Markus Riester
| Snapshot Date: 2025-10-31 13:45 -0400 (Fri, 31 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/PureCN |
| git_branch: RELEASE_3_22 |
| git_last_commit: c7ace8b |
| git_last_commit_date: 2025-10-29 10:31:57 -0400 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-01 12:05 -0400 (Sat, 01 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4901 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4691 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 |
| 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 1666/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| PureCN 2.16.0 (landing page) Markus Riester
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | 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: 2.16.0 |
| 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_2.16.0.tar.gz |
| StartedAt: 2025-10-31 21:32:23 -0400 (Fri, 31 Oct 2025) |
| EndedAt: 2025-10-31 21:38:05 -0400 (Fri, 31 Oct 2025) |
| EllapsedTime: 342.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: PureCN.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PureCN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PureCN_2.16.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/PureCN.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PureCN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PureCN’ version ‘2.16.0’
* 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 14.099 0.181 14.700
segmentationPSCBS 13.253 0.150 13.405
filterIntervals 7.870 0.181 8.077
runAbsoluteCN 5.846 0.107 5.971
segmentationHclust 5.320 0.100 5.434
annotateTargets 4.869 0.192 5.090
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
PureCN.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PureCN ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘PureCN’ ... ** this is package ‘PureCN’ version ‘2.16.0’ ** 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 version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(PureCN)
Loading required package: DNAcopy
Loading required package: VariantAnnotation
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: Seqinfo
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Attaching package: 'VariantAnnotation'
The following object is masked from 'package:base':
tabulate
>
> test_check("PureCN")
WARN [2025-10-31 21:35:49] Attempted adding gene symbols to intervals. Heuristics have been used to pick symbols for overlapping genes.
WARN [2025-10-31 21:35:49] Chromosome naming style of txdb file (UCSC) was different from interval file (Ensembl).
WARN [2025-10-31 21:35:53] Attempted adding gene symbols to intervals. Heuristics have been used to pick symbols for overlapping genes.
FATAL [2025-10-31 21:35:54] tumor.coverage.file and interval.file do not align.
FATAL [2025-10-31 21:35:54]
FATAL [2025-10-31 21:35:54] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:35:54] parameters (PureCN 2.16.0).
WARN [2025-10-31 21:35:54] Cannot find all contig lengths while exporting interval file.
INFO [2025-10-31 21:35:54] Processing seq1:1-21 (1/3)...
INFO [2025-10-31 21:35:54] Processing seq1:1227-1247 (2/3)...
INFO [2025-10-31 21:35:54] Processing seq2:594-614 (3/3)...
WARN [2025-10-31 21:35:55] Large potential mis-calibration of on- and off-target log2 ratios: 0.26
FATAL [2025-10-31 21:35:55] Need either f or purity and ploidy.
FATAL [2025-10-31 21:35:55]
FATAL [2025-10-31 21:35:55] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:35:55] parameters (PureCN 2.16.0).
FATAL [2025-10-31 21:35:55] f not in expected range.
FATAL [2025-10-31 21:35:55]
FATAL [2025-10-31 21:35:55] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:35:55] parameters (PureCN 2.16.0).
FATAL [2025-10-31 21:35:55] coverage not in expected range (>=2)
FATAL [2025-10-31 21:35:55]
FATAL [2025-10-31 21:35:55] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:35:55] parameters (PureCN 2.16.0).
FATAL [2025-10-31 21:35:55] purity not in expected range.
FATAL [2025-10-31 21:35:55]
FATAL [2025-10-31 21:35:55] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:35:55] parameters (PureCN 2.16.0).
FATAL [2025-10-31 21:35:55] ploidy not in expected range.
FATAL [2025-10-31 21:35:55]
FATAL [2025-10-31 21:35:55] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:35:55] parameters (PureCN 2.16.0).
FATAL [2025-10-31 21:35:55] cell.fraction not in expected range.
FATAL [2025-10-31 21:35:55]
FATAL [2025-10-31 21:35:55] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:35:55] parameters (PureCN 2.16.0).
INFO [2025-10-31 21:35:56] 576 on-target bins with low coverage in all samples.
WARN [2025-10-31 21:35:56] You are likely not using the correct baits file!
WARN [2025-10-31 21:35:56] Allosome coverage missing, cannot determine sex.
WARN [2025-10-31 21:35:56] Allosome coverage missing, cannot determine sex.
INFO [2025-10-31 21:35:56] Processing on-target regions...
INFO [2025-10-31 21:35:56] Removing 930 intervals with low coverage in normalDB.
INFO [2025-10-31 21:35:56] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2025-10-31 21:35:57] Tumor/normal noise ratio: 19.041
WARN [2025-10-31 21:35:57] Extensive noise in tumor compared to normals.
INFO [2025-10-31 21:36:11] Tumor/normal noise ratio: 19.041
WARN [2025-10-31 21:36:11] Extensive noise in tumor compared to normals.
INFO [2025-10-31 21:36:13] Using BiocParallel for parallel optimization.
FATAL [2025-10-31 21:36:18] pvalue.cutoff not within expected range or format.
FATAL [2025-10-31 21:36:18]
FATAL [2025-10-31 21:36:18] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:18] parameters (PureCN 2.16.0).
FATAL [2025-10-31 21:36:18] pvalue.cutoff not within expected range or format.
FATAL [2025-10-31 21:36:18]
FATAL [2025-10-31 21:36:18] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:18] parameters (PureCN 2.16.0).
FATAL [2025-10-31 21:36:18] percentile.cutoff not in expected range (0 to 100).
FATAL [2025-10-31 21:36:18]
FATAL [2025-10-31 21:36:18] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:18] parameters (PureCN 2.16.0).
FATAL [2025-10-31 21:36:18] percentile.cutoff not in expected range (0 to 100).
FATAL [2025-10-31 21:36:18]
FATAL [2025-10-31 21:36:18] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:18] parameters (PureCN 2.16.0).
FATAL [2025-10-31 21:36:18] purity not within expected range or format.
FATAL [2025-10-31 21:36:18]
FATAL [2025-10-31 21:36:18] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:18] parameters (PureCN 2.16.0).
FATAL [2025-10-31 21:36:18] purity not within expected range or format.
FATAL [2025-10-31 21:36:18]
FATAL [2025-10-31 21:36:18] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:18] parameters (PureCN 2.16.0).
INFO [2025-10-31 21:36:19] ------------------------------------------------------------
INFO [2025-10-31 21:36:19] PureCN 2.16.0
INFO [2025-10-31 21:36:19] ------------------------------------------------------------
INFO [2025-10-31 21:36:19] Loading coverage files...
INFO [2025-10-31 21:36:19] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-10-31 21:36:19] Allosome coverage missing, cannot determine sex.
WARN [2025-10-31 21:36:19] Allosome coverage missing, cannot determine sex.
INFO [2025-10-31 21:36:19] Removing 228 intervals with missing log.ratio.
INFO [2025-10-31 21:36:19] Removing 22 small (< 5bp) intervals.
INFO [2025-10-31 21:36:19] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-10-31 21:36:19] No normalDB provided. Provide one for better results.
INFO [2025-10-31 21:36:19] Removing 1724 low count (< 100 total reads) intervals.
INFO [2025-10-31 21:36:19] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-10-31 21:36:19] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-10-31 21:36:19] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-10-31 21:36:19] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-10-31 21:36:19] Loading VCF...
INFO [2025-10-31 21:36:19] Found 127 variants in VCF file.
INFO [2025-10-31 21:36:19] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-10-31 21:36:19] LIB-02240e4 is tumor in VCF file.
INFO [2025-10-31 21:36:19] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-10-31 21:36:19] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-10-31 21:36:19] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-10-31 21:36:19] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-10-31 21:36:19] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-10-31 21:36:19] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-10-31 21:36:19] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding).
INFO [2025-10-31 21:36:19] 1.2% of targets contain variants.
INFO [2025-10-31 21:36:19] Removing 4 variants outside intervals.
INFO [2025-10-31 21:36:19] Found SOMATIC annotation in VCF.
INFO [2025-10-31 21:36:19] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-10-31 21:36:19] Found SOMATIC annotation in VCF. Setting mapping bias to 0.972.
INFO [2025-10-31 21:36:19] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-10-31 21:36:19] Sample sex: ?
INFO [2025-10-31 21:36:19] Segmenting data...
INFO [2025-10-31 21:36:19] Loading pre-computed boundaries for DNAcopy...
INFO [2025-10-31 21:36:19] Setting undo.SD parameter to 1.000000.
INFO [2025-10-31 21:36:20] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-10-31 21:36:20] Found 59 segments with median size of 17.67Mb.
INFO [2025-10-31 21:36:20] Using 121 variants.
INFO [2025-10-31 21:36:20] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-10-31 21:36:20] 2D-grid search of purity and ploidy...
INFO [2025-10-31 21:36:20] Local optima: 0.63/1.9, 0.5/2
INFO [2025-10-31 21:36:20] Testing local optimum 1/2 at purity 0.63 and total ploidy 1.90...
INFO [2025-10-31 21:36:21] Testing local optimum 2/2 at purity 0.50 and total ploidy 2.00...
INFO [2025-10-31 21:36:21] Skipping 1 solutions that converged to the same optima.
INFO [2025-10-31 21:36:21] Fitting variants with beta model for local optimum 1/2...
INFO [2025-10-31 21:36:21] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2025-10-31 21:36:22] Optimized purity: 0.65
INFO [2025-10-31 21:36:22] Done.
INFO [2025-10-31 21:36:22] ------------------------------------------------------------
INFO [2025-10-31 21:36:22] Estimating callable regions.
FATAL [2025-10-31 21:36:23] exclude not a GRanges object.
FATAL [2025-10-31 21:36:23]
FATAL [2025-10-31 21:36:23] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:23] parameters (PureCN 2.16.0).
FATAL [2025-10-31 21:36:23] callable not a GRanges object.
FATAL [2025-10-31 21:36:23]
FATAL [2025-10-31 21:36:23] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:23] parameters (PureCN 2.16.0).
WARN [2025-10-31 21:36:25] tumor.coverage.file and interval.file do not align.
INFO [2025-10-31 21:36:26] No Gene column in interval.file. You won't get gene-level calls.
FATAL [2025-10-31 21:36:26] No gc_bias column in interval.file.
FATAL [2025-10-31 21:36:26]
FATAL [2025-10-31 21:36:26] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:26] parameters (PureCN 2.16.0).
FATAL [2025-10-31 21:36:26] Provided coverage is zero, most likely due to a corrupt BAM file.
FATAL [2025-10-31 21:36:26]
FATAL [2025-10-31 21:36:26] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:26] parameters (PureCN 2.16.0).
INFO [2025-10-31 21:36:27] No reptiming column in interval.file.
INFO [2025-10-31 21:36:28] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpt131GW/filef72512b910fa.rds...
INFO [2025-10-31 21:36:29] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpt131GW/filef72512b910fa.rds...
INFO [2025-10-31 21:36:29] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpt131GW/filef72512b910fa.rds...
INFO [2025-10-31 21:36:29] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpt131GW/filef72512b910fa.rds...
INFO [2025-10-31 21:36:29] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpt131GW/filef72512b910fa.rds...
INFO [2025-10-31 21:36:29] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpt131GW/filef72512b910fa.rds...
FATAL [2025-10-31 21:36:29] Purity or Ploidy not numeric or in expected range.
FATAL [2025-10-31 21:36:29]
FATAL [2025-10-31 21:36:29] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:29] parameters (PureCN 2.16.0).
INFO [2025-10-31 21:36:29] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpt131GW/filef72512b910fa.rds...
INFO [2025-10-31 21:36:29] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpt131GW/filef72512b910fa.rds...
FATAL [2025-10-31 21:36:29] 'Failed' column in
FATAL [2025-10-31 21:36:29] /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpt131GW/filef72512b910fa.csv
FATAL [2025-10-31 21:36:29] not logical(1).
FATAL [2025-10-31 21:36:29]
FATAL [2025-10-31 21:36:29] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:29] parameters (PureCN 2.16.0).
INFO [2025-10-31 21:36:29] 576 on-target bins with low coverage in all samples.
WARN [2025-10-31 21:36:29] You are likely not using the correct baits file!
WARN [2025-10-31 21:36:29] Allosome coverage missing, cannot determine sex.
WARN [2025-10-31 21:36:29] Allosome coverage missing, cannot determine sex.
INFO [2025-10-31 21:36:29] Processing on-target regions...
INFO [2025-10-31 21:36:29] Removing 930 intervals with low coverage in normalDB.
INFO [2025-10-31 21:36:29] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2025-10-31 21:36:30] 576 on-target bins with low coverage in all samples.
WARN [2025-10-31 21:36:30] You are likely not using the correct baits file!
WARN [2025-10-31 21:36:30] Allosome coverage missing, cannot determine sex.
WARN [2025-10-31 21:36:30] Allosome coverage missing, cannot determine sex.
INFO [2025-10-31 21:36:31] Processing on-target regions...
INFO [2025-10-31 21:36:31] Removing 930 intervals with low coverage in normalDB.
INFO [2025-10-31 21:36:31] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2025-10-31 21:36:31] 576 on-target bins with low coverage in all samples.
WARN [2025-10-31 21:36:31] You are likely not using the correct baits file!
WARN [2025-10-31 21:36:31] Allosome coverage missing, cannot determine sex.
WARN [2025-10-31 21:36:31] Allosome coverage missing, cannot determine sex.
INFO [2025-10-31 21:36:31] Processing on-target regions...
INFO [2025-10-31 21:36:32] Removing 930 intervals with low coverage in normalDB.
INFO [2025-10-31 21:36:32] Removing 1 intervals with zero coverage in more than 3% of normalDB.
WARN [2025-10-31 21:36:32] Allosome coverage missing, cannot determine sex.
INFO [2025-10-31 21:36:32] Sample sex: NA
WARN [2025-10-31 21:36:32] Allosome coverage missing, cannot determine sex.
INFO [2025-10-31 21:36:32] Sample sex: NA
INFO [2025-10-31 21:36:32] 576 on-target bins with low coverage in all samples.
WARN [2025-10-31 21:36:32] You are likely not using the correct baits file!
WARN [2025-10-31 21:36:32] Allosome coverage missing, cannot determine sex.
WARN [2025-10-31 21:36:32] Allosome coverage missing, cannot determine sex.
FATAL [2025-10-31 21:36:32] Length of normal.coverage.files and sex different
FATAL [2025-10-31 21:36:32]
FATAL [2025-10-31 21:36:32] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:32] parameters (PureCN 2.16.0).
WARN [2025-10-31 21:36:34] Target intervals were not sorted.
INFO [2025-10-31 21:36:34] 560 on-target bins with low coverage in all samples.
WARN [2025-10-31 21:36:34] You are likely not using the correct baits file!
WARN [2025-10-31 21:36:34] Allosome coverage missing, cannot determine sex.
WARN [2025-10-31 21:36:34] Allosome coverage missing, cannot determine sex.
WARN [2025-10-31 21:36:34] Allosome coverage missing, cannot determine sex.
INFO [2025-10-31 21:36:34] Processing on-target regions...
INFO [2025-10-31 21:36:34] Removing 978 intervals with low coverage in normalDB.
INFO [2025-10-31 21:36:34] Removing 11 intervals with zero coverage in more than 3% of normalDB.
FATAL [2025-10-31 21:36:35] tumor.coverage.file and normalDB do not align.
FATAL [2025-10-31 21:36:35]
FATAL [2025-10-31 21:36:35] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:35] parameters (PureCN 2.16.0).
FATAL [2025-10-31 21:36:35] At least 2 normal.coverage.files required.
FATAL [2025-10-31 21:36:35]
FATAL [2025-10-31 21:36:35] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:35] parameters (PureCN 2.16.0).
INFO [2025-10-31 21:36:36] ------------------------------------------------------------
INFO [2025-10-31 21:36:36] PureCN 2.16.0
INFO [2025-10-31 21:36:36] ------------------------------------------------------------
INFO [2025-10-31 21:36:36] Loading coverage files...
INFO [2025-10-31 21:36:36] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-10-31 21:36:36] Allosome coverage missing, cannot determine sex.
WARN [2025-10-31 21:36:36] Allosome coverage missing, cannot determine sex.
INFO [2025-10-31 21:36:36] Removing 228 intervals with missing log.ratio.
FATAL [2025-10-31 21:36:36] normalDB incompatible with this PureCN version. Please re-run
FATAL [2025-10-31 21:36:36] NormalDB.R.
FATAL [2025-10-31 21:36:36]
FATAL [2025-10-31 21:36:36] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:36] parameters (PureCN 2.16.0).
FATAL [2025-10-31 21:36:36] normalDB incompatible with this PureCN version. Please re-run
FATAL [2025-10-31 21:36:36] NormalDB.R.
FATAL [2025-10-31 21:36:36]
FATAL [2025-10-31 21:36:36] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:36] parameters (PureCN 2.16.0).
FATAL [2025-10-31 21:36:36] normal.coverage.files with _coverage.txt and _loess.txt suffix
FATAL [2025-10-31 21:36:36] provided. Provide either only GC-normalized or raw coverage files!
FATAL [2025-10-31 21:36:36]
FATAL [2025-10-31 21:36:36] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:36] parameters (PureCN 2.16.0).
INFO [2025-10-31 21:36:36] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-10-31 21:36:36] Removing 19 low quality variants with non-offset BQ < 25.
INFO [2025-10-31 21:36:36] Base quality scores range from 24 to 35 (offset by 1)
INFO [2025-10-31 21:36:36] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS.
INFO [2025-10-31 21:36:36] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-10-31 21:36:37] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-10-31 21:36:37] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-10-31 21:36:37] Removing 19 low quality variants with non-offset BQ < 25.
INFO [2025-10-31 21:36:37] Base quality scores range from 24 to 35 (offset by 1)
INFO [2025-10-31 21:36:37] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS.
INFO [2025-10-31 21:36:37] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-10-31 21:36:37] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-10-31 21:36:37] Removing 6 blacklisted variants.
INFO [2025-10-31 21:36:37] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-10-31 21:36:37] Removing 19 low quality variants with non-offset BQ < 25.
INFO [2025-10-31 21:36:37] Base quality scores range from 24 to 35 (offset by 1)
INFO [2025-10-31 21:36:37] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS.
INFO [2025-10-31 21:36:37] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-10-31 21:36:37] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
WARN [2025-10-31 21:36:37] MuTect stats file lacks contig and position columns.
INFO [2025-10-31 21:36:37] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-10-31 21:36:37] Removing 19 low quality variants with non-offset BQ < 25.
INFO [2025-10-31 21:36:37] Base quality scores range from 24 to 35 (offset by 1)
INFO [2025-10-31 21:36:37] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS.
INFO [2025-10-31 21:36:37] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-10-31 21:36:37] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
WARN [2025-10-31 21:36:37] MuTect stats file and VCF file do not align perfectly. Will remove 2325 unmatched variants.
WARN [2025-10-31 21:36:37] MuTect stats file lacks failure_reasons column. Keeping all variants listed in stats file.
INFO [2025-10-31 21:36:37] Removing 0 non heterozygous (in matched normal) germline SNPs.
INFO [2025-10-31 21:36:37] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-10-31 21:36:37] Base quality scores range from 31 to 33 (offset by 1)
INFO [2025-10-31 21:36:37] Minimum number of supporting reads ranges from 3 to 4, depending on coverage and BQS.
INFO [2025-10-31 21:36:38] Removing 0 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-10-31 21:36:38] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-10-31 21:36:38] Base quality scores range from 7 to 35 (offset by 1)
INFO [2025-10-31 21:36:38] Minimum number of supporting reads ranges from 1 to 41, depending on coverage and BQS.
INFO [2025-10-31 21:36:38] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-10-31 21:36:38] Removing 49 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-10-31 21:36:38] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-10-31 21:36:38] Base quality scores range from 7 to 35 (offset by 1)
INFO [2025-10-31 21:36:38] Minimum number of supporting reads ranges from 1 to 41, depending on coverage and BQS.
INFO [2025-10-31 21:36:38] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-10-31 21:36:38] Removing 49 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-10-31 21:36:38] Removing 22 non heterozygous (in matched normal) germline SNPs.
WARN [2025-10-31 21:36:38] Many variants removed by min.base.quality (50) filter. You might want to lower the cutoff.
FATAL [2025-10-31 21:36:38] No variants passed filter BQ.
FATAL [2025-10-31 21:36:38]
FATAL [2025-10-31 21:36:38] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:38] parameters (PureCN 2.16.0).
INFO [2025-10-31 21:36:38] Found 11 variants in VCF file.
WARN [2025-10-31 21:36:38] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead.
INFO [2025-10-31 21:36:38] 1 (9.1%) variants annotated as likely germline (DB INFO flag).
INFO [2025-10-31 21:36:39] Found 11 variants in VCF file.
WARN [2025-10-31 21:36:39] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead.
INFO [2025-10-31 21:36:39] 1 (9.1%) variants annotated as likely germline (DB INFO flag).
INFO [2025-10-31 21:36:39] Found 11 variants in VCF file.
WARN [2025-10-31 21:36:39] vcf.file has no DB or POP_AF info field for membership in germline databases. Guessing it based on available dbSNP ID.
INFO [2025-10-31 21:36:39] 1 (9.1%) variants annotated as likely germline (DB INFO flag).
INFO [2025-10-31 21:36:39] Found 1000 variants in VCF file.
INFO [2025-10-31 21:36:39] Removing 2 triallelic sites.
WARN [2025-10-31 21:36:39] Having trouble guessing SOMATIC status...
WARN [2025-10-31 21:36:39] DP FORMAT field contains NAs. Removing 44 variants.
INFO [2025-10-31 21:36:39] 954 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-10-31 21:36:40] Found 12 variants in VCF file.
INFO [2025-10-31 21:36:40] Removing 1 triallelic sites.
WARN [2025-10-31 21:36:40] DP FORMAT field contains NAs. Removing 1 variants.
WARN [2025-10-31 21:36:40] vcf.file has no DB info field for membership in germline databases. Found and used somatic status instead.
INFO [2025-10-31 21:36:40] 8 (80.0%) variants annotated as likely germline (DB INFO flag).
WARN [2025-10-31 21:36:40] BQ FORMAT field contains NAs.
INFO [2025-10-31 21:36:40] Found 2331 variants in VCF file.
INFO [2025-10-31 21:36:40] 2282 (97.9%) variants annotated as likely germline (DB INFO flag).
INFO [2025-10-31 21:36:41] Found 2331 variants in VCF file.
INFO [2025-10-31 21:36:41] 2282 (97.9%) variants annotated as likely germline (DB INFO flag).
WARN [2025-10-31 21:36:41] Did not find base quality scores, will use global error rate of 0.0010 instead.
INFO [2025-10-31 21:36:41] Removing 21 low quality variants with non-offset BQ < 25.
INFO [2025-10-31 21:36:41] Base quality scores range from 24 to 35 (offset by 1)
INFO [2025-10-31 21:36:41] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-10-31 21:36:41] Removing 89 variants with AF < 0.030 or AF >= 0.970 or insufficient supporting reads or depth < 15.
INFO [2025-10-31 21:36:41] Found 2331 variants in VCF file.
INFO [2025-10-31 21:36:41] 2282 (97.9%) variants annotated as likely germline (DB INFO flag).
WARN [2025-10-31 21:36:41] BQ FORMAT field contains NAs.
WARN [2025-10-31 21:36:41] Allosome coverage missing, cannot determine sex.
WARN [2025-10-31 21:36:41] Allosome coverage missing, cannot determine sex.
INFO [2025-10-31 21:36:41] Mean coverages: chrX: 108.58, chrY: 108.58, chr1-22: 104.87.
INFO [2025-10-31 21:36:41] Mean coverages: chrX: 108.58, chrY: 2.17, chr1-22: 104.87.
INFO [2025-10-31 21:36:41] Mean coverages: chrX: 108.58, chrY: 5.17, chr1-22: 104.87.
INFO [2025-10-31 21:36:42] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-10-31 21:36:42] No germline variants in VCF.
FATAL [2025-10-31 21:36:42] No solution with id hello
FATAL [2025-10-31 21:36:42]
FATAL [2025-10-31 21:36:42] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:42] parameters (PureCN 2.16.0).
FATAL [2025-10-31 21:36:42] No solution with id 100
FATAL [2025-10-31 21:36:42]
FATAL [2025-10-31 21:36:42] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:42] parameters (PureCN 2.16.0).
FATAL [2025-10-31 21:36:42] all.data and w have different lengths.
FATAL [2025-10-31 21:36:42]
FATAL [2025-10-31 21:36:42] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:42] parameters (PureCN 2.16.0).
INFO [2025-10-31 21:36:42] Splitting 5 large targets to an average width of 400.
WARN [2025-10-31 21:36:42] No mappability scores provided.
WARN [2025-10-31 21:36:42] No reptiming scores provided.
INFO [2025-10-31 21:36:42] Calculating GC-content...
INFO [2025-10-31 21:36:42] Splitting 5 large targets to an average width of 400.
WARN [2025-10-31 21:36:42] No mappability scores provided.
WARN [2025-10-31 21:36:42] No reptiming scores provided.
INFO [2025-10-31 21:36:42] Calculating GC-content...
INFO [2025-10-31 21:36:43] Splitting 5 large targets to an average width of 400.
INFO [2025-10-31 21:36:43] Removing 1 targets overlapping with exclude.
WARN [2025-10-31 21:36:43] No mappability scores provided.
WARN [2025-10-31 21:36:43] No reptiming scores provided.
INFO [2025-10-31 21:36:43] Calculating GC-content...
WARN [2025-10-31 21:36:43] Found small target regions (< 100bp). Will resize them.
INFO [2025-10-31 21:36:43] Splitting 5 large targets to an average width of 400.
FATAL [2025-10-31 21:36:43] off.target.padding must be negative.
FATAL [2025-10-31 21:36:43]
FATAL [2025-10-31 21:36:43] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:43] parameters (PureCN 2.16.0).
FATAL [2025-10-31 21:36:43] Interval coordinates should start at 1, not at 0
FATAL [2025-10-31 21:36:43]
FATAL [2025-10-31 21:36:43] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:43] parameters (PureCN 2.16.0).
WARN [2025-10-31 21:36:43] Found small target regions (< 100bp). Will resize them.
INFO [2025-10-31 21:36:43] Splitting 5 large targets to an average width of 400.
FATAL [2025-10-31 21:36:43] No off-target regions after filtering for mappability and
FATAL [2025-10-31 21:36:43] off.target.padding
FATAL [2025-10-31 21:36:43]
FATAL [2025-10-31 21:36:43] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:43] parameters (PureCN 2.16.0).
WARN [2025-10-31 21:36:43] Found small target regions (< 100bp). Will resize them.
INFO [2025-10-31 21:36:43] Splitting 5 large targets to an average width of 400.
WARN [2025-10-31 21:36:43] No mappability scores provided.
INFO [2025-10-31 21:36:43] Calculating GC-content...
WARN [2025-10-31 21:36:43] Found small target regions (< 100bp). Will resize them.
INFO [2025-10-31 21:36:43] Averaging reptiming into bins of size 200...
INFO [2025-10-31 21:36:43] Splitting 5 large targets to an average width of 400.
WARN [2025-10-31 21:36:43] No mappability scores provided.
INFO [2025-10-31 21:36:43] Calculating GC-content...
WARN [2025-10-31 21:36:43] Found small target regions (< 100bp). Will resize them.
INFO [2025-10-31 21:36:43] Splitting 6 large targets to an average width of 200.
WARN [2025-10-31 21:36:43] No mappability scores provided.
WARN [2025-10-31 21:36:43] No reptiming scores provided.
INFO [2025-10-31 21:36:43] Calculating GC-content...
WARN [2025-10-31 21:36:43] Found small target regions (< 100bp). Will resize them.
INFO [2025-10-31 21:36:43] Splitting 5 large targets to an average width of 400.
WARN [2025-10-31 21:36:43] No mappability scores provided.
WARN [2025-10-31 21:36:43] No reptiming scores provided.
INFO [2025-10-31 21:36:43] Calculating GC-content...
INFO [2025-10-31 21:36:43] Splitting 5 large targets to an average width of 400.
INFO [2025-10-31 21:36:44] Tiling off-target regions to an average width of 200000.
WARN [2025-10-31 21:36:44] No mappability scores provided.
WARN [2025-10-31 21:36:44] No reptiming scores provided.
INFO [2025-10-31 21:36:44] Calculating GC-content...
WARN [2025-10-31 21:36:44] Intervals contain off-target regions. Will not change intervals.
WARN [2025-10-31 21:36:44] No mappability scores provided.
WARN [2025-10-31 21:36:44] No reptiming scores provided.
INFO [2025-10-31 21:36:44] Calculating GC-content...
INFO [2025-10-31 21:36:44] Splitting 5 large targets to an average width of 400.
WARN [2025-10-31 21:36:44] No reptiming scores provided.
INFO [2025-10-31 21:36:44] Calculating GC-content...
WARN [2025-10-31 21:36:44] Found small target regions (< 100bp). Will resize them.
INFO [2025-10-31 21:36:44] Splitting 5 large targets to an average width of 400.
WARN [2025-10-31 21:36:44] No reptiming scores provided.
INFO [2025-10-31 21:36:44] Calculating GC-content...
WARN [2025-10-31 21:36:44] Found small target regions (< 100bp). Will resize them.
INFO [2025-10-31 21:36:44] Splitting 5 large targets to an average width of 400.
WARN [2025-10-31 21:36:44] 1 intervals without mappability score (1 on-target).
INFO [2025-10-31 21:36:44] Removing 1 intervals with low mappability score (<0.60).
WARN [2025-10-31 21:36:44] No reptiming scores provided.
INFO [2025-10-31 21:36:44] Calculating GC-content...
WARN [2025-10-31 21:36:44] Found small target regions (< 100bp). Will resize them.
INFO [2025-10-31 21:36:44] Splitting 5 large targets to an average width of 400.
INFO [2025-10-31 21:36:44] Tiling off-target regions to an average width of 200000.
WARN [2025-10-31 21:36:44] No reptiming scores provided.
INFO [2025-10-31 21:36:44] Calculating GC-content...
INFO [2025-10-31 21:36:45] Splitting 5 large targets to an average width of 400.
WARN [2025-10-31 21:36:45] No mappability scores provided.
WARN [2025-10-31 21:36:45] No reptiming scores provided.
INFO [2025-10-31 21:36:45] Calculating GC-content...
WARN [2025-10-31 21:36:45] Chromosome naming style of interval file (Ensembl) was different from reference (UCSC).
INFO [2025-10-31 21:36:45] Splitting 5 large targets to an average width of 400.
WARN [2025-10-31 21:36:45] No mappability scores provided.
WARN [2025-10-31 21:36:45] No reptiming scores provided.
INFO [2025-10-31 21:36:45] Calculating GC-content...
FATAL [2025-10-31 21:36:45] Chromosome naming style of interval file unknown, should be UCSC.
FATAL [2025-10-31 21:36:45]
FATAL [2025-10-31 21:36:45] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:45] parameters (PureCN 2.16.0).
WARN [2025-10-31 21:36:45] Chromosome naming style of interval file (Ensembl) was different from reference (UCSC).
WARN [2025-10-31 21:36:45] Chromosome naming style of mappability file (Ensembl) was different from reference (UCSC).
INFO [2025-10-31 21:36:45] Splitting 5 large targets to an average width of 400.
WARN [2025-10-31 21:36:45] No reptiming scores provided.
INFO [2025-10-31 21:36:45] Calculating GC-content...
WARN [2025-10-31 21:36:45] Found small target regions (< 60bp). Will resize them.
INFO [2025-10-31 21:36:45] Splitting 5 large targets to an average width of 400.
WARN [2025-10-31 21:36:45] No mappability scores provided.
WARN [2025-10-31 21:36:45] No reptiming scores provided.
INFO [2025-10-31 21:36:45] Calculating GC-content...
WARN [2025-10-31 21:36:45] Found small target regions (< 60bp). Will drop them.
INFO [2025-10-31 21:36:45] Splitting 4 large targets to an average width of 400.
WARN [2025-10-31 21:36:45] No mappability scores provided.
WARN [2025-10-31 21:36:45] No reptiming scores provided.
INFO [2025-10-31 21:36:45] Calculating GC-content...
WARN [2025-10-31 21:36:45] Found small target regions (< 200bp). Will resize them.
INFO [2025-10-31 21:36:45] Splitting 5 large targets to an average width of 400.
WARN [2025-10-31 21:36:45] No mappability scores provided.
WARN [2025-10-31 21:36:45] No reptiming scores provided.
INFO [2025-10-31 21:36:45] Calculating GC-content...
INFO [2025-10-31 21:36:45] Found 20 variants in VCF file.
INFO [2025-10-31 21:36:46] 20 (100.0%) variants annotated as likely germline (DB INFO flag).
WARN [2025-10-31 21:36:46] Did not find base quality scores, will use global error rate of 0.0010 instead.
Error in read.table(file = file, header = header, sep = sep, quote = quote, :
no lines available in input
FATAL [2025-10-31 21:36:46] Error reading AllelicCountsFile
FATAL [2025-10-31 21:36:46] /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/PureCN/extdata/example_allelic_counts_empty.tsv
FATAL [2025-10-31 21:36:46]
FATAL [2025-10-31 21:36:46] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:46] parameters (PureCN 2.16.0).
INFO [2025-10-31 21:36:46] Found 127 variants in VCF file.
INFO [2025-10-31 21:36:46] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
WARN [2025-10-31 21:36:46] Did not find base quality scores, will use global error rate of 0.0010 instead.
INFO [2025-10-31 21:36:46] ------------------------------------------------------------
INFO [2025-10-31 21:36:46] PureCN 2.16.0
INFO [2025-10-31 21:36:46] ------------------------------------------------------------
INFO [2025-10-31 21:36:46] Loading coverage files...
INFO [2025-10-31 21:36:46] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-10-31 21:36:46] Allosome coverage missing, cannot determine sex.
WARN [2025-10-31 21:36:46] Allosome coverage missing, cannot determine sex.
INFO [2025-10-31 21:36:46] Removing 228 intervals with missing log.ratio.
INFO [2025-10-31 21:36:46] Removing 22 small (< 5bp) intervals.
INFO [2025-10-31 21:36:46] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-10-31 21:36:46] No normalDB provided. Provide one for better results.
INFO [2025-10-31 21:36:46] Removing 1724 low count (< 100 total reads) intervals.
INFO [2025-10-31 21:36:46] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-10-31 21:36:46] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-10-31 21:36:46] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-10-31 21:36:46] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-10-31 21:36:46] Loading VCF...
INFO [2025-10-31 21:36:46] Found 127 variants in VCF file.
INFO [2025-10-31 21:36:46] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-10-31 21:36:46] LIB-02240e4 is tumor in VCF file.
INFO [2025-10-31 21:36:46] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-10-31 21:36:46] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-10-31 21:36:46] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-10-31 21:36:46] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-10-31 21:36:46] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-10-31 21:36:46] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-10-31 21:36:47] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding).
INFO [2025-10-31 21:36:47] 1.2% of targets contain variants.
INFO [2025-10-31 21:36:47] Removing 4 variants outside intervals.
INFO [2025-10-31 21:36:47] Found SOMATIC annotation in VCF.
INFO [2025-10-31 21:36:47] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-10-31 21:36:47] Found SOMATIC annotation in VCF. Setting mapping bias to 0.972.
INFO [2025-10-31 21:36:47] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-10-31 21:36:47] Sample sex: ?
INFO [2025-10-31 21:36:47] Segmenting data...
INFO [2025-10-31 21:36:47] Loading pre-computed boundaries for DNAcopy...
INFO [2025-10-31 21:36:47] Setting undo.SD parameter to 1.000000.
INFO [2025-10-31 21:36:47] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-10-31 21:36:47] Found 59 segments with median size of 17.67Mb.
INFO [2025-10-31 21:36:47] Using 121 variants.
INFO [2025-10-31 21:36:47] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-10-31 21:36:47] 2D-grid search of purity and ploidy...
INFO [2025-10-31 21:36:47] Local optima: 0.65/1.8, 0.52/2
INFO [2025-10-31 21:36:47] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2025-10-31 21:36:48] Testing local optimum 2/2 at purity 0.52 and total ploidy 2.00...
INFO [2025-10-31 21:36:48] Skipping 1 solutions that converged to the same optima.
INFO [2025-10-31 21:36:48] Fitting variants with beta model for local optimum 1/2...
INFO [2025-10-31 21:36:48] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2025-10-31 21:36:49] Optimized purity: 0.65
INFO [2025-10-31 21:36:49] Done.
INFO [2025-10-31 21:36:49] ------------------------------------------------------------
FATAL [2025-10-31 21:36:49] log.ratio NULL in .writeLogRatioFileGATK4
FATAL [2025-10-31 21:36:49]
FATAL [2025-10-31 21:36:49] This runtime error might be caused by invalid input data or parameters.
FATAL [2025-10-31 21:36:49] Please report bug (PureCN 2.16.0).
INFO [2025-10-31 21:36:49] Loaded provided segmentation file example_seg.txt (format DNAcopy).
INFO [2025-10-31 21:36:49] Re-centering provided segment means (offset -0.0033).
INFO [2025-10-31 21:36:49] Loaded provided segmentation file example_gatk4_modelfinal.seg.gz (format GATK4).
WARN [2025-10-31 21:36:49] Expecting numeric chromosome names in seg.file, assuming file is properly sorted.
INFO [2025-10-31 21:36:49] Re-centering provided segment means (offset -0.0037).
INFO [2025-10-31 21:36:50] 576 on-target bins with low coverage in all samples.
WARN [2025-10-31 21:36:50] You are likely not using the correct baits file!
WARN [2025-10-31 21:36:50] Allosome coverage missing, cannot determine sex.
WARN [2025-10-31 21:36:50] Allosome coverage missing, cannot determine sex.
INFO [2025-10-31 21:36:50] Processing on-target regions...
INFO [2025-10-31 21:36:50] Removing 930 intervals with low coverage in normalDB.
INFO [2025-10-31 21:36:50] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2025-10-31 21:36:50] ------------------------------------------------------------
INFO [2025-10-31 21:36:50] PureCN 2.16.0
INFO [2025-10-31 21:36:50] ------------------------------------------------------------
INFO [2025-10-31 21:36:50] Using BiocParallel for parallel optimization.
INFO [2025-10-31 21:36:50] Loading coverage files...
INFO [2025-10-31 21:36:51] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-10-31 21:36:51] Allosome coverage missing, cannot determine sex.
WARN [2025-10-31 21:36:51] Allosome coverage missing, cannot determine sex.
INFO [2025-10-31 21:36:51] Removing 228 intervals with missing log.ratio.
INFO [2025-10-31 21:36:51] Removing 705 intervals excluded in normalDB.
INFO [2025-10-31 21:36:51] normalDB provided. Setting minimum coverage for segmentation to 0.0015X.
INFO [2025-10-31 21:36:51] Removing 1066 low count (< 100 total reads) intervals.
INFO [2025-10-31 21:36:51] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-10-31 21:36:51] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-10-31 21:36:51] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-10-31 21:36:51] Sample sex: ?
INFO [2025-10-31 21:36:51] Segmenting data...
INFO [2025-10-31 21:36:51] Interval weights found, will use weighted CBS.
INFO [2025-10-31 21:36:51] Loading pre-computed boundaries for DNAcopy...
INFO [2025-10-31 21:36:51] Setting undo.SD parameter to 1.000000.
Setting multi-figure configuration
INFO [2025-10-31 21:36:51] Found 52 segments with median size of 29.35Mb.
INFO [2025-10-31 21:36:51] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-10-31 21:36:51] 2D-grid search of purity and ploidy...
INFO [2025-10-31 21:36:51] Local optima: 0.65/1.8, 0.52/2
INFO [2025-10-31 21:36:52] Skipping 1 solutions that converged to the same optima.
INFO [2025-10-31 21:36:52] Done.
INFO [2025-10-31 21:36:52] ------------------------------------------------------------
INFO [2025-10-31 21:36:52] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpt131GW/filef7257e7d171d.rds...
FATAL [2025-10-31 21:36:52] runAbsoluteCN was run without a VCF file.
FATAL [2025-10-31 21:36:52]
FATAL [2025-10-31 21:36:52] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:52] parameters (PureCN 2.16.0).
FATAL [2025-10-31 21:36:52] runAbsoluteCN was run without a VCF file.
FATAL [2025-10-31 21:36:52]
FATAL [2025-10-31 21:36:52] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:52] parameters (PureCN 2.16.0).
INFO [2025-10-31 21:36:52] ------------------------------------------------------------
INFO [2025-10-31 21:36:52] PureCN 2.16.0
INFO [2025-10-31 21:36:52] ------------------------------------------------------------
INFO [2025-10-31 21:36:52] Loading coverage files...
INFO [2025-10-31 21:36:53] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-10-31 21:36:53] Allosome coverage missing, cannot determine sex.
WARN [2025-10-31 21:36:53] Allosome coverage missing, cannot determine sex.
INFO [2025-10-31 21:36:53] Removing 228 intervals with missing log.ratio.
INFO [2025-10-31 21:36:53] Removing 705 intervals excluded in normalDB.
INFO [2025-10-31 21:36:53] normalDB provided. Setting minimum coverage for segmentation to 0.0015X.
INFO [2025-10-31 21:36:53] Removing 1066 low count (< 100 total reads) intervals.
INFO [2025-10-31 21:36:53] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-10-31 21:36:53] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-10-31 21:36:53] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-10-31 21:36:53] Sample sex: ?
INFO [2025-10-31 21:36:53] Segmenting data...
INFO [2025-10-31 21:36:53] Interval weights found, will use weighted PSCBS.
FATAL [2025-10-31 21:36:53] segmentationPSCBS requires VCF file.
FATAL [2025-10-31 21:36:53]
FATAL [2025-10-31 21:36:53] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:53] parameters (PureCN 2.16.0).
INFO [2025-10-31 21:36:55] ------------------------------------------------------------
INFO [2025-10-31 21:36:55] PureCN 2.16.0
INFO [2025-10-31 21:36:55] ------------------------------------------------------------
INFO [2025-10-31 21:36:55] Loading coverage files...
FATAL [2025-10-31 21:36:55] Need a normal coverage file if log.ratio and seg.file are not provided.
FATAL [2025-10-31 21:36:55]
FATAL [2025-10-31 21:36:55] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:55] parameters (PureCN 2.16.0).
INFO [2025-10-31 21:36:55] ------------------------------------------------------------
INFO [2025-10-31 21:36:55] PureCN 2.16.0
INFO [2025-10-31 21:36:55] ------------------------------------------------------------
FATAL [2025-10-31 21:36:55] min.ploidy or max.ploidy not within expected range.
FATAL [2025-10-31 21:36:55]
FATAL [2025-10-31 21:36:55] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:55] parameters (PureCN 2.16.0).
INFO [2025-10-31 21:36:55] ------------------------------------------------------------
INFO [2025-10-31 21:36:55] PureCN 2.16.0
INFO [2025-10-31 21:36:55] ------------------------------------------------------------
FATAL [2025-10-31 21:36:55] min.ploidy or max.ploidy not within expected range.
FATAL [2025-10-31 21:36:55]
FATAL [2025-10-31 21:36:55] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:55] parameters (PureCN 2.16.0).
INFO [2025-10-31 21:36:55] ------------------------------------------------------------
INFO [2025-10-31 21:36:55] PureCN 2.16.0
INFO [2025-10-31 21:36:55] ------------------------------------------------------------
INFO [2025-10-31 21:36:55] ------------------------------------------------------------
INFO [2025-10-31 21:36:55] PureCN 2.16.0
INFO [2025-10-31 21:36:55] ------------------------------------------------------------
INFO [2025-10-31 21:36:55] ------------------------------------------------------------
INFO [2025-10-31 21:36:55] PureCN 2.16.0
INFO [2025-10-31 21:36:55] ------------------------------------------------------------
FATAL [2025-10-31 21:36:55] test.num.copy not within expected range.
FATAL [2025-10-31 21:36:55]
FATAL [2025-10-31 21:36:55] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:55] parameters (PureCN 2.16.0).
INFO [2025-10-31 21:36:55] ------------------------------------------------------------
INFO [2025-10-31 21:36:55] PureCN 2.16.0
INFO [2025-10-31 21:36:55] ------------------------------------------------------------
WARN [2025-10-31 21:36:55] test.num.copy outside recommended range.
FATAL [2025-10-31 21:36:55] max.non.clonal not within expected range or format.
FATAL [2025-10-31 21:36:55]
FATAL [2025-10-31 21:36:55] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:55] parameters (PureCN 2.16.0).
INFO [2025-10-31 21:36:55] ------------------------------------------------------------
INFO [2025-10-31 21:36:55] PureCN 2.16.0
INFO [2025-10-31 21:36:55] ------------------------------------------------------------
WARN [2025-10-31 21:36:55] test.num.copy outside recommended range.
FATAL [2025-10-31 21:36:55] max.non.clonal not within expected range or format.
FATAL [2025-10-31 21:36:55]
FATAL [2025-10-31 21:36:55] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:55] parameters (PureCN 2.16.0).
INFO [2025-10-31 21:36:55] ------------------------------------------------------------
INFO [2025-10-31 21:36:55] PureCN 2.16.0
INFO [2025-10-31 21:36:55] ------------------------------------------------------------
FATAL [2025-10-31 21:36:55] test.purity not within expected range.
FATAL [2025-10-31 21:36:55]
FATAL [2025-10-31 21:36:55] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:55] parameters (PureCN 2.16.0).
INFO [2025-10-31 21:36:55] ------------------------------------------------------------
INFO [2025-10-31 21:36:55] PureCN 2.16.0
INFO [2025-10-31 21:36:55] ------------------------------------------------------------
INFO [2025-10-31 21:36:55] Loading coverage files...
FATAL [2025-10-31 21:36:55] Tumor and normal are identical. This won't give any meaningful results
FATAL [2025-10-31 21:36:55] and I'm stopping here.
FATAL [2025-10-31 21:36:55]
FATAL [2025-10-31 21:36:55] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:55] parameters (PureCN 2.16.0).
INFO [2025-10-31 21:36:55] ------------------------------------------------------------
INFO [2025-10-31 21:36:55] PureCN 2.16.0
INFO [2025-10-31 21:36:55] ------------------------------------------------------------
INFO [2025-10-31 21:36:55] Loading coverage files...
FATAL [2025-10-31 21:36:55] Length of log.ratio different from tumor coverage.
FATAL [2025-10-31 21:36:55]
FATAL [2025-10-31 21:36:55] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:55] parameters (PureCN 2.16.0).
INFO [2025-10-31 21:36:55] ------------------------------------------------------------
INFO [2025-10-31 21:36:55] PureCN 2.16.0
INFO [2025-10-31 21:36:55] ------------------------------------------------------------
FATAL [2025-10-31 21:36:55] prior.purity must have the same length as test.purity.
FATAL [2025-10-31 21:36:55]
FATAL [2025-10-31 21:36:55] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:55] parameters (PureCN 2.16.0).
INFO [2025-10-31 21:36:55] ------------------------------------------------------------
INFO [2025-10-31 21:36:55] PureCN 2.16.0
INFO [2025-10-31 21:36:55] ------------------------------------------------------------
FATAL [2025-10-31 21:36:55] min.gof not within expected range or format.
FATAL [2025-10-31 21:36:55]
FATAL [2025-10-31 21:36:55] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:55] parameters (PureCN 2.16.0).
INFO [2025-10-31 21:36:55] ------------------------------------------------------------
INFO [2025-10-31 21:36:55] PureCN 2.16.0
INFO [2025-10-31 21:36:55] ------------------------------------------------------------
FATAL [2025-10-31 21:36:55] prior.purity not within expected range or format.
FATAL [2025-10-31 21:36:55]
FATAL [2025-10-31 21:36:55] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:55] parameters (PureCN 2.16.0).
INFO [2025-10-31 21:36:55] ------------------------------------------------------------
INFO [2025-10-31 21:36:55] PureCN 2.16.0
INFO [2025-10-31 21:36:55] ------------------------------------------------------------
FATAL [2025-10-31 21:36:55] prior.purity must add to 1. Sum is 1.5
FATAL [2025-10-31 21:36:55]
FATAL [2025-10-31 21:36:55] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:55] parameters (PureCN 2.16.0).
INFO [2025-10-31 21:36:55] ------------------------------------------------------------
INFO [2025-10-31 21:36:55] PureCN 2.16.0
INFO [2025-10-31 21:36:55] ------------------------------------------------------------
FATAL [2025-10-31 21:36:55] max.homozygous.loss not within expected range or format.
FATAL [2025-10-31 21:36:55]
FATAL [2025-10-31 21:36:55] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:55] parameters (PureCN 2.16.0).
INFO [2025-10-31 21:36:55] ------------------------------------------------------------
INFO [2025-10-31 21:36:55] PureCN 2.16.0
INFO [2025-10-31 21:36:55] ------------------------------------------------------------
FATAL [2025-10-31 21:36:55] prior.K not within expected range or format.
FATAL [2025-10-31 21:36:55]
FATAL [2025-10-31 21:36:55] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:55] parameters (PureCN 2.16.0).
INFO [2025-10-31 21:36:55] ------------------------------------------------------------
INFO [2025-10-31 21:36:55] PureCN 2.16.0
INFO [2025-10-31 21:36:55] ------------------------------------------------------------
FATAL [2025-10-31 21:36:55] prior.contamination not within expected range or format.
FATAL [2025-10-31 21:36:55]
FATAL [2025-10-31 21:36:55] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:55] parameters (PureCN 2.16.0).
INFO [2025-10-31 21:36:55] ------------------------------------------------------------
INFO [2025-10-31 21:36:55] PureCN 2.16.0
INFO [2025-10-31 21:36:55] ------------------------------------------------------------
FATAL [2025-10-31 21:36:55] Iterations not in the expected range from 10 to 250.
FATAL [2025-10-31 21:36:55]
FATAL [2025-10-31 21:36:55] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:55] parameters (PureCN 2.16.0).
INFO [2025-10-31 21:36:55] ------------------------------------------------------------
INFO [2025-10-31 21:36:55] PureCN 2.16.0
INFO [2025-10-31 21:36:55] ------------------------------------------------------------
FATAL [2025-10-31 21:36:55] Iterations not in the expected range from 10 to 250.
FATAL [2025-10-31 21:36:55]
FATAL [2025-10-31 21:36:55] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:55] parameters (PureCN 2.16.0).
INFO [2025-10-31 21:36:55] ------------------------------------------------------------
INFO [2025-10-31 21:36:55] PureCN 2.16.0
INFO [2025-10-31 21:36:55] ------------------------------------------------------------
INFO [2025-10-31 21:36:55] Loading coverage files...
FATAL [2025-10-31 21:36:56] Missing tumor.coverage.file requires seg.file or log.ratio and
FATAL [2025-10-31 21:36:56] interval.file.
FATAL [2025-10-31 21:36:56]
FATAL [2025-10-31 21:36:56] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:56] parameters (PureCN 2.16.0).
INFO [2025-10-31 21:36:56] ------------------------------------------------------------
INFO [2025-10-31 21:36:56] PureCN 2.16.0
INFO [2025-10-31 21:36:56] ------------------------------------------------------------
INFO [2025-10-31 21:36:56] ------------------------------------------------------------
INFO [2025-10-31 21:36:56] PureCN 2.16.0
INFO [2025-10-31 21:36:56] ------------------------------------------------------------
INFO [2025-10-31 21:36:56] Loading coverage files...
FATAL [2025-10-31 21:36:56] Interval files in normal and tumor different.
FATAL [2025-10-31 21:36:56]
FATAL [2025-10-31 21:36:56] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:56] parameters (PureCN 2.16.0).
INFO [2025-10-31 21:36:56] ------------------------------------------------------------
INFO [2025-10-31 21:36:56] PureCN 2.16.0
INFO [2025-10-31 21:36:56] ------------------------------------------------------------
INFO [2025-10-31 21:36:56] Loading coverage files...
INFO [2025-10-31 21:36:56] Mean target coverages: 0X (tumor) 99X (normal).
WARN [2025-10-31 21:36:56] Large difference in coverage of tumor and normal.
FATAL [2025-10-31 21:36:56] No finite intervals.
FATAL [2025-10-31 21:36:56]
FATAL [2025-10-31 21:36:56] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:56] parameters (PureCN 2.16.0).
INFO [2025-10-31 21:36:56] ------------------------------------------------------------
INFO [2025-10-31 21:36:56] PureCN 2.16.0
INFO [2025-10-31 21:36:56] ------------------------------------------------------------
INFO [2025-10-31 21:36:56] Loading coverage files...
INFO [2025-10-31 21:36:56] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-10-31 21:36:56] Allosome coverage missing, cannot determine sex.
WARN [2025-10-31 21:36:56] Allosome coverage missing, cannot determine sex.
INFO [2025-10-31 21:36:56] Removing 228 intervals with missing log.ratio.
INFO [2025-10-31 21:36:56] Removing 22 small (< 5bp) intervals.
INFO [2025-10-31 21:36:56] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-10-31 21:36:56] No normalDB provided. Provide one for better results.
INFO [2025-10-31 21:36:56] Removing 1724 low count (< 100 total reads) intervals.
INFO [2025-10-31 21:36:56] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-10-31 21:36:56] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-10-31 21:36:56] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-10-31 21:36:56] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-10-31 21:36:56] Loading VCF...
INFO [2025-10-31 21:36:57] Found 127 variants in VCF file.
INFO [2025-10-31 21:36:57] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-10-31 21:36:57] LIB-02240e4 is tumor in VCF file.
INFO [2025-10-31 21:36:57] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-10-31 21:36:57] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-10-31 21:36:57] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-10-31 21:36:57] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-10-31 21:36:57] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-10-31 21:36:57] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
Error in FileForFormat(resource(con), fileFormat(con)) :
Format 'txt' unsupported
In addition: Warning messages:
1: In for (i in seq_len(n)) { :
closing unused connection 4 (/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/PureCN/extdata/example_allelic_counts_empty.tsv)
2: In UseMethod("median") :
closing unused connection 5 (/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpt131GW/filef7252777f72f.tsv)
3: In UseMethod("median") :
closing unused connection 4 (/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/PureCN/extdata/example_gatk4_denoised_cr.tsv.gz)
FATAL [2025-10-31 21:36:57] Could not import snp.blacklist
FATAL [2025-10-31 21:36:57] /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/PureCN/extdata/example_normal.txt.gz:Error
FATAL [2025-10-31 21:36:57] in FileForFormat(resource(con), fileFormat(con)) : Format 'txt'
FATAL [2025-10-31 21:36:57] unsupported
FATAL [2025-10-31 21:36:57]
FATAL [2025-10-31 21:36:57] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:36:57] parameters (PureCN 2.16.0).
INFO [2025-10-31 21:36:57] ------------------------------------------------------------
INFO [2025-10-31 21:36:57] PureCN 2.16.0
INFO [2025-10-31 21:36:57] ------------------------------------------------------------
INFO [2025-10-31 21:36:57] Loading coverage files...
INFO [2025-10-31 21:36:57] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-10-31 21:36:57] Allosome coverage missing, cannot determine sex.
WARN [2025-10-31 21:36:57] Allosome coverage missing, cannot determine sex.
INFO [2025-10-31 21:36:57] Removing 228 intervals with missing log.ratio.
INFO [2025-10-31 21:36:57] Removing 22 small (< 5bp) intervals.
INFO [2025-10-31 21:36:57] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-10-31 21:36:57] No normalDB provided. Provide one for better results.
INFO [2025-10-31 21:36:57] Removing 233 low coverage (< 15.0000X) intervals.
INFO [2025-10-31 21:36:57] Using 9547 intervals (9547 on-target, 0 off-target).
INFO [2025-10-31 21:36:57] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-10-31 21:36:57] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-10-31 21:36:57] Loading VCF...
INFO [2025-10-31 21:36:57] Found 127 variants in VCF file.
INFO [2025-10-31 21:36:57] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-10-31 21:36:57] LIB-02240e4 is tumor in VCF file.
INFO [2025-10-31 21:36:57] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-10-31 21:36:57] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-10-31 21:36:57] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-10-31 21:36:57] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-10-31 21:36:57] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-10-31 21:36:58] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-10-31 21:36:58] Total size of targeted genomic region: 1.63Mb (2.58Mb with 50bp padding).
INFO [2025-10-31 21:36:58] 1.0% of targets contain variants.
INFO [2025-10-31 21:36:58] Removing 2 variants outside intervals.
INFO [2025-10-31 21:36:58] Found SOMATIC annotation in VCF.
INFO [2025-10-31 21:36:58] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-10-31 21:36:58] Found SOMATIC annotation in VCF. Setting mapping bias to 0.973.
INFO [2025-10-31 21:36:58] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-10-31 21:36:58] Sample sex: ?
INFO [2025-10-31 21:36:58] Segmenting data...
INFO [2025-10-31 21:36:58] Loading pre-computed boundaries for DNAcopy...
INFO [2025-10-31 21:36:58] Setting undo.SD parameter to 1.000000.
INFO [2025-10-31 21:36:59] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-10-31 21:36:59] Found 54 segments with median size of 24.88Mb.
INFO [2025-10-31 21:36:59] Using 123 variants.
INFO [2025-10-31 21:36:59] Mean standard deviation of log-ratios: 0.37 (MAPD: 0.32)
INFO [2025-10-31 21:36:59] 2D-grid search of purity and ploidy...
INFO [2025-10-31 21:36:59] Local optima: 0.62/1.9, 0.3/1.9, 0.32/2
INFO [2025-10-31 21:36:59] Testing local optimum 1/3 at purity 0.62 and total ploidy 1.90...
INFO [2025-10-31 21:36:59] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-10-31 21:37:00] Recalibrating log-ratios...
INFO [2025-10-31 21:37:00] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-10-31 21:37:00] Recalibrating log-ratios...
INFO [2025-10-31 21:37:00] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-10-31 21:37:00] Recalibrating log-ratios...
INFO [2025-10-31 21:37:00] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-10-31 21:37:00] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-10-31 21:37:00] Recalibrating log-ratios...
INFO [2025-10-31 21:37:00] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-10-31 21:37:00] Recalibrating log-ratios...
INFO [2025-10-31 21:37:00] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-10-31 21:37:00] Recalibrating log-ratios...
INFO [2025-10-31 21:37:00] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-10-31 21:37:00] Skipping 1 solutions that converged to the same optima.
INFO [2025-10-31 21:37:00] Skipping 1 solutions exceeding max.non.clonal (0.20): 0.3/1.9 (purity/tumor ploidy)
INFO [2025-10-31 21:37:00] Fitting variants with beta model for local optimum 1/3...
INFO [2025-10-31 21:37:00] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01.
INFO [2025-10-31 21:37:01] Optimized purity: 0.65
INFO [2025-10-31 21:37:01] Done.
INFO [2025-10-31 21:37:01] ------------------------------------------------------------
INFO [2025-10-31 21:37:01] ------------------------------------------------------------
INFO [2025-10-31 21:37:01] PureCN 2.16.0
INFO [2025-10-31 21:37:01] ------------------------------------------------------------
INFO [2025-10-31 21:37:01] Loading coverage files...
INFO [2025-10-31 21:37:02] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-10-31 21:37:02] Allosome coverage missing, cannot determine sex.
WARN [2025-10-31 21:37:02] Allosome coverage missing, cannot determine sex.
INFO [2025-10-31 21:37:02] Removing 228 intervals with missing log.ratio.
INFO [2025-10-31 21:37:02] Removing 22 small (< 5bp) intervals.
INFO [2025-10-31 21:37:02] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-10-31 21:37:02] No normalDB provided. Provide one for better results.
INFO [2025-10-31 21:37:02] Removing 1724 low count (< 100 total reads) intervals.
INFO [2025-10-31 21:37:02] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-10-31 21:37:02] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-10-31 21:37:02] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-10-31 21:37:02] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-10-31 21:37:02] Loading VCF...
INFO [2025-10-31 21:37:02] Found 127 variants in VCF file.
WARN [2025-10-31 21:37:02] DP FORMAT field contains NAs. Removing 3 variants.
WARN [2025-10-31 21:37:02] DB INFO flag contains NAs
INFO [2025-10-31 21:37:02] 119 (96.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-10-31 21:37:02] LIB-02240e4 is tumor in VCF file.
INFO [2025-10-31 21:37:02] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-10-31 21:37:02] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-10-31 21:37:02] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-10-31 21:37:02] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-10-31 21:37:02] Removing 1 variants with AF < 0.030 or AF >= 0.970 or insufficient supporting reads or depth < 15.
INFO [2025-10-31 21:37:02] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding).
INFO [2025-10-31 21:37:02] 1.2% of targets contain variants.
INFO [2025-10-31 21:37:02] Setting somatic prior probabilities for likely germline hits to 0.000500 or to 0.500000 otherwise.
INFO [2025-10-31 21:37:02] Excluding 5 novel or poor quality variants from segmentation.
INFO [2025-10-31 21:37:02] Sample sex: ?
INFO [2025-10-31 21:37:02] Segmenting data...
INFO [2025-10-31 21:37:02] Loading pre-computed boundaries for DNAcopy...
INFO [2025-10-31 21:37:02] Setting undo.SD parameter to 1.000000.
Setting multi-figure configuration
INFO [2025-10-31 21:37:02] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-10-31 21:37:03] Found 59 segments with median size of 17.67Mb.
INFO [2025-10-31 21:37:03] Using 123 variants.
INFO [2025-10-31 21:37:03] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-10-31 21:37:03] 2D-grid search of purity and ploidy...
INFO [2025-10-31 21:37:03] Local optima: 0.62/1.9, 0.3/1.9, 0.32/2
INFO [2025-10-31 21:37:03] Testing local optimum 1/3 at purity 0.62 and total ploidy 1.90...
INFO [2025-10-31 21:37:03] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-10-31 21:37:03] Recalibrating log-ratios...
INFO [2025-10-31 21:37:03] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-10-31 21:37:03] Recalibrating log-ratios...
INFO [2025-10-31 21:37:03] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-10-31 21:37:03] Recalibrating log-ratios...
INFO [2025-10-31 21:37:03] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-10-31 21:37:04] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-10-31 21:37:04] Recalibrating log-ratios...
INFO [2025-10-31 21:37:04] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-10-31 21:37:04] Recalibrating log-ratios...
INFO [2025-10-31 21:37:04] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-10-31 21:37:04] Recalibrating log-ratios...
INFO [2025-10-31 21:37:04] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-10-31 21:37:04] Skipping 2 solutions exceeding max.non.clonal (0.20): 0.3/1.9, 0.35/1.61 (purity/tumor ploidy)
INFO [2025-10-31 21:37:04] Fitting variants with beta model for local optimum 1/3...
INFO [2025-10-31 21:37:04] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2025-10-31 21:37:05] Optimized purity: 0.65
INFO [2025-10-31 21:37:05] Done.
INFO [2025-10-31 21:37:05] ------------------------------------------------------------
INFO [2025-10-31 21:37:05] ------------------------------------------------------------
INFO [2025-10-31 21:37:05] PureCN 2.16.0
INFO [2025-10-31 21:37:05] ------------------------------------------------------------
INFO [2025-10-31 21:37:05] Loading coverage files...
INFO [2025-10-31 21:37:05] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-10-31 21:37:05] Allosome coverage missing, cannot determine sex.
WARN [2025-10-31 21:37:05] Allosome coverage missing, cannot determine sex.
INFO [2025-10-31 21:37:05] No Gene column in interval.file. You won't get gene-level calls.
INFO [2025-10-31 21:37:05] Removing 228 intervals with missing log.ratio.
INFO [2025-10-31 21:37:05] Removing 15 low/high GC targets.
INFO [2025-10-31 21:37:05] Removing 21 small (< 5bp) intervals.
INFO [2025-10-31 21:37:05] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-10-31 21:37:05] No normalDB provided. Provide one for better results.
INFO [2025-10-31 21:37:06] Removing 1718 low count (< 100 total reads) intervals.
INFO [2025-10-31 21:37:06] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-10-31 21:37:06] Removing 36 low mappability intervals.
INFO [2025-10-31 21:37:06] Using 8006 intervals (8006 on-target, 0 off-target).
INFO [2025-10-31 21:37:06] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-10-31 21:37:06] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio).
INFO [2025-10-31 21:37:06] Loading VCF...
INFO [2025-10-31 21:37:06] Found 127 variants in VCF file.
INFO [2025-10-31 21:37:06] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-10-31 21:37:06] LIB-02240e4 is tumor in VCF file.
INFO [2025-10-31 21:37:06] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-10-31 21:37:06] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-10-31 21:37:06] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-10-31 21:37:06] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-10-31 21:37:06] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-10-31 21:37:06] Removing 1 variants with AF < 0.030 or AF >= Inf or insufficient supporting reads or depth < 15.
INFO [2025-10-31 21:37:06] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding).
INFO [2025-10-31 21:37:06] 1.2% of targets contain variants.
INFO [2025-10-31 21:37:06] Removing 11 variants outside intervals.
INFO [2025-10-31 21:37:06] Found SOMATIC annotation in VCF.
INFO [2025-10-31 21:37:06] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-10-31 21:37:06] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970.
INFO [2025-10-31 21:37:06] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-10-31 21:37:06] Sample sex: ?
INFO [2025-10-31 21:37:06] Segmenting data...
INFO [2025-10-31 21:37:06] MAPD of 114 allelic fractions: 0.14 (0.15 adjusted).
INFO [2025-10-31 21:37:06] Using unweighted PSCBS.
INFO [2025-10-31 21:37:06] Setting undo.SD parameter to 1.000000.
INFO [2025-10-31 21:37:16] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-10-31 21:37:16] Found 72 segments with median size of 27.25Mb.
INFO [2025-10-31 21:37:16] Using 114 variants.
INFO [2025-10-31 21:37:16] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-10-31 21:37:16] 2D-grid search of purity and ploidy...
INFO [2025-10-31 21:37:16] Local optima: 0.65/1.8, 0.38/2.2
INFO [2025-10-31 21:37:16] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2025-10-31 21:37:16] Recalibrating log-ratios...
INFO [2025-10-31 21:37:16] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2025-10-31 21:37:17] Recalibrating log-ratios...
INFO [2025-10-31 21:37:17] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2025-10-31 21:37:17] Recalibrating log-ratios...
INFO [2025-10-31 21:37:17] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2025-10-31 21:37:17] Testing local optimum 2/2 at purity 0.38 and total ploidy 2.20...
INFO [2025-10-31 21:37:17] Skipping 1 solutions exceeding max.non.clonal (0.20): 0.65/2.05 (purity/tumor ploidy)
INFO [2025-10-31 21:37:17] Fitting variants with beta model for local optimum 2/2...
INFO [2025-10-31 21:37:17] Fitting variants for purity 0.40, tumor ploidy 2.55 and contamination 0.01.
INFO [2025-10-31 21:37:18] Optimized purity: 0.40
INFO [2025-10-31 21:37:18] Done.
INFO [2025-10-31 21:37:18] ------------------------------------------------------------
FATAL [2025-10-31 21:37:18] This function requires gene-level calls. Please add a column 'Gene'
FATAL [2025-10-31 21:37:18] containing gene symbols to the interval.file.
FATAL [2025-10-31 21:37:18]
FATAL [2025-10-31 21:37:18] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:37:18] parameters (PureCN 2.16.0).
INFO [2025-10-31 21:37:19] ------------------------------------------------------------
INFO [2025-10-31 21:37:19] PureCN 2.16.0
INFO [2025-10-31 21:37:19] ------------------------------------------------------------
INFO [2025-10-31 21:37:19] Loading coverage files...
INFO [2025-10-31 21:37:19] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-10-31 21:37:19] Allosome coverage missing, cannot determine sex.
WARN [2025-10-31 21:37:19] Allosome coverage missing, cannot determine sex.
INFO [2025-10-31 21:37:19] Removing 228 intervals with missing log.ratio.
INFO [2025-10-31 21:37:19] Removing 22 small (< 5bp) intervals.
INFO [2025-10-31 21:37:19] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-10-31 21:37:19] No normalDB provided. Provide one for better results.
INFO [2025-10-31 21:37:19] Removing 1724 low count (< 100 total reads) intervals.
INFO [2025-10-31 21:37:19] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-10-31 21:37:19] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-10-31 21:37:19] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-10-31 21:37:19] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-10-31 21:37:19] Loading VCF...
INFO [2025-10-31 21:37:19] Found 127 variants in VCF file.
INFO [2025-10-31 21:37:19] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
FATAL [2025-10-31 21:37:19] Different chromosome names in coverage and VCF.
FATAL [2025-10-31 21:37:19]
FATAL [2025-10-31 21:37:19] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:37:19] parameters (PureCN 2.16.0).
INFO [2025-10-31 21:37:19] ------------------------------------------------------------
INFO [2025-10-31 21:37:19] PureCN 2.16.0
INFO [2025-10-31 21:37:19] ------------------------------------------------------------
INFO [2025-10-31 21:37:19] Loading coverage files...
INFO [2025-10-31 21:37:19] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-10-31 21:37:19] Allosome coverage missing, cannot determine sex.
WARN [2025-10-31 21:37:19] Allosome coverage missing, cannot determine sex.
FATAL [2025-10-31 21:37:19] tumor.coverage.file and interval.file do not align.
FATAL [2025-10-31 21:37:19]
FATAL [2025-10-31 21:37:19] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:37:19] parameters (PureCN 2.16.0).
INFO [2025-10-31 21:37:20] ------------------------------------------------------------
INFO [2025-10-31 21:37:20] PureCN 2.16.0
INFO [2025-10-31 21:37:20] ------------------------------------------------------------
INFO [2025-10-31 21:37:20] Loading coverage files...
INFO [2025-10-31 21:37:20] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-10-31 21:37:20] Allosome coverage missing, cannot determine sex.
WARN [2025-10-31 21:37:20] Allosome coverage missing, cannot determine sex.
INFO [2025-10-31 21:37:20] Removing 228 intervals with missing log.ratio.
INFO [2025-10-31 21:37:20] Removing 15 low/high GC targets.
INFO [2025-10-31 21:37:20] Removing 21 small (< 5bp) intervals.
INFO [2025-10-31 21:37:20] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-10-31 21:37:20] No normalDB provided. Provide one for better results.
INFO [2025-10-31 21:37:20] Removing 1718 low count (< 100 total reads) intervals.
INFO [2025-10-31 21:37:20] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-10-31 21:37:20] Removing 36 low mappability intervals.
INFO [2025-10-31 21:37:20] Using 8006 intervals (8006 on-target, 0 off-target).
INFO [2025-10-31 21:37:20] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-10-31 21:37:20] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio).
INFO [2025-10-31 21:37:20] Loading VCF...
INFO [2025-10-31 21:37:20] Found 127 variants in VCF file.
INFO [2025-10-31 21:37:20] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-10-31 21:37:20] LIB-02240e4 is tumor in VCF file.
INFO [2025-10-31 21:37:20] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-10-31 21:37:20] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-10-31 21:37:20] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-10-31 21:37:20] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-10-31 21:37:20] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-10-31 21:37:20] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-10-31 21:37:20] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding).
INFO [2025-10-31 21:37:20] 1.2% of targets contain variants.
INFO [2025-10-31 21:37:20] Removing 11 variants outside intervals.
INFO [2025-10-31 21:37:20] Found SOMATIC annotation in VCF.
INFO [2025-10-31 21:37:20] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-10-31 21:37:20] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970.
INFO [2025-10-31 21:37:20] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-10-31 21:37:20] Sample sex: ?
INFO [2025-10-31 21:37:20] Segmenting data...
INFO [2025-10-31 21:37:20] Loading pre-computed boundaries for DNAcopy...
INFO [2025-10-31 21:37:20] Setting undo.SD parameter to 1.000000.
INFO [2025-10-31 21:37:21] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-10-31 21:37:21] Found 59 segments with median size of 17.67Mb.
INFO [2025-10-31 21:37:21] Using 114 variants.
INFO [2025-10-31 21:37:21] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-10-31 21:37:21] 2D-grid search of purity and ploidy...
INFO [2025-10-31 21:37:21] Local optima: 0.63/1.9
INFO [2025-10-31 21:37:21] Testing local optimum 1/1 at purity 0.63 and total ploidy 1.90...
INFO [2025-10-31 21:37:21] Fitting variants with beta model for local optimum 1/1...
INFO [2025-10-31 21:37:21] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2025-10-31 21:37:22] Optimized purity: 0.65
INFO [2025-10-31 21:37:22] Done.
INFO [2025-10-31 21:37:22] ------------------------------------------------------------
INFO [2025-10-31 21:37:22] ------------------------------------------------------------
INFO [2025-10-31 21:37:22] PureCN 2.16.0
INFO [2025-10-31 21:37:22] ------------------------------------------------------------
INFO [2025-10-31 21:37:22] Loading coverage files...
INFO [2025-10-31 21:37:22] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-10-31 21:37:22] Allosome coverage missing, cannot determine sex.
WARN [2025-10-31 21:37:22] Allosome coverage missing, cannot determine sex.
INFO [2025-10-31 21:37:23] Removing 228 intervals with missing log.ratio.
INFO [2025-10-31 21:37:23] Removing 15 low/high GC targets.
INFO [2025-10-31 21:37:23] Removing 21 small (< 5bp) intervals.
INFO [2025-10-31 21:37:23] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-10-31 21:37:23] No normalDB provided. Provide one for better results.
INFO [2025-10-31 21:37:23] Removing 1718 low count (< 100 total reads) intervals.
INFO [2025-10-31 21:37:23] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-10-31 21:37:23] Removing 36 low mappability intervals.
INFO [2025-10-31 21:37:23] Using 8006 intervals (8006 on-target, 0 off-target).
INFO [2025-10-31 21:37:23] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-10-31 21:37:23] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio).
INFO [2025-10-31 21:37:23] Loading VCF...
INFO [2025-10-31 21:37:23] Found 127 variants in VCF file.
INFO [2025-10-31 21:37:23] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-10-31 21:37:23] LIB-02240e4 is tumor in VCF file.
INFO [2025-10-31 21:37:23] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-10-31 21:37:23] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-10-31 21:37:23] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-10-31 21:37:23] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-10-31 21:37:23] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-10-31 21:37:23] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-10-31 21:37:23] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding).
INFO [2025-10-31 21:37:23] 1.2% of targets contain variants.
INFO [2025-10-31 21:37:23] Removing 11 variants outside intervals.
INFO [2025-10-31 21:37:23] Found SOMATIC annotation in VCF.
INFO [2025-10-31 21:37:23] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-10-31 21:37:23] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970.
INFO [2025-10-31 21:37:23] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-10-31 21:37:23] Sample sex: ?
INFO [2025-10-31 21:37:23] Segmenting data...
INFO [2025-10-31 21:37:23] Loading pre-computed boundaries for DNAcopy...
INFO [2025-10-31 21:37:23] Setting undo.SD parameter to 1.000000.
INFO [2025-10-31 21:37:24] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-10-31 21:37:24] Found 59 segments with median size of 17.67Mb.
INFO [2025-10-31 21:37:24] Using 114 variants.
INFO [2025-10-31 21:37:24] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-10-31 21:37:24] 2D-grid search of purity and ploidy...
INFO [2025-10-31 21:37:24] Local optima: 0.63/1.9
INFO [2025-10-31 21:37:24] Testing local optimum 1/1 at purity 0.63 and total ploidy 1.90...
INFO [2025-10-31 21:37:24] Fitting variants with beta model for local optimum 1/1...
WARN [2025-10-31 21:37:24] Some gene symbols found on multiple chromosomes. Use of approved symbols suggested.
INFO [2025-10-31 21:37:24] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2025-10-31 21:37:25] Optimized purity: 0.65
INFO [2025-10-31 21:37:25] Done.
INFO [2025-10-31 21:37:25] ------------------------------------------------------------
FATAL [2025-10-31 21:37:25] chr1 not valid chromosome name(s). Valid names are:
FATAL [2025-10-31 21:37:25] 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22
FATAL [2025-10-31 21:37:25]
FATAL [2025-10-31 21:37:25] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:37:25] parameters (PureCN 2.16.0).
INFO [2025-10-31 21:37:25] ------------------------------------------------------------
INFO [2025-10-31 21:37:25] PureCN 2.16.0
INFO [2025-10-31 21:37:25] ------------------------------------------------------------
INFO [2025-10-31 21:37:25] Loading coverage files...
WARN [2025-10-31 21:37:25] Provided sampleid (Sample2) does not match Sample1 found in segmentation.
WARN [2025-10-31 21:37:25] Allosome coverage missing, cannot determine sex.
WARN [2025-10-31 21:37:25] Allosome coverage missing, cannot determine sex.
INFO [2025-10-31 21:37:25] Removing 10 intervals with missing log.ratio.
INFO [2025-10-31 21:37:25] Using 10039 intervals (10039 on-target, 0 off-target).
INFO [2025-10-31 21:37:25] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-10-31 21:37:25] Loading VCF...
INFO [2025-10-31 21:37:26] Found 127 variants in VCF file.
INFO [2025-10-31 21:37:26] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-10-31 21:37:26] LIB-02240e4 is tumor in VCF file.
INFO [2025-10-31 21:37:26] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-10-31 21:37:26] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-10-31 21:37:26] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-10-31 21:37:26] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-10-31 21:37:26] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-10-31 21:37:26] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-10-31 21:37:26] Total size of targeted genomic region: 1.71Mb (2.70Mb with 50bp padding).
INFO [2025-10-31 21:37:26] 1.0% of targets contain variants.
INFO [2025-10-31 21:37:26] Removing 0 variants outside intervals.
INFO [2025-10-31 21:37:26] Found SOMATIC annotation in VCF.
INFO [2025-10-31 21:37:26] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-10-31 21:37:26] Found SOMATIC annotation in VCF. Setting mapping bias to 0.976.
INFO [2025-10-31 21:37:26] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-10-31 21:37:26] Sample sex: ?
INFO [2025-10-31 21:37:26] Segmenting data...
INFO [2025-10-31 21:37:26] Loaded provided segmentation file example_seg.txt (format DNAcopy).
WARN [2025-10-31 21:37:26] Provided sampleid (Sample2) does not match Sample1 found in segmentation.
INFO [2025-10-31 21:37:26] Re-centering provided segment means (offset -0.0033).
INFO [2025-10-31 21:37:26] Loading pre-computed boundaries for DNAcopy...
INFO [2025-10-31 21:37:26] Setting undo.SD parameter to 0.000000.
Setting multi-figure configuration
INFO [2025-10-31 21:37:26] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-10-31 21:37:26] Found 54 segments with median size of 24.88Mb.
INFO [2025-10-31 21:37:26] Using 125 variants.
INFO [2025-10-31 21:37:26] Mean standard deviation of log-ratios: 0.40 (MAPD: 0.00)
INFO [2025-10-31 21:37:26] 2D-grid search of purity and ploidy...
INFO [2025-10-31 21:37:26] Local optima: 0.6/1.9
INFO [2025-10-31 21:37:26] Testing local optimum 1/1 at purity 0.60 and total ploidy 1.90...
INFO [2025-10-31 21:37:27] Fitting variants with beta model for local optimum 1/1...
INFO [2025-10-31 21:37:27] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01.
INFO [2025-10-31 21:37:28] Optimized purity: 0.65
INFO [2025-10-31 21:37:28] Done.
INFO [2025-10-31 21:37:28] ------------------------------------------------------------
WARN [2025-10-31 21:37:28] Allosome coverage missing, cannot determine sex.
WARN [2025-10-31 21:37:28] Allosome coverage missing, cannot determine sex.
Setting multi-figure configuration
FATAL [2025-10-31 21:37:30] Segmentation file expected with colnames ID, chrom, loc.start, loc.end,
FATAL [2025-10-31 21:37:30] num.mark, seg.mean
FATAL [2025-10-31 21:37:30]
FATAL [2025-10-31 21:37:30] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:37:30] parameters (PureCN 2.16.0).
FATAL [2025-10-31 21:37:31] seg.file contains multiple samples and sampleid missing.
FATAL [2025-10-31 21:37:31]
FATAL [2025-10-31 21:37:31] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:37:31] parameters (PureCN 2.16.0).
FATAL [2025-10-31 21:37:31] seg.file contains multiple samples and sampleid does not match any.
FATAL [2025-10-31 21:37:31]
FATAL [2025-10-31 21:37:31] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:37:31] parameters (PureCN 2.16.0).
WARN [2025-10-31 21:37:31] Allosome coverage missing, cannot determine sex.
WARN [2025-10-31 21:37:31] Allosome coverage missing, cannot determine sex.
WARN [2025-10-31 21:37:33] Allosome coverage missing, cannot determine sex.
WARN [2025-10-31 21:37:33] Allosome coverage missing, cannot determine sex.
WARN [2025-10-31 21:37:33] Provided sampleid (example_tumor.txt.gz) does not match Sample1 found in segmentation.
WARN [2025-10-31 21:37:34] Allosome coverage missing, cannot determine sex.
WARN [2025-10-31 21:37:34] Allosome coverage missing, cannot determine sex.
WARN [2025-10-31 21:37:35] No normalDB provided. Provide one for better results.
WARN [2025-10-31 21:37:37] Allosome coverage missing, cannot determine sex.
WARN [2025-10-31 21:37:37] Allosome coverage missing, cannot determine sex.
WARN [2025-10-31 21:37:38] Provided sampleid (Sample.1) does not match Sample1 found in segmentation.
Setting multi-figure configuration
WARN [2025-10-31 21:37:41] Allosome coverage missing, cannot determine sex.
WARN [2025-10-31 21:37:41] Allosome coverage missing, cannot determine sex.
WARN [2025-10-31 21:37:41] No normalDB provided. Provide one for better results.
WARN [2025-10-31 21:37:41] Sampleid looks like a normal in VCF, not like a tumor.
WARN [2025-10-31 21:37:44] Allosome coverage missing, cannot determine sex.
WARN [2025-10-31 21:37:44] Allosome coverage missing, cannot determine sex.
FATAL [2025-10-31 21:37:44] normalDB not a valid normalDB object. Use createNormalDatabase to
FATAL [2025-10-31 21:37:44] create one.
FATAL [2025-10-31 21:37:44]
FATAL [2025-10-31 21:37:44] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:37:44] parameters (PureCN 2.16.0).
WARN [2025-10-31 21:37:44] You are likely not using the correct baits file!
WARN [2025-10-31 21:37:44] Allosome coverage missing, cannot determine sex.
WARN [2025-10-31 21:37:44] Allosome coverage missing, cannot determine sex.
WARN [2025-10-31 21:37:45] Allosome coverage missing, cannot determine sex.
WARN [2025-10-31 21:37:45] Allosome coverage missing, cannot determine sex.
FATAL [2025-10-31 21:37:45] normalDB appears to be empty.
FATAL [2025-10-31 21:37:45]
FATAL [2025-10-31 21:37:45] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:37:45] parameters (PureCN 2.16.0).
WARN [2025-10-31 21:37:45] Allosome coverage missing, cannot determine sex.
WARN [2025-10-31 21:37:45] Allosome coverage missing, cannot determine sex.
WARN [2025-10-31 21:37:46] Intervals in coverage and interval.file have conflicting on/off-target annotation.
WARN [2025-10-31 21:37:49] Allosome coverage missing, cannot determine sex.
WARN [2025-10-31 21:37:49] Allosome coverage missing, cannot determine sex.
FATAL [2025-10-31 21:37:49] Seqlevels missing in provided segmentation: 6
FATAL [2025-10-31 21:37:49]
FATAL [2025-10-31 21:37:49] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:37:49] parameters (PureCN 2.16.0).
sh: gatk: command not found
WARN [2025-10-31 21:37:50] Cannot find gatk binary in path.
WARN [2025-10-31 21:37:50] Allosome coverage missing, cannot determine sex.
WARN [2025-10-31 21:37:50] Allosome coverage missing, cannot determine sex.
WARN [2025-10-31 21:37:50] No normalDB provided. Provide one for better results.
FATAL [2025-10-31 21:37:50] segmentationHclust requires an input segmentation.
FATAL [2025-10-31 21:37:50]
FATAL [2025-10-31 21:37:50] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:37:50] parameters (PureCN 2.16.0).
WARN [2025-10-31 21:37:50] Allosome coverage missing, cannot determine sex.
WARN [2025-10-31 21:37:50] Allosome coverage missing, cannot determine sex.
WARN [2025-10-31 21:37:50] No normalDB provided. Provide one for better results.
FATAL [2025-10-31 21:37:59] The normal.panel.vcf.file contains only a single sample.
FATAL [2025-10-31 21:37:59]
FATAL [2025-10-31 21:37:59] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:37:59] parameters (PureCN 2.16.0).
FATAL [2025-10-31 21:37:59] mapping.bias.file must be a file with *.rds suffix.
FATAL [2025-10-31 21:37:59]
FATAL [2025-10-31 21:37:59] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:37:59] parameters (PureCN 2.16.0).
Failed with error: 'there is no package called 'genomicsdb''
FATAL [2025-10-31 21:38:00] min.normals (0) must be >= 1.
FATAL [2025-10-31 21:38:00]
FATAL [2025-10-31 21:38:00] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:38:00] parameters (PureCN 2.16.0).
FATAL [2025-10-31 21:38:00] min.normals (10) cannot be larger than min.normals.assign.betafit (3).
FATAL [2025-10-31 21:38:00]
FATAL [2025-10-31 21:38:00] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:38:00] parameters (PureCN 2.16.0).
FATAL [2025-10-31 21:38:00] min.normals.assign.betafit (10) cannot be larger than
FATAL [2025-10-31 21:38:00] min.normals.betafit (7).
FATAL [2025-10-31 21:38:00]
FATAL [2025-10-31 21:38:00] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:38:00] parameters (PureCN 2.16.0).
FATAL [2025-10-31 21:38:00] min.normals.betafit (20) cannot be larger than
FATAL [2025-10-31 21:38:00] min.normals.position.specific.fit (10).
FATAL [2025-10-31 21:38:00]
FATAL [2025-10-31 21:38:00] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:38:00] parameters (PureCN 2.16.0).
FATAL [2025-10-31 21:38:00] min.betafit.rho not within expected range or format.
FATAL [2025-10-31 21:38:00]
FATAL [2025-10-31 21:38:00] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:38:00] parameters (PureCN 2.16.0).
FATAL [2025-10-31 21:38:00] max.betafit.rho not within expected range or format.
FATAL [2025-10-31 21:38:00]
FATAL [2025-10-31 21:38:00] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:38:00] parameters (PureCN 2.16.0).
FATAL [2025-10-31 21:38:00] min.betafit.rho (0.9) cannot be larger than max.betafit.rho (0.2).
FATAL [2025-10-31 21:38:00]
FATAL [2025-10-31 21:38:00] This is most likely a user error due to invalid input data or
FATAL [2025-10-31 21:38:00] parameters (PureCN 2.16.0).
[ 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
149.836 5.092 143.409
PureCN.Rcheck/PureCN-Ex.timings
| name | user | system | elapsed | |
| adjustLogRatio | 0.789 | 0.013 | 0.805 | |
| annotateTargets | 4.869 | 0.192 | 5.090 | |
| bootstrapResults | 0.201 | 0.020 | 0.225 | |
| calculateBamCoverageByInterval | 0.075 | 0.002 | 0.081 | |
| calculateLogRatio | 0.351 | 0.020 | 0.412 | |
| calculateMappingBiasGatk4 | 0.001 | 0.000 | 0.000 | |
| calculateMappingBiasVcf | 0.701 | 0.025 | 0.764 | |
| calculatePowerDetectSomatic | 0.492 | 0.005 | 0.499 | |
| calculateTangentNormal | 1.166 | 0.021 | 1.193 | |
| callAlterations | 0.055 | 0.003 | 0.057 | |
| callAlterationsFromSegmentation | 0.579 | 0.011 | 0.592 | |
| callAmplificationsInLowPurity | 14.099 | 0.181 | 14.700 | |
| callCIN | 0.087 | 0.002 | 0.089 | |
| callLOH | 0.074 | 0.002 | 0.076 | |
| callMutationBurden | 0.624 | 0.019 | 0.642 | |
| centromeres | 0.001 | 0.001 | 0.002 | |
| correctCoverageBias | 0.649 | 0.015 | 0.665 | |
| createCurationFile | 0.154 | 0.004 | 0.160 | |
| createNormalDatabase | 1.008 | 0.015 | 1.030 | |
| filterIntervals | 7.870 | 0.181 | 8.077 | |
| filterVcfBasic | 0.218 | 0.002 | 0.221 | |
| filterVcfMuTect | 0.229 | 0.004 | 0.233 | |
| filterVcfMuTect2 | 0.233 | 0.002 | 0.236 | |
| findFocal | 4.125 | 0.069 | 4.198 | |
| findHighQualitySNPs | 0.556 | 0.008 | 0.564 | |
| getSexFromCoverage | 0.094 | 0.004 | 0.098 | |
| getSexFromVcf | 0.111 | 0.003 | 0.115 | |
| plotAbs | 0.088 | 0.004 | 0.093 | |
| poolCoverage | 0.209 | 0.008 | 0.217 | |
| predictSomatic | 0.173 | 0.003 | 0.174 | |
| preprocessIntervals | 0.232 | 0.005 | 0.238 | |
| processMultipleSamples | 0.857 | 0.021 | 0.879 | |
| readAllelicCountsFile | 0.188 | 0.001 | 0.191 | |
| readCoverageFile | 0.092 | 0.004 | 0.096 | |
| readCurationFile | 0.088 | 0.002 | 0.091 | |
| readIntervalFile | 0.059 | 0.001 | 0.061 | |
| readLogRatioFile | 0.010 | 0.001 | 0.010 | |
| readSegmentationFile | 0.003 | 0.000 | 0.003 | |
| runAbsoluteCN | 5.846 | 0.107 | 5.971 | |
| segmentationCBS | 2.848 | 0.050 | 2.904 | |
| segmentationGATK4 | 0.001 | 0.000 | 0.001 | |
| segmentationHclust | 5.320 | 0.100 | 5.434 | |
| segmentationPSCBS | 13.253 | 0.150 | 13.405 | |
| setMappingBiasVcf | 0.116 | 0.003 | 0.119 | |
| setPriorVcf | 0.099 | 0.002 | 0.101 | |