Markus Riester
| Snapshot Date: 2025-12-04 13:40 -0500 (Thu, 04 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/PureCN |
| git_branch: devel |
| git_last_commit: 3330cff |
| git_last_commit_date: 2025-10-29 10:31:57 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-05 11:35 -0500 (Fri, 05 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4869 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4576 |
| 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 1649/2331 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| PureCN 2.17.0 (landing page) Markus Riester
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | 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: 2.17.0 |
| 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_2.17.0.tar.gz |
| StartedAt: 2025-12-04 21:51:06 -0500 (Thu, 04 Dec 2025) |
| EndedAt: 2025-12-04 21:57:36 -0500 (Thu, 04 Dec 2025) |
| EllapsedTime: 390.3 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_2.17.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/PureCN.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* 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 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PureCN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PureCN’ version ‘2.17.0’
* 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 15.162 0.132 16.745
segmentationPSCBS 14.517 0.192 15.334
filterIntervals 8.753 0.150 9.661
runAbsoluteCN 6.338 0.123 6.804
annotateTargets 6.026 0.255 6.584
segmentationHclust 5.737 0.113 6.322
* 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/4.6-arm64/Resources/library’ * installing *source* package ‘PureCN’ ... ** this is package ‘PureCN’ version ‘2.17.0’ ** 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 Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
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 [2025-12-04 21:55:01] Attempted adding gene symbols to intervals. Heuristics have been used to pick symbols for overlapping genes.
WARN [2025-12-04 21:55:01] Chromosome naming style of txdb file (UCSC) was different from interval file (Ensembl).
WARN [2025-12-04 21:55:06] Attempted adding gene symbols to intervals. Heuristics have been used to pick symbols for overlapping genes.
FATAL [2025-12-04 21:55:07] tumor.coverage.file and interval.file do not align.
FATAL [2025-12-04 21:55:07]
FATAL [2025-12-04 21:55:07] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:55:07] parameters (PureCN 2.17.0).
WARN [2025-12-04 21:55:07] Cannot find all contig lengths while exporting interval file.
INFO [2025-12-04 21:55:07] Processing seq1:1-21 (1/3)...
INFO [2025-12-04 21:55:08] Processing seq1:1227-1247 (2/3)...
INFO [2025-12-04 21:55:08] Processing seq2:594-614 (3/3)...
WARN [2025-12-04 21:55:09] Large potential mis-calibration of on- and off-target log2 ratios: 0.26
FATAL [2025-12-04 21:55:09] Need either f or purity and ploidy.
FATAL [2025-12-04 21:55:09]
FATAL [2025-12-04 21:55:09] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:55:09] parameters (PureCN 2.17.0).
FATAL [2025-12-04 21:55:09] f not in expected range.
FATAL [2025-12-04 21:55:09]
FATAL [2025-12-04 21:55:09] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:55:09] parameters (PureCN 2.17.0).
FATAL [2025-12-04 21:55:09] coverage not in expected range (>=2)
FATAL [2025-12-04 21:55:09]
FATAL [2025-12-04 21:55:09] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:55:09] parameters (PureCN 2.17.0).
FATAL [2025-12-04 21:55:09] purity not in expected range.
FATAL [2025-12-04 21:55:09]
FATAL [2025-12-04 21:55:09] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:55:09] parameters (PureCN 2.17.0).
FATAL [2025-12-04 21:55:09] ploidy not in expected range.
FATAL [2025-12-04 21:55:09]
FATAL [2025-12-04 21:55:09] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:55:09] parameters (PureCN 2.17.0).
FATAL [2025-12-04 21:55:09] cell.fraction not in expected range.
FATAL [2025-12-04 21:55:09]
FATAL [2025-12-04 21:55:09] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:55:09] parameters (PureCN 2.17.0).
INFO [2025-12-04 21:55:10] 576 on-target bins with low coverage in all samples.
WARN [2025-12-04 21:55:10] You are likely not using the correct baits file!
WARN [2025-12-04 21:55:10] Allosome coverage missing, cannot determine sex.
WARN [2025-12-04 21:55:10] Allosome coverage missing, cannot determine sex.
INFO [2025-12-04 21:55:10] Processing on-target regions...
INFO [2025-12-04 21:55:10] Removing 930 intervals with low coverage in normalDB.
INFO [2025-12-04 21:55:10] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2025-12-04 21:55:11] Tumor/normal noise ratio: 19.041
WARN [2025-12-04 21:55:11] Extensive noise in tumor compared to normals.
INFO [2025-12-04 21:55:28] Tumor/normal noise ratio: 19.041
WARN [2025-12-04 21:55:28] Extensive noise in tumor compared to normals.
INFO [2025-12-04 21:55:30] Using BiocParallel for parallel optimization.
FATAL [2025-12-04 21:55:35] pvalue.cutoff not within expected range or format.
FATAL [2025-12-04 21:55:35]
FATAL [2025-12-04 21:55:35] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:55:35] parameters (PureCN 2.17.0).
FATAL [2025-12-04 21:55:35] pvalue.cutoff not within expected range or format.
FATAL [2025-12-04 21:55:35]
FATAL [2025-12-04 21:55:35] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:55:35] parameters (PureCN 2.17.0).
FATAL [2025-12-04 21:55:35] percentile.cutoff not in expected range (0 to 100).
FATAL [2025-12-04 21:55:35]
FATAL [2025-12-04 21:55:35] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:55:35] parameters (PureCN 2.17.0).
FATAL [2025-12-04 21:55:35] percentile.cutoff not in expected range (0 to 100).
FATAL [2025-12-04 21:55:35]
FATAL [2025-12-04 21:55:35] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:55:35] parameters (PureCN 2.17.0).
FATAL [2025-12-04 21:55:35] purity not within expected range or format.
FATAL [2025-12-04 21:55:35]
FATAL [2025-12-04 21:55:35] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:55:35] parameters (PureCN 2.17.0).
FATAL [2025-12-04 21:55:35] purity not within expected range or format.
FATAL [2025-12-04 21:55:35]
FATAL [2025-12-04 21:55:35] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:55:35] parameters (PureCN 2.17.0).
INFO [2025-12-04 21:55:36] ------------------------------------------------------------
INFO [2025-12-04 21:55:36] PureCN 2.17.0
INFO [2025-12-04 21:55:36] ------------------------------------------------------------
INFO [2025-12-04 21:55:36] Loading coverage files...
INFO [2025-12-04 21:55:36] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-12-04 21:55:36] Allosome coverage missing, cannot determine sex.
WARN [2025-12-04 21:55:36] Allosome coverage missing, cannot determine sex.
INFO [2025-12-04 21:55:36] Removing 228 intervals with missing log.ratio.
INFO [2025-12-04 21:55:36] Removing 22 small (< 5bp) intervals.
INFO [2025-12-04 21:55:36] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-12-04 21:55:36] No normalDB provided. Provide one for better results.
INFO [2025-12-04 21:55:36] Removing 1724 low count (< 100 total reads) intervals.
INFO [2025-12-04 21:55:36] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-12-04 21:55:36] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-12-04 21:55:36] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-12-04 21:55:36] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-12-04 21:55:36] Loading VCF...
INFO [2025-12-04 21:55:36] Found 127 variants in VCF file.
INFO [2025-12-04 21:55:36] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-12-04 21:55:36] LIB-02240e4 is tumor in VCF file.
INFO [2025-12-04 21:55:36] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-12-04 21:55:36] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-12-04 21:55:36] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-12-04 21:55:36] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-12-04 21:55:36] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-12-04 21:55:36] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-12-04 21:55:36] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding).
INFO [2025-12-04 21:55:37] 1.2% of targets contain variants.
INFO [2025-12-04 21:55:37] Removing 4 variants outside intervals.
INFO [2025-12-04 21:55:37] Found SOMATIC annotation in VCF.
INFO [2025-12-04 21:55:37] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-12-04 21:55:37] Found SOMATIC annotation in VCF. Setting mapping bias to 0.972.
INFO [2025-12-04 21:55:37] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-12-04 21:55:37] Sample sex: ?
INFO [2025-12-04 21:55:37] Segmenting data...
INFO [2025-12-04 21:55:37] Loading pre-computed boundaries for DNAcopy...
INFO [2025-12-04 21:55:37] Setting undo.SD parameter to 1.000000.
INFO [2025-12-04 21:55:37] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-12-04 21:55:37] Found 59 segments with median size of 17.67Mb.
INFO [2025-12-04 21:55:37] Using 121 variants.
INFO [2025-12-04 21:55:37] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-12-04 21:55:37] 2D-grid search of purity and ploidy...
INFO [2025-12-04 21:55:38] Local optima: 0.63/1.9, 0.5/2
INFO [2025-12-04 21:55:38] Testing local optimum 1/2 at purity 0.63 and total ploidy 1.90...
INFO [2025-12-04 21:55:38] Testing local optimum 2/2 at purity 0.50 and total ploidy 2.00...
INFO [2025-12-04 21:55:39] Skipping 1 solutions that converged to the same optima.
INFO [2025-12-04 21:55:39] Fitting variants with beta model for local optimum 1/2...
INFO [2025-12-04 21:55:39] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2025-12-04 21:55:40] Optimized purity: 0.65
INFO [2025-12-04 21:55:40] Done.
INFO [2025-12-04 21:55:40] ------------------------------------------------------------
INFO [2025-12-04 21:55:40] Estimating callable regions.
FATAL [2025-12-04 21:55:40] exclude not a GRanges object.
FATAL [2025-12-04 21:55:40]
FATAL [2025-12-04 21:55:40] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:55:40] parameters (PureCN 2.17.0).
FATAL [2025-12-04 21:55:40] callable not a GRanges object.
FATAL [2025-12-04 21:55:40]
FATAL [2025-12-04 21:55:40] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:55:40] parameters (PureCN 2.17.0).
WARN [2025-12-04 21:55:43] tumor.coverage.file and interval.file do not align.
INFO [2025-12-04 21:55:44] No Gene column in interval.file. You won't get gene-level calls.
FATAL [2025-12-04 21:55:44] No gc_bias column in interval.file.
FATAL [2025-12-04 21:55:44]
FATAL [2025-12-04 21:55:44] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:55:44] parameters (PureCN 2.17.0).
FATAL [2025-12-04 21:55:44] Provided coverage is zero, most likely due to a corrupt BAM file.
FATAL [2025-12-04 21:55:44]
FATAL [2025-12-04 21:55:44] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:55:44] parameters (PureCN 2.17.0).
INFO [2025-12-04 21:55:45] No reptiming column in interval.file.
INFO [2025-12-04 21:55:47] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpdk23KO/file1645e783461c.rds...
INFO [2025-12-04 21:55:47] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpdk23KO/file1645e783461c.rds...
INFO [2025-12-04 21:55:47] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpdk23KO/file1645e783461c.rds...
INFO [2025-12-04 21:55:47] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpdk23KO/file1645e783461c.rds...
INFO [2025-12-04 21:55:47] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpdk23KO/file1645e783461c.rds...
INFO [2025-12-04 21:55:47] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpdk23KO/file1645e783461c.rds...
FATAL [2025-12-04 21:55:47] Purity or Ploidy not numeric or in expected range.
FATAL [2025-12-04 21:55:47]
FATAL [2025-12-04 21:55:47] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:55:47] parameters (PureCN 2.17.0).
INFO [2025-12-04 21:55:47] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpdk23KO/file1645e783461c.rds...
INFO [2025-12-04 21:55:47] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpdk23KO/file1645e783461c.rds...
FATAL [2025-12-04 21:55:47] 'Failed' column in
FATAL [2025-12-04 21:55:47] /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpdk23KO/file1645e783461c.csv
FATAL [2025-12-04 21:55:47] not logical(1).
FATAL [2025-12-04 21:55:47]
FATAL [2025-12-04 21:55:47] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:55:47] parameters (PureCN 2.17.0).
INFO [2025-12-04 21:55:47] 576 on-target bins with low coverage in all samples.
WARN [2025-12-04 21:55:47] You are likely not using the correct baits file!
WARN [2025-12-04 21:55:47] Allosome coverage missing, cannot determine sex.
WARN [2025-12-04 21:55:47] Allosome coverage missing, cannot determine sex.
INFO [2025-12-04 21:55:47] Processing on-target regions...
INFO [2025-12-04 21:55:48] Removing 930 intervals with low coverage in normalDB.
INFO [2025-12-04 21:55:48] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2025-12-04 21:55:49] 576 on-target bins with low coverage in all samples.
WARN [2025-12-04 21:55:49] You are likely not using the correct baits file!
WARN [2025-12-04 21:55:49] Allosome coverage missing, cannot determine sex.
WARN [2025-12-04 21:55:49] Allosome coverage missing, cannot determine sex.
INFO [2025-12-04 21:55:49] Processing on-target regions...
INFO [2025-12-04 21:55:49] Removing 930 intervals with low coverage in normalDB.
INFO [2025-12-04 21:55:49] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2025-12-04 21:55:50] 576 on-target bins with low coverage in all samples.
WARN [2025-12-04 21:55:50] You are likely not using the correct baits file!
WARN [2025-12-04 21:55:50] Allosome coverage missing, cannot determine sex.
WARN [2025-12-04 21:55:50] Allosome coverage missing, cannot determine sex.
INFO [2025-12-04 21:55:50] Processing on-target regions...
INFO [2025-12-04 21:55:50] Removing 930 intervals with low coverage in normalDB.
INFO [2025-12-04 21:55:50] Removing 1 intervals with zero coverage in more than 3% of normalDB.
WARN [2025-12-04 21:55:50] Allosome coverage missing, cannot determine sex.
INFO [2025-12-04 21:55:50] Sample sex: NA
WARN [2025-12-04 21:55:51] Allosome coverage missing, cannot determine sex.
INFO [2025-12-04 21:55:51] Sample sex: NA
INFO [2025-12-04 21:55:51] 576 on-target bins with low coverage in all samples.
WARN [2025-12-04 21:55:51] You are likely not using the correct baits file!
WARN [2025-12-04 21:55:51] Allosome coverage missing, cannot determine sex.
WARN [2025-12-04 21:55:51] Allosome coverage missing, cannot determine sex.
FATAL [2025-12-04 21:55:51] Length of normal.coverage.files and sex different
FATAL [2025-12-04 21:55:51]
FATAL [2025-12-04 21:55:51] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:55:51] parameters (PureCN 2.17.0).
WARN [2025-12-04 21:55:53] Target intervals were not sorted.
INFO [2025-12-04 21:55:53] 560 on-target bins with low coverage in all samples.
WARN [2025-12-04 21:55:53] You are likely not using the correct baits file!
WARN [2025-12-04 21:55:53] Allosome coverage missing, cannot determine sex.
WARN [2025-12-04 21:55:53] Allosome coverage missing, cannot determine sex.
WARN [2025-12-04 21:55:53] Allosome coverage missing, cannot determine sex.
INFO [2025-12-04 21:55:53] Processing on-target regions...
INFO [2025-12-04 21:55:53] Removing 978 intervals with low coverage in normalDB.
INFO [2025-12-04 21:55:53] Removing 11 intervals with zero coverage in more than 3% of normalDB.
FATAL [2025-12-04 21:55:54] tumor.coverage.file and normalDB do not align.
FATAL [2025-12-04 21:55:54]
FATAL [2025-12-04 21:55:54] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:55:54] parameters (PureCN 2.17.0).
FATAL [2025-12-04 21:55:54] At least 2 normal.coverage.files required.
FATAL [2025-12-04 21:55:54]
FATAL [2025-12-04 21:55:54] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:55:54] parameters (PureCN 2.17.0).
INFO [2025-12-04 21:55:55] ------------------------------------------------------------
INFO [2025-12-04 21:55:55] PureCN 2.17.0
INFO [2025-12-04 21:55:55] ------------------------------------------------------------
INFO [2025-12-04 21:55:55] Loading coverage files...
INFO [2025-12-04 21:55:55] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-12-04 21:55:55] Allosome coverage missing, cannot determine sex.
WARN [2025-12-04 21:55:55] Allosome coverage missing, cannot determine sex.
INFO [2025-12-04 21:55:55] Removing 228 intervals with missing log.ratio.
FATAL [2025-12-04 21:55:55] normalDB incompatible with this PureCN version. Please re-run
FATAL [2025-12-04 21:55:55] NormalDB.R.
FATAL [2025-12-04 21:55:55]
FATAL [2025-12-04 21:55:55] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:55:55] parameters (PureCN 2.17.0).
FATAL [2025-12-04 21:55:55] normalDB incompatible with this PureCN version. Please re-run
FATAL [2025-12-04 21:55:55] NormalDB.R.
FATAL [2025-12-04 21:55:55]
FATAL [2025-12-04 21:55:55] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:55:55] parameters (PureCN 2.17.0).
FATAL [2025-12-04 21:55:55] normal.coverage.files with _coverage.txt and _loess.txt suffix
FATAL [2025-12-04 21:55:55] provided. Provide either only GC-normalized or raw coverage files!
FATAL [2025-12-04 21:55:55]
FATAL [2025-12-04 21:55:55] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:55:55] parameters (PureCN 2.17.0).
INFO [2025-12-04 21:55:55] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-12-04 21:55:55] Removing 19 low quality variants with non-offset BQ < 25.
INFO [2025-12-04 21:55:55] Base quality scores range from 24 to 35 (offset by 1)
INFO [2025-12-04 21:55:55] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS.
INFO [2025-12-04 21:55:56] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-12-04 21:55:56] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-12-04 21:55:56] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-12-04 21:55:56] Removing 19 low quality variants with non-offset BQ < 25.
INFO [2025-12-04 21:55:56] Base quality scores range from 24 to 35 (offset by 1)
INFO [2025-12-04 21:55:56] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS.
INFO [2025-12-04 21:55:57] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-12-04 21:55:57] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-12-04 21:55:57] Removing 6 blacklisted variants.
INFO [2025-12-04 21:55:57] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-12-04 21:55:57] Removing 19 low quality variants with non-offset BQ < 25.
INFO [2025-12-04 21:55:57] Base quality scores range from 24 to 35 (offset by 1)
INFO [2025-12-04 21:55:57] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS.
INFO [2025-12-04 21:55:57] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-12-04 21:55:57] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
WARN [2025-12-04 21:55:57] MuTect stats file lacks contig and position columns.
INFO [2025-12-04 21:55:57] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-12-04 21:55:57] Removing 19 low quality variants with non-offset BQ < 25.
INFO [2025-12-04 21:55:57] Base quality scores range from 24 to 35 (offset by 1)
INFO [2025-12-04 21:55:57] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS.
INFO [2025-12-04 21:55:57] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-12-04 21:55:57] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
WARN [2025-12-04 21:55:57] MuTect stats file and VCF file do not align perfectly. Will remove 2325 unmatched variants.
WARN [2025-12-04 21:55:57] MuTect stats file lacks failure_reasons column. Keeping all variants listed in stats file.
INFO [2025-12-04 21:55:57] Removing 0 non heterozygous (in matched normal) germline SNPs.
INFO [2025-12-04 21:55:57] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-12-04 21:55:57] Base quality scores range from 31 to 33 (offset by 1)
INFO [2025-12-04 21:55:57] Minimum number of supporting reads ranges from 3 to 4, depending on coverage and BQS.
INFO [2025-12-04 21:55:57] Removing 0 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-12-04 21:55:57] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-12-04 21:55:57] Base quality scores range from 7 to 35 (offset by 1)
INFO [2025-12-04 21:55:58] Minimum number of supporting reads ranges from 1 to 41, depending on coverage and BQS.
INFO [2025-12-04 21:55:58] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-12-04 21:55:58] Removing 49 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-12-04 21:55:58] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-12-04 21:55:58] Base quality scores range from 7 to 35 (offset by 1)
INFO [2025-12-04 21:55:58] Minimum number of supporting reads ranges from 1 to 41, depending on coverage and BQS.
INFO [2025-12-04 21:55:58] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-12-04 21:55:58] Removing 49 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-12-04 21:55:58] Removing 22 non heterozygous (in matched normal) germline SNPs.
WARN [2025-12-04 21:55:58] Many variants removed by min.base.quality (50) filter. You might want to lower the cutoff.
FATAL [2025-12-04 21:55:58] No variants passed filter BQ.
FATAL [2025-12-04 21:55:58]
FATAL [2025-12-04 21:55:58] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:55:58] parameters (PureCN 2.17.0).
INFO [2025-12-04 21:55:58] Found 11 variants in VCF file.
WARN [2025-12-04 21:55:58] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead.
INFO [2025-12-04 21:55:58] 1 (9.1%) variants annotated as likely germline (DB INFO flag).
INFO [2025-12-04 21:55:59] Found 11 variants in VCF file.
WARN [2025-12-04 21:55:59] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead.
INFO [2025-12-04 21:55:59] 1 (9.1%) variants annotated as likely germline (DB INFO flag).
INFO [2025-12-04 21:55:59] Found 11 variants in VCF file.
WARN [2025-12-04 21:55:59] vcf.file has no DB or POP_AF info field for membership in germline databases. Guessing it based on available dbSNP ID.
INFO [2025-12-04 21:55:59] 1 (9.1%) variants annotated as likely germline (DB INFO flag).
INFO [2025-12-04 21:55:59] Found 1000 variants in VCF file.
INFO [2025-12-04 21:55:59] Removing 2 triallelic sites.
WARN [2025-12-04 21:55:59] Having trouble guessing SOMATIC status...
WARN [2025-12-04 21:55:59] DP FORMAT field contains NAs. Removing 44 variants.
INFO [2025-12-04 21:56:00] 954 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-12-04 21:56:00] Found 12 variants in VCF file.
INFO [2025-12-04 21:56:00] Removing 1 triallelic sites.
WARN [2025-12-04 21:56:00] DP FORMAT field contains NAs. Removing 1 variants.
WARN [2025-12-04 21:56:00] vcf.file has no DB info field for membership in germline databases. Found and used somatic status instead.
INFO [2025-12-04 21:56:00] 8 (80.0%) variants annotated as likely germline (DB INFO flag).
WARN [2025-12-04 21:56:00] BQ FORMAT field contains NAs.
INFO [2025-12-04 21:56:00] Found 2331 variants in VCF file.
INFO [2025-12-04 21:56:00] 2282 (97.9%) variants annotated as likely germline (DB INFO flag).
INFO [2025-12-04 21:56:01] Found 2331 variants in VCF file.
INFO [2025-12-04 21:56:01] 2282 (97.9%) variants annotated as likely germline (DB INFO flag).
WARN [2025-12-04 21:56:01] Did not find base quality scores, will use global error rate of 0.0010 instead.
INFO [2025-12-04 21:56:01] Removing 21 low quality variants with non-offset BQ < 25.
INFO [2025-12-04 21:56:01] Base quality scores range from 24 to 35 (offset by 1)
INFO [2025-12-04 21:56:01] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-12-04 21:56:01] Removing 89 variants with AF < 0.030 or AF >= 0.970 or insufficient supporting reads or depth < 15.
INFO [2025-12-04 21:56:01] Found 2331 variants in VCF file.
INFO [2025-12-04 21:56:01] 2282 (97.9%) variants annotated as likely germline (DB INFO flag).
WARN [2025-12-04 21:56:01] BQ FORMAT field contains NAs.
WARN [2025-12-04 21:56:01] Allosome coverage missing, cannot determine sex.
WARN [2025-12-04 21:56:02] Allosome coverage missing, cannot determine sex.
INFO [2025-12-04 21:56:02] Mean coverages: chrX: 108.58, chrY: 108.58, chr1-22: 104.87.
INFO [2025-12-04 21:56:02] Mean coverages: chrX: 108.58, chrY: 2.17, chr1-22: 104.87.
INFO [2025-12-04 21:56:02] Mean coverages: chrX: 108.58, chrY: 5.17, chr1-22: 104.87.
INFO [2025-12-04 21:56:02] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-12-04 21:56:02] No germline variants in VCF.
FATAL [2025-12-04 21:56:02] No solution with id hello
FATAL [2025-12-04 21:56:02]
FATAL [2025-12-04 21:56:02] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:56:02] parameters (PureCN 2.17.0).
FATAL [2025-12-04 21:56:02] No solution with id 100
FATAL [2025-12-04 21:56:02]
FATAL [2025-12-04 21:56:02] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:56:02] parameters (PureCN 2.17.0).
FATAL [2025-12-04 21:56:02] all.data and w have different lengths.
FATAL [2025-12-04 21:56:02]
FATAL [2025-12-04 21:56:02] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:56:02] parameters (PureCN 2.17.0).
INFO [2025-12-04 21:56:03] Splitting 5 large targets to an average width of 400.
WARN [2025-12-04 21:56:03] No mappability scores provided.
WARN [2025-12-04 21:56:03] No reptiming scores provided.
INFO [2025-12-04 21:56:03] Calculating GC-content...
INFO [2025-12-04 21:56:03] Splitting 5 large targets to an average width of 400.
WARN [2025-12-04 21:56:03] No mappability scores provided.
WARN [2025-12-04 21:56:03] No reptiming scores provided.
INFO [2025-12-04 21:56:03] Calculating GC-content...
INFO [2025-12-04 21:56:03] Splitting 5 large targets to an average width of 400.
INFO [2025-12-04 21:56:03] Removing 1 targets overlapping with exclude.
WARN [2025-12-04 21:56:03] No mappability scores provided.
WARN [2025-12-04 21:56:03] No reptiming scores provided.
INFO [2025-12-04 21:56:03] Calculating GC-content...
WARN [2025-12-04 21:56:03] Found small target regions (< 100bp). Will resize them.
INFO [2025-12-04 21:56:03] Splitting 5 large targets to an average width of 400.
FATAL [2025-12-04 21:56:03] off.target.padding must be negative.
FATAL [2025-12-04 21:56:03]
FATAL [2025-12-04 21:56:03] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:56:03] parameters (PureCN 2.17.0).
FATAL [2025-12-04 21:56:03] Interval coordinates should start at 1, not at 0
FATAL [2025-12-04 21:56:03]
FATAL [2025-12-04 21:56:03] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:56:03] parameters (PureCN 2.17.0).
WARN [2025-12-04 21:56:03] Found small target regions (< 100bp). Will resize them.
INFO [2025-12-04 21:56:03] Splitting 5 large targets to an average width of 400.
FATAL [2025-12-04 21:56:03] No off-target regions after filtering for mappability and
FATAL [2025-12-04 21:56:03] off.target.padding
FATAL [2025-12-04 21:56:03]
FATAL [2025-12-04 21:56:03] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:56:03] parameters (PureCN 2.17.0).
WARN [2025-12-04 21:56:03] Found small target regions (< 100bp). Will resize them.
INFO [2025-12-04 21:56:03] Splitting 5 large targets to an average width of 400.
WARN [2025-12-04 21:56:03] No mappability scores provided.
INFO [2025-12-04 21:56:03] Calculating GC-content...
WARN [2025-12-04 21:56:03] Found small target regions (< 100bp). Will resize them.
INFO [2025-12-04 21:56:03] Averaging reptiming into bins of size 200...
INFO [2025-12-04 21:56:04] Splitting 5 large targets to an average width of 400.
WARN [2025-12-04 21:56:04] No mappability scores provided.
INFO [2025-12-04 21:56:04] Calculating GC-content...
WARN [2025-12-04 21:56:04] Found small target regions (< 100bp). Will resize them.
INFO [2025-12-04 21:56:04] Splitting 6 large targets to an average width of 200.
WARN [2025-12-04 21:56:04] No mappability scores provided.
WARN [2025-12-04 21:56:04] No reptiming scores provided.
INFO [2025-12-04 21:56:04] Calculating GC-content...
WARN [2025-12-04 21:56:04] Found small target regions (< 100bp). Will resize them.
INFO [2025-12-04 21:56:04] Splitting 5 large targets to an average width of 400.
WARN [2025-12-04 21:56:04] No mappability scores provided.
WARN [2025-12-04 21:56:04] No reptiming scores provided.
INFO [2025-12-04 21:56:04] Calculating GC-content...
INFO [2025-12-04 21:56:04] Splitting 5 large targets to an average width of 400.
INFO [2025-12-04 21:56:04] Tiling off-target regions to an average width of 200000.
WARN [2025-12-04 21:56:04] No mappability scores provided.
WARN [2025-12-04 21:56:04] No reptiming scores provided.
INFO [2025-12-04 21:56:04] Calculating GC-content...
WARN [2025-12-04 21:56:04] Intervals contain off-target regions. Will not change intervals.
WARN [2025-12-04 21:56:04] No mappability scores provided.
WARN [2025-12-04 21:56:04] No reptiming scores provided.
INFO [2025-12-04 21:56:04] Calculating GC-content...
INFO [2025-12-04 21:56:04] Splitting 5 large targets to an average width of 400.
WARN [2025-12-04 21:56:04] No reptiming scores provided.
INFO [2025-12-04 21:56:04] Calculating GC-content...
WARN [2025-12-04 21:56:04] Found small target regions (< 100bp). Will resize them.
INFO [2025-12-04 21:56:04] Splitting 5 large targets to an average width of 400.
WARN [2025-12-04 21:56:04] No reptiming scores provided.
INFO [2025-12-04 21:56:04] Calculating GC-content...
WARN [2025-12-04 21:56:05] Found small target regions (< 100bp). Will resize them.
INFO [2025-12-04 21:56:05] Splitting 5 large targets to an average width of 400.
WARN [2025-12-04 21:56:05] 1 intervals without mappability score (1 on-target).
INFO [2025-12-04 21:56:05] Removing 1 intervals with low mappability score (<0.60).
WARN [2025-12-04 21:56:05] No reptiming scores provided.
INFO [2025-12-04 21:56:05] Calculating GC-content...
WARN [2025-12-04 21:56:05] Found small target regions (< 100bp). Will resize them.
INFO [2025-12-04 21:56:05] Splitting 5 large targets to an average width of 400.
INFO [2025-12-04 21:56:05] Tiling off-target regions to an average width of 200000.
WARN [2025-12-04 21:56:05] No reptiming scores provided.
INFO [2025-12-04 21:56:05] Calculating GC-content...
INFO [2025-12-04 21:56:05] Splitting 5 large targets to an average width of 400.
WARN [2025-12-04 21:56:05] No mappability scores provided.
WARN [2025-12-04 21:56:05] No reptiming scores provided.
INFO [2025-12-04 21:56:05] Calculating GC-content...
WARN [2025-12-04 21:56:05] Chromosome naming style of interval file (Ensembl) was different from reference (UCSC).
INFO [2025-12-04 21:56:05] Splitting 5 large targets to an average width of 400.
WARN [2025-12-04 21:56:05] No mappability scores provided.
WARN [2025-12-04 21:56:05] No reptiming scores provided.
INFO [2025-12-04 21:56:05] Calculating GC-content...
FATAL [2025-12-04 21:56:05] Chromosome naming style of interval file unknown, should be UCSC.
FATAL [2025-12-04 21:56:05]
FATAL [2025-12-04 21:56:05] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:56:05] parameters (PureCN 2.17.0).
WARN [2025-12-04 21:56:05] Chromosome naming style of interval file (Ensembl) was different from reference (UCSC).
WARN [2025-12-04 21:56:05] Chromosome naming style of mappability file (Ensembl) was different from reference (UCSC).
INFO [2025-12-04 21:56:05] Splitting 5 large targets to an average width of 400.
WARN [2025-12-04 21:56:05] No reptiming scores provided.
INFO [2025-12-04 21:56:05] Calculating GC-content...
WARN [2025-12-04 21:56:06] Found small target regions (< 60bp). Will resize them.
INFO [2025-12-04 21:56:06] Splitting 5 large targets to an average width of 400.
WARN [2025-12-04 21:56:06] No mappability scores provided.
WARN [2025-12-04 21:56:06] No reptiming scores provided.
INFO [2025-12-04 21:56:06] Calculating GC-content...
WARN [2025-12-04 21:56:06] Found small target regions (< 60bp). Will drop them.
INFO [2025-12-04 21:56:06] Splitting 4 large targets to an average width of 400.
WARN [2025-12-04 21:56:06] No mappability scores provided.
WARN [2025-12-04 21:56:06] No reptiming scores provided.
INFO [2025-12-04 21:56:06] Calculating GC-content...
WARN [2025-12-04 21:56:06] Found small target regions (< 200bp). Will resize them.
INFO [2025-12-04 21:56:06] Splitting 5 large targets to an average width of 400.
WARN [2025-12-04 21:56:06] No mappability scores provided.
WARN [2025-12-04 21:56:06] No reptiming scores provided.
INFO [2025-12-04 21:56:06] Calculating GC-content...
INFO [2025-12-04 21:56:06] Found 20 variants in VCF file.
INFO [2025-12-04 21:56:06] 20 (100.0%) variants annotated as likely germline (DB INFO flag).
WARN [2025-12-04 21:56:06] 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 [2025-12-04 21:56:06] Error reading AllelicCountsFile
FATAL [2025-12-04 21:56:06] /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/PureCN/extdata/example_allelic_counts_empty.tsv
FATAL [2025-12-04 21:56:06]
FATAL [2025-12-04 21:56:06] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:56:06] parameters (PureCN 2.17.0).
INFO [2025-12-04 21:56:06] Found 127 variants in VCF file.
INFO [2025-12-04 21:56:06] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
WARN [2025-12-04 21:56:06] Did not find base quality scores, will use global error rate of 0.0010 instead.
INFO [2025-12-04 21:56:06] ------------------------------------------------------------
INFO [2025-12-04 21:56:06] PureCN 2.17.0
INFO [2025-12-04 21:56:06] ------------------------------------------------------------
INFO [2025-12-04 21:56:06] Loading coverage files...
INFO [2025-12-04 21:56:07] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-12-04 21:56:07] Allosome coverage missing, cannot determine sex.
WARN [2025-12-04 21:56:07] Allosome coverage missing, cannot determine sex.
INFO [2025-12-04 21:56:07] Removing 228 intervals with missing log.ratio.
INFO [2025-12-04 21:56:07] Removing 22 small (< 5bp) intervals.
INFO [2025-12-04 21:56:07] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-12-04 21:56:07] No normalDB provided. Provide one for better results.
INFO [2025-12-04 21:56:07] Removing 1724 low count (< 100 total reads) intervals.
INFO [2025-12-04 21:56:07] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-12-04 21:56:07] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-12-04 21:56:07] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-12-04 21:56:07] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-12-04 21:56:07] Loading VCF...
INFO [2025-12-04 21:56:07] Found 127 variants in VCF file.
INFO [2025-12-04 21:56:07] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-12-04 21:56:07] LIB-02240e4 is tumor in VCF file.
INFO [2025-12-04 21:56:07] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-12-04 21:56:07] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-12-04 21:56:07] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-12-04 21:56:07] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-12-04 21:56:07] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-12-04 21:56:07] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-12-04 21:56:07] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding).
INFO [2025-12-04 21:56:07] 1.2% of targets contain variants.
INFO [2025-12-04 21:56:07] Removing 4 variants outside intervals.
INFO [2025-12-04 21:56:07] Found SOMATIC annotation in VCF.
INFO [2025-12-04 21:56:07] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-12-04 21:56:07] Found SOMATIC annotation in VCF. Setting mapping bias to 0.972.
INFO [2025-12-04 21:56:07] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-12-04 21:56:07] Sample sex: ?
INFO [2025-12-04 21:56:07] Segmenting data...
INFO [2025-12-04 21:56:07] Loading pre-computed boundaries for DNAcopy...
INFO [2025-12-04 21:56:07] Setting undo.SD parameter to 1.000000.
INFO [2025-12-04 21:56:08] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-12-04 21:56:08] Found 59 segments with median size of 17.67Mb.
INFO [2025-12-04 21:56:08] Using 121 variants.
INFO [2025-12-04 21:56:08] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-12-04 21:56:08] 2D-grid search of purity and ploidy...
INFO [2025-12-04 21:56:08] Local optima: 0.65/1.8, 0.52/2
INFO [2025-12-04 21:56:08] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2025-12-04 21:56:08] Testing local optimum 2/2 at purity 0.52 and total ploidy 2.00...
INFO [2025-12-04 21:56:09] Skipping 1 solutions that converged to the same optima.
INFO [2025-12-04 21:56:09] Fitting variants with beta model for local optimum 1/2...
INFO [2025-12-04 21:56:09] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2025-12-04 21:56:10] Optimized purity: 0.65
INFO [2025-12-04 21:56:10] Done.
INFO [2025-12-04 21:56:10] ------------------------------------------------------------
FATAL [2025-12-04 21:56:10] log.ratio NULL in .writeLogRatioFileGATK4
FATAL [2025-12-04 21:56:10]
FATAL [2025-12-04 21:56:10] This runtime error might be caused by invalid input data or parameters.
FATAL [2025-12-04 21:56:10] Please report bug (PureCN 2.17.0).
INFO [2025-12-04 21:56:10] Loaded provided segmentation file example_seg.txt (format DNAcopy).
INFO [2025-12-04 21:56:10] Re-centering provided segment means (offset -0.0033).
INFO [2025-12-04 21:56:10] Loaded provided segmentation file example_gatk4_modelfinal.seg.gz (format GATK4).
WARN [2025-12-04 21:56:10] Expecting numeric chromosome names in seg.file, assuming file is properly sorted.
INFO [2025-12-04 21:56:10] Re-centering provided segment means (offset -0.0037).
INFO [2025-12-04 21:56:11] 576 on-target bins with low coverage in all samples.
WARN [2025-12-04 21:56:11] You are likely not using the correct baits file!
WARN [2025-12-04 21:56:11] Allosome coverage missing, cannot determine sex.
WARN [2025-12-04 21:56:11] Allosome coverage missing, cannot determine sex.
INFO [2025-12-04 21:56:11] Processing on-target regions...
INFO [2025-12-04 21:56:11] Removing 930 intervals with low coverage in normalDB.
INFO [2025-12-04 21:56:11] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2025-12-04 21:56:12] ------------------------------------------------------------
INFO [2025-12-04 21:56:12] PureCN 2.17.0
INFO [2025-12-04 21:56:12] ------------------------------------------------------------
INFO [2025-12-04 21:56:12] Using BiocParallel for parallel optimization.
INFO [2025-12-04 21:56:12] Loading coverage files...
INFO [2025-12-04 21:56:12] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-12-04 21:56:12] Allosome coverage missing, cannot determine sex.
WARN [2025-12-04 21:56:12] Allosome coverage missing, cannot determine sex.
INFO [2025-12-04 21:56:12] Removing 228 intervals with missing log.ratio.
INFO [2025-12-04 21:56:12] Removing 705 intervals excluded in normalDB.
INFO [2025-12-04 21:56:12] normalDB provided. Setting minimum coverage for segmentation to 0.0015X.
INFO [2025-12-04 21:56:12] Removing 1066 low count (< 100 total reads) intervals.
INFO [2025-12-04 21:56:12] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-12-04 21:56:12] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-12-04 21:56:12] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-12-04 21:56:12] Sample sex: ?
INFO [2025-12-04 21:56:12] Segmenting data...
INFO [2025-12-04 21:56:12] Interval weights found, will use weighted CBS.
INFO [2025-12-04 21:56:12] Loading pre-computed boundaries for DNAcopy...
INFO [2025-12-04 21:56:12] Setting undo.SD parameter to 1.000000.
Setting multi-figure configuration
INFO [2025-12-04 21:56:13] Found 52 segments with median size of 29.35Mb.
INFO [2025-12-04 21:56:13] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-12-04 21:56:13] 2D-grid search of purity and ploidy...
INFO [2025-12-04 21:56:13] Local optima: 0.65/1.8, 0.52/2
INFO [2025-12-04 21:56:14] Skipping 1 solutions that converged to the same optima.
INFO [2025-12-04 21:56:14] Done.
INFO [2025-12-04 21:56:14] ------------------------------------------------------------
INFO [2025-12-04 21:56:14] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpdk23KO/file1645e13111125.rds...
FATAL [2025-12-04 21:56:14] runAbsoluteCN was run without a VCF file.
FATAL [2025-12-04 21:56:14]
FATAL [2025-12-04 21:56:14] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:56:14] parameters (PureCN 2.17.0).
FATAL [2025-12-04 21:56:14] runAbsoluteCN was run without a VCF file.
FATAL [2025-12-04 21:56:14]
FATAL [2025-12-04 21:56:14] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:56:14] parameters (PureCN 2.17.0).
INFO [2025-12-04 21:56:14] ------------------------------------------------------------
INFO [2025-12-04 21:56:14] PureCN 2.17.0
INFO [2025-12-04 21:56:14] ------------------------------------------------------------
INFO [2025-12-04 21:56:14] Loading coverage files...
INFO [2025-12-04 21:56:14] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-12-04 21:56:14] Allosome coverage missing, cannot determine sex.
WARN [2025-12-04 21:56:14] Allosome coverage missing, cannot determine sex.
INFO [2025-12-04 21:56:14] Removing 228 intervals with missing log.ratio.
INFO [2025-12-04 21:56:14] Removing 705 intervals excluded in normalDB.
INFO [2025-12-04 21:56:14] normalDB provided. Setting minimum coverage for segmentation to 0.0015X.
INFO [2025-12-04 21:56:14] Removing 1066 low count (< 100 total reads) intervals.
INFO [2025-12-04 21:56:14] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-12-04 21:56:14] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-12-04 21:56:14] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-12-04 21:56:14] Sample sex: ?
INFO [2025-12-04 21:56:14] Segmenting data...
INFO [2025-12-04 21:56:14] Interval weights found, will use weighted PSCBS.
FATAL [2025-12-04 21:56:14] segmentationPSCBS requires VCF file.
FATAL [2025-12-04 21:56:14]
FATAL [2025-12-04 21:56:14] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:56:14] parameters (PureCN 2.17.0).
INFO [2025-12-04 21:56:17] ------------------------------------------------------------
INFO [2025-12-04 21:56:17] PureCN 2.17.0
INFO [2025-12-04 21:56:17] ------------------------------------------------------------
INFO [2025-12-04 21:56:17] Loading coverage files...
FATAL [2025-12-04 21:56:17] Need a normal coverage file if log.ratio and seg.file are not provided.
FATAL [2025-12-04 21:56:17]
FATAL [2025-12-04 21:56:17] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:56:17] parameters (PureCN 2.17.0).
INFO [2025-12-04 21:56:17] ------------------------------------------------------------
INFO [2025-12-04 21:56:17] PureCN 2.17.0
INFO [2025-12-04 21:56:17] ------------------------------------------------------------
FATAL [2025-12-04 21:56:17] min.ploidy or max.ploidy not within expected range.
FATAL [2025-12-04 21:56:17]
FATAL [2025-12-04 21:56:17] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:56:17] parameters (PureCN 2.17.0).
INFO [2025-12-04 21:56:17] ------------------------------------------------------------
INFO [2025-12-04 21:56:17] PureCN 2.17.0
INFO [2025-12-04 21:56:17] ------------------------------------------------------------
FATAL [2025-12-04 21:56:17] min.ploidy or max.ploidy not within expected range.
FATAL [2025-12-04 21:56:17]
FATAL [2025-12-04 21:56:17] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:56:17] parameters (PureCN 2.17.0).
INFO [2025-12-04 21:56:17] ------------------------------------------------------------
INFO [2025-12-04 21:56:17] PureCN 2.17.0
INFO [2025-12-04 21:56:17] ------------------------------------------------------------
INFO [2025-12-04 21:56:17] ------------------------------------------------------------
INFO [2025-12-04 21:56:17] PureCN 2.17.0
INFO [2025-12-04 21:56:17] ------------------------------------------------------------
INFO [2025-12-04 21:56:17] ------------------------------------------------------------
INFO [2025-12-04 21:56:17] PureCN 2.17.0
INFO [2025-12-04 21:56:17] ------------------------------------------------------------
FATAL [2025-12-04 21:56:17] test.num.copy not within expected range.
FATAL [2025-12-04 21:56:17]
FATAL [2025-12-04 21:56:17] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:56:17] parameters (PureCN 2.17.0).
INFO [2025-12-04 21:56:17] ------------------------------------------------------------
INFO [2025-12-04 21:56:17] PureCN 2.17.0
INFO [2025-12-04 21:56:17] ------------------------------------------------------------
WARN [2025-12-04 21:56:17] test.num.copy outside recommended range.
FATAL [2025-12-04 21:56:17] max.non.clonal not within expected range or format.
FATAL [2025-12-04 21:56:17]
FATAL [2025-12-04 21:56:17] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:56:17] parameters (PureCN 2.17.0).
INFO [2025-12-04 21:56:17] ------------------------------------------------------------
INFO [2025-12-04 21:56:17] PureCN 2.17.0
INFO [2025-12-04 21:56:17] ------------------------------------------------------------
WARN [2025-12-04 21:56:17] test.num.copy outside recommended range.
FATAL [2025-12-04 21:56:17] max.non.clonal not within expected range or format.
FATAL [2025-12-04 21:56:17]
FATAL [2025-12-04 21:56:17] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:56:17] parameters (PureCN 2.17.0).
INFO [2025-12-04 21:56:17] ------------------------------------------------------------
INFO [2025-12-04 21:56:17] PureCN 2.17.0
INFO [2025-12-04 21:56:17] ------------------------------------------------------------
FATAL [2025-12-04 21:56:17] test.purity not within expected range.
FATAL [2025-12-04 21:56:17]
FATAL [2025-12-04 21:56:17] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:56:17] parameters (PureCN 2.17.0).
INFO [2025-12-04 21:56:17] ------------------------------------------------------------
INFO [2025-12-04 21:56:17] PureCN 2.17.0
INFO [2025-12-04 21:56:17] ------------------------------------------------------------
INFO [2025-12-04 21:56:17] Loading coverage files...
FATAL [2025-12-04 21:56:17] Tumor and normal are identical. This won't give any meaningful results
FATAL [2025-12-04 21:56:17] and I'm stopping here.
FATAL [2025-12-04 21:56:17]
FATAL [2025-12-04 21:56:17] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:56:17] parameters (PureCN 2.17.0).
INFO [2025-12-04 21:56:17] ------------------------------------------------------------
INFO [2025-12-04 21:56:17] PureCN 2.17.0
INFO [2025-12-04 21:56:17] ------------------------------------------------------------
INFO [2025-12-04 21:56:17] Loading coverage files...
FATAL [2025-12-04 21:56:17] Length of log.ratio different from tumor coverage.
FATAL [2025-12-04 21:56:17]
FATAL [2025-12-04 21:56:17] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:56:17] parameters (PureCN 2.17.0).
INFO [2025-12-04 21:56:17] ------------------------------------------------------------
INFO [2025-12-04 21:56:17] PureCN 2.17.0
INFO [2025-12-04 21:56:17] ------------------------------------------------------------
FATAL [2025-12-04 21:56:17] prior.purity must have the same length as test.purity.
FATAL [2025-12-04 21:56:17]
FATAL [2025-12-04 21:56:17] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:56:17] parameters (PureCN 2.17.0).
INFO [2025-12-04 21:56:17] ------------------------------------------------------------
INFO [2025-12-04 21:56:17] PureCN 2.17.0
INFO [2025-12-04 21:56:17] ------------------------------------------------------------
FATAL [2025-12-04 21:56:17] min.gof not within expected range or format.
FATAL [2025-12-04 21:56:17]
FATAL [2025-12-04 21:56:17] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:56:17] parameters (PureCN 2.17.0).
INFO [2025-12-04 21:56:17] ------------------------------------------------------------
INFO [2025-12-04 21:56:17] PureCN 2.17.0
INFO [2025-12-04 21:56:17] ------------------------------------------------------------
FATAL [2025-12-04 21:56:17] prior.purity not within expected range or format.
FATAL [2025-12-04 21:56:17]
FATAL [2025-12-04 21:56:17] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:56:17] parameters (PureCN 2.17.0).
INFO [2025-12-04 21:56:17] ------------------------------------------------------------
INFO [2025-12-04 21:56:17] PureCN 2.17.0
INFO [2025-12-04 21:56:17] ------------------------------------------------------------
FATAL [2025-12-04 21:56:17] prior.purity must add to 1. Sum is 1.5
FATAL [2025-12-04 21:56:17]
FATAL [2025-12-04 21:56:17] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:56:17] parameters (PureCN 2.17.0).
INFO [2025-12-04 21:56:17] ------------------------------------------------------------
INFO [2025-12-04 21:56:17] PureCN 2.17.0
INFO [2025-12-04 21:56:17] ------------------------------------------------------------
FATAL [2025-12-04 21:56:17] max.homozygous.loss not within expected range or format.
FATAL [2025-12-04 21:56:17]
FATAL [2025-12-04 21:56:17] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:56:17] parameters (PureCN 2.17.0).
INFO [2025-12-04 21:56:17] ------------------------------------------------------------
INFO [2025-12-04 21:56:17] PureCN 2.17.0
INFO [2025-12-04 21:56:17] ------------------------------------------------------------
FATAL [2025-12-04 21:56:17] prior.K not within expected range or format.
FATAL [2025-12-04 21:56:17]
FATAL [2025-12-04 21:56:17] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:56:17] parameters (PureCN 2.17.0).
INFO [2025-12-04 21:56:17] ------------------------------------------------------------
INFO [2025-12-04 21:56:17] PureCN 2.17.0
INFO [2025-12-04 21:56:17] ------------------------------------------------------------
FATAL [2025-12-04 21:56:17] prior.contamination not within expected range or format.
FATAL [2025-12-04 21:56:17]
FATAL [2025-12-04 21:56:17] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:56:17] parameters (PureCN 2.17.0).
INFO [2025-12-04 21:56:17] ------------------------------------------------------------
INFO [2025-12-04 21:56:17] PureCN 2.17.0
INFO [2025-12-04 21:56:17] ------------------------------------------------------------
FATAL [2025-12-04 21:56:17] Iterations not in the expected range from 10 to 250.
FATAL [2025-12-04 21:56:17]
FATAL [2025-12-04 21:56:17] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:56:17] parameters (PureCN 2.17.0).
INFO [2025-12-04 21:56:17] ------------------------------------------------------------
INFO [2025-12-04 21:56:17] PureCN 2.17.0
INFO [2025-12-04 21:56:17] ------------------------------------------------------------
FATAL [2025-12-04 21:56:17] Iterations not in the expected range from 10 to 250.
FATAL [2025-12-04 21:56:17]
FATAL [2025-12-04 21:56:17] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:56:17] parameters (PureCN 2.17.0).
INFO [2025-12-04 21:56:17] ------------------------------------------------------------
INFO [2025-12-04 21:56:17] PureCN 2.17.0
INFO [2025-12-04 21:56:17] ------------------------------------------------------------
INFO [2025-12-04 21:56:17] Loading coverage files...
FATAL [2025-12-04 21:56:17] Missing tumor.coverage.file requires seg.file or log.ratio and
FATAL [2025-12-04 21:56:17] interval.file.
FATAL [2025-12-04 21:56:17]
FATAL [2025-12-04 21:56:17] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:56:17] parameters (PureCN 2.17.0).
INFO [2025-12-04 21:56:17] ------------------------------------------------------------
INFO [2025-12-04 21:56:17] PureCN 2.17.0
INFO [2025-12-04 21:56:17] ------------------------------------------------------------
INFO [2025-12-04 21:56:18] ------------------------------------------------------------
INFO [2025-12-04 21:56:18] PureCN 2.17.0
INFO [2025-12-04 21:56:18] ------------------------------------------------------------
INFO [2025-12-04 21:56:18] Loading coverage files...
FATAL [2025-12-04 21:56:18] Interval files in normal and tumor different.
FATAL [2025-12-04 21:56:18]
FATAL [2025-12-04 21:56:18] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:56:18] parameters (PureCN 2.17.0).
INFO [2025-12-04 21:56:18] ------------------------------------------------------------
INFO [2025-12-04 21:56:18] PureCN 2.17.0
INFO [2025-12-04 21:56:18] ------------------------------------------------------------
INFO [2025-12-04 21:56:18] Loading coverage files...
INFO [2025-12-04 21:56:18] Mean target coverages: 0X (tumor) 99X (normal).
WARN [2025-12-04 21:56:18] Large difference in coverage of tumor and normal.
FATAL [2025-12-04 21:56:18] No finite intervals.
FATAL [2025-12-04 21:56:18]
FATAL [2025-12-04 21:56:18] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:56:18] parameters (PureCN 2.17.0).
INFO [2025-12-04 21:56:18] ------------------------------------------------------------
INFO [2025-12-04 21:56:18] PureCN 2.17.0
INFO [2025-12-04 21:56:18] ------------------------------------------------------------
INFO [2025-12-04 21:56:18] Loading coverage files...
INFO [2025-12-04 21:56:18] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-12-04 21:56:18] Allosome coverage missing, cannot determine sex.
WARN [2025-12-04 21:56:18] Allosome coverage missing, cannot determine sex.
INFO [2025-12-04 21:56:18] Removing 228 intervals with missing log.ratio.
INFO [2025-12-04 21:56:18] Removing 22 small (< 5bp) intervals.
INFO [2025-12-04 21:56:18] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-12-04 21:56:18] No normalDB provided. Provide one for better results.
INFO [2025-12-04 21:56:18] Removing 1724 low count (< 100 total reads) intervals.
INFO [2025-12-04 21:56:18] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-12-04 21:56:18] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-12-04 21:56:18] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-12-04 21:56:18] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-12-04 21:56:18] Loading VCF...
INFO [2025-12-04 21:56:19] Found 127 variants in VCF file.
INFO [2025-12-04 21:56:19] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-12-04 21:56:19] LIB-02240e4 is tumor in VCF file.
INFO [2025-12-04 21:56:19] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-12-04 21:56:19] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-12-04 21:56:19] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-12-04 21:56:19] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-12-04 21:56:19] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-12-04 21:56:19] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
Error in FileForFormat(resource(con), fileFormat(con)) :
Format 'txt' unsupported
In addition: Warning messages:
1: In for (i in (1L:cols)[do]) { :
closing unused connection 4 (/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/PureCN/extdata/example_allelic_counts_empty.tsv)
2: In for (i in seq_len(n)) { :
closing unused connection 5 (/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpdk23KO/file1645e6f1ad48f.tsv)
3: In for (i in seq_len(n)) { :
closing unused connection 4 (/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/PureCN/extdata/example_gatk4_denoised_cr.tsv.gz)
FATAL [2025-12-04 21:56:19] Could not import snp.blacklist
FATAL [2025-12-04 21:56:19] /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/PureCN/extdata/example_normal.txt.gz:Error
FATAL [2025-12-04 21:56:19] in FileForFormat(resource(con), fileFormat(con)) : Format 'txt'
FATAL [2025-12-04 21:56:19] unsupported
FATAL [2025-12-04 21:56:19]
FATAL [2025-12-04 21:56:19] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:56:19] parameters (PureCN 2.17.0).
INFO [2025-12-04 21:56:19] ------------------------------------------------------------
INFO [2025-12-04 21:56:19] PureCN 2.17.0
INFO [2025-12-04 21:56:19] ------------------------------------------------------------
INFO [2025-12-04 21:56:19] Loading coverage files...
INFO [2025-12-04 21:56:19] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-12-04 21:56:19] Allosome coverage missing, cannot determine sex.
WARN [2025-12-04 21:56:19] Allosome coverage missing, cannot determine sex.
INFO [2025-12-04 21:56:19] Removing 228 intervals with missing log.ratio.
INFO [2025-12-04 21:56:19] Removing 22 small (< 5bp) intervals.
INFO [2025-12-04 21:56:19] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-12-04 21:56:19] No normalDB provided. Provide one for better results.
INFO [2025-12-04 21:56:19] Removing 233 low coverage (< 15.0000X) intervals.
INFO [2025-12-04 21:56:19] Using 9547 intervals (9547 on-target, 0 off-target).
INFO [2025-12-04 21:56:19] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-12-04 21:56:19] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-12-04 21:56:19] Loading VCF...
INFO [2025-12-04 21:56:19] Found 127 variants in VCF file.
INFO [2025-12-04 21:56:19] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-12-04 21:56:19] LIB-02240e4 is tumor in VCF file.
INFO [2025-12-04 21:56:19] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-12-04 21:56:19] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-12-04 21:56:19] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-12-04 21:56:19] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-12-04 21:56:19] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-12-04 21:56:20] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-12-04 21:56:20] Total size of targeted genomic region: 1.63Mb (2.58Mb with 50bp padding).
INFO [2025-12-04 21:56:20] 1.0% of targets contain variants.
INFO [2025-12-04 21:56:20] Removing 2 variants outside intervals.
INFO [2025-12-04 21:56:20] Found SOMATIC annotation in VCF.
INFO [2025-12-04 21:56:20] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-12-04 21:56:20] Found SOMATIC annotation in VCF. Setting mapping bias to 0.973.
INFO [2025-12-04 21:56:20] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-12-04 21:56:20] Sample sex: ?
INFO [2025-12-04 21:56:20] Segmenting data...
INFO [2025-12-04 21:56:20] Loading pre-computed boundaries for DNAcopy...
INFO [2025-12-04 21:56:20] Setting undo.SD parameter to 1.000000.
INFO [2025-12-04 21:56:20] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-12-04 21:56:20] Found 54 segments with median size of 24.88Mb.
INFO [2025-12-04 21:56:20] Using 123 variants.
INFO [2025-12-04 21:56:20] Mean standard deviation of log-ratios: 0.37 (MAPD: 0.32)
INFO [2025-12-04 21:56:20] 2D-grid search of purity and ploidy...
INFO [2025-12-04 21:56:21] Local optima: 0.62/1.9, 0.3/1.9, 0.32/2
INFO [2025-12-04 21:56:21] Testing local optimum 1/3 at purity 0.62 and total ploidy 1.90...
INFO [2025-12-04 21:56:21] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-12-04 21:56:21] Recalibrating log-ratios...
INFO [2025-12-04 21:56:21] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-12-04 21:56:21] Recalibrating log-ratios...
INFO [2025-12-04 21:56:21] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-12-04 21:56:22] Recalibrating log-ratios...
INFO [2025-12-04 21:56:22] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-12-04 21:56:22] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-12-04 21:56:22] Recalibrating log-ratios...
INFO [2025-12-04 21:56:22] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-12-04 21:56:22] Recalibrating log-ratios...
INFO [2025-12-04 21:56:22] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-12-04 21:56:22] Recalibrating log-ratios...
INFO [2025-12-04 21:56:22] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-12-04 21:56:22] Skipping 1 solutions that converged to the same optima.
INFO [2025-12-04 21:56:22] Skipping 1 solutions exceeding max.non.clonal (0.20): 0.3/1.9 (purity/tumor ploidy)
INFO [2025-12-04 21:56:22] Fitting variants with beta model for local optimum 1/3...
INFO [2025-12-04 21:56:22] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01.
INFO [2025-12-04 21:56:23] Optimized purity: 0.65
INFO [2025-12-04 21:56:23] Done.
INFO [2025-12-04 21:56:23] ------------------------------------------------------------
INFO [2025-12-04 21:56:23] ------------------------------------------------------------
INFO [2025-12-04 21:56:23] PureCN 2.17.0
INFO [2025-12-04 21:56:23] ------------------------------------------------------------
INFO [2025-12-04 21:56:23] Loading coverage files...
INFO [2025-12-04 21:56:24] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-12-04 21:56:24] Allosome coverage missing, cannot determine sex.
WARN [2025-12-04 21:56:24] Allosome coverage missing, cannot determine sex.
INFO [2025-12-04 21:56:24] Removing 228 intervals with missing log.ratio.
INFO [2025-12-04 21:56:24] Removing 22 small (< 5bp) intervals.
INFO [2025-12-04 21:56:24] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-12-04 21:56:24] No normalDB provided. Provide one for better results.
INFO [2025-12-04 21:56:24] Removing 1724 low count (< 100 total reads) intervals.
INFO [2025-12-04 21:56:24] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-12-04 21:56:24] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-12-04 21:56:24] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-12-04 21:56:24] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-12-04 21:56:24] Loading VCF...
INFO [2025-12-04 21:56:24] Found 127 variants in VCF file.
WARN [2025-12-04 21:56:24] DP FORMAT field contains NAs. Removing 3 variants.
WARN [2025-12-04 21:56:24] DB INFO flag contains NAs
INFO [2025-12-04 21:56:24] 119 (96.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-12-04 21:56:24] LIB-02240e4 is tumor in VCF file.
INFO [2025-12-04 21:56:24] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-12-04 21:56:24] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-12-04 21:56:24] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-12-04 21:56:24] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-12-04 21:56:24] Removing 1 variants with AF < 0.030 or AF >= 0.970 or insufficient supporting reads or depth < 15.
INFO [2025-12-04 21:56:24] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding).
INFO [2025-12-04 21:56:24] 1.2% of targets contain variants.
INFO [2025-12-04 21:56:24] Setting somatic prior probabilities for likely germline hits to 0.000500 or to 0.500000 otherwise.
INFO [2025-12-04 21:56:24] Excluding 5 novel or poor quality variants from segmentation.
INFO [2025-12-04 21:56:24] Sample sex: ?
INFO [2025-12-04 21:56:24] Segmenting data...
INFO [2025-12-04 21:56:24] Loading pre-computed boundaries for DNAcopy...
INFO [2025-12-04 21:56:24] Setting undo.SD parameter to 1.000000.
Setting multi-figure configuration
INFO [2025-12-04 21:56:25] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-12-04 21:56:25] Found 59 segments with median size of 17.67Mb.
INFO [2025-12-04 21:56:25] Using 123 variants.
INFO [2025-12-04 21:56:25] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-12-04 21:56:25] 2D-grid search of purity and ploidy...
INFO [2025-12-04 21:56:25] Local optima: 0.62/1.9, 0.3/1.9, 0.32/2
INFO [2025-12-04 21:56:25] Testing local optimum 1/3 at purity 0.62 and total ploidy 1.90...
INFO [2025-12-04 21:56:25] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-12-04 21:56:26] Recalibrating log-ratios...
INFO [2025-12-04 21:56:26] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-12-04 21:56:26] Recalibrating log-ratios...
INFO [2025-12-04 21:56:26] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-12-04 21:56:26] Recalibrating log-ratios...
INFO [2025-12-04 21:56:26] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-12-04 21:56:26] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-12-04 21:56:26] Recalibrating log-ratios...
INFO [2025-12-04 21:56:26] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-12-04 21:56:26] Recalibrating log-ratios...
INFO [2025-12-04 21:56:26] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-12-04 21:56:26] Recalibrating log-ratios...
INFO [2025-12-04 21:56:26] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-12-04 21:56:26] Skipping 2 solutions exceeding max.non.clonal (0.20): 0.3/1.9, 0.35/1.61 (purity/tumor ploidy)
INFO [2025-12-04 21:56:26] Fitting variants with beta model for local optimum 1/3...
INFO [2025-12-04 21:56:26] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2025-12-04 21:56:27] Optimized purity: 0.65
INFO [2025-12-04 21:56:27] Done.
INFO [2025-12-04 21:56:27] ------------------------------------------------------------
INFO [2025-12-04 21:56:28] ------------------------------------------------------------
INFO [2025-12-04 21:56:28] PureCN 2.17.0
INFO [2025-12-04 21:56:28] ------------------------------------------------------------
INFO [2025-12-04 21:56:28] Loading coverage files...
INFO [2025-12-04 21:56:28] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-12-04 21:56:28] Allosome coverage missing, cannot determine sex.
WARN [2025-12-04 21:56:28] Allosome coverage missing, cannot determine sex.
INFO [2025-12-04 21:56:28] No Gene column in interval.file. You won't get gene-level calls.
INFO [2025-12-04 21:56:28] Removing 228 intervals with missing log.ratio.
INFO [2025-12-04 21:56:28] Removing 15 low/high GC targets.
INFO [2025-12-04 21:56:28] Removing 21 small (< 5bp) intervals.
INFO [2025-12-04 21:56:28] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-12-04 21:56:28] No normalDB provided. Provide one for better results.
INFO [2025-12-04 21:56:28] Removing 1718 low count (< 100 total reads) intervals.
INFO [2025-12-04 21:56:28] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-12-04 21:56:28] Removing 36 low mappability intervals.
INFO [2025-12-04 21:56:28] Using 8006 intervals (8006 on-target, 0 off-target).
INFO [2025-12-04 21:56:28] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-12-04 21:56:28] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio).
INFO [2025-12-04 21:56:28] Loading VCF...
INFO [2025-12-04 21:56:28] Found 127 variants in VCF file.
INFO [2025-12-04 21:56:28] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-12-04 21:56:28] LIB-02240e4 is tumor in VCF file.
INFO [2025-12-04 21:56:28] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-12-04 21:56:28] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-12-04 21:56:28] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-12-04 21:56:28] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-12-04 21:56:28] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-12-04 21:56:28] Removing 1 variants with AF < 0.030 or AF >= Inf or insufficient supporting reads or depth < 15.
INFO [2025-12-04 21:56:28] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding).
INFO [2025-12-04 21:56:29] 1.2% of targets contain variants.
INFO [2025-12-04 21:56:29] Removing 11 variants outside intervals.
INFO [2025-12-04 21:56:29] Found SOMATIC annotation in VCF.
INFO [2025-12-04 21:56:29] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-12-04 21:56:29] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970.
INFO [2025-12-04 21:56:29] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-12-04 21:56:29] Sample sex: ?
INFO [2025-12-04 21:56:29] Segmenting data...
INFO [2025-12-04 21:56:29] MAPD of 114 allelic fractions: 0.14 (0.15 adjusted).
INFO [2025-12-04 21:56:29] Using unweighted PSCBS.
INFO [2025-12-04 21:56:29] Setting undo.SD parameter to 1.000000.
INFO [2025-12-04 21:56:40] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-12-04 21:56:41] Found 72 segments with median size of 27.25Mb.
INFO [2025-12-04 21:56:41] Using 114 variants.
INFO [2025-12-04 21:56:41] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-12-04 21:56:41] 2D-grid search of purity and ploidy...
INFO [2025-12-04 21:56:41] Local optima: 0.65/1.8, 0.38/2.2
INFO [2025-12-04 21:56:41] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2025-12-04 21:56:41] Recalibrating log-ratios...
INFO [2025-12-04 21:56:41] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2025-12-04 21:56:41] Recalibrating log-ratios...
INFO [2025-12-04 21:56:41] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2025-12-04 21:56:41] Recalibrating log-ratios...
INFO [2025-12-04 21:56:41] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2025-12-04 21:56:41] Testing local optimum 2/2 at purity 0.38 and total ploidy 2.20...
INFO [2025-12-04 21:56:42] Skipping 1 solutions exceeding max.non.clonal (0.20): 0.65/2.05 (purity/tumor ploidy)
INFO [2025-12-04 21:56:42] Fitting variants with beta model for local optimum 2/2...
INFO [2025-12-04 21:56:42] Fitting variants for purity 0.40, tumor ploidy 2.55 and contamination 0.01.
INFO [2025-12-04 21:56:43] Optimized purity: 0.40
INFO [2025-12-04 21:56:43] Done.
INFO [2025-12-04 21:56:43] ------------------------------------------------------------
FATAL [2025-12-04 21:56:43] This function requires gene-level calls. Please add a column 'Gene'
FATAL [2025-12-04 21:56:43] containing gene symbols to the interval.file.
FATAL [2025-12-04 21:56:43]
FATAL [2025-12-04 21:56:43] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:56:43] parameters (PureCN 2.17.0).
INFO [2025-12-04 21:56:44] ------------------------------------------------------------
INFO [2025-12-04 21:56:44] PureCN 2.17.0
INFO [2025-12-04 21:56:44] ------------------------------------------------------------
INFO [2025-12-04 21:56:44] Loading coverage files...
INFO [2025-12-04 21:56:44] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-12-04 21:56:44] Allosome coverage missing, cannot determine sex.
WARN [2025-12-04 21:56:44] Allosome coverage missing, cannot determine sex.
INFO [2025-12-04 21:56:44] Removing 228 intervals with missing log.ratio.
INFO [2025-12-04 21:56:44] Removing 22 small (< 5bp) intervals.
INFO [2025-12-04 21:56:44] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-12-04 21:56:44] No normalDB provided. Provide one for better results.
INFO [2025-12-04 21:56:44] Removing 1724 low count (< 100 total reads) intervals.
INFO [2025-12-04 21:56:44] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-12-04 21:56:44] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-12-04 21:56:44] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-12-04 21:56:44] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-12-04 21:56:44] Loading VCF...
INFO [2025-12-04 21:56:44] Found 127 variants in VCF file.
INFO [2025-12-04 21:56:44] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
FATAL [2025-12-04 21:56:44] Different chromosome names in coverage and VCF.
FATAL [2025-12-04 21:56:44]
FATAL [2025-12-04 21:56:44] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:56:44] parameters (PureCN 2.17.0).
INFO [2025-12-04 21:56:44] ------------------------------------------------------------
INFO [2025-12-04 21:56:44] PureCN 2.17.0
INFO [2025-12-04 21:56:44] ------------------------------------------------------------
INFO [2025-12-04 21:56:44] Loading coverage files...
INFO [2025-12-04 21:56:44] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-12-04 21:56:44] Allosome coverage missing, cannot determine sex.
WARN [2025-12-04 21:56:44] Allosome coverage missing, cannot determine sex.
FATAL [2025-12-04 21:56:44] tumor.coverage.file and interval.file do not align.
FATAL [2025-12-04 21:56:44]
FATAL [2025-12-04 21:56:44] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:56:44] parameters (PureCN 2.17.0).
INFO [2025-12-04 21:56:44] ------------------------------------------------------------
INFO [2025-12-04 21:56:44] PureCN 2.17.0
INFO [2025-12-04 21:56:44] ------------------------------------------------------------
INFO [2025-12-04 21:56:44] Loading coverage files...
INFO [2025-12-04 21:56:44] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-12-04 21:56:44] Allosome coverage missing, cannot determine sex.
WARN [2025-12-04 21:56:44] Allosome coverage missing, cannot determine sex.
INFO [2025-12-04 21:56:45] Removing 228 intervals with missing log.ratio.
INFO [2025-12-04 21:56:45] Removing 15 low/high GC targets.
INFO [2025-12-04 21:56:45] Removing 21 small (< 5bp) intervals.
INFO [2025-12-04 21:56:45] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-12-04 21:56:45] No normalDB provided. Provide one for better results.
INFO [2025-12-04 21:56:45] Removing 1718 low count (< 100 total reads) intervals.
INFO [2025-12-04 21:56:45] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-12-04 21:56:45] Removing 36 low mappability intervals.
INFO [2025-12-04 21:56:45] Using 8006 intervals (8006 on-target, 0 off-target).
INFO [2025-12-04 21:56:45] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-12-04 21:56:45] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio).
INFO [2025-12-04 21:56:45] Loading VCF...
INFO [2025-12-04 21:56:45] Found 127 variants in VCF file.
INFO [2025-12-04 21:56:45] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-12-04 21:56:45] LIB-02240e4 is tumor in VCF file.
INFO [2025-12-04 21:56:45] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-12-04 21:56:45] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-12-04 21:56:45] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-12-04 21:56:45] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-12-04 21:56:45] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-12-04 21:56:45] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-12-04 21:56:45] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding).
INFO [2025-12-04 21:56:45] 1.2% of targets contain variants.
INFO [2025-12-04 21:56:45] Removing 11 variants outside intervals.
INFO [2025-12-04 21:56:45] Found SOMATIC annotation in VCF.
INFO [2025-12-04 21:56:45] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-12-04 21:56:45] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970.
INFO [2025-12-04 21:56:45] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-12-04 21:56:45] Sample sex: ?
INFO [2025-12-04 21:56:45] Segmenting data...
INFO [2025-12-04 21:56:45] Loading pre-computed boundaries for DNAcopy...
INFO [2025-12-04 21:56:45] Setting undo.SD parameter to 1.000000.
INFO [2025-12-04 21:56:46] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-12-04 21:56:46] Found 59 segments with median size of 17.67Mb.
INFO [2025-12-04 21:56:46] Using 114 variants.
INFO [2025-12-04 21:56:46] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-12-04 21:56:46] 2D-grid search of purity and ploidy...
INFO [2025-12-04 21:56:46] Local optima: 0.63/1.9
INFO [2025-12-04 21:56:46] Testing local optimum 1/1 at purity 0.63 and total ploidy 1.90...
INFO [2025-12-04 21:56:46] Fitting variants with beta model for local optimum 1/1...
INFO [2025-12-04 21:56:46] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2025-12-04 21:56:47] Optimized purity: 0.65
INFO [2025-12-04 21:56:47] Done.
INFO [2025-12-04 21:56:47] ------------------------------------------------------------
INFO [2025-12-04 21:56:47] ------------------------------------------------------------
INFO [2025-12-04 21:56:47] PureCN 2.17.0
INFO [2025-12-04 21:56:47] ------------------------------------------------------------
INFO [2025-12-04 21:56:47] Loading coverage files...
INFO [2025-12-04 21:56:47] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-12-04 21:56:48] Allosome coverage missing, cannot determine sex.
WARN [2025-12-04 21:56:48] Allosome coverage missing, cannot determine sex.
INFO [2025-12-04 21:56:48] Removing 228 intervals with missing log.ratio.
INFO [2025-12-04 21:56:48] Removing 15 low/high GC targets.
INFO [2025-12-04 21:56:48] Removing 21 small (< 5bp) intervals.
INFO [2025-12-04 21:56:48] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-12-04 21:56:48] No normalDB provided. Provide one for better results.
INFO [2025-12-04 21:56:48] Removing 1718 low count (< 100 total reads) intervals.
INFO [2025-12-04 21:56:48] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-12-04 21:56:48] Removing 36 low mappability intervals.
INFO [2025-12-04 21:56:48] Using 8006 intervals (8006 on-target, 0 off-target).
INFO [2025-12-04 21:56:48] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-12-04 21:56:48] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio).
INFO [2025-12-04 21:56:48] Loading VCF...
INFO [2025-12-04 21:56:48] Found 127 variants in VCF file.
INFO [2025-12-04 21:56:48] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-12-04 21:56:48] LIB-02240e4 is tumor in VCF file.
INFO [2025-12-04 21:56:48] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-12-04 21:56:48] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-12-04 21:56:48] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-12-04 21:56:48] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-12-04 21:56:48] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-12-04 21:56:48] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-12-04 21:56:48] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding).
INFO [2025-12-04 21:56:48] 1.2% of targets contain variants.
INFO [2025-12-04 21:56:48] Removing 11 variants outside intervals.
INFO [2025-12-04 21:56:48] Found SOMATIC annotation in VCF.
INFO [2025-12-04 21:56:48] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-12-04 21:56:48] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970.
INFO [2025-12-04 21:56:48] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-12-04 21:56:48] Sample sex: ?
INFO [2025-12-04 21:56:48] Segmenting data...
INFO [2025-12-04 21:56:48] Loading pre-computed boundaries for DNAcopy...
INFO [2025-12-04 21:56:48] Setting undo.SD parameter to 1.000000.
INFO [2025-12-04 21:56:49] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-12-04 21:56:49] Found 59 segments with median size of 17.67Mb.
INFO [2025-12-04 21:56:49] Using 114 variants.
INFO [2025-12-04 21:56:49] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-12-04 21:56:49] 2D-grid search of purity and ploidy...
INFO [2025-12-04 21:56:49] Local optima: 0.63/1.9
INFO [2025-12-04 21:56:49] Testing local optimum 1/1 at purity 0.63 and total ploidy 1.90...
INFO [2025-12-04 21:56:50] Fitting variants with beta model for local optimum 1/1...
WARN [2025-12-04 21:56:50] Some gene symbols found on multiple chromosomes. Use of approved symbols suggested.
INFO [2025-12-04 21:56:50] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2025-12-04 21:56:51] Optimized purity: 0.65
INFO [2025-12-04 21:56:51] Done.
INFO [2025-12-04 21:56:51] ------------------------------------------------------------
FATAL [2025-12-04 21:56:51] chr1 not valid chromosome name(s). Valid names are:
FATAL [2025-12-04 21:56:51] 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22
FATAL [2025-12-04 21:56:51]
FATAL [2025-12-04 21:56:51] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:56:51] parameters (PureCN 2.17.0).
INFO [2025-12-04 21:56:51] ------------------------------------------------------------
INFO [2025-12-04 21:56:51] PureCN 2.17.0
INFO [2025-12-04 21:56:51] ------------------------------------------------------------
INFO [2025-12-04 21:56:51] Loading coverage files...
WARN [2025-12-04 21:56:51] Provided sampleid (Sample2) does not match Sample1 found in segmentation.
WARN [2025-12-04 21:56:51] Allosome coverage missing, cannot determine sex.
WARN [2025-12-04 21:56:51] Allosome coverage missing, cannot determine sex.
INFO [2025-12-04 21:56:51] Removing 10 intervals with missing log.ratio.
INFO [2025-12-04 21:56:51] Using 10039 intervals (10039 on-target, 0 off-target).
INFO [2025-12-04 21:56:51] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-12-04 21:56:51] Loading VCF...
INFO [2025-12-04 21:56:51] Found 127 variants in VCF file.
INFO [2025-12-04 21:56:51] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-12-04 21:56:51] LIB-02240e4 is tumor in VCF file.
INFO [2025-12-04 21:56:51] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-12-04 21:56:51] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-12-04 21:56:51] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-12-04 21:56:51] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-12-04 21:56:51] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-12-04 21:56:51] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-12-04 21:56:51] Total size of targeted genomic region: 1.71Mb (2.70Mb with 50bp padding).
INFO [2025-12-04 21:56:52] 1.0% of targets contain variants.
INFO [2025-12-04 21:56:52] Removing 0 variants outside intervals.
INFO [2025-12-04 21:56:52] Found SOMATIC annotation in VCF.
INFO [2025-12-04 21:56:52] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-12-04 21:56:52] Found SOMATIC annotation in VCF. Setting mapping bias to 0.976.
INFO [2025-12-04 21:56:52] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-12-04 21:56:52] Sample sex: ?
INFO [2025-12-04 21:56:52] Segmenting data...
INFO [2025-12-04 21:56:52] Loaded provided segmentation file example_seg.txt (format DNAcopy).
WARN [2025-12-04 21:56:52] Provided sampleid (Sample2) does not match Sample1 found in segmentation.
INFO [2025-12-04 21:56:52] Re-centering provided segment means (offset -0.0033).
INFO [2025-12-04 21:56:52] Loading pre-computed boundaries for DNAcopy...
INFO [2025-12-04 21:56:52] Setting undo.SD parameter to 0.000000.
Setting multi-figure configuration
INFO [2025-12-04 21:56:52] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-12-04 21:56:52] Found 54 segments with median size of 24.88Mb.
INFO [2025-12-04 21:56:52] Using 125 variants.
INFO [2025-12-04 21:56:52] Mean standard deviation of log-ratios: 0.40 (MAPD: 0.00)
INFO [2025-12-04 21:56:52] 2D-grid search of purity and ploidy...
INFO [2025-12-04 21:56:52] Local optima: 0.6/1.9
INFO [2025-12-04 21:56:52] Testing local optimum 1/1 at purity 0.60 and total ploidy 1.90...
INFO [2025-12-04 21:56:53] Fitting variants with beta model for local optimum 1/1...
INFO [2025-12-04 21:56:53] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01.
INFO [2025-12-04 21:56:54] Optimized purity: 0.65
INFO [2025-12-04 21:56:54] Done.
INFO [2025-12-04 21:56:54] ------------------------------------------------------------
WARN [2025-12-04 21:56:54] Allosome coverage missing, cannot determine sex.
WARN [2025-12-04 21:56:54] Allosome coverage missing, cannot determine sex.
Setting multi-figure configuration
FATAL [2025-12-04 21:56:57] Segmentation file expected with colnames ID, chrom, loc.start, loc.end,
FATAL [2025-12-04 21:56:57] num.mark, seg.mean
FATAL [2025-12-04 21:56:57]
FATAL [2025-12-04 21:56:57] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:56:57] parameters (PureCN 2.17.0).
FATAL [2025-12-04 21:56:57] seg.file contains multiple samples and sampleid missing.
FATAL [2025-12-04 21:56:57]
FATAL [2025-12-04 21:56:57] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:56:57] parameters (PureCN 2.17.0).
FATAL [2025-12-04 21:56:57] seg.file contains multiple samples and sampleid does not match any.
FATAL [2025-12-04 21:56:57]
FATAL [2025-12-04 21:56:57] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:56:57] parameters (PureCN 2.17.0).
WARN [2025-12-04 21:56:57] Allosome coverage missing, cannot determine sex.
WARN [2025-12-04 21:56:57] Allosome coverage missing, cannot determine sex.
WARN [2025-12-04 21:57:01] Allosome coverage missing, cannot determine sex.
WARN [2025-12-04 21:57:01] Allosome coverage missing, cannot determine sex.
WARN [2025-12-04 21:57:01] Provided sampleid (example_tumor.txt.gz) does not match Sample1 found in segmentation.
WARN [2025-12-04 21:57:02] Allosome coverage missing, cannot determine sex.
WARN [2025-12-04 21:57:02] Allosome coverage missing, cannot determine sex.
WARN [2025-12-04 21:57:02] No normalDB provided. Provide one for better results.
WARN [2025-12-04 21:57:05] Allosome coverage missing, cannot determine sex.
WARN [2025-12-04 21:57:05] Allosome coverage missing, cannot determine sex.
WARN [2025-12-04 21:57:06] Provided sampleid (Sample.1) does not match Sample1 found in segmentation.
Setting multi-figure configuration
WARN [2025-12-04 21:57:09] Allosome coverage missing, cannot determine sex.
WARN [2025-12-04 21:57:09] Allosome coverage missing, cannot determine sex.
WARN [2025-12-04 21:57:09] No normalDB provided. Provide one for better results.
WARN [2025-12-04 21:57:09] Sampleid looks like a normal in VCF, not like a tumor.
WARN [2025-12-04 21:57:11] Allosome coverage missing, cannot determine sex.
WARN [2025-12-04 21:57:11] Allosome coverage missing, cannot determine sex.
FATAL [2025-12-04 21:57:11] normalDB not a valid normalDB object. Use createNormalDatabase to
FATAL [2025-12-04 21:57:11] create one.
FATAL [2025-12-04 21:57:11]
FATAL [2025-12-04 21:57:11] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:57:11] parameters (PureCN 2.17.0).
WARN [2025-12-04 21:57:11] You are likely not using the correct baits file!
WARN [2025-12-04 21:57:11] Allosome coverage missing, cannot determine sex.
WARN [2025-12-04 21:57:11] Allosome coverage missing, cannot determine sex.
WARN [2025-12-04 21:57:12] Allosome coverage missing, cannot determine sex.
WARN [2025-12-04 21:57:12] Allosome coverage missing, cannot determine sex.
FATAL [2025-12-04 21:57:12] normalDB appears to be empty.
FATAL [2025-12-04 21:57:12]
FATAL [2025-12-04 21:57:12] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:57:12] parameters (PureCN 2.17.0).
WARN [2025-12-04 21:57:13] Allosome coverage missing, cannot determine sex.
WARN [2025-12-04 21:57:13] Allosome coverage missing, cannot determine sex.
WARN [2025-12-04 21:57:13] Intervals in coverage and interval.file have conflicting on/off-target annotation.
WARN [2025-12-04 21:57:17] Allosome coverage missing, cannot determine sex.
WARN [2025-12-04 21:57:17] Allosome coverage missing, cannot determine sex.
FATAL [2025-12-04 21:57:17] Seqlevels missing in provided segmentation: 6
FATAL [2025-12-04 21:57:17]
FATAL [2025-12-04 21:57:17] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:57:17] parameters (PureCN 2.17.0).
sh: gatk: command not found
WARN [2025-12-04 21:57:18] Cannot find gatk binary in path.
WARN [2025-12-04 21:57:18] Allosome coverage missing, cannot determine sex.
WARN [2025-12-04 21:57:18] Allosome coverage missing, cannot determine sex.
WARN [2025-12-04 21:57:18] No normalDB provided. Provide one for better results.
FATAL [2025-12-04 21:57:18] segmentationHclust requires an input segmentation.
FATAL [2025-12-04 21:57:18]
FATAL [2025-12-04 21:57:18] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:57:18] parameters (PureCN 2.17.0).
WARN [2025-12-04 21:57:18] Allosome coverage missing, cannot determine sex.
WARN [2025-12-04 21:57:18] Allosome coverage missing, cannot determine sex.
WARN [2025-12-04 21:57:18] No normalDB provided. Provide one for better results.
FATAL [2025-12-04 21:57:28] The normal.panel.vcf.file contains only a single sample.
FATAL [2025-12-04 21:57:28]
FATAL [2025-12-04 21:57:28] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:57:28] parameters (PureCN 2.17.0).
FATAL [2025-12-04 21:57:28] mapping.bias.file must be a file with *.rds suffix.
FATAL [2025-12-04 21:57:28]
FATAL [2025-12-04 21:57:28] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:57:28] parameters (PureCN 2.17.0).
Failed with error: 'there is no package called 'genomicsdb''
FATAL [2025-12-04 21:57:29] min.normals (0) must be >= 1.
FATAL [2025-12-04 21:57:29]
FATAL [2025-12-04 21:57:29] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:57:29] parameters (PureCN 2.17.0).
FATAL [2025-12-04 21:57:29] min.normals (10) cannot be larger than min.normals.assign.betafit (3).
FATAL [2025-12-04 21:57:29]
FATAL [2025-12-04 21:57:29] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:57:29] parameters (PureCN 2.17.0).
FATAL [2025-12-04 21:57:29] min.normals.assign.betafit (10) cannot be larger than
FATAL [2025-12-04 21:57:29] min.normals.betafit (7).
FATAL [2025-12-04 21:57:29]
FATAL [2025-12-04 21:57:29] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:57:29] parameters (PureCN 2.17.0).
FATAL [2025-12-04 21:57:29] min.normals.betafit (20) cannot be larger than
FATAL [2025-12-04 21:57:29] min.normals.position.specific.fit (10).
FATAL [2025-12-04 21:57:29]
FATAL [2025-12-04 21:57:29] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:57:29] parameters (PureCN 2.17.0).
FATAL [2025-12-04 21:57:29] min.betafit.rho not within expected range or format.
FATAL [2025-12-04 21:57:29]
FATAL [2025-12-04 21:57:29] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:57:29] parameters (PureCN 2.17.0).
FATAL [2025-12-04 21:57:29] max.betafit.rho not within expected range or format.
FATAL [2025-12-04 21:57:29]
FATAL [2025-12-04 21:57:29] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:57:29] parameters (PureCN 2.17.0).
FATAL [2025-12-04 21:57:29] min.betafit.rho (0.9) cannot be larger than max.betafit.rho (0.2).
FATAL [2025-12-04 21:57:29]
FATAL [2025-12-04 21:57:29] This is most likely a user error due to invalid input data or
FATAL [2025-12-04 21:57:29] parameters (PureCN 2.17.0).
[ 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
161.238 5.802 161.580
PureCN.Rcheck/PureCN-Ex.timings
| name | user | system | elapsed | |
| adjustLogRatio | 0.929 | 0.014 | 0.999 | |
| annotateTargets | 6.026 | 0.255 | 6.584 | |
| bootstrapResults | 0.207 | 0.016 | 0.248 | |
| calculateBamCoverageByInterval | 0.077 | 0.002 | 0.089 | |
| calculateLogRatio | 0.335 | 0.017 | 0.372 | |
| calculateMappingBiasGatk4 | 0 | 0 | 0 | |
| calculateMappingBiasVcf | 0.732 | 0.026 | 0.824 | |
| calculatePowerDetectSomatic | 0.556 | 0.004 | 0.583 | |
| calculateTangentNormal | 1.279 | 0.032 | 1.442 | |
| callAlterations | 0.081 | 0.004 | 0.129 | |
| callAlterationsFromSegmentation | 0.649 | 0.015 | 0.772 | |
| callAmplificationsInLowPurity | 15.162 | 0.132 | 16.745 | |
| callCIN | 0.101 | 0.002 | 0.113 | |
| callLOH | 0.082 | 0.002 | 0.088 | |
| callMutationBurden | 0.638 | 0.017 | 0.695 | |
| centromeres | 0.000 | 0.001 | 0.003 | |
| correctCoverageBias | 0.699 | 0.014 | 0.741 | |
| createCurationFile | 0.163 | 0.004 | 0.178 | |
| createNormalDatabase | 1.077 | 0.016 | 1.169 | |
| filterIntervals | 8.753 | 0.150 | 9.661 | |
| filterVcfBasic | 0.259 | 0.004 | 0.274 | |
| filterVcfMuTect | 0.237 | 0.005 | 0.254 | |
| filterVcfMuTect2 | 0.263 | 0.004 | 0.288 | |
| findFocal | 4.440 | 0.061 | 4.679 | |
| findHighQualitySNPs | 0.578 | 0.006 | 0.614 | |
| getSexFromCoverage | 0.106 | 0.005 | 0.125 | |
| getSexFromVcf | 0.128 | 0.003 | 0.145 | |
| plotAbs | 0.092 | 0.003 | 0.100 | |
| poolCoverage | 0.223 | 0.009 | 0.260 | |
| predictSomatic | 0.211 | 0.004 | 0.230 | |
| preprocessIntervals | 0.233 | 0.004 | 0.257 | |
| processMultipleSamples | 0.939 | 0.021 | 1.070 | |
| readAllelicCountsFile | 0.204 | 0.000 | 0.214 | |
| readCoverageFile | 0.101 | 0.006 | 0.111 | |
| readCurationFile | 0.093 | 0.003 | 0.102 | |
| readIntervalFile | 0.073 | 0.002 | 0.076 | |
| readLogRatioFile | 0.022 | 0.001 | 0.023 | |
| readSegmentationFile | 0.003 | 0.001 | 0.003 | |
| runAbsoluteCN | 6.338 | 0.123 | 6.804 | |
| segmentationCBS | 3.073 | 0.038 | 3.253 | |
| segmentationGATK4 | 0.001 | 0.000 | 0.001 | |
| segmentationHclust | 5.737 | 0.113 | 6.322 | |
| segmentationPSCBS | 14.517 | 0.192 | 15.334 | |
| setMappingBiasVcf | 0.130 | 0.003 | 0.134 | |
| setPriorVcf | 0.109 | 0.002 | 0.117 | |