 21:11:16] Removing 22 non heterozygous (in matched normal) germline SNPs. INFO [2025-09-24 21:11:16] Base quality scores range from 7 to 35 (offset by 1) INFO [2025-09-24 21:11:16] Minimum number of supporting reads ranges from 1 to 41, depending on coverage and BQS. INFO [2025-09-24 21:11:16] Initial testing for significant sample cross-contamination: unlikely INFO [2025-09-24 21:11:16] Removing 49 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. INFO [2025-09-24 21:11:16] Removing 22 non heterozygous (in matched normal) germline SNPs. INFO [2025-09-24 21:11:16] Base quality scores range from 7 to 35 (offset by 1) INFO [2025-09-24 21:11:16] Minimum number of supporting reads ranges from 1 to 41, depending on coverage and BQS. INFO [2025-09-24 21:11:16] Initial testing for significant sample cross-contamination: unlikely INFO [2025-09-24 21:11:16] Removing 49 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. INFO [2025-09-24 21:11:16] Removing 22 non heterozygous (in matched normal) germline SNPs. WARN [2025-09-24 21:11:16] Many variants removed by min.base.quality (50) filter. You might want to lower the cutoff. FATAL [2025-09-24 21:11:16] No variants passed filter BQ. FATAL [2025-09-24 21:11:16] FATAL [2025-09-24 21:11:16] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:11:16] parameters (PureCN 2.15.4). INFO [2025-09-24 21:11:16] Found 11 variants in VCF file. WARN [2025-09-24 21:11:16] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead. INFO [2025-09-24 21:11:17] 1 (9.1%) variants annotated as likely germline (DB INFO flag). INFO [2025-09-24 21:11:17] Found 11 variants in VCF file. WARN [2025-09-24 21:11:17] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead. INFO [2025-09-24 21:11:17] 1 (9.1%) variants annotated as likely germline (DB INFO flag). INFO [2025-09-24 21:11:17] Found 11 variants in VCF file. WARN [2025-09-24 21:11:17] vcf.file has no DB or POP_AF info field for membership in germline databases. Guessing it based on available dbSNP ID. INFO [2025-09-24 21:11:17] 1 (9.1%) variants annotated as likely germline (DB INFO flag). INFO [2025-09-24 21:11:18] Found 1000 variants in VCF file. INFO [2025-09-24 21:11:18] Removing 2 triallelic sites. WARN [2025-09-24 21:11:18] Having trouble guessing SOMATIC status... WARN [2025-09-24 21:11:18] DP FORMAT field contains NAs. Removing 44 variants. INFO [2025-09-24 21:11:18] 954 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2025-09-24 21:11:18] Found 12 variants in VCF file. INFO [2025-09-24 21:11:18] Removing 1 triallelic sites. WARN [2025-09-24 21:11:18] DP FORMAT field contains NAs. Removing 1 variants. WARN [2025-09-24 21:11:18] vcf.file has no DB info field for membership in germline databases. Found and used somatic status instead. INFO [2025-09-24 21:11:18] 8 (80.0%) variants annotated as likely germline (DB INFO flag). WARN [2025-09-24 21:11:18] BQ FORMAT field contains NAs. INFO [2025-09-24 21:11:18] Found 2331 variants in VCF file. INFO [2025-09-24 21:11:19] 2282 (97.9%) variants annotated as likely germline (DB INFO flag). INFO [2025-09-24 21:11:19] Found 2331 variants in VCF file. INFO [2025-09-24 21:11:19] 2282 (97.9%) variants annotated as likely germline (DB INFO flag). WARN [2025-09-24 21:11:19] Did not find base quality scores, will use global error rate of 0.0010 instead. INFO [2025-09-24 21:11:19] Removing 21 low quality variants with non-offset BQ < 25. INFO [2025-09-24 21:11:19] Base quality scores range from 24 to 35 (offset by 1) INFO [2025-09-24 21:11:19] Initial testing for significant sample cross-contamination: unlikely INFO [2025-09-24 21:11:19] Removing 89 variants with AF < 0.030 or AF >= 0.970 or insufficient supporting reads or depth < 15. INFO [2025-09-24 21:11:19] Found 2331 variants in VCF file. INFO [2025-09-24 21:11:19] 2282 (97.9%) variants annotated as likely germline (DB INFO flag). WARN [2025-09-24 21:11:19] BQ FORMAT field contains NAs. WARN [2025-09-24 21:11:19] Allosome coverage missing, cannot determine sex. WARN [2025-09-24 21:11:20] Allosome coverage missing, cannot determine sex. INFO [2025-09-24 21:11:20] Mean coverages: chrX: 108.58, chrY: 108.58, chr1-22: 104.87. INFO [2025-09-24 21:11:20] Mean coverages: chrX: 108.58, chrY: 2.17, chr1-22: 104.87. INFO [2025-09-24 21:11:20] Mean coverages: chrX: 108.58, chrY: 5.17, chr1-22: 104.87. INFO [2025-09-24 21:11:20] No homozygous variants in VCF, provide unfiltered VCF. INFO [2025-09-24 21:11:20] No germline variants in VCF. FATAL [2025-09-24 21:11:20] No solution with id hello FATAL [2025-09-24 21:11:20] FATAL [2025-09-24 21:11:20] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:11:20] parameters (PureCN 2.15.4). FATAL [2025-09-24 21:11:20] No solution with id 100 FATAL [2025-09-24 21:11:20] FATAL [2025-09-24 21:11:20] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:11:20] parameters (PureCN 2.15.4). FATAL [2025-09-24 21:11:20] all.data and w have different lengths. FATAL [2025-09-24 21:11:20] FATAL [2025-09-24 21:11:20] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:11:20] parameters (PureCN 2.15.4). INFO [2025-09-24 21:11:21] Splitting 5 large targets to an average width of 400. WARN [2025-09-24 21:11:21] No mappability scores provided. WARN [2025-09-24 21:11:21] No reptiming scores provided. INFO [2025-09-24 21:11:21] Calculating GC-content... INFO [2025-09-24 21:11:21] Splitting 5 large targets to an average width of 400. WARN [2025-09-24 21:11:21] No mappability scores provided. WARN [2025-09-24 21:11:21] No reptiming scores provided. INFO [2025-09-24 21:11:21] Calculating GC-content... INFO [2025-09-24 21:11:21] Splitting 5 large targets to an average width of 400. INFO [2025-09-24 21:11:21] Removing 1 targets overlapping with exclude. WARN [2025-09-24 21:11:21] No mappability scores provided. WARN [2025-09-24 21:11:21] No reptiming scores provided. INFO [2025-09-24 21:11:21] Calculating GC-content... WARN [2025-09-24 21:11:21] Found small target regions (< 100bp). Will resize them. INFO [2025-09-24 21:11:21] Splitting 5 large targets to an average width of 400. FATAL [2025-09-24 21:11:21] off.target.padding must be negative. FATAL [2025-09-24 21:11:21] FATAL [2025-09-24 21:11:21] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:11:21] parameters (PureCN 2.15.4). FATAL [2025-09-24 21:11:21] Interval coordinates should start at 1, not at 0 FATAL [2025-09-24 21:11:21] FATAL [2025-09-24 21:11:21] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:11:21] parameters (PureCN 2.15.4). WARN [2025-09-24 21:11:21] Found small target regions (< 100bp). Will resize them. INFO [2025-09-24 21:11:21] Splitting 5 large targets to an average width of 400. FATAL [2025-09-24 21:11:21] No off-target regions after filtering for mappability and FATAL [2025-09-24 21:11:21] off.target.padding FATAL [2025-09-24 21:11:21] FATAL [2025-09-24 21:11:21] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:11:21] parameters (PureCN 2.15.4). WARN [2025-09-24 21:11:21] Found small target regions (< 100bp). Will resize them. INFO [2025-09-24 21:11:21] Splitting 5 large targets to an average width of 400. WARN [2025-09-24 21:11:21] No mappability scores provided. INFO [2025-09-24 21:11:21] Calculating GC-content... WARN [2025-09-24 21:11:21] Found small target regions (< 100bp). Will resize them. INFO [2025-09-24 21:11:21] Averaging reptiming into bins of size 200... INFO [2025-09-24 21:11:21] Splitting 5 large targets to an average width of 400. WARN [2025-09-24 21:11:21] No mappability scores provided. INFO [2025-09-24 21:11:21] Calculating GC-content... WARN [2025-09-24 21:11:21] Found small target regions (< 100bp). Will resize them. INFO [2025-09-24 21:11:21] Splitting 6 large targets to an average width of 200. WARN [2025-09-24 21:11:21] No mappability scores provided. WARN [2025-09-24 21:11:21] No reptiming scores provided. INFO [2025-09-24 21:11:21] Calculating GC-content... WARN [2025-09-24 21:11:21] Found small target regions (< 100bp). Will resize them. INFO [2025-09-24 21:11:22] Splitting 5 large targets to an average width of 400. WARN [2025-09-24 21:11:22] No mappability scores provided. WARN [2025-09-24 21:11:22] No reptiming scores provided. INFO [2025-09-24 21:11:22] Calculating GC-content... INFO [2025-09-24 21:11:22] Splitting 5 large targets to an average width of 400. INFO [2025-09-24 21:11:22] Tiling off-target regions to an average width of 200000. WARN [2025-09-24 21:11:22] No mappability scores provided. WARN [2025-09-24 21:11:22] No reptiming scores provided. INFO [2025-09-24 21:11:22] Calculating GC-content... WARN [2025-09-24 21:11:22] Intervals contain off-target regions. Will not change intervals. WARN [2025-09-24 21:11:22] No mappability scores provided. WARN [2025-09-24 21:11:22] No reptiming scores provided. INFO [2025-09-24 21:11:22] Calculating GC-content... INFO [2025-09-24 21:11:22] Splitting 5 large targets to an average width of 400. WARN [2025-09-24 21:11:22] No reptiming scores provided. INFO [2025-09-24 21:11:22] Calculating GC-content... WARN [2025-09-24 21:11:22] Found small target regions (< 100bp). Will resize them. INFO [2025-09-24 21:11:22] Splitting 5 large targets to an average width of 400. WARN [2025-09-24 21:11:22] No reptiming scores provided. INFO [2025-09-24 21:11:22] Calculating GC-content... WARN [2025-09-24 21:11:22] Found small target regions (< 100bp). Will resize them. INFO [2025-09-24 21:11:22] Splitting 5 large targets to an average width of 400. WARN [2025-09-24 21:11:22] 1 intervals without mappability score (1 on-target). INFO [2025-09-24 21:11:22] Removing 1 intervals with low mappability score (<0.60). WARN [2025-09-24 21:11:22] No reptiming scores provided. INFO [2025-09-24 21:11:22] Calculating GC-content... WARN [2025-09-24 21:11:22] Found small target regions (< 100bp). Will resize them. INFO [2025-09-24 21:11:22] Splitting 5 large targets to an average width of 400. INFO [2025-09-24 21:11:22] Tiling off-target regions to an average width of 200000. WARN [2025-09-24 21:11:23] No reptiming scores provided. INFO [2025-09-24 21:11:23] Calculating GC-content... INFO [2025-09-24 21:11:23] Splitting 5 large targets to an average width of 400. WARN [2025-09-24 21:11:23] No mappability scores provided. WARN [2025-09-24 21:11:23] No reptiming scores provided. INFO [2025-09-24 21:11:23] Calculating GC-content... WARN [2025-09-24 21:11:23] Chromosome naming style of interval file (Ensembl) was different from reference (UCSC). INFO [2025-09-24 21:11:23] Splitting 5 large targets to an average width of 400. WARN [2025-09-24 21:11:23] No mappability scores provided. WARN [2025-09-24 21:11:23] No reptiming scores provided. INFO [2025-09-24 21:11:23] Calculating GC-content... FATAL [2025-09-24 21:11:23] Chromosome naming style of interval file unknown, should be UCSC. FATAL [2025-09-24 21:11:23] FATAL [2025-09-24 21:11:23] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:11:23] parameters (PureCN 2.15.4). WARN [2025-09-24 21:11:23] Chromosome naming style of interval file (Ensembl) was different from reference (UCSC). WARN [2025-09-24 21:11:23] Chromosome naming style of mappability file (Ensembl) was different from reference (UCSC). INFO [2025-09-24 21:11:23] Splitting 5 large targets to an average width of 400. WARN [2025-09-24 21:11:23] No reptiming scores provided. INFO [2025-09-24 21:11:23] Calculating GC-content... WARN [2025-09-24 21:11:23] Found small target regions (< 60bp). Will resize them. INFO [2025-09-24 21:11:23] Splitting 5 large targets to an average width of 400. WARN [2025-09-24 21:11:23] No mappability scores provided. WARN [2025-09-24 21:11:23] No reptiming scores provided. INFO [2025-09-24 21:11:23] Calculating GC-content... WARN [2025-09-24 21:11:23] Found small target regions (< 60bp). Will drop them. INFO [2025-09-24 21:11:23] Splitting 4 large targets to an average width of 400. WARN [2025-09-24 21:11:23] No mappability scores provided. WARN [2025-09-24 21:11:23] No reptiming scores provided. INFO [2025-09-24 21:11:23] Calculating GC-content... WARN [2025-09-24 21:11:23] Found small target regions (< 200bp). Will resize them. INFO [2025-09-24 21:11:23] Splitting 5 large targets to an average width of 400. WARN [2025-09-24 21:11:23] No mappability scores provided. WARN [2025-09-24 21:11:23] No reptiming scores provided. INFO [2025-09-24 21:11:23] Calculating GC-content... INFO [2025-09-24 21:11:23] Found 20 variants in VCF file. INFO [2025-09-24 21:11:24] 20 (100.0%) variants annotated as likely germline (DB INFO flag). WARN [2025-09-24 21:11:24] 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 [2025-09-24 21:11:24] Error reading AllelicCountsFile FATAL [2025-09-24 21:11:24] /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/PureCN/extdata/example_allelic_counts_empty.tsv FATAL [2025-09-24 21:11:24] FATAL [2025-09-24 21:11:24] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:11:24] parameters (PureCN 2.15.4). INFO [2025-09-24 21:11:24] Found 127 variants in VCF file. INFO [2025-09-24 21:11:24] 127 (100.0%) variants annotated as likely germline (DB INFO flag). WARN [2025-09-24 21:11:24] Did not find base quality scores, will use global error rate of 0.0010 instead. INFO [2025-09-24 21:11:24] ------------------------------------------------------------ INFO [2025-09-24 21:11:24] PureCN 2.15.4 INFO [2025-09-24 21:11:24] ------------------------------------------------------------ INFO [2025-09-24 21:11:24] Loading coverage files... INFO [2025-09-24 21:11:24] Mean target coverages: 112X (tumor) 99X (normal). WARN [2025-09-24 21:11:24] Allosome coverage missing, cannot determine sex. WARN [2025-09-24 21:11:24] Allosome coverage missing, cannot determine sex. INFO [2025-09-24 21:11:24] Removing 228 intervals with missing log.ratio. INFO [2025-09-24 21:11:24] Removing 22 small (< 5bp) intervals. INFO [2025-09-24 21:11:24] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2025-09-24 21:11:24] No normalDB provided. Provide one for better results. INFO [2025-09-24 21:11:24] Removing 1724 low count (< 100 total reads) intervals. INFO [2025-09-24 21:11:24] Removing 6 low coverage (< 15.0000X) intervals. INFO [2025-09-24 21:11:24] Using 8050 intervals (8050 on-target, 0 off-target). INFO [2025-09-24 21:11:24] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2025-09-24 21:11:24] No interval.file provided. Cannot check for any GC-biases. INFO [2025-09-24 21:11:24] Loading VCF... INFO [2025-09-24 21:11:24] Found 127 variants in VCF file. INFO [2025-09-24 21:11:24] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2025-09-24 21:11:24] LIB-02240e4 is tumor in VCF file. INFO [2025-09-24 21:11:24] No homozygous variants in VCF, provide unfiltered VCF. INFO [2025-09-24 21:11:24] Removing 1 non heterozygous (in matched normal) germline SNPs. INFO [2025-09-24 21:11:24] Removing 0 low quality variants with non-offset BQ < 25. INFO [2025-09-24 21:11:24] Base quality scores range from 29 to 35 (offset by 1) INFO [2025-09-24 21:11:24] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS. INFO [2025-09-24 21:11:24] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. INFO [2025-09-24 21:11:24] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding). INFO [2025-09-24 21:11:24] 1.2% of targets contain variants. INFO [2025-09-24 21:11:24] Removing 4 variants outside intervals. INFO [2025-09-24 21:11:24] Found SOMATIC annotation in VCF. INFO [2025-09-24 21:11:24] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. INFO [2025-09-24 21:11:25] Found SOMATIC annotation in VCF. Setting mapping bias to 0.972. INFO [2025-09-24 21:11:25] Excluding 0 novel or poor quality variants from segmentation. INFO [2025-09-24 21:11:25] Sample sex: ? INFO [2025-09-24 21:11:25] Segmenting data... INFO [2025-09-24 21:11:25] Loading pre-computed boundaries for DNAcopy... INFO [2025-09-24 21:11:25] Setting undo.SD parameter to 1.000000. INFO [2025-09-24 21:11:25] Setting prune.hclust.h parameter to 0.200000. INFO [2025-09-24 21:11:25] Found 59 segments with median size of 17.67Mb. INFO [2025-09-24 21:11:25] Using 121 variants. INFO [2025-09-24 21:11:25] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30) INFO [2025-09-24 21:11:25] 2D-grid search of purity and ploidy... INFO [2025-09-24 21:11:25] Local optima: 0.65/1.8, 0.52/2 INFO [2025-09-24 21:11:25] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80... INFO [2025-09-24 21:11:25] Testing local optimum 2/2 at purity 0.52 and total ploidy 2.00... INFO [2025-09-24 21:11:26] Skipping 1 solutions that converged to the same optima. INFO [2025-09-24 21:11:26] Fitting variants with beta model for local optimum 1/2... INFO [2025-09-24 21:11:26] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01. INFO [2025-09-24 21:11:27] Optimized purity: 0.65 INFO [2025-09-24 21:11:27] Done. INFO [2025-09-24 21:11:27] ------------------------------------------------------------ FATAL [2025-09-24 21:11:27] log.ratio NULL in .writeLogRatioFileGATK4 FATAL [2025-09-24 21:11:27] FATAL [2025-09-24 21:11:27] This runtime error might be caused by invalid input data or parameters. FATAL [2025-09-24 21:11:27] Please report bug (PureCN 2.15.4). INFO [2025-09-24 21:11:27] Loaded provided segmentation file example_seg.txt (format DNAcopy). INFO [2025-09-24 21:11:27] Re-centering provided segment means (offset -0.0033). INFO [2025-09-24 21:11:27] Loaded provided segmentation file example_gatk4_modelfinal.seg.gz (format GATK4). WARN [2025-09-24 21:11:27] Expecting numeric chromosome names in seg.file, assuming file is properly sorted. INFO [2025-09-24 21:11:27] Re-centering provided segment means (offset -0.0037). INFO [2025-09-24 21:11:27] 576 on-target bins with low coverage in all samples. WARN [2025-09-24 21:11:27] You are likely not using the correct baits file! WARN [2025-09-24 21:11:27] Allosome coverage missing, cannot determine sex. WARN [2025-09-24 21:11:27] Allosome coverage missing, cannot determine sex. INFO [2025-09-24 21:11:27] Processing on-target regions... INFO [2025-09-24 21:11:28] Removing 930 intervals with low coverage in normalDB. INFO [2025-09-24 21:11:28] Removing 1 intervals with zero coverage in more than 3% of normalDB. INFO [2025-09-24 21:11:28] ------------------------------------------------------------ INFO [2025-09-24 21:11:28] PureCN 2.15.4 INFO [2025-09-24 21:11:28] ------------------------------------------------------------ INFO [2025-09-24 21:11:28] Using BiocParallel for parallel optimization. INFO [2025-09-24 21:11:28] Loading coverage files... INFO [2025-09-24 21:11:28] Mean target coverages: 112X (tumor) 99X (normal). WARN [2025-09-24 21:11:28] Allosome coverage missing, cannot determine sex. WARN [2025-09-24 21:11:28] Allosome coverage missing, cannot determine sex. INFO [2025-09-24 21:11:28] Removing 228 intervals with missing log.ratio. INFO [2025-09-24 21:11:28] Removing 705 intervals excluded in normalDB. INFO [2025-09-24 21:11:28] normalDB provided. Setting minimum coverage for segmentation to 0.0015X. INFO [2025-09-24 21:11:28] Removing 1066 low count (< 100 total reads) intervals. INFO [2025-09-24 21:11:28] Using 8050 intervals (8050 on-target, 0 off-target). INFO [2025-09-24 21:11:28] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2025-09-24 21:11:28] No interval.file provided. Cannot check for any GC-biases. INFO [2025-09-24 21:11:28] Sample sex: ? INFO [2025-09-24 21:11:28] Segmenting data... INFO [2025-09-24 21:11:28] Interval weights found, will use weighted CBS. INFO [2025-09-24 21:11:28] Loading pre-computed boundaries for DNAcopy... INFO [2025-09-24 21:11:28] Setting undo.SD parameter to 1.000000. Setting multi-figure configuration INFO [2025-09-24 21:11:29] Found 52 segments with median size of 29.35Mb. INFO [2025-09-24 21:11:29] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30) INFO [2025-09-24 21:11:29] 2D-grid search of purity and ploidy... INFO [2025-09-24 21:11:29] Local optima: 0.65/1.8, 0.52/2 INFO [2025-09-24 21:11:30] Skipping 1 solutions that converged to the same optima. INFO [2025-09-24 21:11:30] Done. INFO [2025-09-24 21:11:30] ------------------------------------------------------------ INFO [2025-09-24 21:11:30] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpM1a86W/file157cd19d8530e.rds... FATAL [2025-09-24 21:11:30] runAbsoluteCN was run without a VCF file. FATAL [2025-09-24 21:11:30] FATAL [2025-09-24 21:11:30] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:11:30] parameters (PureCN 2.15.4). FATAL [2025-09-24 21:11:30] runAbsoluteCN was run without a VCF file. FATAL [2025-09-24 21:11:30] FATAL [2025-09-24 21:11:30] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:11:30] parameters (PureCN 2.15.4). INFO [2025-09-24 21:11:30] ------------------------------------------------------------ INFO [2025-09-24 21:11:30] PureCN 2.15.4 INFO [2025-09-24 21:11:30] ------------------------------------------------------------ INFO [2025-09-24 21:11:30] Loading coverage files... INFO [2025-09-24 21:11:30] Mean target coverages: 112X (tumor) 99X (normal). WARN [2025-09-24 21:11:30] Allosome coverage missing, cannot determine sex. WARN [2025-09-24 21:11:30] Allosome coverage missing, cannot determine sex. INFO [2025-09-24 21:11:30] Removing 228 intervals with missing log.ratio. INFO [2025-09-24 21:11:30] Removing 705 intervals excluded in normalDB. INFO [2025-09-24 21:11:30] normalDB provided. Setting minimum coverage for segmentation to 0.0015X. INFO [2025-09-24 21:11:30] Removing 1066 low count (< 100 total reads) intervals. INFO [2025-09-24 21:11:30] Using 8050 intervals (8050 on-target, 0 off-target). INFO [2025-09-24 21:11:30] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2025-09-24 21:11:30] No interval.file provided. Cannot check for any GC-biases. INFO [2025-09-24 21:11:30] Sample sex: ? INFO [2025-09-24 21:11:30] Segmenting data... INFO [2025-09-24 21:11:30] Interval weights found, will use weighted PSCBS. FATAL [2025-09-24 21:11:30] segmentationPSCBS requires VCF file. FATAL [2025-09-24 21:11:30] FATAL [2025-09-24 21:11:30] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:11:30] parameters (PureCN 2.15.4). INFO [2025-09-24 21:11:32] ------------------------------------------------------------ INFO [2025-09-24 21:11:33] PureCN 2.15.4 INFO [2025-09-24 21:11:33] ------------------------------------------------------------ INFO [2025-09-24 21:11:33] Loading coverage files... FATAL [2025-09-24 21:11:33] Need a normal coverage file if log.ratio and seg.file are not provided. FATAL [2025-09-24 21:11:33] FATAL [2025-09-24 21:11:33] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:11:33] parameters (PureCN 2.15.4). INFO [2025-09-24 21:11:33] ------------------------------------------------------------ INFO [2025-09-24 21:11:33] PureCN 2.15.4 INFO [2025-09-24 21:11:33] ------------------------------------------------------------ FATAL [2025-09-24 21:11:33] min.ploidy or max.ploidy not within expected range. FATAL [2025-09-24 21:11:33] FATAL [2025-09-24 21:11:33] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:11:33] parameters (PureCN 2.15.4). INFO [2025-09-24 21:11:33] ------------------------------------------------------------ INFO [2025-09-24 21:11:33] PureCN 2.15.4 INFO [2025-09-24 21:11:33] ------------------------------------------------------------ FATAL [2025-09-24 21:11:33] min.ploidy or max.ploidy not within expected range. FATAL [2025-09-24 21:11:33] FATAL [2025-09-24 21:11:33] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:11:33] parameters (PureCN 2.15.4). INFO [2025-09-24 21:11:33] ------------------------------------------------------------ INFO [2025-09-24 21:11:33] PureCN 2.15.4 INFO [2025-09-24 21:11:33] ------------------------------------------------------------ INFO [2025-09-24 21:11:33] ------------------------------------------------------------ INFO [2025-09-24 21:11:33] PureCN 2.15.4 INFO [2025-09-24 21:11:33] ------------------------------------------------------------ INFO [2025-09-24 21:11:33] ------------------------------------------------------------ INFO [2025-09-24 21:11:33] PureCN 2.15.4 INFO [2025-09-24 21:11:33] ------------------------------------------------------------ FATAL [2025-09-24 21:11:33] test.num.copy not within expected range. FATAL [2025-09-24 21:11:33] FATAL [2025-09-24 21:11:33] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:11:33] parameters (PureCN 2.15.4). INFO [2025-09-24 21:11:33] ------------------------------------------------------------ INFO [2025-09-24 21:11:33] PureCN 2.15.4 INFO [2025-09-24 21:11:33] ------------------------------------------------------------ WARN [2025-09-24 21:11:33] test.num.copy outside recommended range. FATAL [2025-09-24 21:11:33] max.non.clonal not within expected range or format. FATAL [2025-09-24 21:11:33] FATAL [2025-09-24 21:11:33] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:11:33] parameters (PureCN 2.15.4). INFO [2025-09-24 21:11:33] ------------------------------------------------------------ INFO [2025-09-24 21:11:33] PureCN 2.15.4 INFO [2025-09-24 21:11:33] ------------------------------------------------------------ WARN [2025-09-24 21:11:33] test.num.copy outside recommended range. FATAL [2025-09-24 21:11:33] max.non.clonal not within expected range or format. FATAL [2025-09-24 21:11:33] FATAL [2025-09-24 21:11:33] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:11:33] parameters (PureCN 2.15.4). INFO [2025-09-24 21:11:33] ------------------------------------------------------------ INFO [2025-09-24 21:11:33] PureCN 2.15.4 INFO [2025-09-24 21:11:33] ------------------------------------------------------------ FATAL [2025-09-24 21:11:33] test.purity not within expected range. FATAL [2025-09-24 21:11:33] FATAL [2025-09-24 21:11:33] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:11:33] parameters (PureCN 2.15.4). INFO [2025-09-24 21:11:33] ------------------------------------------------------------ INFO [2025-09-24 21:11:33] PureCN 2.15.4 INFO [2025-09-24 21:11:33] ------------------------------------------------------------ INFO [2025-09-24 21:11:33] Loading coverage files... FATAL [2025-09-24 21:11:33] Tumor and normal are identical. This won't give any meaningful results FATAL [2025-09-24 21:11:33] and I'm stopping here. FATAL [2025-09-24 21:11:33] FATAL [2025-09-24 21:11:33] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:11:33] parameters (PureCN 2.15.4). INFO [2025-09-24 21:11:33] ------------------------------------------------------------ INFO [2025-09-24 21:11:33] PureCN 2.15.4 INFO [2025-09-24 21:11:33] ------------------------------------------------------------ INFO [2025-09-24 21:11:33] Loading coverage files... FATAL [2025-09-24 21:11:33] Length of log.ratio different from tumor coverage. FATAL [2025-09-24 21:11:33] FATAL [2025-09-24 21:11:33] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:11:33] parameters (PureCN 2.15.4). INFO [2025-09-24 21:11:33] ------------------------------------------------------------ INFO [2025-09-24 21:11:33] PureCN 2.15.4 INFO [2025-09-24 21:11:33] ------------------------------------------------------------ FATAL [2025-09-24 21:11:33] prior.purity must have the same length as test.purity. FATAL [2025-09-24 21:11:33] FATAL [2025-09-24 21:11:33] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:11:33] parameters (PureCN 2.15.4). INFO [2025-09-24 21:11:33] ------------------------------------------------------------ INFO [2025-09-24 21:11:33] PureCN 2.15.4 INFO [2025-09-24 21:11:33] ------------------------------------------------------------ FATAL [2025-09-24 21:11:33] min.gof not within expected range or format. FATAL [2025-09-24 21:11:33] FATAL [2025-09-24 21:11:33] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:11:33] parameters (PureCN 2.15.4). INFO [2025-09-24 21:11:33] ------------------------------------------------------------ INFO [2025-09-24 21:11:33] PureCN 2.15.4 INFO [2025-09-24 21:11:33] ------------------------------------------------------------ FATAL [2025-09-24 21:11:33] prior.purity not within expected range or format. FATAL [2025-09-24 21:11:33] FATAL [2025-09-24 21:11:33] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:11:33] parameters (PureCN 2.15.4). INFO [2025-09-24 21:11:33] ------------------------------------------------------------ INFO [2025-09-24 21:11:33] PureCN 2.15.4 INFO [2025-09-24 21:11:33] ------------------------------------------------------------ FATAL [2025-09-24 21:11:33] prior.purity must add to 1. Sum is 1.5 FATAL [2025-09-24 21:11:33] FATAL [2025-09-24 21:11:33] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:11:33] parameters (PureCN 2.15.4). INFO [2025-09-24 21:11:33] ------------------------------------------------------------ INFO [2025-09-24 21:11:33] PureCN 2.15.4 INFO [2025-09-24 21:11:33] ------------------------------------------------------------ FATAL [2025-09-24 21:11:33] max.homozygous.loss not within expected range or format. FATAL [2025-09-24 21:11:33] FATAL [2025-09-24 21:11:33] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:11:33] parameters (PureCN 2.15.4). INFO [2025-09-24 21:11:33] ------------------------------------------------------------ INFO [2025-09-24 21:11:33] PureCN 2.15.4 INFO [2025-09-24 21:11:33] ------------------------------------------------------------ FATAL [2025-09-24 21:11:33] prior.K not within expected range or format. FATAL [2025-09-24 21:11:33] FATAL [2025-09-24 21:11:33] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:11:33] parameters (PureCN 2.15.4). INFO [2025-09-24 21:11:33] ------------------------------------------------------------ INFO [2025-09-24 21:11:33] PureCN 2.15.4 INFO [2025-09-24 21:11:33] ------------------------------------------------------------ FATAL [2025-09-24 21:11:33] prior.contamination not within expected range or format. FATAL [2025-09-24 21:11:33] FATAL [2025-09-24 21:11:33] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:11:33] parameters (PureCN 2.15.4). INFO [2025-09-24 21:11:33] ------------------------------------------------------------ INFO [2025-09-24 21:11:33] PureCN 2.15.4 INFO [2025-09-24 21:11:33] ------------------------------------------------------------ FATAL [2025-09-24 21:11:33] Iterations not in the expected range from 10 to 250. FATAL [2025-09-24 21:11:33] FATAL [2025-09-24 21:11:33] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:11:33] parameters (PureCN 2.15.4). INFO [2025-09-24 21:11:33] ------------------------------------------------------------ INFO [2025-09-24 21:11:33] PureCN 2.15.4 INFO [2025-09-24 21:11:33] ------------------------------------------------------------ FATAL [2025-09-24 21:11:33] Iterations not in the expected range from 10 to 250. FATAL [2025-09-24 21:11:33] FATAL [2025-09-24 21:11:33] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:11:33] parameters (PureCN 2.15.4). INFO [2025-09-24 21:11:33] ------------------------------------------------------------ INFO [2025-09-24 21:11:33] PureCN 2.15.4 INFO [2025-09-24 21:11:33] ------------------------------------------------------------ INFO [2025-09-24 21:11:33] Loading coverage files... FATAL [2025-09-24 21:11:33] Missing tumor.coverage.file requires seg.file or log.ratio and FATAL [2025-09-24 21:11:33] interval.file. FATAL [2025-09-24 21:11:33] FATAL [2025-09-24 21:11:33] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:11:33] parameters (PureCN 2.15.4). INFO [2025-09-24 21:11:33] ------------------------------------------------------------ INFO [2025-09-24 21:11:33] PureCN 2.15.4 INFO [2025-09-24 21:11:33] ------------------------------------------------------------ INFO [2025-09-24 21:11:33] ------------------------------------------------------------ INFO [2025-09-24 21:11:33] PureCN 2.15.4 INFO [2025-09-24 21:11:33] ------------------------------------------------------------ INFO [2025-09-24 21:11:33] Loading coverage files... FATAL [2025-09-24 21:11:34] Interval files in normal and tumor different. FATAL [2025-09-24 21:11:34] FATAL [2025-09-24 21:11:34] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:11:34] parameters (PureCN 2.15.4). INFO [2025-09-24 21:11:34] ------------------------------------------------------------ INFO [2025-09-24 21:11:34] PureCN 2.15.4 INFO [2025-09-24 21:11:34] ------------------------------------------------------------ INFO [2025-09-24 21:11:34] Loading coverage files... INFO [2025-09-24 21:11:34] Mean target coverages: 0X (tumor) 99X (normal). WARN [2025-09-24 21:11:34] Large difference in coverage of tumor and normal. FATAL [2025-09-24 21:11:34] No finite intervals. FATAL [2025-09-24 21:11:34] FATAL [2025-09-24 21:11:34] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:11:34] parameters (PureCN 2.15.4). INFO [2025-09-24 21:11:34] ------------------------------------------------------------ INFO [2025-09-24 21:11:34] PureCN 2.15.4 INFO [2025-09-24 21:11:34] ------------------------------------------------------------ INFO [2025-09-24 21:11:34] Loading coverage files... INFO [2025-09-24 21:11:34] Mean target coverages: 112X (tumor) 99X (normal). WARN [2025-09-24 21:11:34] Allosome coverage missing, cannot determine sex. WARN [2025-09-24 21:11:34] Allosome coverage missing, cannot determine sex. INFO [2025-09-24 21:11:34] Removing 228 intervals with missing log.ratio. INFO [2025-09-24 21:11:34] Removing 22 small (< 5bp) intervals. INFO [2025-09-24 21:11:34] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2025-09-24 21:11:34] No normalDB provided. Provide one for better results. INFO [2025-09-24 21:11:34] Removing 1724 low count (< 100 total reads) intervals. INFO [2025-09-24 21:11:34] Removing 6 low coverage (< 15.0000X) intervals. INFO [2025-09-24 21:11:34] Using 8050 intervals (8050 on-target, 0 off-target). INFO [2025-09-24 21:11:34] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2025-09-24 21:11:34] No interval.file provided. Cannot check for any GC-biases. INFO [2025-09-24 21:11:34] Loading VCF... INFO [2025-09-24 21:11:34] Found 127 variants in VCF file. INFO [2025-09-24 21:11:34] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2025-09-24 21:11:34] LIB-02240e4 is tumor in VCF file. INFO [2025-09-24 21:11:34] No homozygous variants in VCF, provide unfiltered VCF. INFO [2025-09-24 21:11:34] Removing 1 non heterozygous (in matched normal) germline SNPs. INFO [2025-09-24 21:11:34] Removing 0 low quality variants with non-offset BQ < 25. INFO [2025-09-24 21:11:34] Base quality scores range from 29 to 35 (offset by 1) INFO [2025-09-24 21:11:34] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS. INFO [2025-09-24 21:11:34] 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 for (getMethodName in getMethodNames) { : closing unused connection 5 (/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpM1a86W/file157cd70524c48.tsv) 3: In for (getMethodName in getMethodNames) { : closing unused connection 4 (/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/PureCN/extdata/example_gatk4_denoised_cr.tsv.gz) FATAL [2025-09-24 21:11:34] Could not import snp.blacklist FATAL [2025-09-24 21:11:34] /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/PureCN/extdata/example_normal.txt.gz:Error FATAL [2025-09-24 21:11:34] in FileForFormat(resource(con), fileFormat(con)) : Format 'txt' FATAL [2025-09-24 21:11:34] unsupported FATAL [2025-09-24 21:11:34] FATAL [2025-09-24 21:11:34] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:11:34] parameters (PureCN 2.15.4). INFO [2025-09-24 21:11:34] ------------------------------------------------------------ INFO [2025-09-24 21:11:34] PureCN 2.15.4 INFO [2025-09-24 21:11:34] ------------------------------------------------------------ INFO [2025-09-24 21:11:34] Loading coverage files... INFO [2025-09-24 21:11:35] Mean target coverages: 112X (tumor) 99X (normal). WARN [2025-09-24 21:11:35] Allosome coverage missing, cannot determine sex. WARN [2025-09-24 21:11:35] Allosome coverage missing, cannot determine sex. INFO [2025-09-24 21:11:35] Removing 228 intervals with missing log.ratio. INFO [2025-09-24 21:11:35] Removing 22 small (< 5bp) intervals. INFO [2025-09-24 21:11:35] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2025-09-24 21:11:35] No normalDB provided. Provide one for better results. INFO [2025-09-24 21:11:35] Removing 233 low coverage (< 15.0000X) intervals. INFO [2025-09-24 21:11:35] Using 9547 intervals (9547 on-target, 0 off-target). INFO [2025-09-24 21:11:35] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2025-09-24 21:11:35] No interval.file provided. Cannot check for any GC-biases. INFO [2025-09-24 21:11:35] Loading VCF... INFO [2025-09-24 21:11:35] Found 127 variants in VCF file. INFO [2025-09-24 21:11:35] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2025-09-24 21:11:35] LIB-02240e4 is tumor in VCF file. INFO [2025-09-24 21:11:35] No homozygous variants in VCF, provide unfiltered VCF. INFO [2025-09-24 21:11:35] Removing 1 non heterozygous (in matched normal) germline SNPs. INFO [2025-09-24 21:11:35] Removing 0 low quality variants with non-offset BQ < 25. INFO [2025-09-24 21:11:35] Base quality scores range from 29 to 35 (offset by 1) INFO [2025-09-24 21:11:35] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS. INFO [2025-09-24 21:11:35] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. INFO [2025-09-24 21:11:35] Total size of targeted genomic region: 1.63Mb (2.58Mb with 50bp padding). INFO [2025-09-24 21:11:35] 1.0% of targets contain variants. INFO [2025-09-24 21:11:35] Removing 2 variants outside intervals. INFO [2025-09-24 21:11:35] Found SOMATIC annotation in VCF. INFO [2025-09-24 21:11:35] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. INFO [2025-09-24 21:11:35] Found SOMATIC annotation in VCF. Setting mapping bias to 0.973. INFO [2025-09-24 21:11:35] Excluding 0 novel or poor quality variants from segmentation. INFO [2025-09-24 21:11:35] Sample sex: ? INFO [2025-09-24 21:11:35] Segmenting data... INFO [2025-09-24 21:11:35] Loading pre-computed boundaries for DNAcopy... INFO [2025-09-24 21:11:35] Setting undo.SD parameter to 1.000000. INFO [2025-09-24 21:11:36] Setting prune.hclust.h parameter to 0.200000. INFO [2025-09-24 21:11:36] Found 54 segments with median size of 24.88Mb. INFO [2025-09-24 21:11:36] Using 123 variants. INFO [2025-09-24 21:11:36] Mean standard deviation of log-ratios: 0.37 (MAPD: 0.32) INFO [2025-09-24 21:11:36] 2D-grid search of purity and ploidy... INFO [2025-09-24 21:11:36] Local optima: 0.62/1.9, 0.3/1.9, 0.32/2 INFO [2025-09-24 21:11:36] Testing local optimum 1/3 at purity 0.62 and total ploidy 1.90... INFO [2025-09-24 21:11:37] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90... INFO [2025-09-24 21:11:37] Recalibrating log-ratios... INFO [2025-09-24 21:11:37] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90... INFO [2025-09-24 21:11:37] Recalibrating log-ratios... INFO [2025-09-24 21:11:37] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90... INFO [2025-09-24 21:11:37] Recalibrating log-ratios... INFO [2025-09-24 21:11:37] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90... INFO [2025-09-24 21:11:37] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00... INFO [2025-09-24 21:11:37] Recalibrating log-ratios... INFO [2025-09-24 21:11:37] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00... INFO [2025-09-24 21:11:37] Recalibrating log-ratios... INFO [2025-09-24 21:11:37] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00... INFO [2025-09-24 21:11:38] Recalibrating log-ratios... INFO [2025-09-24 21:11:38] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00... INFO [2025-09-24 21:11:38] Skipping 1 solutions that converged to the same optima. INFO [2025-09-24 21:11:38] Skipping 1 solutions exceeding max.non.clonal (0.20): 0.3/1.9 (purity/tumor ploidy) INFO [2025-09-24 21:11:38] Fitting variants with beta model for local optimum 1/3... INFO [2025-09-24 21:11:38] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01. INFO [2025-09-24 21:11:39] Optimized purity: 0.65 INFO [2025-09-24 21:11:39] Done. INFO [2025-09-24 21:11:39] ------------------------------------------------------------ INFO [2025-09-24 21:11:39] ------------------------------------------------------------ INFO [2025-09-24 21:11:39] PureCN 2.15.4 INFO [2025-09-24 21:11:39] ------------------------------------------------------------ INFO [2025-09-24 21:11:39] Loading coverage files... INFO [2025-09-24 21:11:39] Mean target coverages: 112X (tumor) 99X (normal). WARN [2025-09-24 21:11:39] Allosome coverage missing, cannot determine sex. WARN [2025-09-24 21:11:39] Allosome coverage missing, cannot determine sex. INFO [2025-09-24 21:11:39] Removing 228 intervals with missing log.ratio. INFO [2025-09-24 21:11:39] Removing 22 small (< 5bp) intervals. INFO [2025-09-24 21:11:39] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2025-09-24 21:11:39] No normalDB provided. Provide one for better results. INFO [2025-09-24 21:11:39] Removing 1724 low count (< 100 total reads) intervals. INFO [2025-09-24 21:11:39] Removing 6 low coverage (< 15.0000X) intervals. INFO [2025-09-24 21:11:39] Using 8050 intervals (8050 on-target, 0 off-target). INFO [2025-09-24 21:11:39] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2025-09-24 21:11:39] No interval.file provided. Cannot check for any GC-biases. INFO [2025-09-24 21:11:39] Loading VCF... INFO [2025-09-24 21:11:39] Found 127 variants in VCF file. WARN [2025-09-24 21:11:39] DP FORMAT field contains NAs. Removing 3 variants. WARN [2025-09-24 21:11:39] DB INFO flag contains NAs INFO [2025-09-24 21:11:39] 119 (96.0%) variants annotated as likely germline (DB INFO flag). INFO [2025-09-24 21:11:39] LIB-02240e4 is tumor in VCF file. INFO [2025-09-24 21:11:39] No homozygous variants in VCF, provide unfiltered VCF. INFO [2025-09-24 21:11:39] Removing 0 low quality variants with non-offset BQ < 25. INFO [2025-09-24 21:11:39] Base quality scores range from 29 to 35 (offset by 1) INFO [2025-09-24 21:11:39] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS. INFO [2025-09-24 21:11:39] Removing 1 variants with AF < 0.030 or AF >= 0.970 or insufficient supporting reads or depth < 15. INFO [2025-09-24 21:11:39] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding). INFO [2025-09-24 21:11:39] 1.2% of targets contain variants. INFO [2025-09-24 21:11:39] Setting somatic prior probabilities for likely germline hits to 0.000500 or to 0.500000 otherwise. INFO [2025-09-24 21:11:39] Excluding 5 novel or poor quality variants from segmentation. INFO [2025-09-24 21:11:39] Sample sex: ? INFO [2025-09-24 21:11:39] Segmenting data... INFO [2025-09-24 21:11:39] Loading pre-computed boundaries for DNAcopy... INFO [2025-09-24 21:11:39] Setting undo.SD parameter to 1.000000. Setting multi-figure configuration INFO [2025-09-24 21:11:40] Setting prune.hclust.h parameter to 0.200000. INFO [2025-09-24 21:11:40] Found 59 segments with median size of 17.67Mb. INFO [2025-09-24 21:11:40] Using 123 variants. INFO [2025-09-24 21:11:40] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30) INFO [2025-09-24 21:11:40] 2D-grid search of purity and ploidy... INFO [2025-09-24 21:11:40] Local optima: 0.62/1.9, 0.3/1.9, 0.32/2 INFO [2025-09-24 21:11:40] Testing local optimum 1/3 at purity 0.62 and total ploidy 1.90... INFO [2025-09-24 21:11:41] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90... INFO [2025-09-24 21:11:41] Recalibrating log-ratios... INFO [2025-09-24 21:11:41] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90... INFO [2025-09-24 21:11:41] Recalibrating log-ratios... INFO [2025-09-24 21:11:41] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90... INFO [2025-09-24 21:11:41] Recalibrating log-ratios... INFO [2025-09-24 21:11:41] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90... INFO [2025-09-24 21:11:41] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00... INFO [2025-09-24 21:11:41] Recalibrating log-ratios... INFO [2025-09-24 21:11:41] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00... INFO [2025-09-24 21:11:41] Recalibrating log-ratios... INFO [2025-09-24 21:11:41] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00... INFO [2025-09-24 21:11:41] Recalibrating log-ratios... INFO [2025-09-24 21:11:41] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00... INFO [2025-09-24 21:11:41] Skipping 2 solutions exceeding max.non.clonal (0.20): 0.3/1.9, 0.35/1.61 (purity/tumor ploidy) INFO [2025-09-24 21:11:41] Fitting variants with beta model for local optimum 1/3... INFO [2025-09-24 21:11:41] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01. INFO [2025-09-24 21:11:42] Optimized purity: 0.65 INFO [2025-09-24 21:11:42] Done. INFO [2025-09-24 21:11:42] ------------------------------------------------------------ INFO [2025-09-24 21:11:42] ------------------------------------------------------------ INFO [2025-09-24 21:11:42] PureCN 2.15.4 INFO [2025-09-24 21:11:42] ------------------------------------------------------------ INFO [2025-09-24 21:11:42] Loading coverage files... INFO [2025-09-24 21:11:43] Mean target coverages: 112X (tumor) 99X (normal). WARN [2025-09-24 21:11:43] Allosome coverage missing, cannot determine sex. WARN [2025-09-24 21:11:43] Allosome coverage missing, cannot determine sex. INFO [2025-09-24 21:11:43] No Gene column in interval.file. You won't get gene-level calls. INFO [2025-09-24 21:11:43] Removing 228 intervals with missing log.ratio. INFO [2025-09-24 21:11:43] Removing 15 low/high GC targets. INFO [2025-09-24 21:11:43] Removing 21 small (< 5bp) intervals. INFO [2025-09-24 21:11:43] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2025-09-24 21:11:43] No normalDB provided. Provide one for better results. INFO [2025-09-24 21:11:43] Removing 1718 low count (< 100 total reads) intervals. INFO [2025-09-24 21:11:43] Removing 6 low coverage (< 15.0000X) intervals. INFO [2025-09-24 21:11:43] Removing 36 low mappability intervals. INFO [2025-09-24 21:11:43] Using 8006 intervals (8006 on-target, 0 off-target). INFO [2025-09-24 21:11:43] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2025-09-24 21:11:43] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio). INFO [2025-09-24 21:11:43] Loading VCF... INFO [2025-09-24 21:11:43] Found 127 variants in VCF file. INFO [2025-09-24 21:11:43] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2025-09-24 21:11:43] LIB-02240e4 is tumor in VCF file. INFO [2025-09-24 21:11:43] No homozygous variants in VCF, provide unfiltered VCF. INFO [2025-09-24 21:11:43] Removing 1 non heterozygous (in matched normal) germline SNPs. INFO [2025-09-24 21:11:43] Removing 0 low quality variants with non-offset BQ < 25. INFO [2025-09-24 21:11:43] Base quality scores range from 29 to 35 (offset by 1) INFO [2025-09-24 21:11:43] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS. INFO [2025-09-24 21:11:43] Removing 1 variants with AF < 0.030 or AF >= Inf or insufficient supporting reads or depth < 15. INFO [2025-09-24 21:11:43] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding). INFO [2025-09-24 21:11:43] 1.2% of targets contain variants. INFO [2025-09-24 21:11:43] Removing 11 variants outside intervals. INFO [2025-09-24 21:11:43] Found SOMATIC annotation in VCF. INFO [2025-09-24 21:11:43] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. INFO [2025-09-24 21:11:43] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970. INFO [2025-09-24 21:11:44] Excluding 0 novel or poor quality variants from segmentation. INFO [2025-09-24 21:11:44] Sample sex: ? INFO [2025-09-24 21:11:44] Segmenting data... INFO [2025-09-24 21:11:44] MAPD of 114 allelic fractions: 0.14 (0.15 adjusted). INFO [2025-09-24 21:11:44] Using unweighted PSCBS. INFO [2025-09-24 21:11:44] Setting undo.SD parameter to 1.000000. INFO [2025-09-24 21:11:54] Setting prune.hclust.h parameter to 0.200000. INFO [2025-09-24 21:11:54] Found 72 segments with median size of 27.25Mb. INFO [2025-09-24 21:11:54] Using 114 variants. INFO [2025-09-24 21:11:54] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30) INFO [2025-09-24 21:11:54] 2D-grid search of purity and ploidy... INFO [2025-09-24 21:11:54] Local optima: 0.65/1.8, 0.38/2.2 INFO [2025-09-24 21:11:54] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80... INFO [2025-09-24 21:11:54] Recalibrating log-ratios... INFO [2025-09-24 21:11:54] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80... INFO [2025-09-24 21:11:54] Recalibrating log-ratios... INFO [2025-09-24 21:11:54] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80... INFO [2025-09-24 21:11:54] Recalibrating log-ratios... INFO [2025-09-24 21:11:54] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80... INFO [2025-09-24 21:11:54] Testing local optimum 2/2 at purity 0.38 and total ploidy 2.20... INFO [2025-09-24 21:11:55] Skipping 1 solutions exceeding max.non.clonal (0.20): 0.65/2.05 (purity/tumor ploidy) INFO [2025-09-24 21:11:55] Fitting variants with beta model for local optimum 2/2... INFO [2025-09-24 21:11:55] Fitting variants for purity 0.40, tumor ploidy 2.55 and contamination 0.01. INFO [2025-09-24 21:11:57] Optimized purity: 0.40 INFO [2025-09-24 21:11:57] Done. INFO [2025-09-24 21:11:57] ------------------------------------------------------------ FATAL [2025-09-24 21:11:57] This function requires gene-level calls. Please add a column 'Gene' FATAL [2025-09-24 21:11:57] containing gene symbols to the interval.file. FATAL [2025-09-24 21:11:57] FATAL [2025-09-24 21:11:57] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:11:57] parameters (PureCN 2.15.4). INFO [2025-09-24 21:11:57] ------------------------------------------------------------ INFO [2025-09-24 21:11:57] PureCN 2.15.4 INFO [2025-09-24 21:11:57] ------------------------------------------------------------ INFO [2025-09-24 21:11:57] Loading coverage files... INFO [2025-09-24 21:11:58] Mean target coverages: 112X (tumor) 99X (normal). WARN [2025-09-24 21:11:58] Allosome coverage missing, cannot determine sex. WARN [2025-09-24 21:11:58] Allosome coverage missing, cannot determine sex. INFO [2025-09-24 21:11:58] Removing 228 intervals with missing log.ratio. INFO [2025-09-24 21:11:58] Removing 22 small (< 5bp) intervals. INFO [2025-09-24 21:11:58] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2025-09-24 21:11:58] No normalDB provided. Provide one for better results. INFO [2025-09-24 21:11:58] Removing 1724 low count (< 100 total reads) intervals. INFO [2025-09-24 21:11:58] Removing 6 low coverage (< 15.0000X) intervals. INFO [2025-09-24 21:11:58] Using 8050 intervals (8050 on-target, 0 off-target). INFO [2025-09-24 21:11:58] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2025-09-24 21:11:58] No interval.file provided. Cannot check for any GC-biases. INFO [2025-09-24 21:11:58] Loading VCF... INFO [2025-09-24 21:11:58] Found 127 variants in VCF file. INFO [2025-09-24 21:11:58] 127 (100.0%) variants annotated as likely germline (DB INFO flag). FATAL [2025-09-24 21:11:58] Different chromosome names in coverage and VCF. FATAL [2025-09-24 21:11:58] FATAL [2025-09-24 21:11:58] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:11:58] parameters (PureCN 2.15.4). INFO [2025-09-24 21:11:58] ------------------------------------------------------------ INFO [2025-09-24 21:11:58] PureCN 2.15.4 INFO [2025-09-24 21:11:58] ------------------------------------------------------------ INFO [2025-09-24 21:11:58] Loading coverage files... INFO [2025-09-24 21:11:58] Mean target coverages: 112X (tumor) 99X (normal). WARN [2025-09-24 21:11:58] Allosome coverage missing, cannot determine sex. WARN [2025-09-24 21:11:58] Allosome coverage missing, cannot determine sex. FATAL [2025-09-24 21:11:58] tumor.coverage.file and interval.file do not align. FATAL [2025-09-24 21:11:58] FATAL [2025-09-24 21:11:58] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:11:58] parameters (PureCN 2.15.4). INFO [2025-09-24 21:11:58] ------------------------------------------------------------ INFO [2025-09-24 21:11:58] PureCN 2.15.4 INFO [2025-09-24 21:11:58] ------------------------------------------------------------ INFO [2025-09-24 21:11:58] Loading coverage files... INFO [2025-09-24 21:11:58] Mean target coverages: 112X (tumor) 99X (normal). WARN [2025-09-24 21:11:58] Allosome coverage missing, cannot determine sex. WARN [2025-09-24 21:11:58] Allosome coverage missing, cannot determine sex. INFO [2025-09-24 21:11:58] Removing 228 intervals with missing log.ratio. INFO [2025-09-24 21:11:58] Removing 15 low/high GC targets. INFO [2025-09-24 21:11:58] Removing 21 small (< 5bp) intervals. INFO [2025-09-24 21:11:58] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2025-09-24 21:11:58] No normalDB provided. Provide one for better results. INFO [2025-09-24 21:11:58] Removing 1718 low count (< 100 total reads) intervals. INFO [2025-09-24 21:11:58] Removing 6 low coverage (< 15.0000X) intervals. INFO [2025-09-24 21:11:58] Removing 36 low mappability intervals. INFO [2025-09-24 21:11:58] Using 8006 intervals (8006 on-target, 0 off-target). INFO [2025-09-24 21:11:58] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2025-09-24 21:11:58] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio). INFO [2025-09-24 21:11:58] Loading VCF... INFO [2025-09-24 21:11:58] Found 127 variants in VCF file. INFO [2025-09-24 21:11:58] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2025-09-24 21:11:58] LIB-02240e4 is tumor in VCF file. INFO [2025-09-24 21:11:58] No homozygous variants in VCF, provide unfiltered VCF. INFO [2025-09-24 21:11:59] Removing 1 non heterozygous (in matched normal) germline SNPs. INFO [2025-09-24 21:11:59] Removing 0 low quality variants with non-offset BQ < 25. INFO [2025-09-24 21:11:59] Base quality scores range from 29 to 35 (offset by 1) INFO [2025-09-24 21:11:59] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS. INFO [2025-09-24 21:11:59] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. INFO [2025-09-24 21:11:59] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding). INFO [2025-09-24 21:11:59] 1.2% of targets contain variants. INFO [2025-09-24 21:11:59] Removing 11 variants outside intervals. INFO [2025-09-24 21:11:59] Found SOMATIC annotation in VCF. INFO [2025-09-24 21:11:59] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. INFO [2025-09-24 21:11:59] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970. INFO [2025-09-24 21:11:59] Excluding 0 novel or poor quality variants from segmentation. INFO [2025-09-24 21:11:59] Sample sex: ? INFO [2025-09-24 21:11:59] Segmenting data... INFO [2025-09-24 21:11:59] Loading pre-computed boundaries for DNAcopy... INFO [2025-09-24 21:11:59] Setting undo.SD parameter to 1.000000. INFO [2025-09-24 21:11:59] Setting prune.hclust.h parameter to 0.200000. INFO [2025-09-24 21:11:59] Found 59 segments with median size of 17.67Mb. INFO [2025-09-24 21:11:59] Using 114 variants. INFO [2025-09-24 21:11:59] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30) INFO [2025-09-24 21:11:59] 2D-grid search of purity and ploidy... INFO [2025-09-24 21:12:00] Local optima: 0.63/1.9 INFO [2025-09-24 21:12:00] Testing local optimum 1/1 at purity 0.63 and total ploidy 1.90... INFO [2025-09-24 21:12:00] Fitting variants with beta model for local optimum 1/1... INFO [2025-09-24 21:12:00] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01. INFO [2025-09-24 21:12:01] Optimized purity: 0.65 INFO [2025-09-24 21:12:01] Done. INFO [2025-09-24 21:12:01] ------------------------------------------------------------ INFO [2025-09-24 21:12:01] ------------------------------------------------------------ INFO [2025-09-24 21:12:01] PureCN 2.15.4 INFO [2025-09-24 21:12:01] ------------------------------------------------------------ INFO [2025-09-24 21:12:01] Loading coverage files... INFO [2025-09-24 21:12:01] Mean target coverages: 112X (tumor) 99X (normal). WARN [2025-09-24 21:12:01] Allosome coverage missing, cannot determine sex. WARN [2025-09-24 21:12:01] Allosome coverage missing, cannot determine sex. INFO [2025-09-24 21:12:01] Removing 228 intervals with missing log.ratio. INFO [2025-09-24 21:12:01] Removing 15 low/high GC targets. INFO [2025-09-24 21:12:01] Removing 21 small (< 5bp) intervals. INFO [2025-09-24 21:12:01] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2025-09-24 21:12:01] No normalDB provided. Provide one for better results. INFO [2025-09-24 21:12:01] Removing 1718 low count (< 100 total reads) intervals. INFO [2025-09-24 21:12:01] Removing 6 low coverage (< 15.0000X) intervals. INFO [2025-09-24 21:12:01] Removing 36 low mappability intervals. INFO [2025-09-24 21:12:01] Using 8006 intervals (8006 on-target, 0 off-target). INFO [2025-09-24 21:12:01] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2025-09-24 21:12:01] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio). INFO [2025-09-24 21:12:01] Loading VCF... INFO [2025-09-24 21:12:01] Found 127 variants in VCF file. INFO [2025-09-24 21:12:01] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2025-09-24 21:12:01] LIB-02240e4 is tumor in VCF file. INFO [2025-09-24 21:12:01] No homozygous variants in VCF, provide unfiltered VCF. INFO [2025-09-24 21:12:01] Removing 1 non heterozygous (in matched normal) germline SNPs. INFO [2025-09-24 21:12:01] Removing 0 low quality variants with non-offset BQ < 25. INFO [2025-09-24 21:12:01] Base quality scores range from 29 to 35 (offset by 1) INFO [2025-09-24 21:12:01] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS. INFO [2025-09-24 21:12:02] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. INFO [2025-09-24 21:12:02] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding). INFO [2025-09-24 21:12:02] 1.2% of targets contain variants. INFO [2025-09-24 21:12:02] Removing 11 variants outside intervals. INFO [2025-09-24 21:12:02] Found SOMATIC annotation in VCF. INFO [2025-09-24 21:12:02] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. INFO [2025-09-24 21:12:02] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970. INFO [2025-09-24 21:12:02] Excluding 0 novel or poor quality variants from segmentation. INFO [2025-09-24 21:12:02] Sample sex: ? INFO [2025-09-24 21:12:02] Segmenting data... INFO [2025-09-24 21:12:02] Loading pre-computed boundaries for DNAcopy... INFO [2025-09-24 21:12:02] Setting undo.SD parameter to 1.000000. INFO [2025-09-24 21:12:02] Setting prune.hclust.h parameter to 0.200000. INFO [2025-09-24 21:12:02] Found 59 segments with median size of 17.67Mb. INFO [2025-09-24 21:12:02] Using 114 variants. INFO [2025-09-24 21:12:02] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30) INFO [2025-09-24 21:12:02] 2D-grid search of purity and ploidy... INFO [2025-09-24 21:12:02] Local optima: 0.63/1.9 INFO [2025-09-24 21:12:02] Testing local optimum 1/1 at purity 0.63 and total ploidy 1.90... INFO [2025-09-24 21:12:03] Fitting variants with beta model for local optimum 1/1... WARN [2025-09-24 21:12:03] Some gene symbols found on multiple chromosomes. Use of approved symbols suggested. INFO [2025-09-24 21:12:03] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01. INFO [2025-09-24 21:12:04] Optimized purity: 0.65 INFO [2025-09-24 21:12:04] Done. INFO [2025-09-24 21:12:04] ------------------------------------------------------------ FATAL [2025-09-24 21:12:04] chr1 not valid chromosome name(s). Valid names are: FATAL [2025-09-24 21:12:04] 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22 FATAL [2025-09-24 21:12:04] FATAL [2025-09-24 21:12:04] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:12:04] parameters (PureCN 2.15.4). INFO [2025-09-24 21:12:04] ------------------------------------------------------------ INFO [2025-09-24 21:12:04] PureCN 2.15.4 INFO [2025-09-24 21:12:04] ------------------------------------------------------------ INFO [2025-09-24 21:12:04] Loading coverage files... WARN [2025-09-24 21:12:04] Provided sampleid (Sample2) does not match Sample1 found in segmentation. WARN [2025-09-24 21:12:04] Allosome coverage missing, cannot determine sex. WARN [2025-09-24 21:12:04] Allosome coverage missing, cannot determine sex. INFO [2025-09-24 21:12:04] Removing 10 intervals with missing log.ratio. INFO [2025-09-24 21:12:04] Using 10039 intervals (10039 on-target, 0 off-target). INFO [2025-09-24 21:12:04] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2025-09-24 21:12:04] Loading VCF... INFO [2025-09-24 21:12:04] Found 127 variants in VCF file. INFO [2025-09-24 21:12:04] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2025-09-24 21:12:04] LIB-02240e4 is tumor in VCF file. INFO [2025-09-24 21:12:04] No homozygous variants in VCF, provide unfiltered VCF. INFO [2025-09-24 21:12:04] Removing 1 non heterozygous (in matched normal) germline SNPs. INFO [2025-09-24 21:12:04] Removing 0 low quality variants with non-offset BQ < 25. INFO [2025-09-24 21:12:04] Base quality scores range from 29 to 35 (offset by 1) INFO [2025-09-24 21:12:04] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS. INFO [2025-09-24 21:12:04] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. INFO [2025-09-24 21:12:04] Total size of targeted genomic region: 1.71Mb (2.70Mb with 50bp padding). INFO [2025-09-24 21:12:04] 1.0% of targets contain variants. INFO [2025-09-24 21:12:04] Removing 0 variants outside intervals. INFO [2025-09-24 21:12:04] Found SOMATIC annotation in VCF. INFO [2025-09-24 21:12:04] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. INFO [2025-09-24 21:12:04] Found SOMATIC annotation in VCF. Setting mapping bias to 0.976. INFO [2025-09-24 21:12:04] Excluding 0 novel or poor quality variants from segmentation. INFO [2025-09-24 21:12:04] Sample sex: ? INFO [2025-09-24 21:12:04] Segmenting data... INFO [2025-09-24 21:12:04] Loaded provided segmentation file example_seg.txt (format DNAcopy). WARN [2025-09-24 21:12:04] Provided sampleid (Sample2) does not match Sample1 found in segmentation. INFO [2025-09-24 21:12:04] Re-centering provided segment means (offset -0.0033). INFO [2025-09-24 21:12:04] Loading pre-computed boundaries for DNAcopy... INFO [2025-09-24 21:12:04] Setting undo.SD parameter to 0.000000. Setting multi-figure configuration INFO [2025-09-24 21:12:05] Setting prune.hclust.h parameter to 0.200000. INFO [2025-09-24 21:12:05] Found 54 segments with median size of 24.88Mb. INFO [2025-09-24 21:12:05] Using 125 variants. INFO [2025-09-24 21:12:05] Mean standard deviation of log-ratios: 0.40 (MAPD: 0.00) INFO [2025-09-24 21:12:05] 2D-grid search of purity and ploidy... INFO [2025-09-24 21:12:05] Local optima: 0.6/1.9 INFO [2025-09-24 21:12:05] Testing local optimum 1/1 at purity 0.60 and total ploidy 1.90... INFO [2025-09-24 21:12:05] Fitting variants with beta model for local optimum 1/1... INFO [2025-09-24 21:12:05] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01. INFO [2025-09-24 21:12:06] Optimized purity: 0.65 INFO [2025-09-24 21:12:06] Done. INFO [2025-09-24 21:12:06] ------------------------------------------------------------ WARN [2025-09-24 21:12:06] Allosome coverage missing, cannot determine sex. WARN [2025-09-24 21:12:06] Allosome coverage missing, cannot determine sex. Setting multi-figure configuration FATAL [2025-09-24 21:12:09] Segmentation file expected with colnames ID, chrom, loc.start, loc.end, FATAL [2025-09-24 21:12:09] num.mark, seg.mean FATAL [2025-09-24 21:12:09] FATAL [2025-09-24 21:12:09] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:12:09] parameters (PureCN 2.15.4). FATAL [2025-09-24 21:12:09] seg.file contains multiple samples and sampleid missing. FATAL [2025-09-24 21:12:09] FATAL [2025-09-24 21:12:09] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:12:09] parameters (PureCN 2.15.4). FATAL [2025-09-24 21:12:09] seg.file contains multiple samples and sampleid does not match any. FATAL [2025-09-24 21:12:09] FATAL [2025-09-24 21:12:09] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:12:09] parameters (PureCN 2.15.4). WARN [2025-09-24 21:12:09] Allosome coverage missing, cannot determine sex. WARN [2025-09-24 21:12:09] Allosome coverage missing, cannot determine sex. WARN [2025-09-24 21:12:12] Allosome coverage missing, cannot determine sex. WARN [2025-09-24 21:12:12] Allosome coverage missing, cannot determine sex. WARN [2025-09-24 21:12:12] Provided sampleid (example_tumor.txt.gz) does not match Sample1 found in segmentation. WARN [2025-09-24 21:12:13] Allosome coverage missing, cannot determine sex. WARN [2025-09-24 21:12:13] Allosome coverage missing, cannot determine sex. WARN [2025-09-24 21:12:13] No normalDB provided. Provide one for better results. WARN [2025-09-24 21:12:16] Allosome coverage missing, cannot determine sex. WARN [2025-09-24 21:12:16] Allosome coverage missing, cannot determine sex. WARN [2025-09-24 21:12:17] Provided sampleid (Sample.1) does not match Sample1 found in segmentation. Setting multi-figure configuration WARN [2025-09-24 21:12:19] Allosome coverage missing, cannot determine sex. WARN [2025-09-24 21:12:19] Allosome coverage missing, cannot determine sex. WARN [2025-09-24 21:12:19] No normalDB provided. Provide one for better results. WARN [2025-09-24 21:12:19] Sampleid looks like a normal in VCF, not like a tumor. WARN [2025-09-24 21:12:21] Allosome coverage missing, cannot determine sex. WARN [2025-09-24 21:12:21] Allosome coverage missing, cannot determine sex. FATAL [2025-09-24 21:12:21] normalDB not a valid normalDB object. Use createNormalDatabase to FATAL [2025-09-24 21:12:21] create one. FATAL [2025-09-24 21:12:21] FATAL [2025-09-24 21:12:21] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:12:21] parameters (PureCN 2.15.4). WARN [2025-09-24 21:12:22] You are likely not using the correct baits file! WARN [2025-09-24 21:12:22] Allosome coverage missing, cannot determine sex. WARN [2025-09-24 21:12:22] Allosome coverage missing, cannot determine sex. WARN [2025-09-24 21:12:23] Allosome coverage missing, cannot determine sex. WARN [2025-09-24 21:12:23] Allosome coverage missing, cannot determine sex. FATAL [2025-09-24 21:12:23] normalDB appears to be empty. FATAL [2025-09-24 21:12:23] FATAL [2025-09-24 21:12:23] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:12:23] parameters (PureCN 2.15.4). WARN [2025-09-24 21:12:23] Allosome coverage missing, cannot determine sex. WARN [2025-09-24 21:12:23] Allosome coverage missing, cannot determine sex. WARN [2025-09-24 21:12:23] Intervals in coverage and interval.file have conflicting on/off-target annotation. WARN [2025-09-24 21:12:27] Allosome coverage missing, cannot determine sex. WARN [2025-09-24 21:12:27] Allosome coverage missing, cannot determine sex. FATAL [2025-09-24 21:12:27] Seqlevels missing in provided segmentation: 6 FATAL [2025-09-24 21:12:27] FATAL [2025-09-24 21:12:27] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:12:27] parameters (PureCN 2.15.4). sh: gatk: command not found WARN [2025-09-24 21:12:27] Cannot find gatk binary in path. WARN [2025-09-24 21:12:28] Allosome coverage missing, cannot determine sex. WARN [2025-09-24 21:12:28] Allosome coverage missing, cannot determine sex. WARN [2025-09-24 21:12:28] No normalDB provided. Provide one for better results. FATAL [2025-09-24 21:12:28] segmentationHclust requires an input segmentation. FATAL [2025-09-24 21:12:28] FATAL [2025-09-24 21:12:28] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:12:28] parameters (PureCN 2.15.4). WARN [2025-09-24 21:12:28] Allosome coverage missing, cannot determine sex. WARN [2025-09-24 21:12:28] Allosome coverage missing, cannot determine sex. WARN [2025-09-24 21:12:28] No normalDB provided. Provide one for better results. FATAL [2025-09-24 21:12:37] The normal.panel.vcf.file contains only a single sample. FATAL [2025-09-24 21:12:37] FATAL [2025-09-24 21:12:37] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:12:37] parameters (PureCN 2.15.4). FATAL [2025-09-24 21:12:37] mapping.bias.file must be a file with *.rds suffix. FATAL [2025-09-24 21:12:37] FATAL [2025-09-24 21:12:37] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:12:37] parameters (PureCN 2.15.4). Failed with error: 'there is no package called 'genomicsdb'' FATAL [2025-09-24 21:12:38] min.normals (0) must be >= 1. FATAL [2025-09-24 21:12:38] FATAL [2025-09-24 21:12:38] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:12:38] parameters (PureCN 2.15.4). FATAL [2025-09-24 21:12:38] min.normals (10) cannot be larger than min.normals.assign.betafit (3). FATAL [2025-09-24 21:12:38] FATAL [2025-09-24 21:12:38] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:12:38] parameters (PureCN 2.15.4). FATAL [2025-09-24 21:12:38] min.normals.assign.betafit (10) cannot be larger than FATAL [2025-09-24 21:12:38] min.normals.betafit (7). FATAL [2025-09-24 21:12:38] FATAL [2025-09-24 21:12:38] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:12:38] parameters (PureCN 2.15.4). FATAL [2025-09-24 21:12:38] min.normals.betafit (20) cannot be larger than FATAL [2025-09-24 21:12:38] min.normals.position.specific.fit (10). FATAL [2025-09-24 21:12:38] FATAL [2025-09-24 21:12:38] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:12:38] parameters (PureCN 2.15.4). FATAL [2025-09-24 21:12:38] min.betafit.rho not within expected range or format. FATAL [2025-09-24 21:12:38] FATAL [2025-09-24 21:12:38] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:12:38] parameters (PureCN 2.15.4). FATAL [2025-09-24 21:12:38] max.betafit.rho not within expected range or format. FATAL [2025-09-24 21:12:38] FATAL [2025-09-24 21:12:38] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:12:38] parameters (PureCN 2.15.4). FATAL [2025-09-24 21:12:38] min.betafit.rho (0.9) cannot be larger than max.betafit.rho (0.2). FATAL [2025-09-24 21:12:38] FATAL [2025-09-24 21:12:38] This is most likely a user error due to invalid input data or FATAL [2025-09-24 21:12:38] 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 144.618 4.713 139.233
PureCN.Rcheck/PureCN-Ex.timings
name | user | system | elapsed | |
adjustLogRatio | 0.861 | 0.013 | 0.921 | |
annotateTargets | 2.869 | 0.116 | 3.098 | |
bootstrapResults | 0.258 | 0.026 | 0.287 | |
calculateBamCoverageByInterval | 0.089 | 0.002 | 0.094 | |
calculateLogRatio | 0.261 | 0.015 | 0.302 | |
calculateMappingBiasGatk4 | 0 | 0 | 0 | |
calculateMappingBiasVcf | 0.667 | 0.023 | 0.719 | |
calculatePowerDetectSomatic | 0.957 | 0.004 | 1.018 | |
calculateTangentNormal | 1.027 | 0.021 | 1.078 | |
callAlterations | 0.054 | 0.002 | 0.061 | |
callAlterationsFromSegmentation | 0.521 | 0.013 | 0.557 | |
callAmplificationsInLowPurity | 13.631 | 0.154 | 14.617 | |
callCIN | 0.086 | 0.002 | 0.088 | |
callLOH | 0.073 | 0.002 | 0.076 | |
callMutationBurden | 0.605 | 0.015 | 0.621 | |
centromeres | 0.000 | 0.001 | 0.002 | |
correctCoverageBias | 0.619 | 0.028 | 0.653 | |
createCurationFile | 0.150 | 0.004 | 0.156 | |
createNormalDatabase | 0.874 | 0.015 | 0.898 | |
filterIntervals | 7.441 | 0.146 | 7.654 | |
filterVcfBasic | 0.223 | 0.003 | 0.227 | |
filterVcfMuTect | 0.212 | 0.002 | 0.215 | |
filterVcfMuTect2 | 0.237 | 0.003 | 0.240 | |
findFocal | 4.132 | 0.025 | 4.214 | |
findHighQualitySNPs | 0.548 | 0.008 | 0.557 | |
getSexFromCoverage | 0.106 | 0.005 | 0.111 | |
getSexFromVcf | 0.095 | 0.003 | 0.098 | |
plotAbs | 0.090 | 0.004 | 0.099 | |
poolCoverage | 0.218 | 0.012 | 0.231 | |
predictSomatic | 0.168 | 0.002 | 0.170 | |
preprocessIntervals | 0.232 | 0.006 | 0.239 | |
processMultipleSamples | 0.841 | 0.016 | 0.882 | |
readAllelicCountsFile | 0.195 | 0.001 | 0.207 | |
readCoverageFile | 0.087 | 0.006 | 0.094 | |
readCurationFile | 0.088 | 0.003 | 0.092 | |
readIntervalFile | 0.058 | 0.003 | 0.063 | |
readLogRatioFile | 0.009 | 0.000 | 0.010 | |
readSegmentationFile | 0.003 | 0.000 | 0.004 | |
runAbsoluteCN | 5.818 | 0.118 | 6.005 | |
segmentationCBS | 2.923 | 0.019 | 2.972 | |
segmentationGATK4 | 0.001 | 0.001 | 0.001 | |
segmentationHclust | 5.396 | 0.097 | 5.544 | |
segmentationPSCBS | 13.521 | 0.153 | 13.791 | |
setMappingBiasVcf | 0.124 | 0.003 | 0.128 | |
setPriorVcf | 0.101 | 0.004 | 0.106 | |