Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-09 12:06 -0400 (Thu, 09 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4854 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4642 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4587 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4584 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 1650/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
PureCN 2.15.4 (landing page) Markus Riester
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the PureCN package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PureCN.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: PureCN |
Version: 2.15.4 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PureCN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PureCN_2.15.4.tar.gz |
StartedAt: 2025-10-08 21:16:10 -0400 (Wed, 08 Oct 2025) |
EndedAt: 2025-10-08 21:21:49 -0400 (Wed, 08 Oct 2025) |
EllapsedTime: 339.3 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 14.155 0.204 14.453 segmentationPSCBS 13.038 0.157 13.216 filterIntervals 7.291 0.213 7.523 runAbsoluteCN 6.103 0.118 6.265 segmentationHclust 5.876 0.113 5.993 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK
PureCN.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PureCN ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘PureCN’ ... ** this is package ‘PureCN’ version ‘2.15.4’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (PureCN)
PureCN.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(PureCN) Loading required package: DNAcopy Loading required package: VariantAnnotation Loading required package: BiocGenerics Loading required package: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, unique, unsplit, which.max, which.min Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: Seqinfo Loading required package: GenomicRanges Loading required package: stats4 Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: SummarizedExperiment Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians Loading required package: Rsamtools Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Attaching package: 'VariantAnnotation' The following object is masked from 'package:base': tabulate > > test_check("PureCN") WARN [2025-10-08 21:19:33] Attempted adding gene symbols to intervals. Heuristics have been used to pick symbols for overlapping genes. WARN [2025-10-08 21:19:33] Chromosome naming style of txdb file (UCSC) was different from interval file (Ensembl). WARN [2025-10-08 21:19:37] Attempted adding gene symbols to intervals. Heuristics have been used to pick symbols for overlapping genes. FATAL [2025-10-08 21:19:38] tumor.coverage.file and interval.file do not align. FATAL [2025-10-08 21:19:38] FATAL [2025-10-08 21:19:38] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:19:38] parameters (PureCN 2.15.4). WARN [2025-10-08 21:19:38] Cannot find all contig lengths while exporting interval file. INFO [2025-10-08 21:19:38] Processing seq1:1-21 (1/3)... INFO [2025-10-08 21:19:39] Processing seq1:1227-1247 (2/3)... INFO [2025-10-08 21:19:39] Processing seq2:594-614 (3/3)... WARN [2025-10-08 21:19:39] Large potential mis-calibration of on- and off-target log2 ratios: 0.26 FATAL [2025-10-08 21:19:39] Need either f or purity and ploidy. FATAL [2025-10-08 21:19:39] FATAL [2025-10-08 21:19:39] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:19:39] parameters (PureCN 2.15.4). FATAL [2025-10-08 21:19:39] f not in expected range. FATAL [2025-10-08 21:19:39] FATAL [2025-10-08 21:19:39] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:19:39] parameters (PureCN 2.15.4). FATAL [2025-10-08 21:19:39] coverage not in expected range (>=2) FATAL [2025-10-08 21:19:39] FATAL [2025-10-08 21:19:39] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:19:39] parameters (PureCN 2.15.4). FATAL [2025-10-08 21:19:39] purity not in expected range. FATAL [2025-10-08 21:19:39] FATAL [2025-10-08 21:19:39] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:19:39] parameters (PureCN 2.15.4). FATAL [2025-10-08 21:19:39] ploidy not in expected range. FATAL [2025-10-08 21:19:39] FATAL [2025-10-08 21:19:39] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:19:39] parameters (PureCN 2.15.4). FATAL [2025-10-08 21:19:39] cell.fraction not in expected range. FATAL [2025-10-08 21:19:39] FATAL [2025-10-08 21:19:39] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:19:39] parameters (PureCN 2.15.4). INFO [2025-10-08 21:19:40] 576 on-target bins with low coverage in all samples. WARN [2025-10-08 21:19:40] You are likely not using the correct baits file! WARN [2025-10-08 21:19:40] Allosome coverage missing, cannot determine sex. WARN [2025-10-08 21:19:40] Allosome coverage missing, cannot determine sex. INFO [2025-10-08 21:19:40] Processing on-target regions... INFO [2025-10-08 21:19:40] Removing 930 intervals with low coverage in normalDB. INFO [2025-10-08 21:19:40] Removing 1 intervals with zero coverage in more than 3% of normalDB. INFO [2025-10-08 21:19:41] Tumor/normal noise ratio: 19.041 WARN [2025-10-08 21:19:41] Extensive noise in tumor compared to normals. INFO [2025-10-08 21:19:56] Tumor/normal noise ratio: 19.041 WARN [2025-10-08 21:19:56] Extensive noise in tumor compared to normals. INFO [2025-10-08 21:19:58] Using BiocParallel for parallel optimization. FATAL [2025-10-08 21:20:02] pvalue.cutoff not within expected range or format. FATAL [2025-10-08 21:20:02] FATAL [2025-10-08 21:20:02] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:02] parameters (PureCN 2.15.4). FATAL [2025-10-08 21:20:02] pvalue.cutoff not within expected range or format. FATAL [2025-10-08 21:20:02] FATAL [2025-10-08 21:20:02] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:02] parameters (PureCN 2.15.4). FATAL [2025-10-08 21:20:02] percentile.cutoff not in expected range (0 to 100). FATAL [2025-10-08 21:20:02] FATAL [2025-10-08 21:20:02] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:02] parameters (PureCN 2.15.4). FATAL [2025-10-08 21:20:02] percentile.cutoff not in expected range (0 to 100). FATAL [2025-10-08 21:20:02] FATAL [2025-10-08 21:20:02] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:02] parameters (PureCN 2.15.4). FATAL [2025-10-08 21:20:02] purity not within expected range or format. FATAL [2025-10-08 21:20:02] FATAL [2025-10-08 21:20:02] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:02] parameters (PureCN 2.15.4). FATAL [2025-10-08 21:20:02] purity not within expected range or format. FATAL [2025-10-08 21:20:02] FATAL [2025-10-08 21:20:02] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:02] parameters (PureCN 2.15.4). INFO [2025-10-08 21:20:03] ------------------------------------------------------------ INFO [2025-10-08 21:20:03] PureCN 2.15.4 INFO [2025-10-08 21:20:03] ------------------------------------------------------------ INFO [2025-10-08 21:20:03] Loading coverage files... INFO [2025-10-08 21:20:03] Mean target coverages: 112X (tumor) 99X (normal). WARN [2025-10-08 21:20:03] Allosome coverage missing, cannot determine sex. WARN [2025-10-08 21:20:03] Allosome coverage missing, cannot determine sex. INFO [2025-10-08 21:20:03] Removing 228 intervals with missing log.ratio. INFO [2025-10-08 21:20:03] Removing 22 small (< 5bp) intervals. INFO [2025-10-08 21:20:03] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2025-10-08 21:20:03] No normalDB provided. Provide one for better results. INFO [2025-10-08 21:20:03] Removing 1724 low count (< 100 total reads) intervals. INFO [2025-10-08 21:20:03] Removing 6 low coverage (< 15.0000X) intervals. INFO [2025-10-08 21:20:03] Using 8050 intervals (8050 on-target, 0 off-target). INFO [2025-10-08 21:20:03] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2025-10-08 21:20:03] No interval.file provided. Cannot check for any GC-biases. INFO [2025-10-08 21:20:03] Loading VCF... INFO [2025-10-08 21:20:03] Found 127 variants in VCF file. INFO [2025-10-08 21:20:03] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2025-10-08 21:20:03] LIB-02240e4 is tumor in VCF file. INFO [2025-10-08 21:20:03] No homozygous variants in VCF, provide unfiltered VCF. INFO [2025-10-08 21:20:03] Removing 1 non heterozygous (in matched normal) germline SNPs. INFO [2025-10-08 21:20:03] Removing 0 low quality variants with non-offset BQ < 25. INFO [2025-10-08 21:20:03] Base quality scores range from 29 to 35 (offset by 1) INFO [2025-10-08 21:20:03] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS. INFO [2025-10-08 21:20:03] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. INFO [2025-10-08 21:20:04] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding). INFO [2025-10-08 21:20:04] 1.2% of targets contain variants. INFO [2025-10-08 21:20:04] Removing 4 variants outside intervals. INFO [2025-10-08 21:20:04] Found SOMATIC annotation in VCF. INFO [2025-10-08 21:20:04] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. INFO [2025-10-08 21:20:04] Found SOMATIC annotation in VCF. Setting mapping bias to 0.972. INFO [2025-10-08 21:20:04] Excluding 0 novel or poor quality variants from segmentation. INFO [2025-10-08 21:20:04] Sample sex: ? INFO [2025-10-08 21:20:04] Segmenting data... INFO [2025-10-08 21:20:04] Loading pre-computed boundaries for DNAcopy... INFO [2025-10-08 21:20:04] Setting undo.SD parameter to 1.000000. INFO [2025-10-08 21:20:04] Setting prune.hclust.h parameter to 0.200000. INFO [2025-10-08 21:20:04] Found 59 segments with median size of 17.67Mb. INFO [2025-10-08 21:20:04] Using 121 variants. INFO [2025-10-08 21:20:04] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30) INFO [2025-10-08 21:20:04] 2D-grid search of purity and ploidy... INFO [2025-10-08 21:20:05] Local optima: 0.63/1.9, 0.5/2 INFO [2025-10-08 21:20:05] Testing local optimum 1/2 at purity 0.63 and total ploidy 1.90... INFO [2025-10-08 21:20:05] Testing local optimum 2/2 at purity 0.50 and total ploidy 2.00... INFO [2025-10-08 21:20:05] Skipping 1 solutions that converged to the same optima. INFO [2025-10-08 21:20:05] Fitting variants with beta model for local optimum 1/2... INFO [2025-10-08 21:20:05] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01. INFO [2025-10-08 21:20:06] Optimized purity: 0.65 INFO [2025-10-08 21:20:06] Done. INFO [2025-10-08 21:20:06] ------------------------------------------------------------ INFO [2025-10-08 21:20:06] Estimating callable regions. FATAL [2025-10-08 21:20:07] exclude not a GRanges object. FATAL [2025-10-08 21:20:07] FATAL [2025-10-08 21:20:07] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:07] parameters (PureCN 2.15.4). FATAL [2025-10-08 21:20:07] callable not a GRanges object. FATAL [2025-10-08 21:20:07] FATAL [2025-10-08 21:20:07] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:07] parameters (PureCN 2.15.4). WARN [2025-10-08 21:20:10] tumor.coverage.file and interval.file do not align. INFO [2025-10-08 21:20:10] No Gene column in interval.file. You won't get gene-level calls. FATAL [2025-10-08 21:20:11] No gc_bias column in interval.file. FATAL [2025-10-08 21:20:11] FATAL [2025-10-08 21:20:11] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:11] parameters (PureCN 2.15.4). FATAL [2025-10-08 21:20:11] Provided coverage is zero, most likely due to a corrupt BAM file. FATAL [2025-10-08 21:20:11] FATAL [2025-10-08 21:20:11] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:11] parameters (PureCN 2.15.4). INFO [2025-10-08 21:20:11] No reptiming column in interval.file. INFO [2025-10-08 21:20:13] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpAGVjDt/filef25c322cced0.rds... INFO [2025-10-08 21:20:13] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpAGVjDt/filef25c322cced0.rds... INFO [2025-10-08 21:20:13] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpAGVjDt/filef25c322cced0.rds... INFO [2025-10-08 21:20:13] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpAGVjDt/filef25c322cced0.rds... INFO [2025-10-08 21:20:13] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpAGVjDt/filef25c322cced0.rds... INFO [2025-10-08 21:20:13] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpAGVjDt/filef25c322cced0.rds... FATAL [2025-10-08 21:20:13] Purity or Ploidy not numeric or in expected range. FATAL [2025-10-08 21:20:13] FATAL [2025-10-08 21:20:13] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:13] parameters (PureCN 2.15.4). INFO [2025-10-08 21:20:13] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpAGVjDt/filef25c322cced0.rds... INFO [2025-10-08 21:20:13] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpAGVjDt/filef25c322cced0.rds... FATAL [2025-10-08 21:20:13] 'Failed' column in FATAL [2025-10-08 21:20:13] /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpAGVjDt/filef25c322cced0.csv FATAL [2025-10-08 21:20:13] not logical(1). FATAL [2025-10-08 21:20:13] FATAL [2025-10-08 21:20:13] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:13] parameters (PureCN 2.15.4). INFO [2025-10-08 21:20:13] 576 on-target bins with low coverage in all samples. WARN [2025-10-08 21:20:13] You are likely not using the correct baits file! WARN [2025-10-08 21:20:13] Allosome coverage missing, cannot determine sex. WARN [2025-10-08 21:20:13] Allosome coverage missing, cannot determine sex. INFO [2025-10-08 21:20:13] Processing on-target regions... INFO [2025-10-08 21:20:14] Removing 930 intervals with low coverage in normalDB. INFO [2025-10-08 21:20:14] Removing 1 intervals with zero coverage in more than 3% of normalDB. INFO [2025-10-08 21:20:15] 576 on-target bins with low coverage in all samples. WARN [2025-10-08 21:20:15] You are likely not using the correct baits file! WARN [2025-10-08 21:20:15] Allosome coverage missing, cannot determine sex. WARN [2025-10-08 21:20:15] Allosome coverage missing, cannot determine sex. INFO [2025-10-08 21:20:15] Processing on-target regions... INFO [2025-10-08 21:20:15] Removing 930 intervals with low coverage in normalDB. INFO [2025-10-08 21:20:15] Removing 1 intervals with zero coverage in more than 3% of normalDB. INFO [2025-10-08 21:20:16] 576 on-target bins with low coverage in all samples. WARN [2025-10-08 21:20:16] You are likely not using the correct baits file! WARN [2025-10-08 21:20:16] Allosome coverage missing, cannot determine sex. WARN [2025-10-08 21:20:16] Allosome coverage missing, cannot determine sex. INFO [2025-10-08 21:20:16] Processing on-target regions... INFO [2025-10-08 21:20:16] Removing 930 intervals with low coverage in normalDB. INFO [2025-10-08 21:20:16] Removing 1 intervals with zero coverage in more than 3% of normalDB. WARN [2025-10-08 21:20:17] Allosome coverage missing, cannot determine sex. INFO [2025-10-08 21:20:17] Sample sex: NA WARN [2025-10-08 21:20:17] Allosome coverage missing, cannot determine sex. INFO [2025-10-08 21:20:17] Sample sex: NA INFO [2025-10-08 21:20:17] 576 on-target bins with low coverage in all samples. WARN [2025-10-08 21:20:17] You are likely not using the correct baits file! WARN [2025-10-08 21:20:17] Allosome coverage missing, cannot determine sex. WARN [2025-10-08 21:20:17] Allosome coverage missing, cannot determine sex. FATAL [2025-10-08 21:20:17] Length of normal.coverage.files and sex different FATAL [2025-10-08 21:20:17] FATAL [2025-10-08 21:20:17] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:17] parameters (PureCN 2.15.4). WARN [2025-10-08 21:20:19] Target intervals were not sorted. INFO [2025-10-08 21:20:19] 560 on-target bins with low coverage in all samples. WARN [2025-10-08 21:20:19] You are likely not using the correct baits file! WARN [2025-10-08 21:20:19] Allosome coverage missing, cannot determine sex. WARN [2025-10-08 21:20:19] Allosome coverage missing, cannot determine sex. WARN [2025-10-08 21:20:19] Allosome coverage missing, cannot determine sex. INFO [2025-10-08 21:20:19] Processing on-target regions... INFO [2025-10-08 21:20:19] Removing 978 intervals with low coverage in normalDB. INFO [2025-10-08 21:20:19] Removing 11 intervals with zero coverage in more than 3% of normalDB. FATAL [2025-10-08 21:20:19] tumor.coverage.file and normalDB do not align. FATAL [2025-10-08 21:20:19] FATAL [2025-10-08 21:20:19] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:19] parameters (PureCN 2.15.4). FATAL [2025-10-08 21:20:19] At least 2 normal.coverage.files required. FATAL [2025-10-08 21:20:19] FATAL [2025-10-08 21:20:19] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:19] parameters (PureCN 2.15.4). INFO [2025-10-08 21:20:20] ------------------------------------------------------------ INFO [2025-10-08 21:20:20] PureCN 2.15.4 INFO [2025-10-08 21:20:20] ------------------------------------------------------------ INFO [2025-10-08 21:20:20] Loading coverage files... INFO [2025-10-08 21:20:21] Mean target coverages: 112X (tumor) 99X (normal). WARN [2025-10-08 21:20:21] Allosome coverage missing, cannot determine sex. WARN [2025-10-08 21:20:21] Allosome coverage missing, cannot determine sex. INFO [2025-10-08 21:20:21] Removing 228 intervals with missing log.ratio. FATAL [2025-10-08 21:20:21] normalDB incompatible with this PureCN version. Please re-run FATAL [2025-10-08 21:20:21] NormalDB.R. FATAL [2025-10-08 21:20:21] FATAL [2025-10-08 21:20:21] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:21] parameters (PureCN 2.15.4). FATAL [2025-10-08 21:20:21] normalDB incompatible with this PureCN version. Please re-run FATAL [2025-10-08 21:20:21] NormalDB.R. FATAL [2025-10-08 21:20:21] FATAL [2025-10-08 21:20:21] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:21] parameters (PureCN 2.15.4). FATAL [2025-10-08 21:20:21] normal.coverage.files with _coverage.txt and _loess.txt suffix FATAL [2025-10-08 21:20:21] provided. Provide either only GC-normalized or raw coverage files! FATAL [2025-10-08 21:20:21] FATAL [2025-10-08 21:20:21] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:21] parameters (PureCN 2.15.4). INFO [2025-10-08 21:20:21] Removing 22 non heterozygous (in matched normal) germline SNPs. INFO [2025-10-08 21:20:21] Removing 19 low quality variants with non-offset BQ < 25. INFO [2025-10-08 21:20:21] Base quality scores range from 24 to 35 (offset by 1) INFO [2025-10-08 21:20:21] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS. INFO [2025-10-08 21:20:21] Initial testing for significant sample cross-contamination: unlikely INFO [2025-10-08 21:20:21] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. INFO [2025-10-08 21:20:21] Removing 22 non heterozygous (in matched normal) germline SNPs. INFO [2025-10-08 21:20:21] Removing 19 low quality variants with non-offset BQ < 25. INFO [2025-10-08 21:20:21] Base quality scores range from 24 to 35 (offset by 1) INFO [2025-10-08 21:20:21] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS. INFO [2025-10-08 21:20:21] Initial testing for significant sample cross-contamination: unlikely INFO [2025-10-08 21:20:21] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. INFO [2025-10-08 21:20:21] Removing 6 blacklisted variants. INFO [2025-10-08 21:20:21] Removing 22 non heterozygous (in matched normal) germline SNPs. INFO [2025-10-08 21:20:21] Removing 19 low quality variants with non-offset BQ < 25. INFO [2025-10-08 21:20:21] Base quality scores range from 24 to 35 (offset by 1) INFO [2025-10-08 21:20:21] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS. INFO [2025-10-08 21:20:22] Initial testing for significant sample cross-contamination: unlikely INFO [2025-10-08 21:20:22] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. WARN [2025-10-08 21:20:22] MuTect stats file lacks contig and position columns. INFO [2025-10-08 21:20:22] Removing 22 non heterozygous (in matched normal) germline SNPs. INFO [2025-10-08 21:20:22] Removing 19 low quality variants with non-offset BQ < 25. INFO [2025-10-08 21:20:22] Base quality scores range from 24 to 35 (offset by 1) INFO [2025-10-08 21:20:22] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS. INFO [2025-10-08 21:20:22] Initial testing for significant sample cross-contamination: unlikely INFO [2025-10-08 21:20:22] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. WARN [2025-10-08 21:20:22] MuTect stats file and VCF file do not align perfectly. Will remove 2325 unmatched variants. WARN [2025-10-08 21:20:22] MuTect stats file lacks failure_reasons column. Keeping all variants listed in stats file. INFO [2025-10-08 21:20:22] Removing 0 non heterozygous (in matched normal) germline SNPs. INFO [2025-10-08 21:20:22] Removing 0 low quality variants with non-offset BQ < 25. INFO [2025-10-08 21:20:22] Base quality scores range from 31 to 33 (offset by 1) INFO [2025-10-08 21:20:22] Minimum number of supporting reads ranges from 3 to 4, depending on coverage and BQS. INFO [2025-10-08 21:20:22] Removing 0 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. INFO [2025-10-08 21:20:22] Removing 22 non heterozygous (in matched normal) germline SNPs. INFO [2025-10-08 21:20:22] Base quality scores range from 7 to 35 (offset by 1) INFO [2025-10-08 21:20:22] Minimum number of supporting reads ranges from 1 to 41, depending on coverage and BQS. INFO [2025-10-08 21:20:22] Initial testing for significant sample cross-contamination: unlikely INFO [2025-10-08 21:20:22] Removing 49 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. INFO [2025-10-08 21:20:22] Removing 22 non heterozygous (in matched normal) germline SNPs. INFO [2025-10-08 21:20:22] Base quality scores range from 7 to 35 (offset by 1) INFO [2025-10-08 21:20:22] Minimum number of supporting reads ranges from 1 to 41, depending on coverage and BQS. INFO [2025-10-08 21:20:22] Initial testing for significant sample cross-contamination: unlikely INFO [2025-10-08 21:20:23] Removing 49 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. INFO [2025-10-08 21:20:23] Removing 22 non heterozygous (in matched normal) germline SNPs. WARN [2025-10-08 21:20:23] Many variants removed by min.base.quality (50) filter. You might want to lower the cutoff. FATAL [2025-10-08 21:20:23] No variants passed filter BQ. FATAL [2025-10-08 21:20:23] FATAL [2025-10-08 21:20:23] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:23] parameters (PureCN 2.15.4). INFO [2025-10-08 21:20:23] Found 11 variants in VCF file. WARN [2025-10-08 21:20:23] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead. INFO [2025-10-08 21:20:23] 1 (9.1%) variants annotated as likely germline (DB INFO flag). INFO [2025-10-08 21:20:23] Found 11 variants in VCF file. WARN [2025-10-08 21:20:23] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead. INFO [2025-10-08 21:20:23] 1 (9.1%) variants annotated as likely germline (DB INFO flag). INFO [2025-10-08 21:20:24] Found 11 variants in VCF file. WARN [2025-10-08 21:20:24] vcf.file has no DB or POP_AF info field for membership in germline databases. Guessing it based on available dbSNP ID. INFO [2025-10-08 21:20:24] 1 (9.1%) variants annotated as likely germline (DB INFO flag). INFO [2025-10-08 21:20:24] Found 1000 variants in VCF file. INFO [2025-10-08 21:20:24] Removing 2 triallelic sites. WARN [2025-10-08 21:20:24] Having trouble guessing SOMATIC status... WARN [2025-10-08 21:20:24] DP FORMAT field contains NAs. Removing 44 variants. INFO [2025-10-08 21:20:24] 954 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2025-10-08 21:20:24] Found 12 variants in VCF file. INFO [2025-10-08 21:20:25] Removing 1 triallelic sites. WARN [2025-10-08 21:20:25] DP FORMAT field contains NAs. Removing 1 variants. WARN [2025-10-08 21:20:25] vcf.file has no DB info field for membership in germline databases. Found and used somatic status instead. INFO [2025-10-08 21:20:25] 8 (80.0%) variants annotated as likely germline (DB INFO flag). WARN [2025-10-08 21:20:25] BQ FORMAT field contains NAs. INFO [2025-10-08 21:20:25] Found 2331 variants in VCF file. INFO [2025-10-08 21:20:25] 2282 (97.9%) variants annotated as likely germline (DB INFO flag). INFO [2025-10-08 21:20:25] Found 2331 variants in VCF file. INFO [2025-10-08 21:20:25] 2282 (97.9%) variants annotated as likely germline (DB INFO flag). WARN [2025-10-08 21:20:25] Did not find base quality scores, will use global error rate of 0.0010 instead. INFO [2025-10-08 21:20:25] Removing 21 low quality variants with non-offset BQ < 25. INFO [2025-10-08 21:20:25] Base quality scores range from 24 to 35 (offset by 1) INFO [2025-10-08 21:20:25] Initial testing for significant sample cross-contamination: unlikely INFO [2025-10-08 21:20:25] Removing 89 variants with AF < 0.030 or AF >= 0.970 or insufficient supporting reads or depth < 15. INFO [2025-10-08 21:20:25] Found 2331 variants in VCF file. INFO [2025-10-08 21:20:25] 2282 (97.9%) variants annotated as likely germline (DB INFO flag). WARN [2025-10-08 21:20:25] BQ FORMAT field contains NAs. WARN [2025-10-08 21:20:26] Allosome coverage missing, cannot determine sex. WARN [2025-10-08 21:20:26] Allosome coverage missing, cannot determine sex. INFO [2025-10-08 21:20:26] Mean coverages: chrX: 108.58, chrY: 108.58, chr1-22: 104.87. INFO [2025-10-08 21:20:26] Mean coverages: chrX: 108.58, chrY: 2.17, chr1-22: 104.87. INFO [2025-10-08 21:20:26] Mean coverages: chrX: 108.58, chrY: 5.17, chr1-22: 104.87. INFO [2025-10-08 21:20:26] No homozygous variants in VCF, provide unfiltered VCF. INFO [2025-10-08 21:20:26] No germline variants in VCF. FATAL [2025-10-08 21:20:26] No solution with id hello FATAL [2025-10-08 21:20:26] FATAL [2025-10-08 21:20:26] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:26] parameters (PureCN 2.15.4). FATAL [2025-10-08 21:20:26] No solution with id 100 FATAL [2025-10-08 21:20:26] FATAL [2025-10-08 21:20:26] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:26] parameters (PureCN 2.15.4). FATAL [2025-10-08 21:20:27] all.data and w have different lengths. FATAL [2025-10-08 21:20:27] FATAL [2025-10-08 21:20:27] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:27] parameters (PureCN 2.15.4). INFO [2025-10-08 21:20:27] Splitting 5 large targets to an average width of 400. WARN [2025-10-08 21:20:27] No mappability scores provided. WARN [2025-10-08 21:20:27] No reptiming scores provided. INFO [2025-10-08 21:20:27] Calculating GC-content... INFO [2025-10-08 21:20:27] Splitting 5 large targets to an average width of 400. WARN [2025-10-08 21:20:27] No mappability scores provided. WARN [2025-10-08 21:20:27] No reptiming scores provided. INFO [2025-10-08 21:20:27] Calculating GC-content... INFO [2025-10-08 21:20:27] Splitting 5 large targets to an average width of 400. INFO [2025-10-08 21:20:27] Removing 1 targets overlapping with exclude. WARN [2025-10-08 21:20:27] No mappability scores provided. WARN [2025-10-08 21:20:27] No reptiming scores provided. INFO [2025-10-08 21:20:27] Calculating GC-content... WARN [2025-10-08 21:20:27] Found small target regions (< 100bp). Will resize them. INFO [2025-10-08 21:20:27] Splitting 5 large targets to an average width of 400. FATAL [2025-10-08 21:20:27] off.target.padding must be negative. FATAL [2025-10-08 21:20:27] FATAL [2025-10-08 21:20:27] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:27] parameters (PureCN 2.15.4). FATAL [2025-10-08 21:20:27] Interval coordinates should start at 1, not at 0 FATAL [2025-10-08 21:20:27] FATAL [2025-10-08 21:20:27] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:27] parameters (PureCN 2.15.4). WARN [2025-10-08 21:20:27] Found small target regions (< 100bp). Will resize them. INFO [2025-10-08 21:20:27] Splitting 5 large targets to an average width of 400. FATAL [2025-10-08 21:20:27] No off-target regions after filtering for mappability and FATAL [2025-10-08 21:20:27] off.target.padding FATAL [2025-10-08 21:20:27] FATAL [2025-10-08 21:20:27] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:27] parameters (PureCN 2.15.4). WARN [2025-10-08 21:20:27] Found small target regions (< 100bp). Will resize them. INFO [2025-10-08 21:20:27] Splitting 5 large targets to an average width of 400. WARN [2025-10-08 21:20:27] No mappability scores provided. INFO [2025-10-08 21:20:27] Calculating GC-content... WARN [2025-10-08 21:20:27] Found small target regions (< 100bp). Will resize them. INFO [2025-10-08 21:20:28] Averaging reptiming into bins of size 200... INFO [2025-10-08 21:20:28] Splitting 5 large targets to an average width of 400. WARN [2025-10-08 21:20:28] No mappability scores provided. INFO [2025-10-08 21:20:28] Calculating GC-content... WARN [2025-10-08 21:20:28] Found small target regions (< 100bp). Will resize them. INFO [2025-10-08 21:20:28] Splitting 6 large targets to an average width of 200. WARN [2025-10-08 21:20:28] No mappability scores provided. WARN [2025-10-08 21:20:28] No reptiming scores provided. INFO [2025-10-08 21:20:28] Calculating GC-content... WARN [2025-10-08 21:20:28] Found small target regions (< 100bp). Will resize them. INFO [2025-10-08 21:20:28] Splitting 5 large targets to an average width of 400. WARN [2025-10-08 21:20:28] No mappability scores provided. WARN [2025-10-08 21:20:28] No reptiming scores provided. INFO [2025-10-08 21:20:28] Calculating GC-content... INFO [2025-10-08 21:20:28] Splitting 5 large targets to an average width of 400. INFO [2025-10-08 21:20:28] Tiling off-target regions to an average width of 200000. WARN [2025-10-08 21:20:28] No mappability scores provided. WARN [2025-10-08 21:20:28] No reptiming scores provided. INFO [2025-10-08 21:20:28] Calculating GC-content... WARN [2025-10-08 21:20:28] Intervals contain off-target regions. Will not change intervals. WARN [2025-10-08 21:20:28] No mappability scores provided. WARN [2025-10-08 21:20:28] No reptiming scores provided. INFO [2025-10-08 21:20:28] Calculating GC-content... INFO [2025-10-08 21:20:28] Splitting 5 large targets to an average width of 400. WARN [2025-10-08 21:20:28] No reptiming scores provided. INFO [2025-10-08 21:20:28] Calculating GC-content... WARN [2025-10-08 21:20:28] Found small target regions (< 100bp). Will resize them. INFO [2025-10-08 21:20:28] Splitting 5 large targets to an average width of 400. WARN [2025-10-08 21:20:28] No reptiming scores provided. INFO [2025-10-08 21:20:28] Calculating GC-content... WARN [2025-10-08 21:20:29] Found small target regions (< 100bp). Will resize them. INFO [2025-10-08 21:20:29] Splitting 5 large targets to an average width of 400. WARN [2025-10-08 21:20:29] 1 intervals without mappability score (1 on-target). INFO [2025-10-08 21:20:29] Removing 1 intervals with low mappability score (<0.60). WARN [2025-10-08 21:20:29] No reptiming scores provided. INFO [2025-10-08 21:20:29] Calculating GC-content... WARN [2025-10-08 21:20:29] Found small target regions (< 100bp). Will resize them. INFO [2025-10-08 21:20:29] Splitting 5 large targets to an average width of 400. INFO [2025-10-08 21:20:29] Tiling off-target regions to an average width of 200000. WARN [2025-10-08 21:20:29] No reptiming scores provided. INFO [2025-10-08 21:20:29] Calculating GC-content... INFO [2025-10-08 21:20:29] Splitting 5 large targets to an average width of 400. WARN [2025-10-08 21:20:29] No mappability scores provided. WARN [2025-10-08 21:20:29] No reptiming scores provided. INFO [2025-10-08 21:20:29] Calculating GC-content... WARN [2025-10-08 21:20:29] Chromosome naming style of interval file (Ensembl) was different from reference (UCSC). INFO [2025-10-08 21:20:29] Splitting 5 large targets to an average width of 400. WARN [2025-10-08 21:20:29] No mappability scores provided. WARN [2025-10-08 21:20:29] No reptiming scores provided. INFO [2025-10-08 21:20:29] Calculating GC-content... FATAL [2025-10-08 21:20:29] Chromosome naming style of interval file unknown, should be UCSC. FATAL [2025-10-08 21:20:29] FATAL [2025-10-08 21:20:29] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:29] parameters (PureCN 2.15.4). WARN [2025-10-08 21:20:29] Chromosome naming style of interval file (Ensembl) was different from reference (UCSC). WARN [2025-10-08 21:20:29] Chromosome naming style of mappability file (Ensembl) was different from reference (UCSC). INFO [2025-10-08 21:20:29] Splitting 5 large targets to an average width of 400. WARN [2025-10-08 21:20:29] No reptiming scores provided. INFO [2025-10-08 21:20:29] Calculating GC-content... WARN [2025-10-08 21:20:29] Found small target regions (< 60bp). Will resize them. INFO [2025-10-08 21:20:29] Splitting 5 large targets to an average width of 400. WARN [2025-10-08 21:20:29] No mappability scores provided. WARN [2025-10-08 21:20:29] No reptiming scores provided. INFO [2025-10-08 21:20:29] Calculating GC-content... WARN [2025-10-08 21:20:29] Found small target regions (< 60bp). Will drop them. INFO [2025-10-08 21:20:29] Splitting 4 large targets to an average width of 400. WARN [2025-10-08 21:20:29] No mappability scores provided. WARN [2025-10-08 21:20:29] No reptiming scores provided. INFO [2025-10-08 21:20:29] Calculating GC-content... WARN [2025-10-08 21:20:30] Found small target regions (< 200bp). Will resize them. INFO [2025-10-08 21:20:30] Splitting 5 large targets to an average width of 400. WARN [2025-10-08 21:20:30] No mappability scores provided. WARN [2025-10-08 21:20:30] No reptiming scores provided. INFO [2025-10-08 21:20:30] Calculating GC-content... INFO [2025-10-08 21:20:30] Found 20 variants in VCF file. INFO [2025-10-08 21:20:30] 20 (100.0%) variants annotated as likely germline (DB INFO flag). WARN [2025-10-08 21:20:30] Did not find base quality scores, will use global error rate of 0.0010 instead. Error in read.table(file = file, header = header, sep = sep, quote = quote, : no lines available in input FATAL [2025-10-08 21:20:30] Error reading AllelicCountsFile FATAL [2025-10-08 21:20:30] /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/PureCN/extdata/example_allelic_counts_empty.tsv FATAL [2025-10-08 21:20:30] FATAL [2025-10-08 21:20:30] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:30] parameters (PureCN 2.15.4). INFO [2025-10-08 21:20:30] Found 127 variants in VCF file. INFO [2025-10-08 21:20:30] 127 (100.0%) variants annotated as likely germline (DB INFO flag). WARN [2025-10-08 21:20:30] Did not find base quality scores, will use global error rate of 0.0010 instead. INFO [2025-10-08 21:20:30] ------------------------------------------------------------ INFO [2025-10-08 21:20:30] PureCN 2.15.4 INFO [2025-10-08 21:20:30] ------------------------------------------------------------ INFO [2025-10-08 21:20:30] Loading coverage files... INFO [2025-10-08 21:20:30] Mean target coverages: 112X (tumor) 99X (normal). WARN [2025-10-08 21:20:30] Allosome coverage missing, cannot determine sex. WARN [2025-10-08 21:20:30] Allosome coverage missing, cannot determine sex. INFO [2025-10-08 21:20:30] Removing 228 intervals with missing log.ratio. INFO [2025-10-08 21:20:30] Removing 22 small (< 5bp) intervals. INFO [2025-10-08 21:20:30] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2025-10-08 21:20:30] No normalDB provided. Provide one for better results. INFO [2025-10-08 21:20:30] Removing 1724 low count (< 100 total reads) intervals. INFO [2025-10-08 21:20:30] Removing 6 low coverage (< 15.0000X) intervals. INFO [2025-10-08 21:20:31] Using 8050 intervals (8050 on-target, 0 off-target). INFO [2025-10-08 21:20:31] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2025-10-08 21:20:31] No interval.file provided. Cannot check for any GC-biases. INFO [2025-10-08 21:20:31] Loading VCF... INFO [2025-10-08 21:20:31] Found 127 variants in VCF file. INFO [2025-10-08 21:20:31] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2025-10-08 21:20:31] LIB-02240e4 is tumor in VCF file. INFO [2025-10-08 21:20:31] No homozygous variants in VCF, provide unfiltered VCF. INFO [2025-10-08 21:20:31] Removing 1 non heterozygous (in matched normal) germline SNPs. INFO [2025-10-08 21:20:31] Removing 0 low quality variants with non-offset BQ < 25. INFO [2025-10-08 21:20:31] Base quality scores range from 29 to 35 (offset by 1) INFO [2025-10-08 21:20:31] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS. INFO [2025-10-08 21:20:31] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. INFO [2025-10-08 21:20:31] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding). INFO [2025-10-08 21:20:31] 1.2% of targets contain variants. INFO [2025-10-08 21:20:31] Removing 4 variants outside intervals. INFO [2025-10-08 21:20:31] Found SOMATIC annotation in VCF. INFO [2025-10-08 21:20:31] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. INFO [2025-10-08 21:20:31] Found SOMATIC annotation in VCF. Setting mapping bias to 0.972. INFO [2025-10-08 21:20:31] Excluding 0 novel or poor quality variants from segmentation. INFO [2025-10-08 21:20:31] Sample sex: ? INFO [2025-10-08 21:20:31] Segmenting data... INFO [2025-10-08 21:20:31] Loading pre-computed boundaries for DNAcopy... INFO [2025-10-08 21:20:31] Setting undo.SD parameter to 1.000000. INFO [2025-10-08 21:20:31] Setting prune.hclust.h parameter to 0.200000. INFO [2025-10-08 21:20:31] Found 59 segments with median size of 17.67Mb. INFO [2025-10-08 21:20:31] Using 121 variants. INFO [2025-10-08 21:20:31] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30) INFO [2025-10-08 21:20:31] 2D-grid search of purity and ploidy... INFO [2025-10-08 21:20:31] Local optima: 0.65/1.8, 0.52/2 INFO [2025-10-08 21:20:31] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80... INFO [2025-10-08 21:20:32] Testing local optimum 2/2 at purity 0.52 and total ploidy 2.00... INFO [2025-10-08 21:20:32] Skipping 1 solutions that converged to the same optima. INFO [2025-10-08 21:20:32] Fitting variants with beta model for local optimum 1/2... INFO [2025-10-08 21:20:32] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01. INFO [2025-10-08 21:20:33] Optimized purity: 0.65 INFO [2025-10-08 21:20:33] Done. INFO [2025-10-08 21:20:33] ------------------------------------------------------------ FATAL [2025-10-08 21:20:33] log.ratio NULL in .writeLogRatioFileGATK4 FATAL [2025-10-08 21:20:33] FATAL [2025-10-08 21:20:33] This runtime error might be caused by invalid input data or parameters. FATAL [2025-10-08 21:20:33] Please report bug (PureCN 2.15.4). INFO [2025-10-08 21:20:34] Loaded provided segmentation file example_seg.txt (format DNAcopy). INFO [2025-10-08 21:20:34] Re-centering provided segment means (offset -0.0033). INFO [2025-10-08 21:20:34] Loaded provided segmentation file example_gatk4_modelfinal.seg.gz (format GATK4). WARN [2025-10-08 21:20:34] Expecting numeric chromosome names in seg.file, assuming file is properly sorted. INFO [2025-10-08 21:20:34] Re-centering provided segment means (offset -0.0037). INFO [2025-10-08 21:20:34] 576 on-target bins with low coverage in all samples. WARN [2025-10-08 21:20:34] You are likely not using the correct baits file! WARN [2025-10-08 21:20:34] Allosome coverage missing, cannot determine sex. WARN [2025-10-08 21:20:34] Allosome coverage missing, cannot determine sex. INFO [2025-10-08 21:20:34] Processing on-target regions... INFO [2025-10-08 21:20:34] Removing 930 intervals with low coverage in normalDB. INFO [2025-10-08 21:20:34] Removing 1 intervals with zero coverage in more than 3% of normalDB. INFO [2025-10-08 21:20:35] ------------------------------------------------------------ INFO [2025-10-08 21:20:35] PureCN 2.15.4 INFO [2025-10-08 21:20:35] ------------------------------------------------------------ INFO [2025-10-08 21:20:35] Using BiocParallel for parallel optimization. INFO [2025-10-08 21:20:35] Loading coverage files... INFO [2025-10-08 21:20:35] Mean target coverages: 112X (tumor) 99X (normal). WARN [2025-10-08 21:20:35] Allosome coverage missing, cannot determine sex. WARN [2025-10-08 21:20:35] Allosome coverage missing, cannot determine sex. INFO [2025-10-08 21:20:35] Removing 228 intervals with missing log.ratio. INFO [2025-10-08 21:20:35] Removing 705 intervals excluded in normalDB. INFO [2025-10-08 21:20:35] normalDB provided. Setting minimum coverage for segmentation to 0.0015X. INFO [2025-10-08 21:20:35] Removing 1066 low count (< 100 total reads) intervals. INFO [2025-10-08 21:20:35] Using 8050 intervals (8050 on-target, 0 off-target). INFO [2025-10-08 21:20:35] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2025-10-08 21:20:35] No interval.file provided. Cannot check for any GC-biases. INFO [2025-10-08 21:20:35] Sample sex: ? INFO [2025-10-08 21:20:35] Segmenting data... INFO [2025-10-08 21:20:35] Interval weights found, will use weighted CBS. INFO [2025-10-08 21:20:35] Loading pre-computed boundaries for DNAcopy... INFO [2025-10-08 21:20:35] Setting undo.SD parameter to 1.000000. Setting multi-figure configuration INFO [2025-10-08 21:20:36] Found 52 segments with median size of 29.35Mb. INFO [2025-10-08 21:20:36] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30) INFO [2025-10-08 21:20:36] 2D-grid search of purity and ploidy... INFO [2025-10-08 21:20:36] Local optima: 0.65/1.8, 0.52/2 INFO [2025-10-08 21:20:36] Skipping 1 solutions that converged to the same optima. INFO [2025-10-08 21:20:36] Done. INFO [2025-10-08 21:20:36] ------------------------------------------------------------ INFO [2025-10-08 21:20:36] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpAGVjDt/filef25c6cedce8a.rds... FATAL [2025-10-08 21:20:36] runAbsoluteCN was run without a VCF file. FATAL [2025-10-08 21:20:36] FATAL [2025-10-08 21:20:36] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:36] parameters (PureCN 2.15.4). FATAL [2025-10-08 21:20:36] runAbsoluteCN was run without a VCF file. FATAL [2025-10-08 21:20:36] FATAL [2025-10-08 21:20:36] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:36] parameters (PureCN 2.15.4). INFO [2025-10-08 21:20:36] ------------------------------------------------------------ INFO [2025-10-08 21:20:36] PureCN 2.15.4 INFO [2025-10-08 21:20:36] ------------------------------------------------------------ INFO [2025-10-08 21:20:36] Loading coverage files... INFO [2025-10-08 21:20:37] Mean target coverages: 112X (tumor) 99X (normal). WARN [2025-10-08 21:20:37] Allosome coverage missing, cannot determine sex. WARN [2025-10-08 21:20:37] Allosome coverage missing, cannot determine sex. INFO [2025-10-08 21:20:37] Removing 228 intervals with missing log.ratio. INFO [2025-10-08 21:20:37] Removing 705 intervals excluded in normalDB. INFO [2025-10-08 21:20:37] normalDB provided. Setting minimum coverage for segmentation to 0.0015X. INFO [2025-10-08 21:20:37] Removing 1066 low count (< 100 total reads) intervals. INFO [2025-10-08 21:20:37] Using 8050 intervals (8050 on-target, 0 off-target). INFO [2025-10-08 21:20:37] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2025-10-08 21:20:37] No interval.file provided. Cannot check for any GC-biases. INFO [2025-10-08 21:20:37] Sample sex: ? INFO [2025-10-08 21:20:37] Segmenting data... INFO [2025-10-08 21:20:37] Interval weights found, will use weighted PSCBS. FATAL [2025-10-08 21:20:37] segmentationPSCBS requires VCF file. FATAL [2025-10-08 21:20:37] FATAL [2025-10-08 21:20:37] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:37] parameters (PureCN 2.15.4). INFO [2025-10-08 21:20:39] ------------------------------------------------------------ INFO [2025-10-08 21:20:39] PureCN 2.15.4 INFO [2025-10-08 21:20:39] ------------------------------------------------------------ INFO [2025-10-08 21:20:39] Loading coverage files... FATAL [2025-10-08 21:20:39] Need a normal coverage file if log.ratio and seg.file are not provided. FATAL [2025-10-08 21:20:39] FATAL [2025-10-08 21:20:39] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:39] parameters (PureCN 2.15.4). INFO [2025-10-08 21:20:39] ------------------------------------------------------------ INFO [2025-10-08 21:20:39] PureCN 2.15.4 INFO [2025-10-08 21:20:39] ------------------------------------------------------------ FATAL [2025-10-08 21:20:39] min.ploidy or max.ploidy not within expected range. FATAL [2025-10-08 21:20:39] FATAL [2025-10-08 21:20:39] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:39] parameters (PureCN 2.15.4). INFO [2025-10-08 21:20:39] ------------------------------------------------------------ INFO [2025-10-08 21:20:39] PureCN 2.15.4 INFO [2025-10-08 21:20:39] ------------------------------------------------------------ FATAL [2025-10-08 21:20:39] min.ploidy or max.ploidy not within expected range. FATAL [2025-10-08 21:20:39] FATAL [2025-10-08 21:20:39] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:39] parameters (PureCN 2.15.4). INFO [2025-10-08 21:20:39] ------------------------------------------------------------ INFO [2025-10-08 21:20:39] PureCN 2.15.4 INFO [2025-10-08 21:20:39] ------------------------------------------------------------ INFO [2025-10-08 21:20:39] ------------------------------------------------------------ INFO [2025-10-08 21:20:39] PureCN 2.15.4 INFO [2025-10-08 21:20:39] ------------------------------------------------------------ INFO [2025-10-08 21:20:39] ------------------------------------------------------------ INFO [2025-10-08 21:20:39] PureCN 2.15.4 INFO [2025-10-08 21:20:39] ------------------------------------------------------------ FATAL [2025-10-08 21:20:39] test.num.copy not within expected range. FATAL [2025-10-08 21:20:39] FATAL [2025-10-08 21:20:39] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:39] parameters (PureCN 2.15.4). INFO [2025-10-08 21:20:39] ------------------------------------------------------------ INFO [2025-10-08 21:20:39] PureCN 2.15.4 INFO [2025-10-08 21:20:39] ------------------------------------------------------------ WARN [2025-10-08 21:20:39] test.num.copy outside recommended range. FATAL [2025-10-08 21:20:39] max.non.clonal not within expected range or format. FATAL [2025-10-08 21:20:39] FATAL [2025-10-08 21:20:39] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:39] parameters (PureCN 2.15.4). INFO [2025-10-08 21:20:39] ------------------------------------------------------------ INFO [2025-10-08 21:20:39] PureCN 2.15.4 INFO [2025-10-08 21:20:39] ------------------------------------------------------------ WARN [2025-10-08 21:20:39] test.num.copy outside recommended range. FATAL [2025-10-08 21:20:39] max.non.clonal not within expected range or format. FATAL [2025-10-08 21:20:39] FATAL [2025-10-08 21:20:39] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:39] parameters (PureCN 2.15.4). INFO [2025-10-08 21:20:39] ------------------------------------------------------------ INFO [2025-10-08 21:20:39] PureCN 2.15.4 INFO [2025-10-08 21:20:39] ------------------------------------------------------------ FATAL [2025-10-08 21:20:39] test.purity not within expected range. FATAL [2025-10-08 21:20:39] FATAL [2025-10-08 21:20:39] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:39] parameters (PureCN 2.15.4). INFO [2025-10-08 21:20:39] ------------------------------------------------------------ INFO [2025-10-08 21:20:39] PureCN 2.15.4 INFO [2025-10-08 21:20:39] ------------------------------------------------------------ INFO [2025-10-08 21:20:39] Loading coverage files... FATAL [2025-10-08 21:20:39] Tumor and normal are identical. This won't give any meaningful results FATAL [2025-10-08 21:20:39] and I'm stopping here. FATAL [2025-10-08 21:20:39] FATAL [2025-10-08 21:20:39] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:39] parameters (PureCN 2.15.4). INFO [2025-10-08 21:20:39] ------------------------------------------------------------ INFO [2025-10-08 21:20:39] PureCN 2.15.4 INFO [2025-10-08 21:20:39] ------------------------------------------------------------ INFO [2025-10-08 21:20:39] Loading coverage files... FATAL [2025-10-08 21:20:39] Length of log.ratio different from tumor coverage. FATAL [2025-10-08 21:20:39] FATAL [2025-10-08 21:20:39] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:39] parameters (PureCN 2.15.4). INFO [2025-10-08 21:20:40] ------------------------------------------------------------ INFO [2025-10-08 21:20:40] PureCN 2.15.4 INFO [2025-10-08 21:20:40] ------------------------------------------------------------ FATAL [2025-10-08 21:20:40] prior.purity must have the same length as test.purity. FATAL [2025-10-08 21:20:40] FATAL [2025-10-08 21:20:40] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:40] parameters (PureCN 2.15.4). INFO [2025-10-08 21:20:40] ------------------------------------------------------------ INFO [2025-10-08 21:20:40] PureCN 2.15.4 INFO [2025-10-08 21:20:40] ------------------------------------------------------------ FATAL [2025-10-08 21:20:40] min.gof not within expected range or format. FATAL [2025-10-08 21:20:40] FATAL [2025-10-08 21:20:40] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:40] parameters (PureCN 2.15.4). INFO [2025-10-08 21:20:40] ------------------------------------------------------------ INFO [2025-10-08 21:20:40] PureCN 2.15.4 INFO [2025-10-08 21:20:40] ------------------------------------------------------------ FATAL [2025-10-08 21:20:40] prior.purity not within expected range or format. FATAL [2025-10-08 21:20:40] FATAL [2025-10-08 21:20:40] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:40] parameters (PureCN 2.15.4). INFO [2025-10-08 21:20:40] ------------------------------------------------------------ INFO [2025-10-08 21:20:40] PureCN 2.15.4 INFO [2025-10-08 21:20:40] ------------------------------------------------------------ FATAL [2025-10-08 21:20:40] prior.purity must add to 1. Sum is 1.5 FATAL [2025-10-08 21:20:40] FATAL [2025-10-08 21:20:40] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:40] parameters (PureCN 2.15.4). INFO [2025-10-08 21:20:40] ------------------------------------------------------------ INFO [2025-10-08 21:20:40] PureCN 2.15.4 INFO [2025-10-08 21:20:40] ------------------------------------------------------------ FATAL [2025-10-08 21:20:40] max.homozygous.loss not within expected range or format. FATAL [2025-10-08 21:20:40] FATAL [2025-10-08 21:20:40] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:40] parameters (PureCN 2.15.4). INFO [2025-10-08 21:20:40] ------------------------------------------------------------ INFO [2025-10-08 21:20:40] PureCN 2.15.4 INFO [2025-10-08 21:20:40] ------------------------------------------------------------ FATAL [2025-10-08 21:20:40] prior.K not within expected range or format. FATAL [2025-10-08 21:20:40] FATAL [2025-10-08 21:20:40] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:40] parameters (PureCN 2.15.4). INFO [2025-10-08 21:20:40] ------------------------------------------------------------ INFO [2025-10-08 21:20:40] PureCN 2.15.4 INFO [2025-10-08 21:20:40] ------------------------------------------------------------ FATAL [2025-10-08 21:20:40] prior.contamination not within expected range or format. FATAL [2025-10-08 21:20:40] FATAL [2025-10-08 21:20:40] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:40] parameters (PureCN 2.15.4). INFO [2025-10-08 21:20:40] ------------------------------------------------------------ INFO [2025-10-08 21:20:40] PureCN 2.15.4 INFO [2025-10-08 21:20:40] ------------------------------------------------------------ FATAL [2025-10-08 21:20:40] Iterations not in the expected range from 10 to 250. FATAL [2025-10-08 21:20:40] FATAL [2025-10-08 21:20:40] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:40] parameters (PureCN 2.15.4). INFO [2025-10-08 21:20:40] ------------------------------------------------------------ INFO [2025-10-08 21:20:40] PureCN 2.15.4 INFO [2025-10-08 21:20:40] ------------------------------------------------------------ FATAL [2025-10-08 21:20:40] Iterations not in the expected range from 10 to 250. FATAL [2025-10-08 21:20:40] FATAL [2025-10-08 21:20:40] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:40] parameters (PureCN 2.15.4). INFO [2025-10-08 21:20:40] ------------------------------------------------------------ INFO [2025-10-08 21:20:40] PureCN 2.15.4 INFO [2025-10-08 21:20:40] ------------------------------------------------------------ INFO [2025-10-08 21:20:40] Loading coverage files... FATAL [2025-10-08 21:20:40] Missing tumor.coverage.file requires seg.file or log.ratio and FATAL [2025-10-08 21:20:40] interval.file. FATAL [2025-10-08 21:20:40] FATAL [2025-10-08 21:20:40] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:40] parameters (PureCN 2.15.4). INFO [2025-10-08 21:20:40] ------------------------------------------------------------ INFO [2025-10-08 21:20:40] PureCN 2.15.4 INFO [2025-10-08 21:20:40] ------------------------------------------------------------ INFO [2025-10-08 21:20:40] ------------------------------------------------------------ INFO [2025-10-08 21:20:40] PureCN 2.15.4 INFO [2025-10-08 21:20:40] ------------------------------------------------------------ INFO [2025-10-08 21:20:40] Loading coverage files... FATAL [2025-10-08 21:20:40] Interval files in normal and tumor different. FATAL [2025-10-08 21:20:40] FATAL [2025-10-08 21:20:40] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:40] parameters (PureCN 2.15.4). INFO [2025-10-08 21:20:40] ------------------------------------------------------------ INFO [2025-10-08 21:20:40] PureCN 2.15.4 INFO [2025-10-08 21:20:40] ------------------------------------------------------------ INFO [2025-10-08 21:20:40] Loading coverage files... INFO [2025-10-08 21:20:40] Mean target coverages: 0X (tumor) 99X (normal). WARN [2025-10-08 21:20:40] Large difference in coverage of tumor and normal. FATAL [2025-10-08 21:20:40] No finite intervals. FATAL [2025-10-08 21:20:40] FATAL [2025-10-08 21:20:40] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:40] parameters (PureCN 2.15.4). INFO [2025-10-08 21:20:40] ------------------------------------------------------------ INFO [2025-10-08 21:20:40] PureCN 2.15.4 INFO [2025-10-08 21:20:40] ------------------------------------------------------------ INFO [2025-10-08 21:20:40] Loading coverage files... INFO [2025-10-08 21:20:40] Mean target coverages: 112X (tumor) 99X (normal). WARN [2025-10-08 21:20:40] Allosome coverage missing, cannot determine sex. WARN [2025-10-08 21:20:40] Allosome coverage missing, cannot determine sex. INFO [2025-10-08 21:20:41] Removing 228 intervals with missing log.ratio. INFO [2025-10-08 21:20:41] Removing 22 small (< 5bp) intervals. INFO [2025-10-08 21:20:41] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2025-10-08 21:20:41] No normalDB provided. Provide one for better results. INFO [2025-10-08 21:20:41] Removing 1724 low count (< 100 total reads) intervals. INFO [2025-10-08 21:20:41] Removing 6 low coverage (< 15.0000X) intervals. INFO [2025-10-08 21:20:41] Using 8050 intervals (8050 on-target, 0 off-target). INFO [2025-10-08 21:20:41] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2025-10-08 21:20:41] No interval.file provided. Cannot check for any GC-biases. INFO [2025-10-08 21:20:41] Loading VCF... INFO [2025-10-08 21:20:41] Found 127 variants in VCF file. INFO [2025-10-08 21:20:41] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2025-10-08 21:20:41] LIB-02240e4 is tumor in VCF file. INFO [2025-10-08 21:20:41] No homozygous variants in VCF, provide unfiltered VCF. INFO [2025-10-08 21:20:41] Removing 1 non heterozygous (in matched normal) germline SNPs. INFO [2025-10-08 21:20:41] Removing 0 low quality variants with non-offset BQ < 25. INFO [2025-10-08 21:20:41] Base quality scores range from 29 to 35 (offset by 1) INFO [2025-10-08 21:20:41] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS. INFO [2025-10-08 21:20:41] 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 if (!is.numeric(x) && !is.complex(x) && !is.logical(x)) { : closing unused connection 5 (/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpAGVjDt/filef25c52ae97fd.tsv) 3: In if (!is.numeric(x) && !is.complex(x) && !is.logical(x)) { : closing unused connection 4 (/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/PureCN/extdata/example_gatk4_denoised_cr.tsv.gz) FATAL [2025-10-08 21:20:41] Could not import snp.blacklist FATAL [2025-10-08 21:20:41] /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/PureCN/extdata/example_normal.txt.gz:Error FATAL [2025-10-08 21:20:41] in FileForFormat(resource(con), fileFormat(con)) : Format 'txt' FATAL [2025-10-08 21:20:41] unsupported FATAL [2025-10-08 21:20:41] FATAL [2025-10-08 21:20:41] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:20:41] parameters (PureCN 2.15.4). INFO [2025-10-08 21:20:41] ------------------------------------------------------------ INFO [2025-10-08 21:20:41] PureCN 2.15.4 INFO [2025-10-08 21:20:41] ------------------------------------------------------------ INFO [2025-10-08 21:20:41] Loading coverage files... INFO [2025-10-08 21:20:41] Mean target coverages: 112X (tumor) 99X (normal). WARN [2025-10-08 21:20:41] Allosome coverage missing, cannot determine sex. WARN [2025-10-08 21:20:41] Allosome coverage missing, cannot determine sex. INFO [2025-10-08 21:20:41] Removing 228 intervals with missing log.ratio. INFO [2025-10-08 21:20:41] Removing 22 small (< 5bp) intervals. INFO [2025-10-08 21:20:41] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2025-10-08 21:20:41] No normalDB provided. Provide one for better results. INFO [2025-10-08 21:20:41] Removing 233 low coverage (< 15.0000X) intervals. INFO [2025-10-08 21:20:41] Using 9547 intervals (9547 on-target, 0 off-target). INFO [2025-10-08 21:20:41] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2025-10-08 21:20:41] No interval.file provided. Cannot check for any GC-biases. INFO [2025-10-08 21:20:41] Loading VCF... INFO [2025-10-08 21:20:41] Found 127 variants in VCF file. INFO [2025-10-08 21:20:41] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2025-10-08 21:20:41] LIB-02240e4 is tumor in VCF file. INFO [2025-10-08 21:20:41] No homozygous variants in VCF, provide unfiltered VCF. INFO [2025-10-08 21:20:41] Removing 1 non heterozygous (in matched normal) germline SNPs. INFO [2025-10-08 21:20:41] Removing 0 low quality variants with non-offset BQ < 25. INFO [2025-10-08 21:20:41] Base quality scores range from 29 to 35 (offset by 1) INFO [2025-10-08 21:20:42] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS. INFO [2025-10-08 21:20:42] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. INFO [2025-10-08 21:20:42] Total size of targeted genomic region: 1.63Mb (2.58Mb with 50bp padding). INFO [2025-10-08 21:20:42] 1.0% of targets contain variants. INFO [2025-10-08 21:20:42] Removing 2 variants outside intervals. INFO [2025-10-08 21:20:42] Found SOMATIC annotation in VCF. INFO [2025-10-08 21:20:42] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. INFO [2025-10-08 21:20:42] Found SOMATIC annotation in VCF. Setting mapping bias to 0.973. INFO [2025-10-08 21:20:42] Excluding 0 novel or poor quality variants from segmentation. INFO [2025-10-08 21:20:42] Sample sex: ? INFO [2025-10-08 21:20:42] Segmenting data... INFO [2025-10-08 21:20:42] Loading pre-computed boundaries for DNAcopy... INFO [2025-10-08 21:20:42] Setting undo.SD parameter to 1.000000. INFO [2025-10-08 21:20:42] Setting prune.hclust.h parameter to 0.200000. INFO [2025-10-08 21:20:42] Found 54 segments with median size of 24.88Mb. INFO [2025-10-08 21:20:42] Using 123 variants. INFO [2025-10-08 21:20:42] Mean standard deviation of log-ratios: 0.37 (MAPD: 0.32) INFO [2025-10-08 21:20:42] 2D-grid search of purity and ploidy... INFO [2025-10-08 21:20:43] Local optima: 0.62/1.9, 0.3/1.9, 0.32/2 INFO [2025-10-08 21:20:43] Testing local optimum 1/3 at purity 0.62 and total ploidy 1.90... INFO [2025-10-08 21:20:43] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90... INFO [2025-10-08 21:20:43] Recalibrating log-ratios... INFO [2025-10-08 21:20:43] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90... INFO [2025-10-08 21:20:43] Recalibrating log-ratios... INFO [2025-10-08 21:20:43] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90... INFO [2025-10-08 21:20:43] Recalibrating log-ratios... INFO [2025-10-08 21:20:43] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90... INFO [2025-10-08 21:20:43] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00... INFO [2025-10-08 21:20:43] Recalibrating log-ratios... INFO [2025-10-08 21:20:43] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00... INFO [2025-10-08 21:20:44] Recalibrating log-ratios... INFO [2025-10-08 21:20:44] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00... INFO [2025-10-08 21:20:44] Recalibrating log-ratios... INFO [2025-10-08 21:20:44] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00... INFO [2025-10-08 21:20:44] Skipping 1 solutions that converged to the same optima. INFO [2025-10-08 21:20:44] Skipping 1 solutions exceeding max.non.clonal (0.20): 0.3/1.9 (purity/tumor ploidy) INFO [2025-10-08 21:20:44] Fitting variants with beta model for local optimum 1/3... INFO [2025-10-08 21:20:44] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01. INFO [2025-10-08 21:20:45] Optimized purity: 0.65 INFO [2025-10-08 21:20:45] Done. INFO [2025-10-08 21:20:45] ------------------------------------------------------------ INFO [2025-10-08 21:20:45] ------------------------------------------------------------ INFO [2025-10-08 21:20:45] PureCN 2.15.4 INFO [2025-10-08 21:20:45] ------------------------------------------------------------ INFO [2025-10-08 21:20:45] Loading coverage files... INFO [2025-10-08 21:20:45] Mean target coverages: 112X (tumor) 99X (normal). WARN [2025-10-08 21:20:45] Allosome coverage missing, cannot determine sex. WARN [2025-10-08 21:20:45] Allosome coverage missing, cannot determine sex. INFO [2025-10-08 21:20:45] Removing 228 intervals with missing log.ratio. INFO [2025-10-08 21:20:45] Removing 22 small (< 5bp) intervals. INFO [2025-10-08 21:20:45] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2025-10-08 21:20:45] No normalDB provided. Provide one for better results. INFO [2025-10-08 21:20:45] Removing 1724 low count (< 100 total reads) intervals. INFO [2025-10-08 21:20:45] Removing 6 low coverage (< 15.0000X) intervals. INFO [2025-10-08 21:20:45] Using 8050 intervals (8050 on-target, 0 off-target). INFO [2025-10-08 21:20:45] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2025-10-08 21:20:45] No interval.file provided. Cannot check for any GC-biases. INFO [2025-10-08 21:20:45] Loading VCF... INFO [2025-10-08 21:20:45] Found 127 variants in VCF file. WARN [2025-10-08 21:20:45] DP FORMAT field contains NAs. Removing 3 variants. WARN [2025-10-08 21:20:45] DB INFO flag contains NAs INFO [2025-10-08 21:20:45] 119 (96.0%) variants annotated as likely germline (DB INFO flag). INFO [2025-10-08 21:20:45] LIB-02240e4 is tumor in VCF file. INFO [2025-10-08 21:20:45] No homozygous variants in VCF, provide unfiltered VCF. INFO [2025-10-08 21:20:45] Removing 0 low quality variants with non-offset BQ < 25. INFO [2025-10-08 21:20:45] Base quality scores range from 29 to 35 (offset by 1) INFO [2025-10-08 21:20:45] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS. INFO [2025-10-08 21:20:45] Removing 1 variants with AF < 0.030 or AF >= 0.970 or insufficient supporting reads or depth < 15. INFO [2025-10-08 21:20:45] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding). INFO [2025-10-08 21:20:46] 1.2% of targets contain variants. INFO [2025-10-08 21:20:46] Setting somatic prior probabilities for likely germline hits to 0.000500 or to 0.500000 otherwise. INFO [2025-10-08 21:20:46] Excluding 5 novel or poor quality variants from segmentation. INFO [2025-10-08 21:20:46] Sample sex: ? INFO [2025-10-08 21:20:46] Segmenting data... INFO [2025-10-08 21:20:46] Loading pre-computed boundaries for DNAcopy... INFO [2025-10-08 21:20:46] Setting undo.SD parameter to 1.000000. Setting multi-figure configuration INFO [2025-10-08 21:20:46] Setting prune.hclust.h parameter to 0.200000. INFO [2025-10-08 21:20:46] Found 59 segments with median size of 17.67Mb. INFO [2025-10-08 21:20:46] Using 123 variants. INFO [2025-10-08 21:20:46] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30) INFO [2025-10-08 21:20:46] 2D-grid search of purity and ploidy... INFO [2025-10-08 21:20:46] Local optima: 0.62/1.9, 0.3/1.9, 0.32/2 INFO [2025-10-08 21:20:46] Testing local optimum 1/3 at purity 0.62 and total ploidy 1.90... INFO [2025-10-08 21:20:47] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90... INFO [2025-10-08 21:20:47] Recalibrating log-ratios... INFO [2025-10-08 21:20:47] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90... INFO [2025-10-08 21:20:47] Recalibrating log-ratios... INFO [2025-10-08 21:20:47] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90... INFO [2025-10-08 21:20:47] Recalibrating log-ratios... INFO [2025-10-08 21:20:47] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90... INFO [2025-10-08 21:20:47] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00... INFO [2025-10-08 21:20:47] Recalibrating log-ratios... INFO [2025-10-08 21:20:47] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00... INFO [2025-10-08 21:20:47] Recalibrating log-ratios... INFO [2025-10-08 21:20:47] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00... INFO [2025-10-08 21:20:47] Recalibrating log-ratios... INFO [2025-10-08 21:20:47] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00... INFO [2025-10-08 21:20:48] Skipping 2 solutions exceeding max.non.clonal (0.20): 0.3/1.9, 0.35/1.61 (purity/tumor ploidy) INFO [2025-10-08 21:20:48] Fitting variants with beta model for local optimum 1/3... INFO [2025-10-08 21:20:48] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01. INFO [2025-10-08 21:20:49] Optimized purity: 0.65 INFO [2025-10-08 21:20:49] Done. INFO [2025-10-08 21:20:49] ------------------------------------------------------------ INFO [2025-10-08 21:20:49] ------------------------------------------------------------ INFO [2025-10-08 21:20:49] PureCN 2.15.4 INFO [2025-10-08 21:20:49] ------------------------------------------------------------ INFO [2025-10-08 21:20:49] Loading coverage files... INFO [2025-10-08 21:20:49] Mean target coverages: 112X (tumor) 99X (normal). WARN [2025-10-08 21:20:49] Allosome coverage missing, cannot determine sex. WARN [2025-10-08 21:20:49] Allosome coverage missing, cannot determine sex. INFO [2025-10-08 21:20:49] No Gene column in interval.file. You won't get gene-level calls. INFO [2025-10-08 21:20:49] Removing 228 intervals with missing log.ratio. INFO [2025-10-08 21:20:49] Removing 15 low/high GC targets. INFO [2025-10-08 21:20:49] Removing 21 small (< 5bp) intervals. INFO [2025-10-08 21:20:49] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2025-10-08 21:20:49] No normalDB provided. Provide one for better results. INFO [2025-10-08 21:20:49] Removing 1718 low count (< 100 total reads) intervals. INFO [2025-10-08 21:20:49] Removing 6 low coverage (< 15.0000X) intervals. INFO [2025-10-08 21:20:49] Removing 36 low mappability intervals. INFO [2025-10-08 21:20:49] Using 8006 intervals (8006 on-target, 0 off-target). INFO [2025-10-08 21:20:49] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2025-10-08 21:20:49] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio). INFO [2025-10-08 21:20:49] Loading VCF... INFO [2025-10-08 21:20:49] Found 127 variants in VCF file. INFO [2025-10-08 21:20:49] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2025-10-08 21:20:49] LIB-02240e4 is tumor in VCF file. INFO [2025-10-08 21:20:49] No homozygous variants in VCF, provide unfiltered VCF. INFO [2025-10-08 21:20:49] Removing 1 non heterozygous (in matched normal) germline SNPs. INFO [2025-10-08 21:20:49] Removing 0 low quality variants with non-offset BQ < 25. INFO [2025-10-08 21:20:49] Base quality scores range from 29 to 35 (offset by 1) INFO [2025-10-08 21:20:49] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS. INFO [2025-10-08 21:20:49] Removing 1 variants with AF < 0.030 or AF >= Inf or insufficient supporting reads or depth < 15. INFO [2025-10-08 21:20:49] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding). INFO [2025-10-08 21:20:50] 1.2% of targets contain variants. INFO [2025-10-08 21:20:50] Removing 11 variants outside intervals. INFO [2025-10-08 21:20:50] Found SOMATIC annotation in VCF. INFO [2025-10-08 21:20:50] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. INFO [2025-10-08 21:20:50] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970. INFO [2025-10-08 21:20:50] Excluding 0 novel or poor quality variants from segmentation. INFO [2025-10-08 21:20:50] Sample sex: ? INFO [2025-10-08 21:20:50] Segmenting data... INFO [2025-10-08 21:20:50] MAPD of 114 allelic fractions: 0.14 (0.15 adjusted). INFO [2025-10-08 21:20:50] Using unweighted PSCBS. INFO [2025-10-08 21:20:50] Setting undo.SD parameter to 1.000000. INFO [2025-10-08 21:21:00] Setting prune.hclust.h parameter to 0.200000. INFO [2025-10-08 21:21:00] Found 72 segments with median size of 27.25Mb. INFO [2025-10-08 21:21:00] Using 114 variants. INFO [2025-10-08 21:21:00] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30) INFO [2025-10-08 21:21:00] 2D-grid search of purity and ploidy... INFO [2025-10-08 21:21:00] Local optima: 0.65/1.8, 0.38/2.2 INFO [2025-10-08 21:21:00] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80... INFO [2025-10-08 21:21:00] Recalibrating log-ratios... INFO [2025-10-08 21:21:00] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80... INFO [2025-10-08 21:21:00] Recalibrating log-ratios... INFO [2025-10-08 21:21:00] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80... INFO [2025-10-08 21:21:00] Recalibrating log-ratios... INFO [2025-10-08 21:21:00] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80... INFO [2025-10-08 21:21:00] Testing local optimum 2/2 at purity 0.38 and total ploidy 2.20... INFO [2025-10-08 21:21:01] Skipping 1 solutions exceeding max.non.clonal (0.20): 0.65/2.05 (purity/tumor ploidy) INFO [2025-10-08 21:21:01] Fitting variants with beta model for local optimum 2/2... INFO [2025-10-08 21:21:01] Fitting variants for purity 0.40, tumor ploidy 2.55 and contamination 0.01. INFO [2025-10-08 21:21:02] Optimized purity: 0.40 INFO [2025-10-08 21:21:02] Done. INFO [2025-10-08 21:21:02] ------------------------------------------------------------ FATAL [2025-10-08 21:21:02] This function requires gene-level calls. Please add a column 'Gene' FATAL [2025-10-08 21:21:02] containing gene symbols to the interval.file. FATAL [2025-10-08 21:21:02] FATAL [2025-10-08 21:21:02] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:21:02] parameters (PureCN 2.15.4). INFO [2025-10-08 21:21:03] ------------------------------------------------------------ INFO [2025-10-08 21:21:03] PureCN 2.15.4 INFO [2025-10-08 21:21:03] ------------------------------------------------------------ INFO [2025-10-08 21:21:03] Loading coverage files... INFO [2025-10-08 21:21:03] Mean target coverages: 112X (tumor) 99X (normal). WARN [2025-10-08 21:21:03] Allosome coverage missing, cannot determine sex. WARN [2025-10-08 21:21:03] Allosome coverage missing, cannot determine sex. INFO [2025-10-08 21:21:03] Removing 228 intervals with missing log.ratio. INFO [2025-10-08 21:21:03] Removing 22 small (< 5bp) intervals. INFO [2025-10-08 21:21:03] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2025-10-08 21:21:03] No normalDB provided. Provide one for better results. INFO [2025-10-08 21:21:03] Removing 1724 low count (< 100 total reads) intervals. INFO [2025-10-08 21:21:03] Removing 6 low coverage (< 15.0000X) intervals. INFO [2025-10-08 21:21:03] Using 8050 intervals (8050 on-target, 0 off-target). INFO [2025-10-08 21:21:03] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2025-10-08 21:21:03] No interval.file provided. Cannot check for any GC-biases. INFO [2025-10-08 21:21:03] Loading VCF... INFO [2025-10-08 21:21:03] Found 127 variants in VCF file. INFO [2025-10-08 21:21:03] 127 (100.0%) variants annotated as likely germline (DB INFO flag). FATAL [2025-10-08 21:21:03] Different chromosome names in coverage and VCF. FATAL [2025-10-08 21:21:03] FATAL [2025-10-08 21:21:03] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:21:03] parameters (PureCN 2.15.4). INFO [2025-10-08 21:21:03] ------------------------------------------------------------ INFO [2025-10-08 21:21:03] PureCN 2.15.4 INFO [2025-10-08 21:21:03] ------------------------------------------------------------ INFO [2025-10-08 21:21:03] Loading coverage files... INFO [2025-10-08 21:21:03] Mean target coverages: 112X (tumor) 99X (normal). WARN [2025-10-08 21:21:03] Allosome coverage missing, cannot determine sex. WARN [2025-10-08 21:21:03] Allosome coverage missing, cannot determine sex. FATAL [2025-10-08 21:21:03] tumor.coverage.file and interval.file do not align. FATAL [2025-10-08 21:21:03] FATAL [2025-10-08 21:21:03] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:21:03] parameters (PureCN 2.15.4). INFO [2025-10-08 21:21:03] ------------------------------------------------------------ INFO [2025-10-08 21:21:03] PureCN 2.15.4 INFO [2025-10-08 21:21:03] ------------------------------------------------------------ INFO [2025-10-08 21:21:03] Loading coverage files... INFO [2025-10-08 21:21:03] Mean target coverages: 112X (tumor) 99X (normal). WARN [2025-10-08 21:21:03] Allosome coverage missing, cannot determine sex. WARN [2025-10-08 21:21:03] Allosome coverage missing, cannot determine sex. INFO [2025-10-08 21:21:04] Removing 228 intervals with missing log.ratio. INFO [2025-10-08 21:21:04] Removing 15 low/high GC targets. INFO [2025-10-08 21:21:04] Removing 21 small (< 5bp) intervals. INFO [2025-10-08 21:21:04] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2025-10-08 21:21:04] No normalDB provided. Provide one for better results. INFO [2025-10-08 21:21:04] Removing 1718 low count (< 100 total reads) intervals. INFO [2025-10-08 21:21:04] Removing 6 low coverage (< 15.0000X) intervals. INFO [2025-10-08 21:21:04] Removing 36 low mappability intervals. INFO [2025-10-08 21:21:04] Using 8006 intervals (8006 on-target, 0 off-target). INFO [2025-10-08 21:21:04] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2025-10-08 21:21:04] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio). INFO [2025-10-08 21:21:04] Loading VCF... INFO [2025-10-08 21:21:04] Found 127 variants in VCF file. INFO [2025-10-08 21:21:04] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2025-10-08 21:21:04] LIB-02240e4 is tumor in VCF file. INFO [2025-10-08 21:21:04] No homozygous variants in VCF, provide unfiltered VCF. INFO [2025-10-08 21:21:04] Removing 1 non heterozygous (in matched normal) germline SNPs. INFO [2025-10-08 21:21:04] Removing 0 low quality variants with non-offset BQ < 25. INFO [2025-10-08 21:21:04] Base quality scores range from 29 to 35 (offset by 1) INFO [2025-10-08 21:21:04] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS. INFO [2025-10-08 21:21:04] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. INFO [2025-10-08 21:21:04] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding). INFO [2025-10-08 21:21:04] 1.2% of targets contain variants. INFO [2025-10-08 21:21:04] Removing 11 variants outside intervals. INFO [2025-10-08 21:21:04] Found SOMATIC annotation in VCF. INFO [2025-10-08 21:21:04] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. INFO [2025-10-08 21:21:04] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970. INFO [2025-10-08 21:21:04] Excluding 0 novel or poor quality variants from segmentation. INFO [2025-10-08 21:21:04] Sample sex: ? INFO [2025-10-08 21:21:04] Segmenting data... INFO [2025-10-08 21:21:04] Loading pre-computed boundaries for DNAcopy... INFO [2025-10-08 21:21:04] Setting undo.SD parameter to 1.000000. INFO [2025-10-08 21:21:05] Setting prune.hclust.h parameter to 0.200000. INFO [2025-10-08 21:21:05] Found 59 segments with median size of 17.67Mb. INFO [2025-10-08 21:21:05] Using 114 variants. INFO [2025-10-08 21:21:05] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30) INFO [2025-10-08 21:21:05] 2D-grid search of purity and ploidy... INFO [2025-10-08 21:21:05] Local optima: 0.63/1.9 INFO [2025-10-08 21:21:05] Testing local optimum 1/1 at purity 0.63 and total ploidy 1.90... INFO [2025-10-08 21:21:05] Fitting variants with beta model for local optimum 1/1... INFO [2025-10-08 21:21:05] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01. INFO [2025-10-08 21:21:06] Optimized purity: 0.65 INFO [2025-10-08 21:21:06] Done. INFO [2025-10-08 21:21:06] ------------------------------------------------------------ INFO [2025-10-08 21:21:06] ------------------------------------------------------------ INFO [2025-10-08 21:21:06] PureCN 2.15.4 INFO [2025-10-08 21:21:06] ------------------------------------------------------------ INFO [2025-10-08 21:21:06] Loading coverage files... INFO [2025-10-08 21:21:06] Mean target coverages: 112X (tumor) 99X (normal). WARN [2025-10-08 21:21:06] Allosome coverage missing, cannot determine sex. WARN [2025-10-08 21:21:06] Allosome coverage missing, cannot determine sex. INFO [2025-10-08 21:21:07] Removing 228 intervals with missing log.ratio. INFO [2025-10-08 21:21:07] Removing 15 low/high GC targets. INFO [2025-10-08 21:21:07] Removing 21 small (< 5bp) intervals. INFO [2025-10-08 21:21:07] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2025-10-08 21:21:07] No normalDB provided. Provide one for better results. INFO [2025-10-08 21:21:07] Removing 1718 low count (< 100 total reads) intervals. INFO [2025-10-08 21:21:07] Removing 6 low coverage (< 15.0000X) intervals. INFO [2025-10-08 21:21:07] Removing 36 low mappability intervals. INFO [2025-10-08 21:21:07] Using 8006 intervals (8006 on-target, 0 off-target). INFO [2025-10-08 21:21:07] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2025-10-08 21:21:07] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio). INFO [2025-10-08 21:21:07] Loading VCF... INFO [2025-10-08 21:21:07] Found 127 variants in VCF file. INFO [2025-10-08 21:21:07] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2025-10-08 21:21:07] LIB-02240e4 is tumor in VCF file. INFO [2025-10-08 21:21:07] No homozygous variants in VCF, provide unfiltered VCF. INFO [2025-10-08 21:21:07] Removing 1 non heterozygous (in matched normal) germline SNPs. INFO [2025-10-08 21:21:07] Removing 0 low quality variants with non-offset BQ < 25. INFO [2025-10-08 21:21:07] Base quality scores range from 29 to 35 (offset by 1) INFO [2025-10-08 21:21:07] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS. INFO [2025-10-08 21:21:07] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. INFO [2025-10-08 21:21:07] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding). INFO [2025-10-08 21:21:07] 1.2% of targets contain variants. INFO [2025-10-08 21:21:07] Removing 11 variants outside intervals. INFO [2025-10-08 21:21:07] Found SOMATIC annotation in VCF. INFO [2025-10-08 21:21:07] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. INFO [2025-10-08 21:21:07] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970. INFO [2025-10-08 21:21:07] Excluding 0 novel or poor quality variants from segmentation. INFO [2025-10-08 21:21:07] Sample sex: ? INFO [2025-10-08 21:21:07] Segmenting data... INFO [2025-10-08 21:21:07] Loading pre-computed boundaries for DNAcopy... INFO [2025-10-08 21:21:07] Setting undo.SD parameter to 1.000000. INFO [2025-10-08 21:21:08] Setting prune.hclust.h parameter to 0.200000. INFO [2025-10-08 21:21:08] Found 59 segments with median size of 17.67Mb. INFO [2025-10-08 21:21:08] Using 114 variants. INFO [2025-10-08 21:21:08] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30) INFO [2025-10-08 21:21:08] 2D-grid search of purity and ploidy... INFO [2025-10-08 21:21:08] Local optima: 0.63/1.9 INFO [2025-10-08 21:21:08] Testing local optimum 1/1 at purity 0.63 and total ploidy 1.90... INFO [2025-10-08 21:21:08] Fitting variants with beta model for local optimum 1/1... WARN [2025-10-08 21:21:08] Some gene symbols found on multiple chromosomes. Use of approved symbols suggested. INFO [2025-10-08 21:21:08] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01. INFO [2025-10-08 21:21:09] Optimized purity: 0.65 INFO [2025-10-08 21:21:09] Done. INFO [2025-10-08 21:21:09] ------------------------------------------------------------ FATAL [2025-10-08 21:21:09] chr1 not valid chromosome name(s). Valid names are: FATAL [2025-10-08 21:21:09] 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22 FATAL [2025-10-08 21:21:09] FATAL [2025-10-08 21:21:09] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:21:09] parameters (PureCN 2.15.4). INFO [2025-10-08 21:21:09] ------------------------------------------------------------ INFO [2025-10-08 21:21:09] PureCN 2.15.4 INFO [2025-10-08 21:21:09] ------------------------------------------------------------ INFO [2025-10-08 21:21:09] Loading coverage files... WARN [2025-10-08 21:21:10] Provided sampleid (Sample2) does not match Sample1 found in segmentation. WARN [2025-10-08 21:21:10] Allosome coverage missing, cannot determine sex. WARN [2025-10-08 21:21:10] Allosome coverage missing, cannot determine sex. INFO [2025-10-08 21:21:10] Removing 10 intervals with missing log.ratio. INFO [2025-10-08 21:21:10] Using 10039 intervals (10039 on-target, 0 off-target). INFO [2025-10-08 21:21:10] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2025-10-08 21:21:10] Loading VCF... INFO [2025-10-08 21:21:10] Found 127 variants in VCF file. INFO [2025-10-08 21:21:10] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2025-10-08 21:21:10] LIB-02240e4 is tumor in VCF file. INFO [2025-10-08 21:21:10] No homozygous variants in VCF, provide unfiltered VCF. INFO [2025-10-08 21:21:10] Removing 1 non heterozygous (in matched normal) germline SNPs. INFO [2025-10-08 21:21:10] Removing 0 low quality variants with non-offset BQ < 25. INFO [2025-10-08 21:21:10] Base quality scores range from 29 to 35 (offset by 1) INFO [2025-10-08 21:21:10] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS. INFO [2025-10-08 21:21:10] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. INFO [2025-10-08 21:21:10] Total size of targeted genomic region: 1.71Mb (2.70Mb with 50bp padding). INFO [2025-10-08 21:21:10] 1.0% of targets contain variants. INFO [2025-10-08 21:21:10] Removing 0 variants outside intervals. INFO [2025-10-08 21:21:10] Found SOMATIC annotation in VCF. INFO [2025-10-08 21:21:10] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. INFO [2025-10-08 21:21:10] Found SOMATIC annotation in VCF. Setting mapping bias to 0.976. INFO [2025-10-08 21:21:10] Excluding 0 novel or poor quality variants from segmentation. INFO [2025-10-08 21:21:10] Sample sex: ? INFO [2025-10-08 21:21:10] Segmenting data... INFO [2025-10-08 21:21:10] Loaded provided segmentation file example_seg.txt (format DNAcopy). WARN [2025-10-08 21:21:10] Provided sampleid (Sample2) does not match Sample1 found in segmentation. INFO [2025-10-08 21:21:10] Re-centering provided segment means (offset -0.0033). INFO [2025-10-08 21:21:10] Loading pre-computed boundaries for DNAcopy... INFO [2025-10-08 21:21:10] Setting undo.SD parameter to 0.000000. Setting multi-figure configuration INFO [2025-10-08 21:21:10] Setting prune.hclust.h parameter to 0.200000. INFO [2025-10-08 21:21:10] Found 54 segments with median size of 24.88Mb. INFO [2025-10-08 21:21:10] Using 125 variants. INFO [2025-10-08 21:21:10] Mean standard deviation of log-ratios: 0.40 (MAPD: 0.00) INFO [2025-10-08 21:21:10] 2D-grid search of purity and ploidy... INFO [2025-10-08 21:21:11] Local optima: 0.6/1.9 INFO [2025-10-08 21:21:11] Testing local optimum 1/1 at purity 0.60 and total ploidy 1.90... INFO [2025-10-08 21:21:11] Fitting variants with beta model for local optimum 1/1... INFO [2025-10-08 21:21:11] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01. INFO [2025-10-08 21:21:12] Optimized purity: 0.65 INFO [2025-10-08 21:21:12] Done. INFO [2025-10-08 21:21:12] ------------------------------------------------------------ WARN [2025-10-08 21:21:12] Allosome coverage missing, cannot determine sex. WARN [2025-10-08 21:21:12] Allosome coverage missing, cannot determine sex. Setting multi-figure configuration FATAL [2025-10-08 21:21:15] Segmentation file expected with colnames ID, chrom, loc.start, loc.end, FATAL [2025-10-08 21:21:15] num.mark, seg.mean FATAL [2025-10-08 21:21:15] FATAL [2025-10-08 21:21:15] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:21:15] parameters (PureCN 2.15.4). FATAL [2025-10-08 21:21:15] seg.file contains multiple samples and sampleid missing. FATAL [2025-10-08 21:21:15] FATAL [2025-10-08 21:21:15] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:21:15] parameters (PureCN 2.15.4). FATAL [2025-10-08 21:21:15] seg.file contains multiple samples and sampleid does not match any. FATAL [2025-10-08 21:21:15] FATAL [2025-10-08 21:21:15] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:21:15] parameters (PureCN 2.15.4). WARN [2025-10-08 21:21:15] Allosome coverage missing, cannot determine sex. WARN [2025-10-08 21:21:15] Allosome coverage missing, cannot determine sex. WARN [2025-10-08 21:21:18] Allosome coverage missing, cannot determine sex. WARN [2025-10-08 21:21:18] Allosome coverage missing, cannot determine sex. WARN [2025-10-08 21:21:18] Provided sampleid (example_tumor.txt.gz) does not match Sample1 found in segmentation. WARN [2025-10-08 21:21:19] Allosome coverage missing, cannot determine sex. WARN [2025-10-08 21:21:19] Allosome coverage missing, cannot determine sex. WARN [2025-10-08 21:21:19] No normalDB provided. Provide one for better results. WARN [2025-10-08 21:21:22] Allosome coverage missing, cannot determine sex. WARN [2025-10-08 21:21:22] Allosome coverage missing, cannot determine sex. WARN [2025-10-08 21:21:23] Provided sampleid (Sample.1) does not match Sample1 found in segmentation. Setting multi-figure configuration WARN [2025-10-08 21:21:26] Allosome coverage missing, cannot determine sex. WARN [2025-10-08 21:21:26] Allosome coverage missing, cannot determine sex. WARN [2025-10-08 21:21:26] No normalDB provided. Provide one for better results. WARN [2025-10-08 21:21:26] Sampleid looks like a normal in VCF, not like a tumor. WARN [2025-10-08 21:21:28] Allosome coverage missing, cannot determine sex. WARN [2025-10-08 21:21:28] Allosome coverage missing, cannot determine sex. FATAL [2025-10-08 21:21:28] normalDB not a valid normalDB object. Use createNormalDatabase to FATAL [2025-10-08 21:21:28] create one. FATAL [2025-10-08 21:21:28] FATAL [2025-10-08 21:21:28] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:21:28] parameters (PureCN 2.15.4). WARN [2025-10-08 21:21:28] You are likely not using the correct baits file! WARN [2025-10-08 21:21:28] Allosome coverage missing, cannot determine sex. WARN [2025-10-08 21:21:28] Allosome coverage missing, cannot determine sex. WARN [2025-10-08 21:21:29] Allosome coverage missing, cannot determine sex. WARN [2025-10-08 21:21:29] Allosome coverage missing, cannot determine sex. FATAL [2025-10-08 21:21:29] normalDB appears to be empty. FATAL [2025-10-08 21:21:29] FATAL [2025-10-08 21:21:29] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:21:29] parameters (PureCN 2.15.4). WARN [2025-10-08 21:21:29] Allosome coverage missing, cannot determine sex. WARN [2025-10-08 21:21:29] Allosome coverage missing, cannot determine sex. WARN [2025-10-08 21:21:30] Intervals in coverage and interval.file have conflicting on/off-target annotation. WARN [2025-10-08 21:21:33] Allosome coverage missing, cannot determine sex. WARN [2025-10-08 21:21:33] Allosome coverage missing, cannot determine sex. FATAL [2025-10-08 21:21:33] Seqlevels missing in provided segmentation: 6 FATAL [2025-10-08 21:21:33] FATAL [2025-10-08 21:21:33] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:21:33] parameters (PureCN 2.15.4). sh: gatk: command not found WARN [2025-10-08 21:21:34] Cannot find gatk binary in path. WARN [2025-10-08 21:21:34] Allosome coverage missing, cannot determine sex. WARN [2025-10-08 21:21:34] Allosome coverage missing, cannot determine sex. WARN [2025-10-08 21:21:34] No normalDB provided. Provide one for better results. FATAL [2025-10-08 21:21:34] segmentationHclust requires an input segmentation. FATAL [2025-10-08 21:21:34] FATAL [2025-10-08 21:21:34] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:21:34] parameters (PureCN 2.15.4). WARN [2025-10-08 21:21:34] Allosome coverage missing, cannot determine sex. WARN [2025-10-08 21:21:34] Allosome coverage missing, cannot determine sex. WARN [2025-10-08 21:21:34] No normalDB provided. Provide one for better results. FATAL [2025-10-08 21:21:43] The normal.panel.vcf.file contains only a single sample. FATAL [2025-10-08 21:21:43] FATAL [2025-10-08 21:21:43] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:21:43] parameters (PureCN 2.15.4). FATAL [2025-10-08 21:21:43] mapping.bias.file must be a file with *.rds suffix. FATAL [2025-10-08 21:21:43] FATAL [2025-10-08 21:21:43] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:21:43] parameters (PureCN 2.15.4). Failed with error: 'there is no package called 'genomicsdb'' FATAL [2025-10-08 21:21:44] min.normals (0) must be >= 1. FATAL [2025-10-08 21:21:44] FATAL [2025-10-08 21:21:44] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:21:44] parameters (PureCN 2.15.4). FATAL [2025-10-08 21:21:44] min.normals (10) cannot be larger than min.normals.assign.betafit (3). FATAL [2025-10-08 21:21:44] FATAL [2025-10-08 21:21:44] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:21:44] parameters (PureCN 2.15.4). FATAL [2025-10-08 21:21:44] min.normals.assign.betafit (10) cannot be larger than FATAL [2025-10-08 21:21:44] min.normals.betafit (7). FATAL [2025-10-08 21:21:44] FATAL [2025-10-08 21:21:44] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:21:44] parameters (PureCN 2.15.4). FATAL [2025-10-08 21:21:44] min.normals.betafit (20) cannot be larger than FATAL [2025-10-08 21:21:44] min.normals.position.specific.fit (10). FATAL [2025-10-08 21:21:44] FATAL [2025-10-08 21:21:44] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:21:44] parameters (PureCN 2.15.4). FATAL [2025-10-08 21:21:44] min.betafit.rho not within expected range or format. FATAL [2025-10-08 21:21:44] FATAL [2025-10-08 21:21:44] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:21:44] parameters (PureCN 2.15.4). FATAL [2025-10-08 21:21:44] max.betafit.rho not within expected range or format. FATAL [2025-10-08 21:21:44] FATAL [2025-10-08 21:21:44] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:21:44] parameters (PureCN 2.15.4). FATAL [2025-10-08 21:21:44] min.betafit.rho (0.9) cannot be larger than max.betafit.rho (0.2). FATAL [2025-10-08 21:21:44] FATAL [2025-10-08 21:21:44] This is most likely a user error due to invalid input data or FATAL [2025-10-08 21:21:44] 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 148.978 5.568 143.337
PureCN.Rcheck/PureCN-Ex.timings
name | user | system | elapsed | |
adjustLogRatio | 0.806 | 0.014 | 0.823 | |
annotateTargets | 4.748 | 0.174 | 4.952 | |
bootstrapResults | 0.234 | 0.017 | 0.252 | |
calculateBamCoverageByInterval | 0.076 | 0.002 | 0.080 | |
calculateLogRatio | 0.324 | 0.017 | 0.344 | |
calculateMappingBiasGatk4 | 0 | 0 | 0 | |
calculateMappingBiasVcf | 0.647 | 0.019 | 0.669 | |
calculatePowerDetectSomatic | 0.527 | 0.007 | 0.537 | |
calculateTangentNormal | 1.189 | 0.022 | 1.214 | |
callAlterations | 0.085 | 0.006 | 0.092 | |
callAlterationsFromSegmentation | 0.608 | 0.015 | 0.624 | |
callAmplificationsInLowPurity | 14.155 | 0.204 | 14.453 | |
callCIN | 0.085 | 0.002 | 0.087 | |
callLOH | 0.073 | 0.002 | 0.075 | |
callMutationBurden | 0.600 | 0.016 | 0.623 | |
centromeres | 0.000 | 0.001 | 0.002 | |
correctCoverageBias | 0.598 | 0.016 | 0.625 | |
createCurationFile | 0.151 | 0.004 | 0.172 | |
createNormalDatabase | 0.844 | 0.011 | 0.855 | |
filterIntervals | 7.291 | 0.213 | 7.523 | |
filterVcfBasic | 0.210 | 0.003 | 0.213 | |
filterVcfMuTect | 0.235 | 0.003 | 0.238 | |
filterVcfMuTect2 | 0.230 | 0.004 | 0.234 | |
findFocal | 3.659 | 0.027 | 3.698 | |
findHighQualitySNPs | 0.560 | 0.011 | 0.572 | |
getSexFromCoverage | 0.091 | 0.004 | 0.095 | |
getSexFromVcf | 0.091 | 0.003 | 0.096 | |
plotAbs | 0.090 | 0.005 | 0.095 | |
poolCoverage | 0.238 | 0.011 | 0.249 | |
predictSomatic | 0.169 | 0.002 | 0.172 | |
preprocessIntervals | 0.244 | 0.004 | 0.254 | |
processMultipleSamples | 0.883 | 0.017 | 0.900 | |
readAllelicCountsFile | 0.208 | 0.000 | 0.208 | |
readCoverageFile | 0.090 | 0.003 | 0.093 | |
readCurationFile | 0.088 | 0.002 | 0.090 | |
readIntervalFile | 0.060 | 0.001 | 0.062 | |
readLogRatioFile | 0.010 | 0.001 | 0.010 | |
readSegmentationFile | 0.003 | 0.000 | 0.004 | |
runAbsoluteCN | 6.103 | 0.118 | 6.265 | |
segmentationCBS | 2.894 | 0.022 | 2.918 | |
segmentationGATK4 | 0.001 | 0.000 | 0.001 | |
segmentationHclust | 5.876 | 0.113 | 5.993 | |
segmentationPSCBS | 13.038 | 0.157 | 13.216 | |
setMappingBiasVcf | 0.112 | 0.003 | 0.116 | |
setPriorVcf | 0.095 | 0.004 | 0.100 | |