Markus Riester
| Snapshot Date: 2025-12-05 13:40 -0500 (Fri, 05 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 2025-12-06 11:35 -0500 (Sat, 06 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: 2025-12-05 21:47:57 -0500 (Fri, 05 Dec 2025) |
| EndedAt: 2025-12-05 21:54:23 -0500 (Fri, 05 Dec 2025) |
| EllapsedTime: 386.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: PureCN.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PureCN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PureCN_2.17.0.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 15.294 0.156 16.750
segmentationPSCBS 14.371 0.168 15.035
filterIntervals 8.552 0.125 9.100
annotateTargets 6.156 0.268 6.739
runAbsoluteCN 6.293 0.116 6.738
segmentationHclust 5.692 0.105 6.167
* 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 [2025-12-05 21:51:50] Attempted adding gene symbols to intervals. Heuristics have been used to pick symbols for overlapping genes.
WARN [2025-12-05 21:51:50] Chromosome naming style of txdb file (UCSC) was different from interval file (Ensembl).
WARN [2025-12-05 21:51:55] Attempted adding gene symbols to intervals. Heuristics have been used to pick symbols for overlapping genes.
FATAL [2025-12-05 21:51:56] tumor.coverage.file and interval.file do not align.
FATAL [2025-12-05 21:51:56]
FATAL [2025-12-05 21:51:56] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:51:56] parameters (PureCN 2.17.0).
WARN [2025-12-05 21:51:56] Cannot find all contig lengths while exporting interval file.
INFO [2025-12-05 21:51:56] Processing seq1:1-21 (1/3)...
INFO [2025-12-05 21:51:57] Processing seq1:1227-1247 (2/3)...
INFO [2025-12-05 21:51:57] Processing seq2:594-614 (3/3)...
WARN [2025-12-05 21:51:57] Large potential mis-calibration of on- and off-target log2 ratios: 0.26
FATAL [2025-12-05 21:51:58] Need either f or purity and ploidy.
FATAL [2025-12-05 21:51:58]
FATAL [2025-12-05 21:51:58] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:51:58] parameters (PureCN 2.17.0).
FATAL [2025-12-05 21:51:58] f not in expected range.
FATAL [2025-12-05 21:51:58]
FATAL [2025-12-05 21:51:58] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:51:58] parameters (PureCN 2.17.0).
FATAL [2025-12-05 21:51:58] coverage not in expected range (>=2)
FATAL [2025-12-05 21:51:58]
FATAL [2025-12-05 21:51:58] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:51:58] parameters (PureCN 2.17.0).
FATAL [2025-12-05 21:51:58] purity not in expected range.
FATAL [2025-12-05 21:51:58]
FATAL [2025-12-05 21:51:58] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:51:58] parameters (PureCN 2.17.0).
FATAL [2025-12-05 21:51:58] ploidy not in expected range.
FATAL [2025-12-05 21:51:58]
FATAL [2025-12-05 21:51:58] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:51:58] parameters (PureCN 2.17.0).
FATAL [2025-12-05 21:51:58] cell.fraction not in expected range.
FATAL [2025-12-05 21:51:58]
FATAL [2025-12-05 21:51:58] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:51:58] parameters (PureCN 2.17.0).
INFO [2025-12-05 21:51:59] 576 on-target bins with low coverage in all samples.
WARN [2025-12-05 21:51:59] You are likely not using the correct baits file!
WARN [2025-12-05 21:51:59] Allosome coverage missing, cannot determine sex.
WARN [2025-12-05 21:51:59] Allosome coverage missing, cannot determine sex.
INFO [2025-12-05 21:51:59] Processing on-target regions...
INFO [2025-12-05 21:51:59] Removing 930 intervals with low coverage in normalDB.
INFO [2025-12-05 21:51:59] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2025-12-05 21:51:59] Tumor/normal noise ratio: 19.041
WARN [2025-12-05 21:51:59] Extensive noise in tumor compared to normals.
INFO [2025-12-05 21:52:16] Tumor/normal noise ratio: 19.041
WARN [2025-12-05 21:52:16] Extensive noise in tumor compared to normals.
INFO [2025-12-05 21:52:18] Using BiocParallel for parallel optimization.
FATAL [2025-12-05 21:52:23] pvalue.cutoff not within expected range or format.
FATAL [2025-12-05 21:52:23]
FATAL [2025-12-05 21:52:23] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:52:23] parameters (PureCN 2.17.0).
FATAL [2025-12-05 21:52:23] pvalue.cutoff not within expected range or format.
FATAL [2025-12-05 21:52:23]
FATAL [2025-12-05 21:52:23] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:52:23] parameters (PureCN 2.17.0).
FATAL [2025-12-05 21:52:23] percentile.cutoff not in expected range (0 to 100).
FATAL [2025-12-05 21:52:23]
FATAL [2025-12-05 21:52:23] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:52:23] parameters (PureCN 2.17.0).
FATAL [2025-12-05 21:52:23] percentile.cutoff not in expected range (0 to 100).
FATAL [2025-12-05 21:52:23]
FATAL [2025-12-05 21:52:23] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:52:23] parameters (PureCN 2.17.0).
FATAL [2025-12-05 21:52:23] purity not within expected range or format.
FATAL [2025-12-05 21:52:23]
FATAL [2025-12-05 21:52:23] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:52:23] parameters (PureCN 2.17.0).
FATAL [2025-12-05 21:52:23] purity not within expected range or format.
FATAL [2025-12-05 21:52:23]
FATAL [2025-12-05 21:52:23] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:52:23] parameters (PureCN 2.17.0).
INFO [2025-12-05 21:52:24] ------------------------------------------------------------
INFO [2025-12-05 21:52:24] PureCN 2.17.0
INFO [2025-12-05 21:52:24] ------------------------------------------------------------
INFO [2025-12-05 21:52:24] Loading coverage files...
INFO [2025-12-05 21:52:24] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-12-05 21:52:24] Allosome coverage missing, cannot determine sex.
WARN [2025-12-05 21:52:24] Allosome coverage missing, cannot determine sex.
INFO [2025-12-05 21:52:24] Removing 228 intervals with missing log.ratio.
INFO [2025-12-05 21:52:24] Removing 22 small (< 5bp) intervals.
INFO [2025-12-05 21:52:24] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-12-05 21:52:24] No normalDB provided. Provide one for better results.
INFO [2025-12-05 21:52:24] Removing 1724 low count (< 100 total reads) intervals.
INFO [2025-12-05 21:52:24] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-12-05 21:52:24] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-12-05 21:52:24] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-12-05 21:52:24] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-12-05 21:52:24] Loading VCF...
INFO [2025-12-05 21:52:24] Found 127 variants in VCF file.
INFO [2025-12-05 21:52:24] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-12-05 21:52:24] LIB-02240e4 is tumor in VCF file.
INFO [2025-12-05 21:52:25] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-12-05 21:52:25] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-12-05 21:52:25] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-12-05 21:52:25] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-12-05 21:52:25] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-12-05 21:52:25] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-12-05 21:52:25] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding).
INFO [2025-12-05 21:52:25] 1.2% of targets contain variants.
INFO [2025-12-05 21:52:25] Removing 4 variants outside intervals.
INFO [2025-12-05 21:52:25] Found SOMATIC annotation in VCF.
INFO [2025-12-05 21:52:25] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-12-05 21:52:25] Found SOMATIC annotation in VCF. Setting mapping bias to 0.972.
INFO [2025-12-05 21:52:25] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-12-05 21:52:25] Sample sex: ?
INFO [2025-12-05 21:52:25] Segmenting data...
INFO [2025-12-05 21:52:25] Loading pre-computed boundaries for DNAcopy...
INFO [2025-12-05 21:52:25] Setting undo.SD parameter to 1.000000.
INFO [2025-12-05 21:52:25] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-12-05 21:52:25] Found 59 segments with median size of 17.67Mb.
INFO [2025-12-05 21:52:25] Using 121 variants.
INFO [2025-12-05 21:52:25] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-12-05 21:52:25] 2D-grid search of purity and ploidy...
INFO [2025-12-05 21:52:26] Local optima: 0.63/1.9, 0.5/2
INFO [2025-12-05 21:52:26] Testing local optimum 1/2 at purity 0.63 and total ploidy 1.90...
INFO [2025-12-05 21:52:26] Testing local optimum 2/2 at purity 0.50 and total ploidy 2.00...
INFO [2025-12-05 21:52:27] Skipping 1 solutions that converged to the same optima.
INFO [2025-12-05 21:52:27] Fitting variants with beta model for local optimum 1/2...
INFO [2025-12-05 21:52:27] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2025-12-05 21:52:28] Optimized purity: 0.65
INFO [2025-12-05 21:52:28] Done.
INFO [2025-12-05 21:52:28] ------------------------------------------------------------
INFO [2025-12-05 21:52:28] Estimating callable regions.
FATAL [2025-12-05 21:52:29] exclude not a GRanges object.
FATAL [2025-12-05 21:52:29]
FATAL [2025-12-05 21:52:29] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:52:29] parameters (PureCN 2.17.0).
FATAL [2025-12-05 21:52:29] callable not a GRanges object.
FATAL [2025-12-05 21:52:29]
FATAL [2025-12-05 21:52:29] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:52:29] parameters (PureCN 2.17.0).
WARN [2025-12-05 21:52:31] tumor.coverage.file and interval.file do not align.
INFO [2025-12-05 21:52:32] No Gene column in interval.file. You won't get gene-level calls.
FATAL [2025-12-05 21:52:32] No gc_bias column in interval.file.
FATAL [2025-12-05 21:52:32]
FATAL [2025-12-05 21:52:32] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:52:32] parameters (PureCN 2.17.0).
FATAL [2025-12-05 21:52:32] Provided coverage is zero, most likely due to a corrupt BAM file.
FATAL [2025-12-05 21:52:32]
FATAL [2025-12-05 21:52:32] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:52:32] parameters (PureCN 2.17.0).
INFO [2025-12-05 21:52:33] No reptiming column in interval.file.
INFO [2025-12-05 21:52:35] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpAQvgYA/file162ab3e0c4de2.rds...
INFO [2025-12-05 21:52:35] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpAQvgYA/file162ab3e0c4de2.rds...
INFO [2025-12-05 21:52:35] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpAQvgYA/file162ab3e0c4de2.rds...
INFO [2025-12-05 21:52:35] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpAQvgYA/file162ab3e0c4de2.rds...
INFO [2025-12-05 21:52:35] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpAQvgYA/file162ab3e0c4de2.rds...
INFO [2025-12-05 21:52:35] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpAQvgYA/file162ab3e0c4de2.rds...
FATAL [2025-12-05 21:52:35] Purity or Ploidy not numeric or in expected range.
FATAL [2025-12-05 21:52:35]
FATAL [2025-12-05 21:52:35] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:52:35] parameters (PureCN 2.17.0).
INFO [2025-12-05 21:52:35] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpAQvgYA/file162ab3e0c4de2.rds...
INFO [2025-12-05 21:52:35] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpAQvgYA/file162ab3e0c4de2.rds...
FATAL [2025-12-05 21:52:35] 'Failed' column in
FATAL [2025-12-05 21:52:35] /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpAQvgYA/file162ab3e0c4de2.csv
FATAL [2025-12-05 21:52:35] not logical(1).
FATAL [2025-12-05 21:52:35]
FATAL [2025-12-05 21:52:35] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:52:35] parameters (PureCN 2.17.0).
INFO [2025-12-05 21:52:36] 576 on-target bins with low coverage in all samples.
WARN [2025-12-05 21:52:36] You are likely not using the correct baits file!
WARN [2025-12-05 21:52:36] Allosome coverage missing, cannot determine sex.
WARN [2025-12-05 21:52:36] Allosome coverage missing, cannot determine sex.
INFO [2025-12-05 21:52:36] Processing on-target regions...
INFO [2025-12-05 21:52:36] Removing 930 intervals with low coverage in normalDB.
INFO [2025-12-05 21:52:36] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2025-12-05 21:52:37] 576 on-target bins with low coverage in all samples.
WARN [2025-12-05 21:52:37] You are likely not using the correct baits file!
WARN [2025-12-05 21:52:37] Allosome coverage missing, cannot determine sex.
WARN [2025-12-05 21:52:37] Allosome coverage missing, cannot determine sex.
INFO [2025-12-05 21:52:37] Processing on-target regions...
INFO [2025-12-05 21:52:37] Removing 930 intervals with low coverage in normalDB.
INFO [2025-12-05 21:52:37] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2025-12-05 21:52:38] 576 on-target bins with low coverage in all samples.
WARN [2025-12-05 21:52:38] You are likely not using the correct baits file!
WARN [2025-12-05 21:52:38] Allosome coverage missing, cannot determine sex.
WARN [2025-12-05 21:52:38] Allosome coverage missing, cannot determine sex.
INFO [2025-12-05 21:52:38] Processing on-target regions...
INFO [2025-12-05 21:52:38] Removing 930 intervals with low coverage in normalDB.
INFO [2025-12-05 21:52:38] Removing 1 intervals with zero coverage in more than 3% of normalDB.
WARN [2025-12-05 21:52:39] Allosome coverage missing, cannot determine sex.
INFO [2025-12-05 21:52:39] Sample sex: NA
WARN [2025-12-05 21:52:39] Allosome coverage missing, cannot determine sex.
INFO [2025-12-05 21:52:39] Sample sex: NA
INFO [2025-12-05 21:52:39] 576 on-target bins with low coverage in all samples.
WARN [2025-12-05 21:52:39] You are likely not using the correct baits file!
WARN [2025-12-05 21:52:39] Allosome coverage missing, cannot determine sex.
WARN [2025-12-05 21:52:39] Allosome coverage missing, cannot determine sex.
FATAL [2025-12-05 21:52:39] Length of normal.coverage.files and sex different
FATAL [2025-12-05 21:52:39]
FATAL [2025-12-05 21:52:39] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:52:39] parameters (PureCN 2.17.0).
WARN [2025-12-05 21:52:41] Target intervals were not sorted.
INFO [2025-12-05 21:52:41] 560 on-target bins with low coverage in all samples.
WARN [2025-12-05 21:52:41] You are likely not using the correct baits file!
WARN [2025-12-05 21:52:41] Allosome coverage missing, cannot determine sex.
WARN [2025-12-05 21:52:41] Allosome coverage missing, cannot determine sex.
WARN [2025-12-05 21:52:41] Allosome coverage missing, cannot determine sex.
INFO [2025-12-05 21:52:41] Processing on-target regions...
INFO [2025-12-05 21:52:41] Removing 978 intervals with low coverage in normalDB.
INFO [2025-12-05 21:52:41] Removing 11 intervals with zero coverage in more than 3% of normalDB.
FATAL [2025-12-05 21:52:42] tumor.coverage.file and normalDB do not align.
FATAL [2025-12-05 21:52:42]
FATAL [2025-12-05 21:52:42] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:52:42] parameters (PureCN 2.17.0).
FATAL [2025-12-05 21:52:42] At least 2 normal.coverage.files required.
FATAL [2025-12-05 21:52:42]
FATAL [2025-12-05 21:52:42] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:52:42] parameters (PureCN 2.17.0).
INFO [2025-12-05 21:52:43] ------------------------------------------------------------
INFO [2025-12-05 21:52:43] PureCN 2.17.0
INFO [2025-12-05 21:52:43] ------------------------------------------------------------
INFO [2025-12-05 21:52:43] Loading coverage files...
INFO [2025-12-05 21:52:43] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-12-05 21:52:43] Allosome coverage missing, cannot determine sex.
WARN [2025-12-05 21:52:43] Allosome coverage missing, cannot determine sex.
INFO [2025-12-05 21:52:43] Removing 228 intervals with missing log.ratio.
FATAL [2025-12-05 21:52:43] normalDB incompatible with this PureCN version. Please re-run
FATAL [2025-12-05 21:52:43] NormalDB.R.
FATAL [2025-12-05 21:52:43]
FATAL [2025-12-05 21:52:43] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:52:43] parameters (PureCN 2.17.0).
FATAL [2025-12-05 21:52:43] normalDB incompatible with this PureCN version. Please re-run
FATAL [2025-12-05 21:52:43] NormalDB.R.
FATAL [2025-12-05 21:52:43]
FATAL [2025-12-05 21:52:43] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:52:43] parameters (PureCN 2.17.0).
FATAL [2025-12-05 21:52:43] normal.coverage.files with _coverage.txt and _loess.txt suffix
FATAL [2025-12-05 21:52:43] provided. Provide either only GC-normalized or raw coverage files!
FATAL [2025-12-05 21:52:43]
FATAL [2025-12-05 21:52:43] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:52:43] parameters (PureCN 2.17.0).
INFO [2025-12-05 21:52:44] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-12-05 21:52:44] Removing 19 low quality variants with non-offset BQ < 25.
INFO [2025-12-05 21:52:44] Base quality scores range from 24 to 35 (offset by 1)
INFO [2025-12-05 21:52:44] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS.
INFO [2025-12-05 21:52:44] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-12-05 21:52:44] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-12-05 21:52:44] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-12-05 21:52:44] Removing 19 low quality variants with non-offset BQ < 25.
INFO [2025-12-05 21:52:44] Base quality scores range from 24 to 35 (offset by 1)
INFO [2025-12-05 21:52:44] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS.
INFO [2025-12-05 21:52:45] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-12-05 21:52:45] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-12-05 21:52:45] Removing 6 blacklisted variants.
INFO [2025-12-05 21:52:45] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-12-05 21:52:45] Removing 19 low quality variants with non-offset BQ < 25.
INFO [2025-12-05 21:52:45] Base quality scores range from 24 to 35 (offset by 1)
INFO [2025-12-05 21:52:45] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS.
INFO [2025-12-05 21:52:45] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-12-05 21:52:45] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
WARN [2025-12-05 21:52:45] MuTect stats file lacks contig and position columns.
INFO [2025-12-05 21:52:45] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-12-05 21:52:45] Removing 19 low quality variants with non-offset BQ < 25.
INFO [2025-12-05 21:52:45] Base quality scores range from 24 to 35 (offset by 1)
INFO [2025-12-05 21:52:45] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS.
INFO [2025-12-05 21:52:45] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-12-05 21:52:45] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
WARN [2025-12-05 21:52:46] MuTect stats file and VCF file do not align perfectly. Will remove 2325 unmatched variants.
WARN [2025-12-05 21:52:46] MuTect stats file lacks failure_reasons column. Keeping all variants listed in stats file.
INFO [2025-12-05 21:52:46] Removing 0 non heterozygous (in matched normal) germline SNPs.
INFO [2025-12-05 21:52:46] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-12-05 21:52:46] Base quality scores range from 31 to 33 (offset by 1)
INFO [2025-12-05 21:52:46] Minimum number of supporting reads ranges from 3 to 4, depending on coverage and BQS.
INFO [2025-12-05 21:52:46] Removing 0 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-12-05 21:52:46] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-12-05 21:52:46] Base quality scores range from 7 to 35 (offset by 1)
INFO [2025-12-05 21:52:46] Minimum number of supporting reads ranges from 1 to 41, depending on coverage and BQS.
INFO [2025-12-05 21:52:46] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-12-05 21:52:46] Removing 49 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-12-05 21:52:46] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-12-05 21:52:46] Base quality scores range from 7 to 35 (offset by 1)
INFO [2025-12-05 21:52:46] Minimum number of supporting reads ranges from 1 to 41, depending on coverage and BQS.
INFO [2025-12-05 21:52:46] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-12-05 21:52:46] Removing 49 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-12-05 21:52:46] Removing 22 non heterozygous (in matched normal) germline SNPs.
WARN [2025-12-05 21:52:46] Many variants removed by min.base.quality (50) filter. You might want to lower the cutoff.
FATAL [2025-12-05 21:52:46] No variants passed filter BQ.
FATAL [2025-12-05 21:52:46]
FATAL [2025-12-05 21:52:46] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:52:46] parameters (PureCN 2.17.0).
INFO [2025-12-05 21:52:46] Found 11 variants in VCF file.
WARN [2025-12-05 21:52:46] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead.
INFO [2025-12-05 21:52:47] 1 (9.1%) variants annotated as likely germline (DB INFO flag).
INFO [2025-12-05 21:52:47] Found 11 variants in VCF file.
WARN [2025-12-05 21:52:47] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead.
INFO [2025-12-05 21:52:47] 1 (9.1%) variants annotated as likely germline (DB INFO flag).
INFO [2025-12-05 21:52:48] Found 11 variants in VCF file.
WARN [2025-12-05 21:52:48] vcf.file has no DB or POP_AF info field for membership in germline databases. Guessing it based on available dbSNP ID.
INFO [2025-12-05 21:52:48] 1 (9.1%) variants annotated as likely germline (DB INFO flag).
INFO [2025-12-05 21:52:48] Found 1000 variants in VCF file.
INFO [2025-12-05 21:52:48] Removing 2 triallelic sites.
WARN [2025-12-05 21:52:48] Having trouble guessing SOMATIC status...
WARN [2025-12-05 21:52:48] DP FORMAT field contains NAs. Removing 44 variants.
INFO [2025-12-05 21:52:48] 954 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-12-05 21:52:48] Found 12 variants in VCF file.
INFO [2025-12-05 21:52:48] Removing 1 triallelic sites.
WARN [2025-12-05 21:52:49] DP FORMAT field contains NAs. Removing 1 variants.
WARN [2025-12-05 21:52:49] vcf.file has no DB info field for membership in germline databases. Found and used somatic status instead.
INFO [2025-12-05 21:52:49] 8 (80.0%) variants annotated as likely germline (DB INFO flag).
WARN [2025-12-05 21:52:49] BQ FORMAT field contains NAs.
INFO [2025-12-05 21:52:49] Found 2331 variants in VCF file.
INFO [2025-12-05 21:52:49] 2282 (97.9%) variants annotated as likely germline (DB INFO flag).
INFO [2025-12-05 21:52:49] Found 2331 variants in VCF file.
INFO [2025-12-05 21:52:49] 2282 (97.9%) variants annotated as likely germline (DB INFO flag).
WARN [2025-12-05 21:52:49] Did not find base quality scores, will use global error rate of 0.0010 instead.
INFO [2025-12-05 21:52:49] Removing 21 low quality variants with non-offset BQ < 25.
INFO [2025-12-05 21:52:49] Base quality scores range from 24 to 35 (offset by 1)
INFO [2025-12-05 21:52:49] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-12-05 21:52:49] Removing 89 variants with AF < 0.030 or AF >= 0.970 or insufficient supporting reads or depth < 15.
INFO [2025-12-05 21:52:49] Found 2331 variants in VCF file.
INFO [2025-12-05 21:52:49] 2282 (97.9%) variants annotated as likely germline (DB INFO flag).
WARN [2025-12-05 21:52:49] BQ FORMAT field contains NAs.
WARN [2025-12-05 21:52:50] Allosome coverage missing, cannot determine sex.
WARN [2025-12-05 21:52:50] Allosome coverage missing, cannot determine sex.
INFO [2025-12-05 21:52:50] Mean coverages: chrX: 108.58, chrY: 108.58, chr1-22: 104.87.
INFO [2025-12-05 21:52:50] Mean coverages: chrX: 108.58, chrY: 2.17, chr1-22: 104.87.
INFO [2025-12-05 21:52:50] Mean coverages: chrX: 108.58, chrY: 5.17, chr1-22: 104.87.
INFO [2025-12-05 21:52:50] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-12-05 21:52:50] No germline variants in VCF.
FATAL [2025-12-05 21:52:50] No solution with id hello
FATAL [2025-12-05 21:52:50]
FATAL [2025-12-05 21:52:50] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:52:50] parameters (PureCN 2.17.0).
FATAL [2025-12-05 21:52:50] No solution with id 100
FATAL [2025-12-05 21:52:50]
FATAL [2025-12-05 21:52:50] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:52:50] parameters (PureCN 2.17.0).
FATAL [2025-12-05 21:52:51] all.data and w have different lengths.
FATAL [2025-12-05 21:52:51]
FATAL [2025-12-05 21:52:51] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:52:51] parameters (PureCN 2.17.0).
INFO [2025-12-05 21:52:51] Splitting 5 large targets to an average width of 400.
WARN [2025-12-05 21:52:51] No mappability scores provided.
WARN [2025-12-05 21:52:51] No reptiming scores provided.
INFO [2025-12-05 21:52:51] Calculating GC-content...
INFO [2025-12-05 21:52:51] Splitting 5 large targets to an average width of 400.
WARN [2025-12-05 21:52:51] No mappability scores provided.
WARN [2025-12-05 21:52:51] No reptiming scores provided.
INFO [2025-12-05 21:52:51] Calculating GC-content...
INFO [2025-12-05 21:52:51] Splitting 5 large targets to an average width of 400.
INFO [2025-12-05 21:52:51] Removing 1 targets overlapping with exclude.
WARN [2025-12-05 21:52:51] No mappability scores provided.
WARN [2025-12-05 21:52:51] No reptiming scores provided.
INFO [2025-12-05 21:52:51] Calculating GC-content...
WARN [2025-12-05 21:52:51] Found small target regions (< 100bp). Will resize them.
INFO [2025-12-05 21:52:51] Splitting 5 large targets to an average width of 400.
FATAL [2025-12-05 21:52:51] off.target.padding must be negative.
FATAL [2025-12-05 21:52:51]
FATAL [2025-12-05 21:52:51] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:52:51] parameters (PureCN 2.17.0).
FATAL [2025-12-05 21:52:51] Interval coordinates should start at 1, not at 0
FATAL [2025-12-05 21:52:51]
FATAL [2025-12-05 21:52:51] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:52:51] parameters (PureCN 2.17.0).
WARN [2025-12-05 21:52:51] Found small target regions (< 100bp). Will resize them.
INFO [2025-12-05 21:52:52] Splitting 5 large targets to an average width of 400.
FATAL [2025-12-05 21:52:52] No off-target regions after filtering for mappability and
FATAL [2025-12-05 21:52:52] off.target.padding
FATAL [2025-12-05 21:52:52]
FATAL [2025-12-05 21:52:52] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:52:52] parameters (PureCN 2.17.0).
WARN [2025-12-05 21:52:52] Found small target regions (< 100bp). Will resize them.
INFO [2025-12-05 21:52:52] Splitting 5 large targets to an average width of 400.
WARN [2025-12-05 21:52:52] No mappability scores provided.
INFO [2025-12-05 21:52:52] Calculating GC-content...
WARN [2025-12-05 21:52:52] Found small target regions (< 100bp). Will resize them.
INFO [2025-12-05 21:52:52] Averaging reptiming into bins of size 200...
INFO [2025-12-05 21:52:52] Splitting 5 large targets to an average width of 400.
WARN [2025-12-05 21:52:52] No mappability scores provided.
INFO [2025-12-05 21:52:52] Calculating GC-content...
WARN [2025-12-05 21:52:52] Found small target regions (< 100bp). Will resize them.
INFO [2025-12-05 21:52:52] Splitting 6 large targets to an average width of 200.
WARN [2025-12-05 21:52:52] No mappability scores provided.
WARN [2025-12-05 21:52:52] No reptiming scores provided.
INFO [2025-12-05 21:52:52] Calculating GC-content...
WARN [2025-12-05 21:52:52] Found small target regions (< 100bp). Will resize them.
INFO [2025-12-05 21:52:52] Splitting 5 large targets to an average width of 400.
WARN [2025-12-05 21:52:52] No mappability scores provided.
WARN [2025-12-05 21:52:52] No reptiming scores provided.
INFO [2025-12-05 21:52:52] Calculating GC-content...
INFO [2025-12-05 21:52:52] Splitting 5 large targets to an average width of 400.
INFO [2025-12-05 21:52:52] Tiling off-target regions to an average width of 200000.
WARN [2025-12-05 21:52:52] No mappability scores provided.
WARN [2025-12-05 21:52:52] No reptiming scores provided.
INFO [2025-12-05 21:52:52] Calculating GC-content...
WARN [2025-12-05 21:52:52] Intervals contain off-target regions. Will not change intervals.
WARN [2025-12-05 21:52:52] No mappability scores provided.
WARN [2025-12-05 21:52:52] No reptiming scores provided.
INFO [2025-12-05 21:52:52] Calculating GC-content...
INFO [2025-12-05 21:52:52] Splitting 5 large targets to an average width of 400.
WARN [2025-12-05 21:52:52] No reptiming scores provided.
INFO [2025-12-05 21:52:52] Calculating GC-content...
WARN [2025-12-05 21:52:52] Found small target regions (< 100bp). Will resize them.
INFO [2025-12-05 21:52:53] Splitting 5 large targets to an average width of 400.
WARN [2025-12-05 21:52:53] No reptiming scores provided.
INFO [2025-12-05 21:52:53] Calculating GC-content...
WARN [2025-12-05 21:52:53] Found small target regions (< 100bp). Will resize them.
INFO [2025-12-05 21:52:53] Splitting 5 large targets to an average width of 400.
WARN [2025-12-05 21:52:53] 1 intervals without mappability score (1 on-target).
INFO [2025-12-05 21:52:53] Removing 1 intervals with low mappability score (<0.60).
WARN [2025-12-05 21:52:53] No reptiming scores provided.
INFO [2025-12-05 21:52:53] Calculating GC-content...
WARN [2025-12-05 21:52:53] Found small target regions (< 100bp). Will resize them.
INFO [2025-12-05 21:52:53] Splitting 5 large targets to an average width of 400.
INFO [2025-12-05 21:52:53] Tiling off-target regions to an average width of 200000.
WARN [2025-12-05 21:52:53] No reptiming scores provided.
INFO [2025-12-05 21:52:53] Calculating GC-content...
INFO [2025-12-05 21:52:53] Splitting 5 large targets to an average width of 400.
WARN [2025-12-05 21:52:53] No mappability scores provided.
WARN [2025-12-05 21:52:53] No reptiming scores provided.
INFO [2025-12-05 21:52:53] Calculating GC-content...
WARN [2025-12-05 21:52:53] Chromosome naming style of interval file (Ensembl) was different from reference (UCSC).
INFO [2025-12-05 21:52:53] Splitting 5 large targets to an average width of 400.
WARN [2025-12-05 21:52:53] No mappability scores provided.
WARN [2025-12-05 21:52:53] No reptiming scores provided.
INFO [2025-12-05 21:52:53] Calculating GC-content...
FATAL [2025-12-05 21:52:54] Chromosome naming style of interval file unknown, should be UCSC.
FATAL [2025-12-05 21:52:54]
FATAL [2025-12-05 21:52:54] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:52:54] parameters (PureCN 2.17.0).
WARN [2025-12-05 21:52:54] Chromosome naming style of interval file (Ensembl) was different from reference (UCSC).
WARN [2025-12-05 21:52:54] Chromosome naming style of mappability file (Ensembl) was different from reference (UCSC).
INFO [2025-12-05 21:52:54] Splitting 5 large targets to an average width of 400.
WARN [2025-12-05 21:52:54] No reptiming scores provided.
INFO [2025-12-05 21:52:54] Calculating GC-content...
WARN [2025-12-05 21:52:54] Found small target regions (< 60bp). Will resize them.
INFO [2025-12-05 21:52:54] Splitting 5 large targets to an average width of 400.
WARN [2025-12-05 21:52:54] No mappability scores provided.
WARN [2025-12-05 21:52:54] No reptiming scores provided.
INFO [2025-12-05 21:52:54] Calculating GC-content...
WARN [2025-12-05 21:52:54] Found small target regions (< 60bp). Will drop them.
INFO [2025-12-05 21:52:54] Splitting 4 large targets to an average width of 400.
WARN [2025-12-05 21:52:54] No mappability scores provided.
WARN [2025-12-05 21:52:54] No reptiming scores provided.
INFO [2025-12-05 21:52:54] Calculating GC-content...
WARN [2025-12-05 21:52:54] Found small target regions (< 200bp). Will resize them.
INFO [2025-12-05 21:52:54] Splitting 5 large targets to an average width of 400.
WARN [2025-12-05 21:52:54] No mappability scores provided.
WARN [2025-12-05 21:52:54] No reptiming scores provided.
INFO [2025-12-05 21:52:54] Calculating GC-content...
INFO [2025-12-05 21:52:54] Found 20 variants in VCF file.
INFO [2025-12-05 21:52:54] 20 (100.0%) variants annotated as likely germline (DB INFO flag).
WARN [2025-12-05 21:52:54] 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 [2025-12-05 21:52:54] Error reading AllelicCountsFile
FATAL [2025-12-05 21:52:54] /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/PureCN/extdata/example_allelic_counts_empty.tsv
FATAL [2025-12-05 21:52:54]
FATAL [2025-12-05 21:52:54] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:52:54] parameters (PureCN 2.17.0).
INFO [2025-12-05 21:52:55] Found 127 variants in VCF file.
INFO [2025-12-05 21:52:55] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
WARN [2025-12-05 21:52:55] Did not find base quality scores, will use global error rate of 0.0010 instead.
INFO [2025-12-05 21:52:55] ------------------------------------------------------------
INFO [2025-12-05 21:52:55] PureCN 2.17.0
INFO [2025-12-05 21:52:55] ------------------------------------------------------------
INFO [2025-12-05 21:52:55] Loading coverage files...
INFO [2025-12-05 21:52:55] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-12-05 21:52:55] Allosome coverage missing, cannot determine sex.
WARN [2025-12-05 21:52:55] Allosome coverage missing, cannot determine sex.
INFO [2025-12-05 21:52:55] Removing 228 intervals with missing log.ratio.
INFO [2025-12-05 21:52:55] Removing 22 small (< 5bp) intervals.
INFO [2025-12-05 21:52:55] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-12-05 21:52:55] No normalDB provided. Provide one for better results.
INFO [2025-12-05 21:52:55] Removing 1724 low count (< 100 total reads) intervals.
INFO [2025-12-05 21:52:55] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-12-05 21:52:55] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-12-05 21:52:55] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-12-05 21:52:55] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-12-05 21:52:55] Loading VCF...
INFO [2025-12-05 21:52:55] Found 127 variants in VCF file.
INFO [2025-12-05 21:52:55] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-12-05 21:52:55] LIB-02240e4 is tumor in VCF file.
INFO [2025-12-05 21:52:55] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-12-05 21:52:55] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-12-05 21:52:55] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-12-05 21:52:55] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-12-05 21:52:55] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-12-05 21:52:55] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-12-05 21:52:55] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding).
INFO [2025-12-05 21:52:55] 1.2% of targets contain variants.
INFO [2025-12-05 21:52:55] Removing 4 variants outside intervals.
INFO [2025-12-05 21:52:55] Found SOMATIC annotation in VCF.
INFO [2025-12-05 21:52:55] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-12-05 21:52:55] Found SOMATIC annotation in VCF. Setting mapping bias to 0.972.
INFO [2025-12-05 21:52:55] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-12-05 21:52:56] Sample sex: ?
INFO [2025-12-05 21:52:56] Segmenting data...
INFO [2025-12-05 21:52:56] Loading pre-computed boundaries for DNAcopy...
INFO [2025-12-05 21:52:56] Setting undo.SD parameter to 1.000000.
INFO [2025-12-05 21:52:56] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-12-05 21:52:56] Found 59 segments with median size of 17.67Mb.
INFO [2025-12-05 21:52:56] Using 121 variants.
INFO [2025-12-05 21:52:56] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-12-05 21:52:56] 2D-grid search of purity and ploidy...
INFO [2025-12-05 21:52:56] Local optima: 0.65/1.8, 0.52/2
INFO [2025-12-05 21:52:56] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2025-12-05 21:52:56] Testing local optimum 2/2 at purity 0.52 and total ploidy 2.00...
INFO [2025-12-05 21:52:57] Skipping 1 solutions that converged to the same optima.
INFO [2025-12-05 21:52:57] Fitting variants with beta model for local optimum 1/2...
INFO [2025-12-05 21:52:57] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2025-12-05 21:52:58] Optimized purity: 0.65
INFO [2025-12-05 21:52:58] Done.
INFO [2025-12-05 21:52:58] ------------------------------------------------------------
FATAL [2025-12-05 21:52:58] log.ratio NULL in .writeLogRatioFileGATK4
FATAL [2025-12-05 21:52:58]
FATAL [2025-12-05 21:52:58] This runtime error might be caused by invalid input data or parameters.
FATAL [2025-12-05 21:52:58] Please report bug (PureCN 2.17.0).
INFO [2025-12-05 21:52:59] Loaded provided segmentation file example_seg.txt (format DNAcopy).
INFO [2025-12-05 21:52:59] Re-centering provided segment means (offset -0.0033).
INFO [2025-12-05 21:52:59] Loaded provided segmentation file example_gatk4_modelfinal.seg.gz (format GATK4).
WARN [2025-12-05 21:52:59] Expecting numeric chromosome names in seg.file, assuming file is properly sorted.
INFO [2025-12-05 21:52:59] Re-centering provided segment means (offset -0.0037).
INFO [2025-12-05 21:52:59] 576 on-target bins with low coverage in all samples.
WARN [2025-12-05 21:52:59] You are likely not using the correct baits file!
WARN [2025-12-05 21:52:59] Allosome coverage missing, cannot determine sex.
WARN [2025-12-05 21:52:59] Allosome coverage missing, cannot determine sex.
INFO [2025-12-05 21:52:59] Processing on-target regions...
INFO [2025-12-05 21:52:59] Removing 930 intervals with low coverage in normalDB.
INFO [2025-12-05 21:52:59] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2025-12-05 21:53:00] ------------------------------------------------------------
INFO [2025-12-05 21:53:00] PureCN 2.17.0
INFO [2025-12-05 21:53:00] ------------------------------------------------------------
INFO [2025-12-05 21:53:00] Using BiocParallel for parallel optimization.
INFO [2025-12-05 21:53:00] Loading coverage files...
INFO [2025-12-05 21:53:00] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-12-05 21:53:00] Allosome coverage missing, cannot determine sex.
WARN [2025-12-05 21:53:00] Allosome coverage missing, cannot determine sex.
INFO [2025-12-05 21:53:00] Removing 228 intervals with missing log.ratio.
INFO [2025-12-05 21:53:00] Removing 705 intervals excluded in normalDB.
INFO [2025-12-05 21:53:00] normalDB provided. Setting minimum coverage for segmentation to 0.0015X.
INFO [2025-12-05 21:53:00] Removing 1066 low count (< 100 total reads) intervals.
INFO [2025-12-05 21:53:00] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-12-05 21:53:00] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-12-05 21:53:00] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-12-05 21:53:00] Sample sex: ?
INFO [2025-12-05 21:53:00] Segmenting data...
INFO [2025-12-05 21:53:00] Interval weights found, will use weighted CBS.
INFO [2025-12-05 21:53:00] Loading pre-computed boundaries for DNAcopy...
INFO [2025-12-05 21:53:00] Setting undo.SD parameter to 1.000000.
Setting multi-figure configuration
INFO [2025-12-05 21:53:01] Found 52 segments with median size of 29.35Mb.
INFO [2025-12-05 21:53:01] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-12-05 21:53:01] 2D-grid search of purity and ploidy...
INFO [2025-12-05 21:53:01] Local optima: 0.65/1.8, 0.52/2
INFO [2025-12-05 21:53:02] Skipping 1 solutions that converged to the same optima.
INFO [2025-12-05 21:53:02] Done.
INFO [2025-12-05 21:53:02] ------------------------------------------------------------
INFO [2025-12-05 21:53:02] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpAQvgYA/file162abcda8e86.rds...
FATAL [2025-12-05 21:53:02] runAbsoluteCN was run without a VCF file.
FATAL [2025-12-05 21:53:02]
FATAL [2025-12-05 21:53:02] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:53:02] parameters (PureCN 2.17.0).
FATAL [2025-12-05 21:53:02] runAbsoluteCN was run without a VCF file.
FATAL [2025-12-05 21:53:02]
FATAL [2025-12-05 21:53:02] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:53:02] parameters (PureCN 2.17.0).
INFO [2025-12-05 21:53:02] ------------------------------------------------------------
INFO [2025-12-05 21:53:02] PureCN 2.17.0
INFO [2025-12-05 21:53:02] ------------------------------------------------------------
INFO [2025-12-05 21:53:02] Loading coverage files...
INFO [2025-12-05 21:53:02] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-12-05 21:53:02] Allosome coverage missing, cannot determine sex.
WARN [2025-12-05 21:53:02] Allosome coverage missing, cannot determine sex.
INFO [2025-12-05 21:53:02] Removing 228 intervals with missing log.ratio.
INFO [2025-12-05 21:53:02] Removing 705 intervals excluded in normalDB.
INFO [2025-12-05 21:53:02] normalDB provided. Setting minimum coverage for segmentation to 0.0015X.
INFO [2025-12-05 21:53:02] Removing 1066 low count (< 100 total reads) intervals.
INFO [2025-12-05 21:53:02] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-12-05 21:53:02] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-12-05 21:53:02] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-12-05 21:53:02] Sample sex: ?
INFO [2025-12-05 21:53:02] Segmenting data...
INFO [2025-12-05 21:53:02] Interval weights found, will use weighted PSCBS.
FATAL [2025-12-05 21:53:02] segmentationPSCBS requires VCF file.
FATAL [2025-12-05 21:53:02]
FATAL [2025-12-05 21:53:02] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:53:02] parameters (PureCN 2.17.0).
INFO [2025-12-05 21:53:05] ------------------------------------------------------------
INFO [2025-12-05 21:53:05] PureCN 2.17.0
INFO [2025-12-05 21:53:05] ------------------------------------------------------------
INFO [2025-12-05 21:53:05] Loading coverage files...
FATAL [2025-12-05 21:53:05] Need a normal coverage file if log.ratio and seg.file are not provided.
FATAL [2025-12-05 21:53:05]
FATAL [2025-12-05 21:53:05] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:53:05] parameters (PureCN 2.17.0).
INFO [2025-12-05 21:53:05] ------------------------------------------------------------
INFO [2025-12-05 21:53:05] PureCN 2.17.0
INFO [2025-12-05 21:53:05] ------------------------------------------------------------
FATAL [2025-12-05 21:53:05] min.ploidy or max.ploidy not within expected range.
FATAL [2025-12-05 21:53:05]
FATAL [2025-12-05 21:53:05] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:53:05] parameters (PureCN 2.17.0).
INFO [2025-12-05 21:53:05] ------------------------------------------------------------
INFO [2025-12-05 21:53:05] PureCN 2.17.0
INFO [2025-12-05 21:53:05] ------------------------------------------------------------
FATAL [2025-12-05 21:53:05] min.ploidy or max.ploidy not within expected range.
FATAL [2025-12-05 21:53:05]
FATAL [2025-12-05 21:53:05] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:53:05] parameters (PureCN 2.17.0).
INFO [2025-12-05 21:53:05] ------------------------------------------------------------
INFO [2025-12-05 21:53:05] PureCN 2.17.0
INFO [2025-12-05 21:53:05] ------------------------------------------------------------
INFO [2025-12-05 21:53:05] ------------------------------------------------------------
INFO [2025-12-05 21:53:05] PureCN 2.17.0
INFO [2025-12-05 21:53:05] ------------------------------------------------------------
INFO [2025-12-05 21:53:05] ------------------------------------------------------------
INFO [2025-12-05 21:53:05] PureCN 2.17.0
INFO [2025-12-05 21:53:05] ------------------------------------------------------------
FATAL [2025-12-05 21:53:05] test.num.copy not within expected range.
FATAL [2025-12-05 21:53:05]
FATAL [2025-12-05 21:53:05] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:53:05] parameters (PureCN 2.17.0).
INFO [2025-12-05 21:53:05] ------------------------------------------------------------
INFO [2025-12-05 21:53:05] PureCN 2.17.0
INFO [2025-12-05 21:53:05] ------------------------------------------------------------
WARN [2025-12-05 21:53:05] test.num.copy outside recommended range.
FATAL [2025-12-05 21:53:05] max.non.clonal not within expected range or format.
FATAL [2025-12-05 21:53:05]
FATAL [2025-12-05 21:53:05] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:53:05] parameters (PureCN 2.17.0).
INFO [2025-12-05 21:53:05] ------------------------------------------------------------
INFO [2025-12-05 21:53:05] PureCN 2.17.0
INFO [2025-12-05 21:53:05] ------------------------------------------------------------
WARN [2025-12-05 21:53:05] test.num.copy outside recommended range.
FATAL [2025-12-05 21:53:05] max.non.clonal not within expected range or format.
FATAL [2025-12-05 21:53:05]
FATAL [2025-12-05 21:53:05] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:53:05] parameters (PureCN 2.17.0).
INFO [2025-12-05 21:53:05] ------------------------------------------------------------
INFO [2025-12-05 21:53:05] PureCN 2.17.0
INFO [2025-12-05 21:53:05] ------------------------------------------------------------
FATAL [2025-12-05 21:53:05] test.purity not within expected range.
FATAL [2025-12-05 21:53:05]
FATAL [2025-12-05 21:53:05] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:53:05] parameters (PureCN 2.17.0).
INFO [2025-12-05 21:53:05] ------------------------------------------------------------
INFO [2025-12-05 21:53:05] PureCN 2.17.0
INFO [2025-12-05 21:53:05] ------------------------------------------------------------
INFO [2025-12-05 21:53:05] Loading coverage files...
FATAL [2025-12-05 21:53:05] Tumor and normal are identical. This won't give any meaningful results
FATAL [2025-12-05 21:53:05] and I'm stopping here.
FATAL [2025-12-05 21:53:05]
FATAL [2025-12-05 21:53:05] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:53:05] parameters (PureCN 2.17.0).
INFO [2025-12-05 21:53:05] ------------------------------------------------------------
INFO [2025-12-05 21:53:05] PureCN 2.17.0
INFO [2025-12-05 21:53:05] ------------------------------------------------------------
INFO [2025-12-05 21:53:05] Loading coverage files...
FATAL [2025-12-05 21:53:05] Length of log.ratio different from tumor coverage.
FATAL [2025-12-05 21:53:05]
FATAL [2025-12-05 21:53:05] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:53:05] parameters (PureCN 2.17.0).
INFO [2025-12-05 21:53:05] ------------------------------------------------------------
INFO [2025-12-05 21:53:05] PureCN 2.17.0
INFO [2025-12-05 21:53:05] ------------------------------------------------------------
FATAL [2025-12-05 21:53:05] prior.purity must have the same length as test.purity.
FATAL [2025-12-05 21:53:05]
FATAL [2025-12-05 21:53:05] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:53:05] parameters (PureCN 2.17.0).
INFO [2025-12-05 21:53:05] ------------------------------------------------------------
INFO [2025-12-05 21:53:05] PureCN 2.17.0
INFO [2025-12-05 21:53:05] ------------------------------------------------------------
FATAL [2025-12-05 21:53:05] min.gof not within expected range or format.
FATAL [2025-12-05 21:53:05]
FATAL [2025-12-05 21:53:05] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:53:05] parameters (PureCN 2.17.0).
INFO [2025-12-05 21:53:05] ------------------------------------------------------------
INFO [2025-12-05 21:53:05] PureCN 2.17.0
INFO [2025-12-05 21:53:05] ------------------------------------------------------------
FATAL [2025-12-05 21:53:05] prior.purity not within expected range or format.
FATAL [2025-12-05 21:53:05]
FATAL [2025-12-05 21:53:05] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:53:05] parameters (PureCN 2.17.0).
INFO [2025-12-05 21:53:05] ------------------------------------------------------------
INFO [2025-12-05 21:53:05] PureCN 2.17.0
INFO [2025-12-05 21:53:05] ------------------------------------------------------------
FATAL [2025-12-05 21:53:05] prior.purity must add to 1. Sum is 1.5
FATAL [2025-12-05 21:53:05]
FATAL [2025-12-05 21:53:05] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:53:05] parameters (PureCN 2.17.0).
INFO [2025-12-05 21:53:05] ------------------------------------------------------------
INFO [2025-12-05 21:53:05] PureCN 2.17.0
INFO [2025-12-05 21:53:05] ------------------------------------------------------------
FATAL [2025-12-05 21:53:05] max.homozygous.loss not within expected range or format.
FATAL [2025-12-05 21:53:05]
FATAL [2025-12-05 21:53:05] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:53:05] parameters (PureCN 2.17.0).
INFO [2025-12-05 21:53:05] ------------------------------------------------------------
INFO [2025-12-05 21:53:05] PureCN 2.17.0
INFO [2025-12-05 21:53:05] ------------------------------------------------------------
FATAL [2025-12-05 21:53:05] prior.K not within expected range or format.
FATAL [2025-12-05 21:53:05]
FATAL [2025-12-05 21:53:05] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:53:05] parameters (PureCN 2.17.0).
INFO [2025-12-05 21:53:05] ------------------------------------------------------------
INFO [2025-12-05 21:53:05] PureCN 2.17.0
INFO [2025-12-05 21:53:05] ------------------------------------------------------------
FATAL [2025-12-05 21:53:05] prior.contamination not within expected range or format.
FATAL [2025-12-05 21:53:05]
FATAL [2025-12-05 21:53:05] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:53:05] parameters (PureCN 2.17.0).
INFO [2025-12-05 21:53:05] ------------------------------------------------------------
INFO [2025-12-05 21:53:05] PureCN 2.17.0
INFO [2025-12-05 21:53:05] ------------------------------------------------------------
FATAL [2025-12-05 21:53:05] Iterations not in the expected range from 10 to 250.
FATAL [2025-12-05 21:53:05]
FATAL [2025-12-05 21:53:05] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:53:05] parameters (PureCN 2.17.0).
INFO [2025-12-05 21:53:05] ------------------------------------------------------------
INFO [2025-12-05 21:53:05] PureCN 2.17.0
INFO [2025-12-05 21:53:05] ------------------------------------------------------------
FATAL [2025-12-05 21:53:05] Iterations not in the expected range from 10 to 250.
FATAL [2025-12-05 21:53:05]
FATAL [2025-12-05 21:53:05] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:53:05] parameters (PureCN 2.17.0).
INFO [2025-12-05 21:53:05] ------------------------------------------------------------
INFO [2025-12-05 21:53:05] PureCN 2.17.0
INFO [2025-12-05 21:53:05] ------------------------------------------------------------
INFO [2025-12-05 21:53:05] Loading coverage files...
FATAL [2025-12-05 21:53:05] Missing tumor.coverage.file requires seg.file or log.ratio and
FATAL [2025-12-05 21:53:05] interval.file.
FATAL [2025-12-05 21:53:05]
FATAL [2025-12-05 21:53:05] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:53:05] parameters (PureCN 2.17.0).
INFO [2025-12-05 21:53:05] ------------------------------------------------------------
INFO [2025-12-05 21:53:05] PureCN 2.17.0
INFO [2025-12-05 21:53:05] ------------------------------------------------------------
INFO [2025-12-05 21:53:05] ------------------------------------------------------------
INFO [2025-12-05 21:53:05] PureCN 2.17.0
INFO [2025-12-05 21:53:05] ------------------------------------------------------------
INFO [2025-12-05 21:53:05] Loading coverage files...
FATAL [2025-12-05 21:53:06] Interval files in normal and tumor different.
FATAL [2025-12-05 21:53:06]
FATAL [2025-12-05 21:53:06] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:53:06] parameters (PureCN 2.17.0).
INFO [2025-12-05 21:53:06] ------------------------------------------------------------
INFO [2025-12-05 21:53:06] PureCN 2.17.0
INFO [2025-12-05 21:53:06] ------------------------------------------------------------
INFO [2025-12-05 21:53:06] Loading coverage files...
INFO [2025-12-05 21:53:06] Mean target coverages: 0X (tumor) 99X (normal).
WARN [2025-12-05 21:53:06] Large difference in coverage of tumor and normal.
FATAL [2025-12-05 21:53:06] No finite intervals.
FATAL [2025-12-05 21:53:06]
FATAL [2025-12-05 21:53:06] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:53:06] parameters (PureCN 2.17.0).
INFO [2025-12-05 21:53:06] ------------------------------------------------------------
INFO [2025-12-05 21:53:06] PureCN 2.17.0
INFO [2025-12-05 21:53:06] ------------------------------------------------------------
INFO [2025-12-05 21:53:06] Loading coverage files...
INFO [2025-12-05 21:53:06] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-12-05 21:53:06] Allosome coverage missing, cannot determine sex.
WARN [2025-12-05 21:53:06] Allosome coverage missing, cannot determine sex.
INFO [2025-12-05 21:53:06] Removing 228 intervals with missing log.ratio.
INFO [2025-12-05 21:53:06] Removing 22 small (< 5bp) intervals.
INFO [2025-12-05 21:53:06] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-12-05 21:53:06] No normalDB provided. Provide one for better results.
INFO [2025-12-05 21:53:06] Removing 1724 low count (< 100 total reads) intervals.
INFO [2025-12-05 21:53:06] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-12-05 21:53:06] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-12-05 21:53:06] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-12-05 21:53:06] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-12-05 21:53:06] Loading VCF...
INFO [2025-12-05 21:53:06] Found 127 variants in VCF file.
INFO [2025-12-05 21:53:06] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-12-05 21:53:06] LIB-02240e4 is tumor in VCF file.
INFO [2025-12-05 21:53:07] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-12-05 21:53:07] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-12-05 21:53:07] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-12-05 21:53:07] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-12-05 21:53:07] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-12-05 21:53:07] 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: closing unused connection 5 (/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpAQvgYA/file162ab27e2eee6.tsv)
3: closing unused connection 4 (/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/PureCN/extdata/example_gatk4_denoised_cr.tsv.gz)
FATAL [2025-12-05 21:53:07] Could not import snp.blacklist
FATAL [2025-12-05 21:53:07] /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/PureCN/extdata/example_normal.txt.gz:Error
FATAL [2025-12-05 21:53:07] in FileForFormat(resource(con), fileFormat(con)) : Format 'txt'
FATAL [2025-12-05 21:53:07] unsupported
FATAL [2025-12-05 21:53:07]
FATAL [2025-12-05 21:53:07] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:53:07] parameters (PureCN 2.17.0).
INFO [2025-12-05 21:53:07] ------------------------------------------------------------
INFO [2025-12-05 21:53:07] PureCN 2.17.0
INFO [2025-12-05 21:53:07] ------------------------------------------------------------
INFO [2025-12-05 21:53:07] Loading coverage files...
INFO [2025-12-05 21:53:07] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-12-05 21:53:07] Allosome coverage missing, cannot determine sex.
WARN [2025-12-05 21:53:07] Allosome coverage missing, cannot determine sex.
INFO [2025-12-05 21:53:07] Removing 228 intervals with missing log.ratio.
INFO [2025-12-05 21:53:07] Removing 22 small (< 5bp) intervals.
INFO [2025-12-05 21:53:07] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-12-05 21:53:07] No normalDB provided. Provide one for better results.
INFO [2025-12-05 21:53:07] Removing 233 low coverage (< 15.0000X) intervals.
INFO [2025-12-05 21:53:07] Using 9547 intervals (9547 on-target, 0 off-target).
INFO [2025-12-05 21:53:07] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-12-05 21:53:07] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-12-05 21:53:07] Loading VCF...
INFO [2025-12-05 21:53:07] Found 127 variants in VCF file.
INFO [2025-12-05 21:53:07] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-12-05 21:53:07] LIB-02240e4 is tumor in VCF file.
INFO [2025-12-05 21:53:07] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-12-05 21:53:07] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-12-05 21:53:07] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-12-05 21:53:07] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-12-05 21:53:07] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-12-05 21:53:07] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-12-05 21:53:07] Total size of targeted genomic region: 1.63Mb (2.58Mb with 50bp padding).
INFO [2025-12-05 21:53:08] 1.0% of targets contain variants.
INFO [2025-12-05 21:53:08] Removing 2 variants outside intervals.
INFO [2025-12-05 21:53:08] Found SOMATIC annotation in VCF.
INFO [2025-12-05 21:53:08] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-12-05 21:53:08] Found SOMATIC annotation in VCF. Setting mapping bias to 0.973.
INFO [2025-12-05 21:53:08] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-12-05 21:53:08] Sample sex: ?
INFO [2025-12-05 21:53:08] Segmenting data...
INFO [2025-12-05 21:53:08] Loading pre-computed boundaries for DNAcopy...
INFO [2025-12-05 21:53:08] Setting undo.SD parameter to 1.000000.
INFO [2025-12-05 21:53:08] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-12-05 21:53:08] Found 54 segments with median size of 24.88Mb.
INFO [2025-12-05 21:53:08] Using 123 variants.
INFO [2025-12-05 21:53:08] Mean standard deviation of log-ratios: 0.37 (MAPD: 0.32)
INFO [2025-12-05 21:53:08] 2D-grid search of purity and ploidy...
INFO [2025-12-05 21:53:09] Local optima: 0.62/1.9, 0.3/1.9, 0.32/2
INFO [2025-12-05 21:53:09] Testing local optimum 1/3 at purity 0.62 and total ploidy 1.90...
INFO [2025-12-05 21:53:09] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-12-05 21:53:09] Recalibrating log-ratios...
INFO [2025-12-05 21:53:09] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-12-05 21:53:09] Recalibrating log-ratios...
INFO [2025-12-05 21:53:09] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-12-05 21:53:09] Recalibrating log-ratios...
INFO [2025-12-05 21:53:09] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-12-05 21:53:10] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-12-05 21:53:10] Recalibrating log-ratios...
INFO [2025-12-05 21:53:10] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-12-05 21:53:10] Recalibrating log-ratios...
INFO [2025-12-05 21:53:10] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-12-05 21:53:10] Recalibrating log-ratios...
INFO [2025-12-05 21:53:10] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-12-05 21:53:10] Skipping 1 solutions that converged to the same optima.
INFO [2025-12-05 21:53:10] Skipping 1 solutions exceeding max.non.clonal (0.20): 0.3/1.9 (purity/tumor ploidy)
INFO [2025-12-05 21:53:10] Fitting variants with beta model for local optimum 1/3...
INFO [2025-12-05 21:53:10] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01.
INFO [2025-12-05 21:53:11] Optimized purity: 0.65
INFO [2025-12-05 21:53:11] Done.
INFO [2025-12-05 21:53:11] ------------------------------------------------------------
INFO [2025-12-05 21:53:11] ------------------------------------------------------------
INFO [2025-12-05 21:53:11] PureCN 2.17.0
INFO [2025-12-05 21:53:11] ------------------------------------------------------------
INFO [2025-12-05 21:53:11] Loading coverage files...
INFO [2025-12-05 21:53:11] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-12-05 21:53:11] Allosome coverage missing, cannot determine sex.
WARN [2025-12-05 21:53:11] Allosome coverage missing, cannot determine sex.
INFO [2025-12-05 21:53:11] Removing 228 intervals with missing log.ratio.
INFO [2025-12-05 21:53:11] Removing 22 small (< 5bp) intervals.
INFO [2025-12-05 21:53:11] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-12-05 21:53:11] No normalDB provided. Provide one for better results.
INFO [2025-12-05 21:53:11] Removing 1724 low count (< 100 total reads) intervals.
INFO [2025-12-05 21:53:11] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-12-05 21:53:11] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-12-05 21:53:11] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-12-05 21:53:12] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-12-05 21:53:12] Loading VCF...
INFO [2025-12-05 21:53:12] Found 127 variants in VCF file.
WARN [2025-12-05 21:53:12] DP FORMAT field contains NAs. Removing 3 variants.
WARN [2025-12-05 21:53:12] DB INFO flag contains NAs
INFO [2025-12-05 21:53:12] 119 (96.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-12-05 21:53:12] LIB-02240e4 is tumor in VCF file.
INFO [2025-12-05 21:53:12] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-12-05 21:53:12] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-12-05 21:53:12] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-12-05 21:53:12] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-12-05 21:53:12] Removing 1 variants with AF < 0.030 or AF >= 0.970 or insufficient supporting reads or depth < 15.
INFO [2025-12-05 21:53:12] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding).
INFO [2025-12-05 21:53:12] 1.2% of targets contain variants.
INFO [2025-12-05 21:53:12] Setting somatic prior probabilities for likely germline hits to 0.000500 or to 0.500000 otherwise.
INFO [2025-12-05 21:53:12] Excluding 5 novel or poor quality variants from segmentation.
INFO [2025-12-05 21:53:12] Sample sex: ?
INFO [2025-12-05 21:53:12] Segmenting data...
INFO [2025-12-05 21:53:12] Loading pre-computed boundaries for DNAcopy...
INFO [2025-12-05 21:53:12] Setting undo.SD parameter to 1.000000.
Setting multi-figure configuration
INFO [2025-12-05 21:53:12] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-12-05 21:53:13] Found 59 segments with median size of 17.67Mb.
INFO [2025-12-05 21:53:13] Using 123 variants.
INFO [2025-12-05 21:53:13] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-12-05 21:53:13] 2D-grid search of purity and ploidy...
INFO [2025-12-05 21:53:13] Local optima: 0.62/1.9, 0.3/1.9, 0.32/2
INFO [2025-12-05 21:53:13] Testing local optimum 1/3 at purity 0.62 and total ploidy 1.90...
INFO [2025-12-05 21:53:13] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-12-05 21:53:13] Recalibrating log-ratios...
INFO [2025-12-05 21:53:13] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-12-05 21:53:14] Recalibrating log-ratios...
INFO [2025-12-05 21:53:14] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-12-05 21:53:14] Recalibrating log-ratios...
INFO [2025-12-05 21:53:14] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-12-05 21:53:14] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-12-05 21:53:14] Recalibrating log-ratios...
INFO [2025-12-05 21:53:14] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-12-05 21:53:14] Recalibrating log-ratios...
INFO [2025-12-05 21:53:14] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-12-05 21:53:14] Recalibrating log-ratios...
INFO [2025-12-05 21:53:14] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-12-05 21:53:14] Skipping 2 solutions exceeding max.non.clonal (0.20): 0.3/1.9, 0.35/1.61 (purity/tumor ploidy)
INFO [2025-12-05 21:53:14] Fitting variants with beta model for local optimum 1/3...
INFO [2025-12-05 21:53:14] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2025-12-05 21:53:15] Optimized purity: 0.65
INFO [2025-12-05 21:53:15] Done.
INFO [2025-12-05 21:53:15] ------------------------------------------------------------
INFO [2025-12-05 21:53:15] ------------------------------------------------------------
INFO [2025-12-05 21:53:15] PureCN 2.17.0
INFO [2025-12-05 21:53:15] ------------------------------------------------------------
INFO [2025-12-05 21:53:15] Loading coverage files...
INFO [2025-12-05 21:53:16] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-12-05 21:53:16] Allosome coverage missing, cannot determine sex.
WARN [2025-12-05 21:53:16] Allosome coverage missing, cannot determine sex.
INFO [2025-12-05 21:53:16] No Gene column in interval.file. You won't get gene-level calls.
INFO [2025-12-05 21:53:16] Removing 228 intervals with missing log.ratio.
INFO [2025-12-05 21:53:16] Removing 15 low/high GC targets.
INFO [2025-12-05 21:53:16] Removing 21 small (< 5bp) intervals.
INFO [2025-12-05 21:53:16] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-12-05 21:53:16] No normalDB provided. Provide one for better results.
INFO [2025-12-05 21:53:16] Removing 1718 low count (< 100 total reads) intervals.
INFO [2025-12-05 21:53:16] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-12-05 21:53:16] Removing 36 low mappability intervals.
INFO [2025-12-05 21:53:16] Using 8006 intervals (8006 on-target, 0 off-target).
INFO [2025-12-05 21:53:16] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-12-05 21:53:16] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio).
INFO [2025-12-05 21:53:16] Loading VCF...
INFO [2025-12-05 21:53:16] Found 127 variants in VCF file.
INFO [2025-12-05 21:53:16] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-12-05 21:53:16] LIB-02240e4 is tumor in VCF file.
INFO [2025-12-05 21:53:16] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-12-05 21:53:16] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-12-05 21:53:16] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-12-05 21:53:16] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-12-05 21:53:16] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-12-05 21:53:16] Removing 1 variants with AF < 0.030 or AF >= Inf or insufficient supporting reads or depth < 15.
INFO [2025-12-05 21:53:16] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding).
INFO [2025-12-05 21:53:16] 1.2% of targets contain variants.
INFO [2025-12-05 21:53:16] Removing 11 variants outside intervals.
INFO [2025-12-05 21:53:16] Found SOMATIC annotation in VCF.
INFO [2025-12-05 21:53:16] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-12-05 21:53:16] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970.
INFO [2025-12-05 21:53:17] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-12-05 21:53:17] Sample sex: ?
INFO [2025-12-05 21:53:17] Segmenting data...
INFO [2025-12-05 21:53:17] MAPD of 114 allelic fractions: 0.14 (0.15 adjusted).
INFO [2025-12-05 21:53:17] Using unweighted PSCBS.
INFO [2025-12-05 21:53:17] Setting undo.SD parameter to 1.000000.
INFO [2025-12-05 21:53:28] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-12-05 21:53:28] Found 72 segments with median size of 27.25Mb.
INFO [2025-12-05 21:53:28] Using 114 variants.
INFO [2025-12-05 21:53:28] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-12-05 21:53:28] 2D-grid search of purity and ploidy...
INFO [2025-12-05 21:53:28] Local optima: 0.65/1.8, 0.38/2.2
INFO [2025-12-05 21:53:28] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2025-12-05 21:53:28] Recalibrating log-ratios...
INFO [2025-12-05 21:53:28] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2025-12-05 21:53:28] Recalibrating log-ratios...
INFO [2025-12-05 21:53:28] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2025-12-05 21:53:28] Recalibrating log-ratios...
INFO [2025-12-05 21:53:28] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2025-12-05 21:53:29] Testing local optimum 2/2 at purity 0.38 and total ploidy 2.20...
INFO [2025-12-05 21:53:29] Skipping 1 solutions exceeding max.non.clonal (0.20): 0.65/2.05 (purity/tumor ploidy)
INFO [2025-12-05 21:53:29] Fitting variants with beta model for local optimum 2/2...
INFO [2025-12-05 21:53:29] Fitting variants for purity 0.40, tumor ploidy 2.55 and contamination 0.01.
INFO [2025-12-05 21:53:30] Optimized purity: 0.40
INFO [2025-12-05 21:53:30] Done.
INFO [2025-12-05 21:53:30] ------------------------------------------------------------
FATAL [2025-12-05 21:53:30] This function requires gene-level calls. Please add a column 'Gene'
FATAL [2025-12-05 21:53:30] containing gene symbols to the interval.file.
FATAL [2025-12-05 21:53:30]
FATAL [2025-12-05 21:53:30] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:53:30] parameters (PureCN 2.17.0).
INFO [2025-12-05 21:53:31] ------------------------------------------------------------
INFO [2025-12-05 21:53:31] PureCN 2.17.0
INFO [2025-12-05 21:53:31] ------------------------------------------------------------
INFO [2025-12-05 21:53:31] Loading coverage files...
INFO [2025-12-05 21:53:31] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-12-05 21:53:31] Allosome coverage missing, cannot determine sex.
WARN [2025-12-05 21:53:31] Allosome coverage missing, cannot determine sex.
INFO [2025-12-05 21:53:31] Removing 228 intervals with missing log.ratio.
INFO [2025-12-05 21:53:31] Removing 22 small (< 5bp) intervals.
INFO [2025-12-05 21:53:31] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-12-05 21:53:31] No normalDB provided. Provide one for better results.
INFO [2025-12-05 21:53:31] Removing 1724 low count (< 100 total reads) intervals.
INFO [2025-12-05 21:53:31] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-12-05 21:53:31] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-12-05 21:53:31] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-12-05 21:53:31] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-12-05 21:53:31] Loading VCF...
INFO [2025-12-05 21:53:31] Found 127 variants in VCF file.
INFO [2025-12-05 21:53:31] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
FATAL [2025-12-05 21:53:31] Different chromosome names in coverage and VCF.
FATAL [2025-12-05 21:53:31]
FATAL [2025-12-05 21:53:31] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:53:31] parameters (PureCN 2.17.0).
INFO [2025-12-05 21:53:31] ------------------------------------------------------------
INFO [2025-12-05 21:53:31] PureCN 2.17.0
INFO [2025-12-05 21:53:31] ------------------------------------------------------------
INFO [2025-12-05 21:53:31] Loading coverage files...
INFO [2025-12-05 21:53:31] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-12-05 21:53:31] Allosome coverage missing, cannot determine sex.
WARN [2025-12-05 21:53:31] Allosome coverage missing, cannot determine sex.
FATAL [2025-12-05 21:53:32] tumor.coverage.file and interval.file do not align.
FATAL [2025-12-05 21:53:32]
FATAL [2025-12-05 21:53:32] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:53:32] parameters (PureCN 2.17.0).
INFO [2025-12-05 21:53:32] ------------------------------------------------------------
INFO [2025-12-05 21:53:32] PureCN 2.17.0
INFO [2025-12-05 21:53:32] ------------------------------------------------------------
INFO [2025-12-05 21:53:32] Loading coverage files...
INFO [2025-12-05 21:53:32] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-12-05 21:53:32] Allosome coverage missing, cannot determine sex.
WARN [2025-12-05 21:53:32] Allosome coverage missing, cannot determine sex.
INFO [2025-12-05 21:53:32] Removing 228 intervals with missing log.ratio.
INFO [2025-12-05 21:53:32] Removing 15 low/high GC targets.
INFO [2025-12-05 21:53:32] Removing 21 small (< 5bp) intervals.
INFO [2025-12-05 21:53:32] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-12-05 21:53:32] No normalDB provided. Provide one for better results.
INFO [2025-12-05 21:53:32] Removing 1718 low count (< 100 total reads) intervals.
INFO [2025-12-05 21:53:32] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-12-05 21:53:32] Removing 36 low mappability intervals.
INFO [2025-12-05 21:53:32] Using 8006 intervals (8006 on-target, 0 off-target).
INFO [2025-12-05 21:53:32] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-12-05 21:53:32] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio).
INFO [2025-12-05 21:53:32] Loading VCF...
INFO [2025-12-05 21:53:32] Found 127 variants in VCF file.
INFO [2025-12-05 21:53:32] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-12-05 21:53:32] LIB-02240e4 is tumor in VCF file.
INFO [2025-12-05 21:53:32] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-12-05 21:53:32] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-12-05 21:53:32] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-12-05 21:53:32] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-12-05 21:53:32] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-12-05 21:53:32] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-12-05 21:53:32] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding).
INFO [2025-12-05 21:53:32] 1.2% of targets contain variants.
INFO [2025-12-05 21:53:33] Removing 11 variants outside intervals.
INFO [2025-12-05 21:53:33] Found SOMATIC annotation in VCF.
INFO [2025-12-05 21:53:33] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-12-05 21:53:33] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970.
INFO [2025-12-05 21:53:33] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-12-05 21:53:33] Sample sex: ?
INFO [2025-12-05 21:53:33] Segmenting data...
INFO [2025-12-05 21:53:33] Loading pre-computed boundaries for DNAcopy...
INFO [2025-12-05 21:53:33] Setting undo.SD parameter to 1.000000.
INFO [2025-12-05 21:53:33] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-12-05 21:53:33] Found 59 segments with median size of 17.67Mb.
INFO [2025-12-05 21:53:33] Using 114 variants.
INFO [2025-12-05 21:53:33] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-12-05 21:53:33] 2D-grid search of purity and ploidy...
INFO [2025-12-05 21:53:33] Local optima: 0.63/1.9
INFO [2025-12-05 21:53:33] Testing local optimum 1/1 at purity 0.63 and total ploidy 1.90...
INFO [2025-12-05 21:53:34] Fitting variants with beta model for local optimum 1/1...
INFO [2025-12-05 21:53:34] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2025-12-05 21:53:35] Optimized purity: 0.65
INFO [2025-12-05 21:53:35] Done.
INFO [2025-12-05 21:53:35] ------------------------------------------------------------
INFO [2025-12-05 21:53:35] ------------------------------------------------------------
INFO [2025-12-05 21:53:35] PureCN 2.17.0
INFO [2025-12-05 21:53:35] ------------------------------------------------------------
INFO [2025-12-05 21:53:35] Loading coverage files...
INFO [2025-12-05 21:53:35] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-12-05 21:53:35] Allosome coverage missing, cannot determine sex.
WARN [2025-12-05 21:53:35] Allosome coverage missing, cannot determine sex.
INFO [2025-12-05 21:53:35] Removing 228 intervals with missing log.ratio.
INFO [2025-12-05 21:53:35] Removing 15 low/high GC targets.
INFO [2025-12-05 21:53:35] Removing 21 small (< 5bp) intervals.
INFO [2025-12-05 21:53:35] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-12-05 21:53:35] No normalDB provided. Provide one for better results.
INFO [2025-12-05 21:53:35] Removing 1718 low count (< 100 total reads) intervals.
INFO [2025-12-05 21:53:35] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-12-05 21:53:35] Removing 36 low mappability intervals.
INFO [2025-12-05 21:53:35] Using 8006 intervals (8006 on-target, 0 off-target).
INFO [2025-12-05 21:53:35] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-12-05 21:53:35] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio).
INFO [2025-12-05 21:53:35] Loading VCF...
INFO [2025-12-05 21:53:35] Found 127 variants in VCF file.
INFO [2025-12-05 21:53:35] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-12-05 21:53:35] LIB-02240e4 is tumor in VCF file.
INFO [2025-12-05 21:53:35] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-12-05 21:53:35] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-12-05 21:53:35] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-12-05 21:53:35] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-12-05 21:53:35] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-12-05 21:53:36] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-12-05 21:53:36] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding).
INFO [2025-12-05 21:53:36] 1.2% of targets contain variants.
INFO [2025-12-05 21:53:36] Removing 11 variants outside intervals.
INFO [2025-12-05 21:53:36] Found SOMATIC annotation in VCF.
INFO [2025-12-05 21:53:36] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-12-05 21:53:36] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970.
INFO [2025-12-05 21:53:36] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-12-05 21:53:36] Sample sex: ?
INFO [2025-12-05 21:53:36] Segmenting data...
INFO [2025-12-05 21:53:36] Loading pre-computed boundaries for DNAcopy...
INFO [2025-12-05 21:53:36] Setting undo.SD parameter to 1.000000.
INFO [2025-12-05 21:53:36] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-12-05 21:53:36] Found 59 segments with median size of 17.67Mb.
INFO [2025-12-05 21:53:36] Using 114 variants.
INFO [2025-12-05 21:53:36] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-12-05 21:53:36] 2D-grid search of purity and ploidy...
INFO [2025-12-05 21:53:37] Local optima: 0.63/1.9
INFO [2025-12-05 21:53:37] Testing local optimum 1/1 at purity 0.63 and total ploidy 1.90...
INFO [2025-12-05 21:53:37] Fitting variants with beta model for local optimum 1/1...
WARN [2025-12-05 21:53:37] Some gene symbols found on multiple chromosomes. Use of approved symbols suggested.
INFO [2025-12-05 21:53:37] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2025-12-05 21:53:38] Optimized purity: 0.65
INFO [2025-12-05 21:53:38] Done.
INFO [2025-12-05 21:53:38] ------------------------------------------------------------
FATAL [2025-12-05 21:53:38] chr1 not valid chromosome name(s). Valid names are:
FATAL [2025-12-05 21:53:38] 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22
FATAL [2025-12-05 21:53:38]
FATAL [2025-12-05 21:53:38] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:53:38] parameters (PureCN 2.17.0).
INFO [2025-12-05 21:53:38] ------------------------------------------------------------
INFO [2025-12-05 21:53:38] PureCN 2.17.0
INFO [2025-12-05 21:53:38] ------------------------------------------------------------
INFO [2025-12-05 21:53:38] Loading coverage files...
WARN [2025-12-05 21:53:38] Provided sampleid (Sample2) does not match Sample1 found in segmentation.
WARN [2025-12-05 21:53:38] Allosome coverage missing, cannot determine sex.
WARN [2025-12-05 21:53:38] Allosome coverage missing, cannot determine sex.
INFO [2025-12-05 21:53:38] Removing 10 intervals with missing log.ratio.
INFO [2025-12-05 21:53:38] Using 10039 intervals (10039 on-target, 0 off-target).
INFO [2025-12-05 21:53:38] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-12-05 21:53:38] Loading VCF...
INFO [2025-12-05 21:53:38] Found 127 variants in VCF file.
INFO [2025-12-05 21:53:38] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-12-05 21:53:38] LIB-02240e4 is tumor in VCF file.
INFO [2025-12-05 21:53:38] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-12-05 21:53:38] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-12-05 21:53:38] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-12-05 21:53:38] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-12-05 21:53:38] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-12-05 21:53:39] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-12-05 21:53:39] Total size of targeted genomic region: 1.71Mb (2.70Mb with 50bp padding).
INFO [2025-12-05 21:53:39] 1.0% of targets contain variants.
INFO [2025-12-05 21:53:39] Removing 0 variants outside intervals.
INFO [2025-12-05 21:53:39] Found SOMATIC annotation in VCF.
INFO [2025-12-05 21:53:39] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-12-05 21:53:39] Found SOMATIC annotation in VCF. Setting mapping bias to 0.976.
INFO [2025-12-05 21:53:39] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-12-05 21:53:39] Sample sex: ?
INFO [2025-12-05 21:53:39] Segmenting data...
INFO [2025-12-05 21:53:39] Loaded provided segmentation file example_seg.txt (format DNAcopy).
WARN [2025-12-05 21:53:39] Provided sampleid (Sample2) does not match Sample1 found in segmentation.
INFO [2025-12-05 21:53:39] Re-centering provided segment means (offset -0.0033).
INFO [2025-12-05 21:53:39] Loading pre-computed boundaries for DNAcopy...
INFO [2025-12-05 21:53:39] Setting undo.SD parameter to 0.000000.
Setting multi-figure configuration
INFO [2025-12-05 21:53:39] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-12-05 21:53:39] Found 54 segments with median size of 24.88Mb.
INFO [2025-12-05 21:53:39] Using 125 variants.
INFO [2025-12-05 21:53:39] Mean standard deviation of log-ratios: 0.40 (MAPD: 0.00)
INFO [2025-12-05 21:53:39] 2D-grid search of purity and ploidy...
INFO [2025-12-05 21:53:39] Local optima: 0.6/1.9
INFO [2025-12-05 21:53:39] Testing local optimum 1/1 at purity 0.60 and total ploidy 1.90...
INFO [2025-12-05 21:53:40] Fitting variants with beta model for local optimum 1/1...
INFO [2025-12-05 21:53:40] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01.
INFO [2025-12-05 21:53:41] Optimized purity: 0.65
INFO [2025-12-05 21:53:41] Done.
INFO [2025-12-05 21:53:41] ------------------------------------------------------------
WARN [2025-12-05 21:53:41] Allosome coverage missing, cannot determine sex.
WARN [2025-12-05 21:53:41] Allosome coverage missing, cannot determine sex.
Setting multi-figure configuration
FATAL [2025-12-05 21:53:44] Segmentation file expected with colnames ID, chrom, loc.start, loc.end,
FATAL [2025-12-05 21:53:44] num.mark, seg.mean
FATAL [2025-12-05 21:53:44]
FATAL [2025-12-05 21:53:44] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:53:44] parameters (PureCN 2.17.0).
FATAL [2025-12-05 21:53:44] seg.file contains multiple samples and sampleid missing.
FATAL [2025-12-05 21:53:44]
FATAL [2025-12-05 21:53:44] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:53:44] parameters (PureCN 2.17.0).
FATAL [2025-12-05 21:53:44] seg.file contains multiple samples and sampleid does not match any.
FATAL [2025-12-05 21:53:44]
FATAL [2025-12-05 21:53:44] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:53:44] parameters (PureCN 2.17.0).
WARN [2025-12-05 21:53:44] Allosome coverage missing, cannot determine sex.
WARN [2025-12-05 21:53:44] Allosome coverage missing, cannot determine sex.
WARN [2025-12-05 21:53:48] Allosome coverage missing, cannot determine sex.
WARN [2025-12-05 21:53:48] Allosome coverage missing, cannot determine sex.
WARN [2025-12-05 21:53:48] Provided sampleid (example_tumor.txt.gz) does not match Sample1 found in segmentation.
WARN [2025-12-05 21:53:49] Allosome coverage missing, cannot determine sex.
WARN [2025-12-05 21:53:49] Allosome coverage missing, cannot determine sex.
WARN [2025-12-05 21:53:49] No normalDB provided. Provide one for better results.
WARN [2025-12-05 21:53:52] Allosome coverage missing, cannot determine sex.
WARN [2025-12-05 21:53:52] Allosome coverage missing, cannot determine sex.
WARN [2025-12-05 21:53:53] Provided sampleid (Sample.1) does not match Sample1 found in segmentation.
Setting multi-figure configuration
WARN [2025-12-05 21:53:55] Allosome coverage missing, cannot determine sex.
WARN [2025-12-05 21:53:55] Allosome coverage missing, cannot determine sex.
WARN [2025-12-05 21:53:55] No normalDB provided. Provide one for better results.
WARN [2025-12-05 21:53:56] Sampleid looks like a normal in VCF, not like a tumor.
WARN [2025-12-05 21:53:58] Allosome coverage missing, cannot determine sex.
WARN [2025-12-05 21:53:58] Allosome coverage missing, cannot determine sex.
FATAL [2025-12-05 21:53:58] normalDB not a valid normalDB object. Use createNormalDatabase to
FATAL [2025-12-05 21:53:58] create one.
FATAL [2025-12-05 21:53:58]
FATAL [2025-12-05 21:53:58] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:53:58] parameters (PureCN 2.17.0).
WARN [2025-12-05 21:53:58] You are likely not using the correct baits file!
WARN [2025-12-05 21:53:58] Allosome coverage missing, cannot determine sex.
WARN [2025-12-05 21:53:58] Allosome coverage missing, cannot determine sex.
WARN [2025-12-05 21:53:59] Allosome coverage missing, cannot determine sex.
WARN [2025-12-05 21:53:59] Allosome coverage missing, cannot determine sex.
FATAL [2025-12-05 21:53:59] normalDB appears to be empty.
FATAL [2025-12-05 21:53:59]
FATAL [2025-12-05 21:53:59] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:53:59] parameters (PureCN 2.17.0).
WARN [2025-12-05 21:54:00] Allosome coverage missing, cannot determine sex.
WARN [2025-12-05 21:54:00] Allosome coverage missing, cannot determine sex.
WARN [2025-12-05 21:54:00] Intervals in coverage and interval.file have conflicting on/off-target annotation.
WARN [2025-12-05 21:54:04] Allosome coverage missing, cannot determine sex.
WARN [2025-12-05 21:54:04] Allosome coverage missing, cannot determine sex.
FATAL [2025-12-05 21:54:04] Seqlevels missing in provided segmentation: 6
FATAL [2025-12-05 21:54:04]
FATAL [2025-12-05 21:54:04] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:54:04] parameters (PureCN 2.17.0).
sh: gatk: command not found
WARN [2025-12-05 21:54:05] Cannot find gatk binary in path.
WARN [2025-12-05 21:54:05] Allosome coverage missing, cannot determine sex.
WARN [2025-12-05 21:54:05] Allosome coverage missing, cannot determine sex.
WARN [2025-12-05 21:54:05] No normalDB provided. Provide one for better results.
FATAL [2025-12-05 21:54:05] segmentationHclust requires an input segmentation.
FATAL [2025-12-05 21:54:05]
FATAL [2025-12-05 21:54:05] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:54:05] parameters (PureCN 2.17.0).
WARN [2025-12-05 21:54:05] Allosome coverage missing, cannot determine sex.
WARN [2025-12-05 21:54:05] Allosome coverage missing, cannot determine sex.
WARN [2025-12-05 21:54:05] No normalDB provided. Provide one for better results.
FATAL [2025-12-05 21:54:15] The normal.panel.vcf.file contains only a single sample.
FATAL [2025-12-05 21:54:15]
FATAL [2025-12-05 21:54:15] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:54:15] parameters (PureCN 2.17.0).
FATAL [2025-12-05 21:54:15] mapping.bias.file must be a file with *.rds suffix.
FATAL [2025-12-05 21:54:15]
FATAL [2025-12-05 21:54:15] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:54:15] parameters (PureCN 2.17.0).
Failed with error: 'there is no package called 'genomicsdb''
FATAL [2025-12-05 21:54:16] min.normals (0) must be >= 1.
FATAL [2025-12-05 21:54:16]
FATAL [2025-12-05 21:54:16] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:54:16] parameters (PureCN 2.17.0).
FATAL [2025-12-05 21:54:16] min.normals (10) cannot be larger than min.normals.assign.betafit (3).
FATAL [2025-12-05 21:54:16]
FATAL [2025-12-05 21:54:16] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:54:16] parameters (PureCN 2.17.0).
FATAL [2025-12-05 21:54:16] min.normals.assign.betafit (10) cannot be larger than
FATAL [2025-12-05 21:54:16] min.normals.betafit (7).
FATAL [2025-12-05 21:54:16]
FATAL [2025-12-05 21:54:16] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:54:16] parameters (PureCN 2.17.0).
FATAL [2025-12-05 21:54:16] min.normals.betafit (20) cannot be larger than
FATAL [2025-12-05 21:54:16] min.normals.position.specific.fit (10).
FATAL [2025-12-05 21:54:16]
FATAL [2025-12-05 21:54:16] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:54:16] parameters (PureCN 2.17.0).
FATAL [2025-12-05 21:54:16] min.betafit.rho not within expected range or format.
FATAL [2025-12-05 21:54:16]
FATAL [2025-12-05 21:54:16] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:54:16] parameters (PureCN 2.17.0).
FATAL [2025-12-05 21:54:16] max.betafit.rho not within expected range or format.
FATAL [2025-12-05 21:54:16]
FATAL [2025-12-05 21:54:16] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:54:16] parameters (PureCN 2.17.0).
FATAL [2025-12-05 21:54:16] min.betafit.rho (0.9) cannot be larger than max.betafit.rho (0.2).
FATAL [2025-12-05 21:54:16]
FATAL [2025-12-05 21:54:16] This is most likely a user error due to invalid input data or
FATAL [2025-12-05 21:54:16] 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
160.202 5.666 159.407
PureCN.Rcheck/PureCN-Ex.timings
| name | user | system | elapsed | |
| adjustLogRatio | 0.946 | 0.015 | 1.104 | |
| annotateTargets | 6.156 | 0.268 | 6.739 | |
| bootstrapResults | 0.206 | 0.015 | 0.239 | |
| calculateBamCoverageByInterval | 0.080 | 0.003 | 0.097 | |
| calculateLogRatio | 0.333 | 0.014 | 0.387 | |
| calculateMappingBiasGatk4 | 0 | 0 | 0 | |
| calculateMappingBiasVcf | 0.707 | 0.026 | 0.809 | |
| calculatePowerDetectSomatic | 0.592 | 0.004 | 0.605 | |
| calculateTangentNormal | 1.273 | 0.020 | 1.342 | |
| callAlterations | 0.080 | 0.005 | 0.090 | |
| callAlterationsFromSegmentation | 0.615 | 0.013 | 0.675 | |
| callAmplificationsInLowPurity | 15.294 | 0.156 | 16.750 | |
| callCIN | 0.089 | 0.002 | 0.096 | |
| callLOH | 0.084 | 0.002 | 0.091 | |
| callMutationBurden | 0.646 | 0.016 | 0.679 | |
| centromeres | 0.001 | 0.002 | 0.002 | |
| correctCoverageBias | 0.697 | 0.014 | 0.754 | |
| createCurationFile | 0.159 | 0.004 | 0.168 | |
| createNormalDatabase | 1.047 | 0.013 | 1.133 | |
| filterIntervals | 8.552 | 0.125 | 9.100 | |
| filterVcfBasic | 0.262 | 0.003 | 0.264 | |
| filterVcfMuTect | 0.236 | 0.005 | 0.246 | |
| filterVcfMuTect2 | 0.282 | 0.002 | 0.296 | |
| findFocal | 4.461 | 0.054 | 4.833 | |
| findHighQualitySNPs | 0.564 | 0.007 | 0.600 | |
| getSexFromCoverage | 0.099 | 0.006 | 0.113 | |
| getSexFromVcf | 0.117 | 0.004 | 0.131 | |
| plotAbs | 0.096 | 0.004 | 0.101 | |
| poolCoverage | 0.227 | 0.008 | 0.261 | |
| predictSomatic | 0.197 | 0.005 | 0.214 | |
| preprocessIntervals | 0.244 | 0.004 | 0.269 | |
| processMultipleSamples | 0.920 | 0.020 | 0.991 | |
| readAllelicCountsFile | 0.209 | 0.000 | 0.222 | |
| readCoverageFile | 0.093 | 0.004 | 0.101 | |
| readCurationFile | 0.093 | 0.004 | 0.098 | |
| readIntervalFile | 0.061 | 0.002 | 0.074 | |
| readLogRatioFile | 0.010 | 0.001 | 0.010 | |
| readSegmentationFile | 0.003 | 0.000 | 0.004 | |
| runAbsoluteCN | 6.293 | 0.116 | 6.738 | |
| segmentationCBS | 3.133 | 0.038 | 3.297 | |
| segmentationGATK4 | 0.001 | 0.001 | 0.002 | |
| segmentationHclust | 5.692 | 0.105 | 6.167 | |
| segmentationPSCBS | 14.371 | 0.168 | 15.035 | |
| setMappingBiasVcf | 0.132 | 0.004 | 0.140 | |
| setPriorVcf | 0.106 | 0.004 | 0.117 | |