Markus Riester
| Snapshot Date: 2025-11-13 13:40 -0500 (Thu, 13 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/PureCN |
| git_branch: devel |
| git_last_commit: 3330cff |
| git_last_commit_date: 2025-10-29 10:31:57 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-14 11:36 -0500 (Fri, 14 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4825 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4547 |
| 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 1644/2325 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| PureCN 2.17.0 (landing page) Markus Riester
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the PureCN package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PureCN.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: PureCN |
| Version: 2.17.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PureCN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PureCN_2.17.0.tar.gz |
| StartedAt: 2025-11-13 21:54:56 -0500 (Thu, 13 Nov 2025) |
| EndedAt: 2025-11-13 22:01:25 -0500 (Thu, 13 Nov 2025) |
| EllapsedTime: 389.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: PureCN.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PureCN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PureCN_2.17.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/PureCN.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PureCN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PureCN’ version ‘2.17.0’
* checking package namespace information ... OK
* checking package dependencies ... INFO
Package which this enhances but not available for checking: ‘genomicsdb’
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘PureCN’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
callAmplificationsInLowPurity 15.188 0.155 16.326
segmentationPSCBS 14.324 0.164 15.033
filterIntervals 8.379 0.153 8.822
runAbsoluteCN 6.375 0.121 6.827
segmentationHclust 5.757 0.113 6.086
annotateTargets 5.644 0.223 6.066
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
PureCN.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PureCN ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’ * installing *source* package ‘PureCN’ ... ** this is package ‘PureCN’ version ‘2.17.0’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (PureCN)
PureCN.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(PureCN)
Loading required package: DNAcopy
Loading required package: VariantAnnotation
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: Seqinfo
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Attaching package: 'VariantAnnotation'
The following object is masked from 'package:base':
tabulate
>
> test_check("PureCN")
WARN [2025-11-13 21:58:51] Attempted adding gene symbols to intervals. Heuristics have been used to pick symbols for overlapping genes.
WARN [2025-11-13 21:58:51] Chromosome naming style of txdb file (UCSC) was different from interval file (Ensembl).
WARN [2025-11-13 21:58:57] Attempted adding gene symbols to intervals. Heuristics have been used to pick symbols for overlapping genes.
FATAL [2025-11-13 21:58:58] tumor.coverage.file and interval.file do not align.
FATAL [2025-11-13 21:58:58]
FATAL [2025-11-13 21:58:58] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 21:58:58] parameters (PureCN 2.17.0).
WARN [2025-11-13 21:58:58] Cannot find all contig lengths while exporting interval file.
INFO [2025-11-13 21:58:58] Processing seq1:1-21 (1/3)...
INFO [2025-11-13 21:58:59] Processing seq1:1227-1247 (2/3)...
INFO [2025-11-13 21:58:59] Processing seq2:594-614 (3/3)...
WARN [2025-11-13 21:58:59] Large potential mis-calibration of on- and off-target log2 ratios: 0.26
FATAL [2025-11-13 21:58:59] Need either f or purity and ploidy.
FATAL [2025-11-13 21:58:59]
FATAL [2025-11-13 21:58:59] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 21:58:59] parameters (PureCN 2.17.0).
FATAL [2025-11-13 21:58:59] f not in expected range.
FATAL [2025-11-13 21:58:59]
FATAL [2025-11-13 21:58:59] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 21:58:59] parameters (PureCN 2.17.0).
FATAL [2025-11-13 21:58:59] coverage not in expected range (>=2)
FATAL [2025-11-13 21:58:59]
FATAL [2025-11-13 21:58:59] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 21:58:59] parameters (PureCN 2.17.0).
FATAL [2025-11-13 21:58:59] purity not in expected range.
FATAL [2025-11-13 21:58:59]
FATAL [2025-11-13 21:58:59] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 21:58:59] parameters (PureCN 2.17.0).
FATAL [2025-11-13 21:58:59] ploidy not in expected range.
FATAL [2025-11-13 21:58:59]
FATAL [2025-11-13 21:58:59] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 21:58:59] parameters (PureCN 2.17.0).
FATAL [2025-11-13 21:58:59] cell.fraction not in expected range.
FATAL [2025-11-13 21:58:59]
FATAL [2025-11-13 21:58:59] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 21:58:59] parameters (PureCN 2.17.0).
INFO [2025-11-13 21:59:00] 576 on-target bins with low coverage in all samples.
WARN [2025-11-13 21:59:00] You are likely not using the correct baits file!
WARN [2025-11-13 21:59:00] Allosome coverage missing, cannot determine sex.
WARN [2025-11-13 21:59:00] Allosome coverage missing, cannot determine sex.
INFO [2025-11-13 21:59:00] Processing on-target regions...
INFO [2025-11-13 21:59:00] Removing 930 intervals with low coverage in normalDB.
INFO [2025-11-13 21:59:00] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2025-11-13 21:59:01] Tumor/normal noise ratio: 19.041
WARN [2025-11-13 21:59:01] Extensive noise in tumor compared to normals.
INFO [2025-11-13 21:59:18] Tumor/normal noise ratio: 19.041
WARN [2025-11-13 21:59:18] Extensive noise in tumor compared to normals.
INFO [2025-11-13 21:59:20] Using BiocParallel for parallel optimization.
FATAL [2025-11-13 21:59:25] pvalue.cutoff not within expected range or format.
FATAL [2025-11-13 21:59:25]
FATAL [2025-11-13 21:59:25] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 21:59:25] parameters (PureCN 2.17.0).
FATAL [2025-11-13 21:59:25] pvalue.cutoff not within expected range or format.
FATAL [2025-11-13 21:59:25]
FATAL [2025-11-13 21:59:25] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 21:59:25] parameters (PureCN 2.17.0).
FATAL [2025-11-13 21:59:25] percentile.cutoff not in expected range (0 to 100).
FATAL [2025-11-13 21:59:25]
FATAL [2025-11-13 21:59:25] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 21:59:25] parameters (PureCN 2.17.0).
FATAL [2025-11-13 21:59:25] percentile.cutoff not in expected range (0 to 100).
FATAL [2025-11-13 21:59:25]
FATAL [2025-11-13 21:59:25] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 21:59:25] parameters (PureCN 2.17.0).
FATAL [2025-11-13 21:59:25] purity not within expected range or format.
FATAL [2025-11-13 21:59:25]
FATAL [2025-11-13 21:59:25] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 21:59:25] parameters (PureCN 2.17.0).
FATAL [2025-11-13 21:59:25] purity not within expected range or format.
FATAL [2025-11-13 21:59:25]
FATAL [2025-11-13 21:59:25] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 21:59:25] parameters (PureCN 2.17.0).
INFO [2025-11-13 21:59:26] ------------------------------------------------------------
INFO [2025-11-13 21:59:26] PureCN 2.17.0
INFO [2025-11-13 21:59:26] ------------------------------------------------------------
INFO [2025-11-13 21:59:26] Loading coverage files...
INFO [2025-11-13 21:59:26] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-11-13 21:59:26] Allosome coverage missing, cannot determine sex.
WARN [2025-11-13 21:59:26] Allosome coverage missing, cannot determine sex.
INFO [2025-11-13 21:59:26] Removing 228 intervals with missing log.ratio.
INFO [2025-11-13 21:59:26] Removing 22 small (< 5bp) intervals.
INFO [2025-11-13 21:59:26] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-11-13 21:59:26] No normalDB provided. Provide one for better results.
INFO [2025-11-13 21:59:26] Removing 1724 low count (< 100 total reads) intervals.
INFO [2025-11-13 21:59:26] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-11-13 21:59:26] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-11-13 21:59:26] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-11-13 21:59:26] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-11-13 21:59:26] Loading VCF...
INFO [2025-11-13 21:59:26] Found 127 variants in VCF file.
INFO [2025-11-13 21:59:26] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-11-13 21:59:26] LIB-02240e4 is tumor in VCF file.
INFO [2025-11-13 21:59:27] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-11-13 21:59:27] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-11-13 21:59:27] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-11-13 21:59:27] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-11-13 21:59:27] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-11-13 21:59:27] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-11-13 21:59:27] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding).
INFO [2025-11-13 21:59:27] 1.2% of targets contain variants.
INFO [2025-11-13 21:59:27] Removing 4 variants outside intervals.
INFO [2025-11-13 21:59:27] Found SOMATIC annotation in VCF.
INFO [2025-11-13 21:59:27] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-11-13 21:59:27] Found SOMATIC annotation in VCF. Setting mapping bias to 0.972.
INFO [2025-11-13 21:59:27] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-11-13 21:59:27] Sample sex: ?
INFO [2025-11-13 21:59:27] Segmenting data...
INFO [2025-11-13 21:59:27] Loading pre-computed boundaries for DNAcopy...
INFO [2025-11-13 21:59:27] Setting undo.SD parameter to 1.000000.
INFO [2025-11-13 21:59:27] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-11-13 21:59:27] Found 59 segments with median size of 17.67Mb.
INFO [2025-11-13 21:59:27] Using 121 variants.
INFO [2025-11-13 21:59:27] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-11-13 21:59:27] 2D-grid search of purity and ploidy...
INFO [2025-11-13 21:59:28] Local optima: 0.63/1.9, 0.5/2
INFO [2025-11-13 21:59:28] Testing local optimum 1/2 at purity 0.63 and total ploidy 1.90...
INFO [2025-11-13 21:59:28] Testing local optimum 2/2 at purity 0.50 and total ploidy 2.00...
INFO [2025-11-13 21:59:29] Skipping 1 solutions that converged to the same optima.
INFO [2025-11-13 21:59:29] Fitting variants with beta model for local optimum 1/2...
INFO [2025-11-13 21:59:29] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2025-11-13 21:59:30] Optimized purity: 0.65
INFO [2025-11-13 21:59:30] Done.
INFO [2025-11-13 21:59:30] ------------------------------------------------------------
INFO [2025-11-13 21:59:30] Estimating callable regions.
FATAL [2025-11-13 21:59:30] exclude not a GRanges object.
FATAL [2025-11-13 21:59:30]
FATAL [2025-11-13 21:59:30] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 21:59:30] parameters (PureCN 2.17.0).
FATAL [2025-11-13 21:59:31] callable not a GRanges object.
FATAL [2025-11-13 21:59:31]
FATAL [2025-11-13 21:59:31] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 21:59:31] parameters (PureCN 2.17.0).
WARN [2025-11-13 21:59:33] tumor.coverage.file and interval.file do not align.
INFO [2025-11-13 21:59:34] No Gene column in interval.file. You won't get gene-level calls.
FATAL [2025-11-13 21:59:34] No gc_bias column in interval.file.
FATAL [2025-11-13 21:59:34]
FATAL [2025-11-13 21:59:34] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 21:59:34] parameters (PureCN 2.17.0).
FATAL [2025-11-13 21:59:34] Provided coverage is zero, most likely due to a corrupt BAM file.
FATAL [2025-11-13 21:59:34]
FATAL [2025-11-13 21:59:34] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 21:59:34] parameters (PureCN 2.17.0).
INFO [2025-11-13 21:59:35] No reptiming column in interval.file.
INFO [2025-11-13 21:59:37] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpGil4ER/file107ca4e2f55df.rds...
INFO [2025-11-13 21:59:37] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpGil4ER/file107ca4e2f55df.rds...
INFO [2025-11-13 21:59:37] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpGil4ER/file107ca4e2f55df.rds...
INFO [2025-11-13 21:59:37] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpGil4ER/file107ca4e2f55df.rds...
INFO [2025-11-13 21:59:37] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpGil4ER/file107ca4e2f55df.rds...
INFO [2025-11-13 21:59:37] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpGil4ER/file107ca4e2f55df.rds...
FATAL [2025-11-13 21:59:37] Purity or Ploidy not numeric or in expected range.
FATAL [2025-11-13 21:59:37]
FATAL [2025-11-13 21:59:37] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 21:59:37] parameters (PureCN 2.17.0).
INFO [2025-11-13 21:59:37] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpGil4ER/file107ca4e2f55df.rds...
INFO [2025-11-13 21:59:37] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpGil4ER/file107ca4e2f55df.rds...
FATAL [2025-11-13 21:59:37] 'Failed' column in
FATAL [2025-11-13 21:59:37] /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpGil4ER/file107ca4e2f55df.csv
FATAL [2025-11-13 21:59:37] not logical(1).
FATAL [2025-11-13 21:59:37]
FATAL [2025-11-13 21:59:37] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 21:59:37] parameters (PureCN 2.17.0).
INFO [2025-11-13 21:59:38] 576 on-target bins with low coverage in all samples.
WARN [2025-11-13 21:59:38] You are likely not using the correct baits file!
WARN [2025-11-13 21:59:38] Allosome coverage missing, cannot determine sex.
WARN [2025-11-13 21:59:38] Allosome coverage missing, cannot determine sex.
INFO [2025-11-13 21:59:38] Processing on-target regions...
INFO [2025-11-13 21:59:38] Removing 930 intervals with low coverage in normalDB.
INFO [2025-11-13 21:59:38] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2025-11-13 21:59:39] 576 on-target bins with low coverage in all samples.
WARN [2025-11-13 21:59:39] You are likely not using the correct baits file!
WARN [2025-11-13 21:59:39] Allosome coverage missing, cannot determine sex.
WARN [2025-11-13 21:59:39] Allosome coverage missing, cannot determine sex.
INFO [2025-11-13 21:59:39] Processing on-target regions...
INFO [2025-11-13 21:59:39] Removing 930 intervals with low coverage in normalDB.
INFO [2025-11-13 21:59:39] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2025-11-13 21:59:40] 576 on-target bins with low coverage in all samples.
WARN [2025-11-13 21:59:40] You are likely not using the correct baits file!
WARN [2025-11-13 21:59:40] Allosome coverage missing, cannot determine sex.
WARN [2025-11-13 21:59:40] Allosome coverage missing, cannot determine sex.
INFO [2025-11-13 21:59:40] Processing on-target regions...
INFO [2025-11-13 21:59:40] Removing 930 intervals with low coverage in normalDB.
INFO [2025-11-13 21:59:40] Removing 1 intervals with zero coverage in more than 3% of normalDB.
WARN [2025-11-13 21:59:40] Allosome coverage missing, cannot determine sex.
INFO [2025-11-13 21:59:40] Sample sex: NA
WARN [2025-11-13 21:59:41] Allosome coverage missing, cannot determine sex.
INFO [2025-11-13 21:59:41] Sample sex: NA
INFO [2025-11-13 21:59:41] 576 on-target bins with low coverage in all samples.
WARN [2025-11-13 21:59:41] You are likely not using the correct baits file!
WARN [2025-11-13 21:59:41] Allosome coverage missing, cannot determine sex.
WARN [2025-11-13 21:59:41] Allosome coverage missing, cannot determine sex.
FATAL [2025-11-13 21:59:41] Length of normal.coverage.files and sex different
FATAL [2025-11-13 21:59:41]
FATAL [2025-11-13 21:59:41] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 21:59:41] parameters (PureCN 2.17.0).
WARN [2025-11-13 21:59:43] Target intervals were not sorted.
INFO [2025-11-13 21:59:43] 560 on-target bins with low coverage in all samples.
WARN [2025-11-13 21:59:43] You are likely not using the correct baits file!
WARN [2025-11-13 21:59:43] Allosome coverage missing, cannot determine sex.
WARN [2025-11-13 21:59:43] Allosome coverage missing, cannot determine sex.
WARN [2025-11-13 21:59:43] Allosome coverage missing, cannot determine sex.
INFO [2025-11-13 21:59:43] Processing on-target regions...
INFO [2025-11-13 21:59:43] Removing 978 intervals with low coverage in normalDB.
INFO [2025-11-13 21:59:43] Removing 11 intervals with zero coverage in more than 3% of normalDB.
FATAL [2025-11-13 21:59:44] tumor.coverage.file and normalDB do not align.
FATAL [2025-11-13 21:59:44]
FATAL [2025-11-13 21:59:44] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 21:59:44] parameters (PureCN 2.17.0).
FATAL [2025-11-13 21:59:44] At least 2 normal.coverage.files required.
FATAL [2025-11-13 21:59:44]
FATAL [2025-11-13 21:59:44] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 21:59:44] parameters (PureCN 2.17.0).
INFO [2025-11-13 21:59:45] ------------------------------------------------------------
INFO [2025-11-13 21:59:45] PureCN 2.17.0
INFO [2025-11-13 21:59:45] ------------------------------------------------------------
INFO [2025-11-13 21:59:45] Loading coverage files...
INFO [2025-11-13 21:59:45] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-11-13 21:59:45] Allosome coverage missing, cannot determine sex.
WARN [2025-11-13 21:59:45] Allosome coverage missing, cannot determine sex.
INFO [2025-11-13 21:59:45] Removing 228 intervals with missing log.ratio.
FATAL [2025-11-13 21:59:45] normalDB incompatible with this PureCN version. Please re-run
FATAL [2025-11-13 21:59:45] NormalDB.R.
FATAL [2025-11-13 21:59:45]
FATAL [2025-11-13 21:59:45] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 21:59:45] parameters (PureCN 2.17.0).
FATAL [2025-11-13 21:59:45] normalDB incompatible with this PureCN version. Please re-run
FATAL [2025-11-13 21:59:45] NormalDB.R.
FATAL [2025-11-13 21:59:45]
FATAL [2025-11-13 21:59:45] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 21:59:45] parameters (PureCN 2.17.0).
FATAL [2025-11-13 21:59:45] normal.coverage.files with _coverage.txt and _loess.txt suffix
FATAL [2025-11-13 21:59:45] provided. Provide either only GC-normalized or raw coverage files!
FATAL [2025-11-13 21:59:45]
FATAL [2025-11-13 21:59:45] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 21:59:45] parameters (PureCN 2.17.0).
INFO [2025-11-13 21:59:45] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-11-13 21:59:45] Removing 19 low quality variants with non-offset BQ < 25.
INFO [2025-11-13 21:59:45] Base quality scores range from 24 to 35 (offset by 1)
INFO [2025-11-13 21:59:45] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS.
INFO [2025-11-13 21:59:45] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-11-13 21:59:45] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-11-13 21:59:45] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-11-13 21:59:45] Removing 19 low quality variants with non-offset BQ < 25.
INFO [2025-11-13 21:59:45] Base quality scores range from 24 to 35 (offset by 1)
INFO [2025-11-13 21:59:46] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS.
INFO [2025-11-13 21:59:46] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-11-13 21:59:46] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-11-13 21:59:46] Removing 6 blacklisted variants.
INFO [2025-11-13 21:59:46] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-11-13 21:59:46] Removing 19 low quality variants with non-offset BQ < 25.
INFO [2025-11-13 21:59:46] Base quality scores range from 24 to 35 (offset by 1)
INFO [2025-11-13 21:59:46] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS.
INFO [2025-11-13 21:59:46] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-11-13 21:59:46] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
WARN [2025-11-13 21:59:46] MuTect stats file lacks contig and position columns.
INFO [2025-11-13 21:59:46] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-11-13 21:59:46] Removing 19 low quality variants with non-offset BQ < 25.
INFO [2025-11-13 21:59:46] Base quality scores range from 24 to 35 (offset by 1)
INFO [2025-11-13 21:59:46] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS.
INFO [2025-11-13 21:59:46] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-11-13 21:59:46] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
WARN [2025-11-13 21:59:46] MuTect stats file and VCF file do not align perfectly. Will remove 2325 unmatched variants.
WARN [2025-11-13 21:59:46] MuTect stats file lacks failure_reasons column. Keeping all variants listed in stats file.
INFO [2025-11-13 21:59:46] Removing 0 non heterozygous (in matched normal) germline SNPs.
INFO [2025-11-13 21:59:46] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-11-13 21:59:46] Base quality scores range from 31 to 33 (offset by 1)
INFO [2025-11-13 21:59:46] Minimum number of supporting reads ranges from 3 to 4, depending on coverage and BQS.
INFO [2025-11-13 21:59:47] Removing 0 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-11-13 21:59:47] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-11-13 21:59:47] Base quality scores range from 7 to 35 (offset by 1)
INFO [2025-11-13 21:59:47] Minimum number of supporting reads ranges from 1 to 41, depending on coverage and BQS.
INFO [2025-11-13 21:59:47] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-11-13 21:59:47] Removing 49 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-11-13 21:59:47] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-11-13 21:59:47] Base quality scores range from 7 to 35 (offset by 1)
INFO [2025-11-13 21:59:47] Minimum number of supporting reads ranges from 1 to 41, depending on coverage and BQS.
INFO [2025-11-13 21:59:47] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-11-13 21:59:47] Removing 49 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-11-13 21:59:47] Removing 22 non heterozygous (in matched normal) germline SNPs.
WARN [2025-11-13 21:59:47] Many variants removed by min.base.quality (50) filter. You might want to lower the cutoff.
FATAL [2025-11-13 21:59:47] No variants passed filter BQ.
FATAL [2025-11-13 21:59:47]
FATAL [2025-11-13 21:59:47] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 21:59:47] parameters (PureCN 2.17.0).
INFO [2025-11-13 21:59:47] Found 11 variants in VCF file.
WARN [2025-11-13 21:59:47] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead.
INFO [2025-11-13 21:59:47] 1 (9.1%) variants annotated as likely germline (DB INFO flag).
INFO [2025-11-13 21:59:48] Found 11 variants in VCF file.
WARN [2025-11-13 21:59:48] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead.
INFO [2025-11-13 21:59:48] 1 (9.1%) variants annotated as likely germline (DB INFO flag).
INFO [2025-11-13 21:59:48] Found 11 variants in VCF file.
WARN [2025-11-13 21:59:48] vcf.file has no DB or POP_AF info field for membership in germline databases. Guessing it based on available dbSNP ID.
INFO [2025-11-13 21:59:49] 1 (9.1%) variants annotated as likely germline (DB INFO flag).
INFO [2025-11-13 21:59:49] Found 1000 variants in VCF file.
INFO [2025-11-13 21:59:49] Removing 2 triallelic sites.
WARN [2025-11-13 21:59:49] Having trouble guessing SOMATIC status...
WARN [2025-11-13 21:59:49] DP FORMAT field contains NAs. Removing 44 variants.
INFO [2025-11-13 21:59:49] 954 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-11-13 21:59:49] Found 12 variants in VCF file.
INFO [2025-11-13 21:59:49] Removing 1 triallelic sites.
WARN [2025-11-13 21:59:49] DP FORMAT field contains NAs. Removing 1 variants.
WARN [2025-11-13 21:59:50] vcf.file has no DB info field for membership in germline databases. Found and used somatic status instead.
INFO [2025-11-13 21:59:50] 8 (80.0%) variants annotated as likely germline (DB INFO flag).
WARN [2025-11-13 21:59:50] BQ FORMAT field contains NAs.
INFO [2025-11-13 21:59:50] Found 2331 variants in VCF file.
INFO [2025-11-13 21:59:50] 2282 (97.9%) variants annotated as likely germline (DB INFO flag).
INFO [2025-11-13 21:59:50] Found 2331 variants in VCF file.
INFO [2025-11-13 21:59:50] 2282 (97.9%) variants annotated as likely germline (DB INFO flag).
WARN [2025-11-13 21:59:50] Did not find base quality scores, will use global error rate of 0.0010 instead.
INFO [2025-11-13 21:59:50] Removing 21 low quality variants with non-offset BQ < 25.
INFO [2025-11-13 21:59:50] Base quality scores range from 24 to 35 (offset by 1)
INFO [2025-11-13 21:59:50] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-11-13 21:59:50] Removing 89 variants with AF < 0.030 or AF >= 0.970 or insufficient supporting reads or depth < 15.
INFO [2025-11-13 21:59:50] Found 2331 variants in VCF file.
INFO [2025-11-13 21:59:50] 2282 (97.9%) variants annotated as likely germline (DB INFO flag).
WARN [2025-11-13 21:59:50] BQ FORMAT field contains NAs.
WARN [2025-11-13 21:59:51] Allosome coverage missing, cannot determine sex.
WARN [2025-11-13 21:59:51] Allosome coverage missing, cannot determine sex.
INFO [2025-11-13 21:59:51] Mean coverages: chrX: 108.58, chrY: 108.58, chr1-22: 104.87.
INFO [2025-11-13 21:59:51] Mean coverages: chrX: 108.58, chrY: 2.17, chr1-22: 104.87.
INFO [2025-11-13 21:59:51] Mean coverages: chrX: 108.58, chrY: 5.17, chr1-22: 104.87.
INFO [2025-11-13 21:59:51] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-11-13 21:59:51] No germline variants in VCF.
FATAL [2025-11-13 21:59:51] No solution with id hello
FATAL [2025-11-13 21:59:51]
FATAL [2025-11-13 21:59:51] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 21:59:51] parameters (PureCN 2.17.0).
FATAL [2025-11-13 21:59:51] No solution with id 100
FATAL [2025-11-13 21:59:51]
FATAL [2025-11-13 21:59:51] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 21:59:51] parameters (PureCN 2.17.0).
FATAL [2025-11-13 21:59:52] all.data and w have different lengths.
FATAL [2025-11-13 21:59:52]
FATAL [2025-11-13 21:59:52] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 21:59:52] parameters (PureCN 2.17.0).
INFO [2025-11-13 21:59:52] Splitting 5 large targets to an average width of 400.
WARN [2025-11-13 21:59:52] No mappability scores provided.
WARN [2025-11-13 21:59:52] No reptiming scores provided.
INFO [2025-11-13 21:59:52] Calculating GC-content...
INFO [2025-11-13 21:59:52] Splitting 5 large targets to an average width of 400.
WARN [2025-11-13 21:59:52] No mappability scores provided.
WARN [2025-11-13 21:59:52] No reptiming scores provided.
INFO [2025-11-13 21:59:52] Calculating GC-content...
INFO [2025-11-13 21:59:52] Splitting 5 large targets to an average width of 400.
INFO [2025-11-13 21:59:52] Removing 1 targets overlapping with exclude.
WARN [2025-11-13 21:59:52] No mappability scores provided.
WARN [2025-11-13 21:59:52] No reptiming scores provided.
INFO [2025-11-13 21:59:52] Calculating GC-content...
WARN [2025-11-13 21:59:52] Found small target regions (< 100bp). Will resize them.
INFO [2025-11-13 21:59:52] Splitting 5 large targets to an average width of 400.
FATAL [2025-11-13 21:59:52] off.target.padding must be negative.
FATAL [2025-11-13 21:59:52]
FATAL [2025-11-13 21:59:52] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 21:59:52] parameters (PureCN 2.17.0).
FATAL [2025-11-13 21:59:52] Interval coordinates should start at 1, not at 0
FATAL [2025-11-13 21:59:52]
FATAL [2025-11-13 21:59:52] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 21:59:52] parameters (PureCN 2.17.0).
WARN [2025-11-13 21:59:53] Found small target regions (< 100bp). Will resize them.
INFO [2025-11-13 21:59:53] Splitting 5 large targets to an average width of 400.
FATAL [2025-11-13 21:59:53] No off-target regions after filtering for mappability and
FATAL [2025-11-13 21:59:53] off.target.padding
FATAL [2025-11-13 21:59:53]
FATAL [2025-11-13 21:59:53] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 21:59:53] parameters (PureCN 2.17.0).
WARN [2025-11-13 21:59:53] Found small target regions (< 100bp). Will resize them.
INFO [2025-11-13 21:59:53] Splitting 5 large targets to an average width of 400.
WARN [2025-11-13 21:59:53] No mappability scores provided.
INFO [2025-11-13 21:59:53] Calculating GC-content...
WARN [2025-11-13 21:59:53] Found small target regions (< 100bp). Will resize them.
INFO [2025-11-13 21:59:53] Averaging reptiming into bins of size 200...
INFO [2025-11-13 21:59:53] Splitting 5 large targets to an average width of 400.
WARN [2025-11-13 21:59:53] No mappability scores provided.
INFO [2025-11-13 21:59:53] Calculating GC-content...
WARN [2025-11-13 21:59:53] Found small target regions (< 100bp). Will resize them.
INFO [2025-11-13 21:59:53] Splitting 6 large targets to an average width of 200.
WARN [2025-11-13 21:59:53] No mappability scores provided.
WARN [2025-11-13 21:59:53] No reptiming scores provided.
INFO [2025-11-13 21:59:53] Calculating GC-content...
WARN [2025-11-13 21:59:53] Found small target regions (< 100bp). Will resize them.
INFO [2025-11-13 21:59:53] Splitting 5 large targets to an average width of 400.
WARN [2025-11-13 21:59:53] No mappability scores provided.
WARN [2025-11-13 21:59:53] No reptiming scores provided.
INFO [2025-11-13 21:59:53] Calculating GC-content...
INFO [2025-11-13 21:59:53] Splitting 5 large targets to an average width of 400.
INFO [2025-11-13 21:59:53] Tiling off-target regions to an average width of 200000.
WARN [2025-11-13 21:59:53] No mappability scores provided.
WARN [2025-11-13 21:59:53] No reptiming scores provided.
INFO [2025-11-13 21:59:53] Calculating GC-content...
WARN [2025-11-13 21:59:53] Intervals contain off-target regions. Will not change intervals.
WARN [2025-11-13 21:59:53] No mappability scores provided.
WARN [2025-11-13 21:59:53] No reptiming scores provided.
INFO [2025-11-13 21:59:53] Calculating GC-content...
INFO [2025-11-13 21:59:53] Splitting 5 large targets to an average width of 400.
WARN [2025-11-13 21:59:53] No reptiming scores provided.
INFO [2025-11-13 21:59:53] Calculating GC-content...
WARN [2025-11-13 21:59:54] Found small target regions (< 100bp). Will resize them.
INFO [2025-11-13 21:59:54] Splitting 5 large targets to an average width of 400.
WARN [2025-11-13 21:59:54] No reptiming scores provided.
INFO [2025-11-13 21:59:54] Calculating GC-content...
WARN [2025-11-13 21:59:54] Found small target regions (< 100bp). Will resize them.
INFO [2025-11-13 21:59:54] Splitting 5 large targets to an average width of 400.
WARN [2025-11-13 21:59:54] 1 intervals without mappability score (1 on-target).
INFO [2025-11-13 21:59:54] Removing 1 intervals with low mappability score (<0.60).
WARN [2025-11-13 21:59:54] No reptiming scores provided.
INFO [2025-11-13 21:59:54] Calculating GC-content...
WARN [2025-11-13 21:59:54] Found small target regions (< 100bp). Will resize them.
INFO [2025-11-13 21:59:54] Splitting 5 large targets to an average width of 400.
INFO [2025-11-13 21:59:54] Tiling off-target regions to an average width of 200000.
WARN [2025-11-13 21:59:54] No reptiming scores provided.
INFO [2025-11-13 21:59:54] Calculating GC-content...
INFO [2025-11-13 21:59:54] Splitting 5 large targets to an average width of 400.
WARN [2025-11-13 21:59:54] No mappability scores provided.
WARN [2025-11-13 21:59:54] No reptiming scores provided.
INFO [2025-11-13 21:59:54] Calculating GC-content...
WARN [2025-11-13 21:59:55] Chromosome naming style of interval file (Ensembl) was different from reference (UCSC).
INFO [2025-11-13 21:59:55] Splitting 5 large targets to an average width of 400.
WARN [2025-11-13 21:59:55] No mappability scores provided.
WARN [2025-11-13 21:59:55] No reptiming scores provided.
INFO [2025-11-13 21:59:55] Calculating GC-content...
FATAL [2025-11-13 21:59:55] Chromosome naming style of interval file unknown, should be UCSC.
FATAL [2025-11-13 21:59:55]
FATAL [2025-11-13 21:59:55] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 21:59:55] parameters (PureCN 2.17.0).
WARN [2025-11-13 21:59:55] Chromosome naming style of interval file (Ensembl) was different from reference (UCSC).
WARN [2025-11-13 21:59:55] Chromosome naming style of mappability file (Ensembl) was different from reference (UCSC).
INFO [2025-11-13 21:59:55] Splitting 5 large targets to an average width of 400.
WARN [2025-11-13 21:59:55] No reptiming scores provided.
INFO [2025-11-13 21:59:55] Calculating GC-content...
WARN [2025-11-13 21:59:55] Found small target regions (< 60bp). Will resize them.
INFO [2025-11-13 21:59:55] Splitting 5 large targets to an average width of 400.
WARN [2025-11-13 21:59:55] No mappability scores provided.
WARN [2025-11-13 21:59:55] No reptiming scores provided.
INFO [2025-11-13 21:59:55] Calculating GC-content...
WARN [2025-11-13 21:59:55] Found small target regions (< 60bp). Will drop them.
INFO [2025-11-13 21:59:55] Splitting 4 large targets to an average width of 400.
WARN [2025-11-13 21:59:55] No mappability scores provided.
WARN [2025-11-13 21:59:55] No reptiming scores provided.
INFO [2025-11-13 21:59:55] Calculating GC-content...
WARN [2025-11-13 21:59:55] Found small target regions (< 200bp). Will resize them.
INFO [2025-11-13 21:59:55] Splitting 5 large targets to an average width of 400.
WARN [2025-11-13 21:59:55] No mappability scores provided.
WARN [2025-11-13 21:59:55] No reptiming scores provided.
INFO [2025-11-13 21:59:55] Calculating GC-content...
INFO [2025-11-13 21:59:55] Found 20 variants in VCF file.
INFO [2025-11-13 21:59:55] 20 (100.0%) variants annotated as likely germline (DB INFO flag).
WARN [2025-11-13 21:59:56] 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 [2025-11-13 21:59:56] Error reading AllelicCountsFile
FATAL [2025-11-13 21:59:56] /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/PureCN/extdata/example_allelic_counts_empty.tsv
FATAL [2025-11-13 21:59:56]
FATAL [2025-11-13 21:59:56] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 21:59:56] parameters (PureCN 2.17.0).
INFO [2025-11-13 21:59:56] Found 127 variants in VCF file.
INFO [2025-11-13 21:59:56] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
WARN [2025-11-13 21:59:56] Did not find base quality scores, will use global error rate of 0.0010 instead.
INFO [2025-11-13 21:59:56] ------------------------------------------------------------
INFO [2025-11-13 21:59:56] PureCN 2.17.0
INFO [2025-11-13 21:59:56] ------------------------------------------------------------
INFO [2025-11-13 21:59:56] Loading coverage files...
INFO [2025-11-13 21:59:56] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-11-13 21:59:56] Allosome coverage missing, cannot determine sex.
WARN [2025-11-13 21:59:56] Allosome coverage missing, cannot determine sex.
INFO [2025-11-13 21:59:56] Removing 228 intervals with missing log.ratio.
INFO [2025-11-13 21:59:56] Removing 22 small (< 5bp) intervals.
INFO [2025-11-13 21:59:56] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-11-13 21:59:56] No normalDB provided. Provide one for better results.
INFO [2025-11-13 21:59:56] Removing 1724 low count (< 100 total reads) intervals.
INFO [2025-11-13 21:59:56] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-11-13 21:59:56] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-11-13 21:59:56] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-11-13 21:59:56] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-11-13 21:59:56] Loading VCF...
INFO [2025-11-13 21:59:56] Found 127 variants in VCF file.
INFO [2025-11-13 21:59:56] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-11-13 21:59:56] LIB-02240e4 is tumor in VCF file.
INFO [2025-11-13 21:59:56] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-11-13 21:59:56] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-11-13 21:59:56] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-11-13 21:59:56] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-11-13 21:59:56] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-11-13 21:59:56] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-11-13 21:59:56] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding).
INFO [2025-11-13 21:59:57] 1.2% of targets contain variants.
INFO [2025-11-13 21:59:57] Removing 4 variants outside intervals.
INFO [2025-11-13 21:59:57] Found SOMATIC annotation in VCF.
INFO [2025-11-13 21:59:57] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-11-13 21:59:57] Found SOMATIC annotation in VCF. Setting mapping bias to 0.972.
INFO [2025-11-13 21:59:57] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-11-13 21:59:57] Sample sex: ?
INFO [2025-11-13 21:59:57] Segmenting data...
INFO [2025-11-13 21:59:57] Loading pre-computed boundaries for DNAcopy...
INFO [2025-11-13 21:59:57] Setting undo.SD parameter to 1.000000.
INFO [2025-11-13 21:59:57] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-11-13 21:59:57] Found 59 segments with median size of 17.67Mb.
INFO [2025-11-13 21:59:57] Using 121 variants.
INFO [2025-11-13 21:59:57] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-11-13 21:59:57] 2D-grid search of purity and ploidy...
INFO [2025-11-13 21:59:57] Local optima: 0.65/1.8, 0.52/2
INFO [2025-11-13 21:59:57] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2025-11-13 21:59:58] Testing local optimum 2/2 at purity 0.52 and total ploidy 2.00...
INFO [2025-11-13 21:59:58] Skipping 1 solutions that converged to the same optima.
INFO [2025-11-13 21:59:58] Fitting variants with beta model for local optimum 1/2...
INFO [2025-11-13 21:59:58] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2025-11-13 21:59:59] Optimized purity: 0.65
INFO [2025-11-13 21:59:59] Done.
INFO [2025-11-13 21:59:59] ------------------------------------------------------------
FATAL [2025-11-13 22:00:00] log.ratio NULL in .writeLogRatioFileGATK4
FATAL [2025-11-13 22:00:00]
FATAL [2025-11-13 22:00:00] This runtime error might be caused by invalid input data or parameters.
FATAL [2025-11-13 22:00:00] Please report bug (PureCN 2.17.0).
INFO [2025-11-13 22:00:00] Loaded provided segmentation file example_seg.txt (format DNAcopy).
INFO [2025-11-13 22:00:00] Re-centering provided segment means (offset -0.0033).
INFO [2025-11-13 22:00:00] Loaded provided segmentation file example_gatk4_modelfinal.seg.gz (format GATK4).
WARN [2025-11-13 22:00:00] Expecting numeric chromosome names in seg.file, assuming file is properly sorted.
INFO [2025-11-13 22:00:00] Re-centering provided segment means (offset -0.0037).
INFO [2025-11-13 22:00:00] 576 on-target bins with low coverage in all samples.
WARN [2025-11-13 22:00:00] You are likely not using the correct baits file!
WARN [2025-11-13 22:00:00] Allosome coverage missing, cannot determine sex.
WARN [2025-11-13 22:00:00] Allosome coverage missing, cannot determine sex.
INFO [2025-11-13 22:00:00] Processing on-target regions...
INFO [2025-11-13 22:00:00] Removing 930 intervals with low coverage in normalDB.
INFO [2025-11-13 22:00:00] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2025-11-13 22:00:01] ------------------------------------------------------------
INFO [2025-11-13 22:00:01] PureCN 2.17.0
INFO [2025-11-13 22:00:01] ------------------------------------------------------------
INFO [2025-11-13 22:00:01] Using BiocParallel for parallel optimization.
INFO [2025-11-13 22:00:01] Loading coverage files...
INFO [2025-11-13 22:00:01] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-11-13 22:00:01] Allosome coverage missing, cannot determine sex.
WARN [2025-11-13 22:00:01] Allosome coverage missing, cannot determine sex.
INFO [2025-11-13 22:00:01] Removing 228 intervals with missing log.ratio.
INFO [2025-11-13 22:00:01] Removing 705 intervals excluded in normalDB.
INFO [2025-11-13 22:00:01] normalDB provided. Setting minimum coverage for segmentation to 0.0015X.
INFO [2025-11-13 22:00:01] Removing 1066 low count (< 100 total reads) intervals.
INFO [2025-11-13 22:00:01] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-11-13 22:00:01] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-11-13 22:00:01] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-11-13 22:00:01] Sample sex: ?
INFO [2025-11-13 22:00:01] Segmenting data...
INFO [2025-11-13 22:00:01] Interval weights found, will use weighted CBS.
INFO [2025-11-13 22:00:01] Loading pre-computed boundaries for DNAcopy...
INFO [2025-11-13 22:00:01] Setting undo.SD parameter to 1.000000.
Setting multi-figure configuration
INFO [2025-11-13 22:00:02] Found 52 segments with median size of 29.35Mb.
INFO [2025-11-13 22:00:02] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-11-13 22:00:02] 2D-grid search of purity and ploidy...
INFO [2025-11-13 22:00:02] Local optima: 0.65/1.8, 0.52/2
INFO [2025-11-13 22:00:03] Skipping 1 solutions that converged to the same optima.
INFO [2025-11-13 22:00:03] Done.
INFO [2025-11-13 22:00:03] ------------------------------------------------------------
INFO [2025-11-13 22:00:03] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpGil4ER/file107ca76bef55a.rds...
FATAL [2025-11-13 22:00:03] runAbsoluteCN was run without a VCF file.
FATAL [2025-11-13 22:00:03]
FATAL [2025-11-13 22:00:03] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 22:00:03] parameters (PureCN 2.17.0).
FATAL [2025-11-13 22:00:03] runAbsoluteCN was run without a VCF file.
FATAL [2025-11-13 22:00:03]
FATAL [2025-11-13 22:00:03] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 22:00:03] parameters (PureCN 2.17.0).
INFO [2025-11-13 22:00:03] ------------------------------------------------------------
INFO [2025-11-13 22:00:03] PureCN 2.17.0
INFO [2025-11-13 22:00:03] ------------------------------------------------------------
INFO [2025-11-13 22:00:03] Loading coverage files...
INFO [2025-11-13 22:00:03] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-11-13 22:00:03] Allosome coverage missing, cannot determine sex.
WARN [2025-11-13 22:00:03] Allosome coverage missing, cannot determine sex.
INFO [2025-11-13 22:00:03] Removing 228 intervals with missing log.ratio.
INFO [2025-11-13 22:00:03] Removing 705 intervals excluded in normalDB.
INFO [2025-11-13 22:00:03] normalDB provided. Setting minimum coverage for segmentation to 0.0015X.
INFO [2025-11-13 22:00:03] Removing 1066 low count (< 100 total reads) intervals.
INFO [2025-11-13 22:00:04] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-11-13 22:00:04] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-11-13 22:00:04] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-11-13 22:00:04] Sample sex: ?
INFO [2025-11-13 22:00:04] Segmenting data...
INFO [2025-11-13 22:00:04] Interval weights found, will use weighted PSCBS.
FATAL [2025-11-13 22:00:04] segmentationPSCBS requires VCF file.
FATAL [2025-11-13 22:00:04]
FATAL [2025-11-13 22:00:04] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 22:00:04] parameters (PureCN 2.17.0).
INFO [2025-11-13 22:00:06] ------------------------------------------------------------
INFO [2025-11-13 22:00:06] PureCN 2.17.0
INFO [2025-11-13 22:00:06] ------------------------------------------------------------
INFO [2025-11-13 22:00:06] Loading coverage files...
FATAL [2025-11-13 22:00:06] Need a normal coverage file if log.ratio and seg.file are not provided.
FATAL [2025-11-13 22:00:06]
FATAL [2025-11-13 22:00:06] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 22:00:06] parameters (PureCN 2.17.0).
INFO [2025-11-13 22:00:06] ------------------------------------------------------------
INFO [2025-11-13 22:00:06] PureCN 2.17.0
INFO [2025-11-13 22:00:06] ------------------------------------------------------------
FATAL [2025-11-13 22:00:06] min.ploidy or max.ploidy not within expected range.
FATAL [2025-11-13 22:00:06]
FATAL [2025-11-13 22:00:06] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 22:00:06] parameters (PureCN 2.17.0).
INFO [2025-11-13 22:00:06] ------------------------------------------------------------
INFO [2025-11-13 22:00:06] PureCN 2.17.0
INFO [2025-11-13 22:00:06] ------------------------------------------------------------
FATAL [2025-11-13 22:00:06] min.ploidy or max.ploidy not within expected range.
FATAL [2025-11-13 22:00:06]
FATAL [2025-11-13 22:00:06] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 22:00:06] parameters (PureCN 2.17.0).
INFO [2025-11-13 22:00:06] ------------------------------------------------------------
INFO [2025-11-13 22:00:06] PureCN 2.17.0
INFO [2025-11-13 22:00:06] ------------------------------------------------------------
INFO [2025-11-13 22:00:06] ------------------------------------------------------------
INFO [2025-11-13 22:00:06] PureCN 2.17.0
INFO [2025-11-13 22:00:06] ------------------------------------------------------------
INFO [2025-11-13 22:00:06] ------------------------------------------------------------
INFO [2025-11-13 22:00:06] PureCN 2.17.0
INFO [2025-11-13 22:00:06] ------------------------------------------------------------
FATAL [2025-11-13 22:00:06] test.num.copy not within expected range.
FATAL [2025-11-13 22:00:06]
FATAL [2025-11-13 22:00:06] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 22:00:06] parameters (PureCN 2.17.0).
INFO [2025-11-13 22:00:06] ------------------------------------------------------------
INFO [2025-11-13 22:00:06] PureCN 2.17.0
INFO [2025-11-13 22:00:06] ------------------------------------------------------------
WARN [2025-11-13 22:00:06] test.num.copy outside recommended range.
FATAL [2025-11-13 22:00:06] max.non.clonal not within expected range or format.
FATAL [2025-11-13 22:00:06]
FATAL [2025-11-13 22:00:06] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 22:00:06] parameters (PureCN 2.17.0).
INFO [2025-11-13 22:00:06] ------------------------------------------------------------
INFO [2025-11-13 22:00:06] PureCN 2.17.0
INFO [2025-11-13 22:00:06] ------------------------------------------------------------
WARN [2025-11-13 22:00:06] test.num.copy outside recommended range.
FATAL [2025-11-13 22:00:06] max.non.clonal not within expected range or format.
FATAL [2025-11-13 22:00:06]
FATAL [2025-11-13 22:00:06] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 22:00:06] parameters (PureCN 2.17.0).
INFO [2025-11-13 22:00:06] ------------------------------------------------------------
INFO [2025-11-13 22:00:06] PureCN 2.17.0
INFO [2025-11-13 22:00:06] ------------------------------------------------------------
FATAL [2025-11-13 22:00:06] test.purity not within expected range.
FATAL [2025-11-13 22:00:06]
FATAL [2025-11-13 22:00:06] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 22:00:06] parameters (PureCN 2.17.0).
INFO [2025-11-13 22:00:06] ------------------------------------------------------------
INFO [2025-11-13 22:00:06] PureCN 2.17.0
INFO [2025-11-13 22:00:06] ------------------------------------------------------------
INFO [2025-11-13 22:00:06] Loading coverage files...
FATAL [2025-11-13 22:00:07] Tumor and normal are identical. This won't give any meaningful results
FATAL [2025-11-13 22:00:07] and I'm stopping here.
FATAL [2025-11-13 22:00:07]
FATAL [2025-11-13 22:00:07] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 22:00:07] parameters (PureCN 2.17.0).
INFO [2025-11-13 22:00:07] ------------------------------------------------------------
INFO [2025-11-13 22:00:07] PureCN 2.17.0
INFO [2025-11-13 22:00:07] ------------------------------------------------------------
INFO [2025-11-13 22:00:07] Loading coverage files...
FATAL [2025-11-13 22:00:07] Length of log.ratio different from tumor coverage.
FATAL [2025-11-13 22:00:07]
FATAL [2025-11-13 22:00:07] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 22:00:07] parameters (PureCN 2.17.0).
INFO [2025-11-13 22:00:07] ------------------------------------------------------------
INFO [2025-11-13 22:00:07] PureCN 2.17.0
INFO [2025-11-13 22:00:07] ------------------------------------------------------------
FATAL [2025-11-13 22:00:07] prior.purity must have the same length as test.purity.
FATAL [2025-11-13 22:00:07]
FATAL [2025-11-13 22:00:07] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 22:00:07] parameters (PureCN 2.17.0).
INFO [2025-11-13 22:00:07] ------------------------------------------------------------
INFO [2025-11-13 22:00:07] PureCN 2.17.0
INFO [2025-11-13 22:00:07] ------------------------------------------------------------
FATAL [2025-11-13 22:00:07] min.gof not within expected range or format.
FATAL [2025-11-13 22:00:07]
FATAL [2025-11-13 22:00:07] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 22:00:07] parameters (PureCN 2.17.0).
INFO [2025-11-13 22:00:07] ------------------------------------------------------------
INFO [2025-11-13 22:00:07] PureCN 2.17.0
INFO [2025-11-13 22:00:07] ------------------------------------------------------------
FATAL [2025-11-13 22:00:07] prior.purity not within expected range or format.
FATAL [2025-11-13 22:00:07]
FATAL [2025-11-13 22:00:07] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 22:00:07] parameters (PureCN 2.17.0).
INFO [2025-11-13 22:00:07] ------------------------------------------------------------
INFO [2025-11-13 22:00:07] PureCN 2.17.0
INFO [2025-11-13 22:00:07] ------------------------------------------------------------
FATAL [2025-11-13 22:00:07] prior.purity must add to 1. Sum is 1.5
FATAL [2025-11-13 22:00:07]
FATAL [2025-11-13 22:00:07] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 22:00:07] parameters (PureCN 2.17.0).
INFO [2025-11-13 22:00:07] ------------------------------------------------------------
INFO [2025-11-13 22:00:07] PureCN 2.17.0
INFO [2025-11-13 22:00:07] ------------------------------------------------------------
FATAL [2025-11-13 22:00:07] max.homozygous.loss not within expected range or format.
FATAL [2025-11-13 22:00:07]
FATAL [2025-11-13 22:00:07] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 22:00:07] parameters (PureCN 2.17.0).
INFO [2025-11-13 22:00:07] ------------------------------------------------------------
INFO [2025-11-13 22:00:07] PureCN 2.17.0
INFO [2025-11-13 22:00:07] ------------------------------------------------------------
FATAL [2025-11-13 22:00:07] prior.K not within expected range or format.
FATAL [2025-11-13 22:00:07]
FATAL [2025-11-13 22:00:07] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 22:00:07] parameters (PureCN 2.17.0).
INFO [2025-11-13 22:00:07] ------------------------------------------------------------
INFO [2025-11-13 22:00:07] PureCN 2.17.0
INFO [2025-11-13 22:00:07] ------------------------------------------------------------
FATAL [2025-11-13 22:00:07] prior.contamination not within expected range or format.
FATAL [2025-11-13 22:00:07]
FATAL [2025-11-13 22:00:07] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 22:00:07] parameters (PureCN 2.17.0).
INFO [2025-11-13 22:00:07] ------------------------------------------------------------
INFO [2025-11-13 22:00:07] PureCN 2.17.0
INFO [2025-11-13 22:00:07] ------------------------------------------------------------
FATAL [2025-11-13 22:00:07] Iterations not in the expected range from 10 to 250.
FATAL [2025-11-13 22:00:07]
FATAL [2025-11-13 22:00:07] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 22:00:07] parameters (PureCN 2.17.0).
INFO [2025-11-13 22:00:07] ------------------------------------------------------------
INFO [2025-11-13 22:00:07] PureCN 2.17.0
INFO [2025-11-13 22:00:07] ------------------------------------------------------------
FATAL [2025-11-13 22:00:07] Iterations not in the expected range from 10 to 250.
FATAL [2025-11-13 22:00:07]
FATAL [2025-11-13 22:00:07] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 22:00:07] parameters (PureCN 2.17.0).
INFO [2025-11-13 22:00:07] ------------------------------------------------------------
INFO [2025-11-13 22:00:07] PureCN 2.17.0
INFO [2025-11-13 22:00:07] ------------------------------------------------------------
INFO [2025-11-13 22:00:07] Loading coverage files...
FATAL [2025-11-13 22:00:07] Missing tumor.coverage.file requires seg.file or log.ratio and
FATAL [2025-11-13 22:00:07] interval.file.
FATAL [2025-11-13 22:00:07]
FATAL [2025-11-13 22:00:07] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 22:00:07] parameters (PureCN 2.17.0).
INFO [2025-11-13 22:00:07] ------------------------------------------------------------
INFO [2025-11-13 22:00:07] PureCN 2.17.0
INFO [2025-11-13 22:00:07] ------------------------------------------------------------
INFO [2025-11-13 22:00:07] ------------------------------------------------------------
INFO [2025-11-13 22:00:07] PureCN 2.17.0
INFO [2025-11-13 22:00:07] ------------------------------------------------------------
INFO [2025-11-13 22:00:07] Loading coverage files...
FATAL [2025-11-13 22:00:07] Interval files in normal and tumor different.
FATAL [2025-11-13 22:00:07]
FATAL [2025-11-13 22:00:07] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 22:00:07] parameters (PureCN 2.17.0).
INFO [2025-11-13 22:00:07] ------------------------------------------------------------
INFO [2025-11-13 22:00:07] PureCN 2.17.0
INFO [2025-11-13 22:00:07] ------------------------------------------------------------
INFO [2025-11-13 22:00:07] Loading coverage files...
INFO [2025-11-13 22:00:08] Mean target coverages: 0X (tumor) 99X (normal).
WARN [2025-11-13 22:00:08] Large difference in coverage of tumor and normal.
FATAL [2025-11-13 22:00:08] No finite intervals.
FATAL [2025-11-13 22:00:08]
FATAL [2025-11-13 22:00:08] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 22:00:08] parameters (PureCN 2.17.0).
INFO [2025-11-13 22:00:08] ------------------------------------------------------------
INFO [2025-11-13 22:00:08] PureCN 2.17.0
INFO [2025-11-13 22:00:08] ------------------------------------------------------------
INFO [2025-11-13 22:00:08] Loading coverage files...
INFO [2025-11-13 22:00:08] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-11-13 22:00:08] Allosome coverage missing, cannot determine sex.
WARN [2025-11-13 22:00:08] Allosome coverage missing, cannot determine sex.
INFO [2025-11-13 22:00:08] Removing 228 intervals with missing log.ratio.
INFO [2025-11-13 22:00:08] Removing 22 small (< 5bp) intervals.
INFO [2025-11-13 22:00:08] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-11-13 22:00:08] No normalDB provided. Provide one for better results.
INFO [2025-11-13 22:00:08] Removing 1724 low count (< 100 total reads) intervals.
INFO [2025-11-13 22:00:08] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-11-13 22:00:08] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-11-13 22:00:08] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-11-13 22:00:08] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-11-13 22:00:08] Loading VCF...
INFO [2025-11-13 22:00:08] Found 127 variants in VCF file.
INFO [2025-11-13 22:00:08] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-11-13 22:00:08] LIB-02240e4 is tumor in VCF file.
INFO [2025-11-13 22:00:08] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-11-13 22:00:08] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-11-13 22:00:08] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-11-13 22:00:08] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-11-13 22:00:08] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-11-13 22:00:08] 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/4.6-arm64/Resources/library/PureCN/extdata/example_allelic_counts_empty.tsv)
2: In UseMethod("mean") :
closing unused connection 5 (/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpGil4ER/file107ca458b2d72.tsv)
3: In UseMethod("mean") :
closing unused connection 4 (/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/PureCN/extdata/example_gatk4_denoised_cr.tsv.gz)
FATAL [2025-11-13 22:00:08] Could not import snp.blacklist
FATAL [2025-11-13 22:00:08] /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/PureCN/extdata/example_normal.txt.gz:Error
FATAL [2025-11-13 22:00:08] in FileForFormat(resource(con), fileFormat(con)) : Format 'txt'
FATAL [2025-11-13 22:00:08] unsupported
FATAL [2025-11-13 22:00:08]
FATAL [2025-11-13 22:00:08] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 22:00:08] parameters (PureCN 2.17.0).
INFO [2025-11-13 22:00:08] ------------------------------------------------------------
INFO [2025-11-13 22:00:08] PureCN 2.17.0
INFO [2025-11-13 22:00:08] ------------------------------------------------------------
INFO [2025-11-13 22:00:08] Loading coverage files...
INFO [2025-11-13 22:00:09] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-11-13 22:00:09] Allosome coverage missing, cannot determine sex.
WARN [2025-11-13 22:00:09] Allosome coverage missing, cannot determine sex.
INFO [2025-11-13 22:00:09] Removing 228 intervals with missing log.ratio.
INFO [2025-11-13 22:00:09] Removing 22 small (< 5bp) intervals.
INFO [2025-11-13 22:00:09] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-11-13 22:00:09] No normalDB provided. Provide one for better results.
INFO [2025-11-13 22:00:09] Removing 233 low coverage (< 15.0000X) intervals.
INFO [2025-11-13 22:00:09] Using 9547 intervals (9547 on-target, 0 off-target).
INFO [2025-11-13 22:00:09] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-11-13 22:00:09] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-11-13 22:00:09] Loading VCF...
INFO [2025-11-13 22:00:09] Found 127 variants in VCF file.
INFO [2025-11-13 22:00:09] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-11-13 22:00:09] LIB-02240e4 is tumor in VCF file.
INFO [2025-11-13 22:00:09] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-11-13 22:00:09] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-11-13 22:00:09] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-11-13 22:00:09] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-11-13 22:00:09] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-11-13 22:00:09] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-11-13 22:00:09] Total size of targeted genomic region: 1.63Mb (2.58Mb with 50bp padding).
INFO [2025-11-13 22:00:09] 1.0% of targets contain variants.
INFO [2025-11-13 22:00:09] Removing 2 variants outside intervals.
INFO [2025-11-13 22:00:09] Found SOMATIC annotation in VCF.
INFO [2025-11-13 22:00:09] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-11-13 22:00:09] Found SOMATIC annotation in VCF. Setting mapping bias to 0.973.
INFO [2025-11-13 22:00:09] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-11-13 22:00:09] Sample sex: ?
INFO [2025-11-13 22:00:09] Segmenting data...
INFO [2025-11-13 22:00:09] Loading pre-computed boundaries for DNAcopy...
INFO [2025-11-13 22:00:09] Setting undo.SD parameter to 1.000000.
INFO [2025-11-13 22:00:10] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-11-13 22:00:10] Found 54 segments with median size of 24.88Mb.
INFO [2025-11-13 22:00:10] Using 123 variants.
INFO [2025-11-13 22:00:10] Mean standard deviation of log-ratios: 0.37 (MAPD: 0.32)
INFO [2025-11-13 22:00:10] 2D-grid search of purity and ploidy...
INFO [2025-11-13 22:00:10] Local optima: 0.62/1.9, 0.3/1.9, 0.32/2
INFO [2025-11-13 22:00:10] Testing local optimum 1/3 at purity 0.62 and total ploidy 1.90...
INFO [2025-11-13 22:00:11] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-11-13 22:00:11] Recalibrating log-ratios...
INFO [2025-11-13 22:00:11] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-11-13 22:00:11] Recalibrating log-ratios...
INFO [2025-11-13 22:00:11] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-11-13 22:00:11] Recalibrating log-ratios...
INFO [2025-11-13 22:00:11] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-11-13 22:00:11] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-11-13 22:00:11] Recalibrating log-ratios...
INFO [2025-11-13 22:00:11] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-11-13 22:00:11] Recalibrating log-ratios...
INFO [2025-11-13 22:00:11] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-11-13 22:00:12] Recalibrating log-ratios...
INFO [2025-11-13 22:00:12] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-11-13 22:00:12] Skipping 1 solutions that converged to the same optima.
INFO [2025-11-13 22:00:12] Skipping 1 solutions exceeding max.non.clonal (0.20): 0.3/1.9 (purity/tumor ploidy)
INFO [2025-11-13 22:00:12] Fitting variants with beta model for local optimum 1/3...
INFO [2025-11-13 22:00:12] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01.
INFO [2025-11-13 22:00:13] Optimized purity: 0.65
INFO [2025-11-13 22:00:13] Done.
INFO [2025-11-13 22:00:13] ------------------------------------------------------------
INFO [2025-11-13 22:00:13] ------------------------------------------------------------
INFO [2025-11-13 22:00:13] PureCN 2.17.0
INFO [2025-11-13 22:00:13] ------------------------------------------------------------
INFO [2025-11-13 22:00:13] Loading coverage files...
INFO [2025-11-13 22:00:13] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-11-13 22:00:13] Allosome coverage missing, cannot determine sex.
WARN [2025-11-13 22:00:13] Allosome coverage missing, cannot determine sex.
INFO [2025-11-13 22:00:13] Removing 228 intervals with missing log.ratio.
INFO [2025-11-13 22:00:13] Removing 22 small (< 5bp) intervals.
INFO [2025-11-13 22:00:13] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-11-13 22:00:13] No normalDB provided. Provide one for better results.
INFO [2025-11-13 22:00:13] Removing 1724 low count (< 100 total reads) intervals.
INFO [2025-11-13 22:00:13] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-11-13 22:00:13] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-11-13 22:00:13] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-11-13 22:00:13] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-11-13 22:00:13] Loading VCF...
INFO [2025-11-13 22:00:13] Found 127 variants in VCF file.
WARN [2025-11-13 22:00:13] DP FORMAT field contains NAs. Removing 3 variants.
WARN [2025-11-13 22:00:13] DB INFO flag contains NAs
INFO [2025-11-13 22:00:13] 119 (96.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-11-13 22:00:13] LIB-02240e4 is tumor in VCF file.
INFO [2025-11-13 22:00:13] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-11-13 22:00:14] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-11-13 22:00:14] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-11-13 22:00:14] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-11-13 22:00:14] Removing 1 variants with AF < 0.030 or AF >= 0.970 or insufficient supporting reads or depth < 15.
INFO [2025-11-13 22:00:14] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding).
INFO [2025-11-13 22:00:14] 1.2% of targets contain variants.
INFO [2025-11-13 22:00:14] Setting somatic prior probabilities for likely germline hits to 0.000500 or to 0.500000 otherwise.
INFO [2025-11-13 22:00:14] Excluding 5 novel or poor quality variants from segmentation.
INFO [2025-11-13 22:00:14] Sample sex: ?
INFO [2025-11-13 22:00:14] Segmenting data...
INFO [2025-11-13 22:00:14] Loading pre-computed boundaries for DNAcopy...
INFO [2025-11-13 22:00:14] Setting undo.SD parameter to 1.000000.
Setting multi-figure configuration
INFO [2025-11-13 22:00:14] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-11-13 22:00:14] Found 59 segments with median size of 17.67Mb.
INFO [2025-11-13 22:00:14] Using 123 variants.
INFO [2025-11-13 22:00:14] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-11-13 22:00:14] 2D-grid search of purity and ploidy...
INFO [2025-11-13 22:00:15] Local optima: 0.62/1.9, 0.3/1.9, 0.32/2
INFO [2025-11-13 22:00:15] Testing local optimum 1/3 at purity 0.62 and total ploidy 1.90...
INFO [2025-11-13 22:00:15] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-11-13 22:00:15] Recalibrating log-ratios...
INFO [2025-11-13 22:00:15] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-11-13 22:00:15] Recalibrating log-ratios...
INFO [2025-11-13 22:00:15] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-11-13 22:00:16] Recalibrating log-ratios...
INFO [2025-11-13 22:00:16] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-11-13 22:00:16] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-11-13 22:00:16] Recalibrating log-ratios...
INFO [2025-11-13 22:00:16] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-11-13 22:00:16] Recalibrating log-ratios...
INFO [2025-11-13 22:00:16] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-11-13 22:00:16] Recalibrating log-ratios...
INFO [2025-11-13 22:00:16] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-11-13 22:00:16] Skipping 2 solutions exceeding max.non.clonal (0.20): 0.3/1.9, 0.35/1.61 (purity/tumor ploidy)
INFO [2025-11-13 22:00:16] Fitting variants with beta model for local optimum 1/3...
INFO [2025-11-13 22:00:16] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2025-11-13 22:00:17] Optimized purity: 0.65
INFO [2025-11-13 22:00:17] Done.
INFO [2025-11-13 22:00:17] ------------------------------------------------------------
INFO [2025-11-13 22:00:17] ------------------------------------------------------------
INFO [2025-11-13 22:00:17] PureCN 2.17.0
INFO [2025-11-13 22:00:17] ------------------------------------------------------------
INFO [2025-11-13 22:00:17] Loading coverage files...
INFO [2025-11-13 22:00:18] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-11-13 22:00:18] Allosome coverage missing, cannot determine sex.
WARN [2025-11-13 22:00:18] Allosome coverage missing, cannot determine sex.
INFO [2025-11-13 22:00:18] No Gene column in interval.file. You won't get gene-level calls.
INFO [2025-11-13 22:00:18] Removing 228 intervals with missing log.ratio.
INFO [2025-11-13 22:00:18] Removing 15 low/high GC targets.
INFO [2025-11-13 22:00:18] Removing 21 small (< 5bp) intervals.
INFO [2025-11-13 22:00:18] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-11-13 22:00:18] No normalDB provided. Provide one for better results.
INFO [2025-11-13 22:00:18] Removing 1718 low count (< 100 total reads) intervals.
INFO [2025-11-13 22:00:18] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-11-13 22:00:18] Removing 36 low mappability intervals.
INFO [2025-11-13 22:00:18] Using 8006 intervals (8006 on-target, 0 off-target).
INFO [2025-11-13 22:00:18] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-11-13 22:00:18] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio).
INFO [2025-11-13 22:00:18] Loading VCF...
INFO [2025-11-13 22:00:18] Found 127 variants in VCF file.
INFO [2025-11-13 22:00:18] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-11-13 22:00:18] LIB-02240e4 is tumor in VCF file.
INFO [2025-11-13 22:00:18] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-11-13 22:00:18] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-11-13 22:00:18] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-11-13 22:00:18] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-11-13 22:00:18] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-11-13 22:00:18] Removing 1 variants with AF < 0.030 or AF >= Inf or insufficient supporting reads or depth < 15.
INFO [2025-11-13 22:00:18] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding).
INFO [2025-11-13 22:00:18] 1.2% of targets contain variants.
INFO [2025-11-13 22:00:18] Removing 11 variants outside intervals.
INFO [2025-11-13 22:00:18] Found SOMATIC annotation in VCF.
INFO [2025-11-13 22:00:18] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-11-13 22:00:18] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970.
INFO [2025-11-13 22:00:19] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-11-13 22:00:19] Sample sex: ?
INFO [2025-11-13 22:00:19] Segmenting data...
INFO [2025-11-13 22:00:19] MAPD of 114 allelic fractions: 0.14 (0.15 adjusted).
INFO [2025-11-13 22:00:19] Using unweighted PSCBS.
INFO [2025-11-13 22:00:19] Setting undo.SD parameter to 1.000000.
INFO [2025-11-13 22:00:31] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-11-13 22:00:31] Found 72 segments with median size of 27.25Mb.
INFO [2025-11-13 22:00:31] Using 114 variants.
INFO [2025-11-13 22:00:31] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-11-13 22:00:31] 2D-grid search of purity and ploidy...
INFO [2025-11-13 22:00:31] Local optima: 0.65/1.8, 0.38/2.2
INFO [2025-11-13 22:00:31] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2025-11-13 22:00:31] Recalibrating log-ratios...
INFO [2025-11-13 22:00:31] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2025-11-13 22:00:31] Recalibrating log-ratios...
INFO [2025-11-13 22:00:31] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2025-11-13 22:00:31] Recalibrating log-ratios...
INFO [2025-11-13 22:00:31] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2025-11-13 22:00:31] Testing local optimum 2/2 at purity 0.38 and total ploidy 2.20...
INFO [2025-11-13 22:00:32] Skipping 1 solutions exceeding max.non.clonal (0.20): 0.65/2.05 (purity/tumor ploidy)
INFO [2025-11-13 22:00:32] Fitting variants with beta model for local optimum 2/2...
INFO [2025-11-13 22:00:32] Fitting variants for purity 0.40, tumor ploidy 2.55 and contamination 0.01.
INFO [2025-11-13 22:00:33] Optimized purity: 0.40
INFO [2025-11-13 22:00:33] Done.
INFO [2025-11-13 22:00:33] ------------------------------------------------------------
FATAL [2025-11-13 22:00:33] This function requires gene-level calls. Please add a column 'Gene'
FATAL [2025-11-13 22:00:33] containing gene symbols to the interval.file.
FATAL [2025-11-13 22:00:33]
FATAL [2025-11-13 22:00:33] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 22:00:33] parameters (PureCN 2.17.0).
INFO [2025-11-13 22:00:33] ------------------------------------------------------------
INFO [2025-11-13 22:00:33] PureCN 2.17.0
INFO [2025-11-13 22:00:33] ------------------------------------------------------------
INFO [2025-11-13 22:00:34] Loading coverage files...
INFO [2025-11-13 22:00:34] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-11-13 22:00:34] Allosome coverage missing, cannot determine sex.
WARN [2025-11-13 22:00:34] Allosome coverage missing, cannot determine sex.
INFO [2025-11-13 22:00:34] Removing 228 intervals with missing log.ratio.
INFO [2025-11-13 22:00:34] Removing 22 small (< 5bp) intervals.
INFO [2025-11-13 22:00:34] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-11-13 22:00:34] No normalDB provided. Provide one for better results.
INFO [2025-11-13 22:00:34] Removing 1724 low count (< 100 total reads) intervals.
INFO [2025-11-13 22:00:34] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-11-13 22:00:34] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-11-13 22:00:34] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-11-13 22:00:34] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-11-13 22:00:34] Loading VCF...
INFO [2025-11-13 22:00:34] Found 127 variants in VCF file.
INFO [2025-11-13 22:00:34] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
FATAL [2025-11-13 22:00:34] Different chromosome names in coverage and VCF.
FATAL [2025-11-13 22:00:34]
FATAL [2025-11-13 22:00:34] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 22:00:34] parameters (PureCN 2.17.0).
INFO [2025-11-13 22:00:34] ------------------------------------------------------------
INFO [2025-11-13 22:00:34] PureCN 2.17.0
INFO [2025-11-13 22:00:34] ------------------------------------------------------------
INFO [2025-11-13 22:00:34] Loading coverage files...
INFO [2025-11-13 22:00:34] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-11-13 22:00:34] Allosome coverage missing, cannot determine sex.
WARN [2025-11-13 22:00:34] Allosome coverage missing, cannot determine sex.
FATAL [2025-11-13 22:00:34] tumor.coverage.file and interval.file do not align.
FATAL [2025-11-13 22:00:34]
FATAL [2025-11-13 22:00:34] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 22:00:34] parameters (PureCN 2.17.0).
INFO [2025-11-13 22:00:34] ------------------------------------------------------------
INFO [2025-11-13 22:00:34] PureCN 2.17.0
INFO [2025-11-13 22:00:34] ------------------------------------------------------------
INFO [2025-11-13 22:00:34] Loading coverage files...
INFO [2025-11-13 22:00:34] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-11-13 22:00:34] Allosome coverage missing, cannot determine sex.
WARN [2025-11-13 22:00:34] Allosome coverage missing, cannot determine sex.
INFO [2025-11-13 22:00:35] Removing 228 intervals with missing log.ratio.
INFO [2025-11-13 22:00:35] Removing 15 low/high GC targets.
INFO [2025-11-13 22:00:35] Removing 21 small (< 5bp) intervals.
INFO [2025-11-13 22:00:35] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-11-13 22:00:35] No normalDB provided. Provide one for better results.
INFO [2025-11-13 22:00:35] Removing 1718 low count (< 100 total reads) intervals.
INFO [2025-11-13 22:00:35] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-11-13 22:00:35] Removing 36 low mappability intervals.
INFO [2025-11-13 22:00:35] Using 8006 intervals (8006 on-target, 0 off-target).
INFO [2025-11-13 22:00:35] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-11-13 22:00:35] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio).
INFO [2025-11-13 22:00:35] Loading VCF...
INFO [2025-11-13 22:00:35] Found 127 variants in VCF file.
INFO [2025-11-13 22:00:35] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-11-13 22:00:35] LIB-02240e4 is tumor in VCF file.
INFO [2025-11-13 22:00:35] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-11-13 22:00:35] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-11-13 22:00:35] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-11-13 22:00:35] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-11-13 22:00:35] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-11-13 22:00:35] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-11-13 22:00:35] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding).
INFO [2025-11-13 22:00:35] 1.2% of targets contain variants.
INFO [2025-11-13 22:00:35] Removing 11 variants outside intervals.
INFO [2025-11-13 22:00:35] Found SOMATIC annotation in VCF.
INFO [2025-11-13 22:00:35] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-11-13 22:00:35] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970.
INFO [2025-11-13 22:00:35] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-11-13 22:00:35] Sample sex: ?
INFO [2025-11-13 22:00:35] Segmenting data...
INFO [2025-11-13 22:00:35] Loading pre-computed boundaries for DNAcopy...
INFO [2025-11-13 22:00:35] Setting undo.SD parameter to 1.000000.
INFO [2025-11-13 22:00:36] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-11-13 22:00:36] Found 59 segments with median size of 17.67Mb.
INFO [2025-11-13 22:00:36] Using 114 variants.
INFO [2025-11-13 22:00:36] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-11-13 22:00:36] 2D-grid search of purity and ploidy...
INFO [2025-11-13 22:00:36] Local optima: 0.63/1.9
INFO [2025-11-13 22:00:36] Testing local optimum 1/1 at purity 0.63 and total ploidy 1.90...
INFO [2025-11-13 22:00:36] Fitting variants with beta model for local optimum 1/1...
INFO [2025-11-13 22:00:36] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2025-11-13 22:00:37] Optimized purity: 0.65
INFO [2025-11-13 22:00:37] Done.
INFO [2025-11-13 22:00:37] ------------------------------------------------------------
INFO [2025-11-13 22:00:37] ------------------------------------------------------------
INFO [2025-11-13 22:00:37] PureCN 2.17.0
INFO [2025-11-13 22:00:37] ------------------------------------------------------------
INFO [2025-11-13 22:00:37] Loading coverage files...
INFO [2025-11-13 22:00:37] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-11-13 22:00:37] Allosome coverage missing, cannot determine sex.
WARN [2025-11-13 22:00:37] Allosome coverage missing, cannot determine sex.
INFO [2025-11-13 22:00:38] Removing 228 intervals with missing log.ratio.
INFO [2025-11-13 22:00:38] Removing 15 low/high GC targets.
INFO [2025-11-13 22:00:38] Removing 21 small (< 5bp) intervals.
INFO [2025-11-13 22:00:38] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-11-13 22:00:38] No normalDB provided. Provide one for better results.
INFO [2025-11-13 22:00:38] Removing 1718 low count (< 100 total reads) intervals.
INFO [2025-11-13 22:00:38] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-11-13 22:00:38] Removing 36 low mappability intervals.
INFO [2025-11-13 22:00:38] Using 8006 intervals (8006 on-target, 0 off-target).
INFO [2025-11-13 22:00:38] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-11-13 22:00:38] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio).
INFO [2025-11-13 22:00:38] Loading VCF...
INFO [2025-11-13 22:00:38] Found 127 variants in VCF file.
INFO [2025-11-13 22:00:38] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-11-13 22:00:38] LIB-02240e4 is tumor in VCF file.
INFO [2025-11-13 22:00:38] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-11-13 22:00:38] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-11-13 22:00:38] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-11-13 22:00:38] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-11-13 22:00:38] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-11-13 22:00:38] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-11-13 22:00:38] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding).
INFO [2025-11-13 22:00:38] 1.2% of targets contain variants.
INFO [2025-11-13 22:00:38] Removing 11 variants outside intervals.
INFO [2025-11-13 22:00:38] Found SOMATIC annotation in VCF.
INFO [2025-11-13 22:00:38] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-11-13 22:00:38] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970.
INFO [2025-11-13 22:00:38] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-11-13 22:00:38] Sample sex: ?
INFO [2025-11-13 22:00:38] Segmenting data...
INFO [2025-11-13 22:00:38] Loading pre-computed boundaries for DNAcopy...
INFO [2025-11-13 22:00:38] Setting undo.SD parameter to 1.000000.
INFO [2025-11-13 22:00:39] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-11-13 22:00:39] Found 59 segments with median size of 17.67Mb.
INFO [2025-11-13 22:00:39] Using 114 variants.
INFO [2025-11-13 22:00:39] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-11-13 22:00:39] 2D-grid search of purity and ploidy...
INFO [2025-11-13 22:00:39] Local optima: 0.63/1.9
INFO [2025-11-13 22:00:39] Testing local optimum 1/1 at purity 0.63 and total ploidy 1.90...
INFO [2025-11-13 22:00:39] Fitting variants with beta model for local optimum 1/1...
WARN [2025-11-13 22:00:39] Some gene symbols found on multiple chromosomes. Use of approved symbols suggested.
INFO [2025-11-13 22:00:39] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2025-11-13 22:00:41] Optimized purity: 0.65
INFO [2025-11-13 22:00:41] Done.
INFO [2025-11-13 22:00:41] ------------------------------------------------------------
FATAL [2025-11-13 22:00:41] chr1 not valid chromosome name(s). Valid names are:
FATAL [2025-11-13 22:00:41] 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22
FATAL [2025-11-13 22:00:41]
FATAL [2025-11-13 22:00:41] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 22:00:41] parameters (PureCN 2.17.0).
INFO [2025-11-13 22:00:41] ------------------------------------------------------------
INFO [2025-11-13 22:00:41] PureCN 2.17.0
INFO [2025-11-13 22:00:41] ------------------------------------------------------------
INFO [2025-11-13 22:00:41] Loading coverage files...
WARN [2025-11-13 22:00:41] Provided sampleid (Sample2) does not match Sample1 found in segmentation.
WARN [2025-11-13 22:00:41] Allosome coverage missing, cannot determine sex.
WARN [2025-11-13 22:00:41] Allosome coverage missing, cannot determine sex.
INFO [2025-11-13 22:00:41] Removing 10 intervals with missing log.ratio.
INFO [2025-11-13 22:00:41] Using 10039 intervals (10039 on-target, 0 off-target).
INFO [2025-11-13 22:00:41] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-11-13 22:00:41] Loading VCF...
INFO [2025-11-13 22:00:41] Found 127 variants in VCF file.
INFO [2025-11-13 22:00:41] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-11-13 22:00:41] LIB-02240e4 is tumor in VCF file.
INFO [2025-11-13 22:00:41] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-11-13 22:00:41] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-11-13 22:00:41] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-11-13 22:00:41] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-11-13 22:00:41] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-11-13 22:00:41] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-11-13 22:00:41] Total size of targeted genomic region: 1.71Mb (2.70Mb with 50bp padding).
INFO [2025-11-13 22:00:41] 1.0% of targets contain variants.
INFO [2025-11-13 22:00:41] Removing 0 variants outside intervals.
INFO [2025-11-13 22:00:41] Found SOMATIC annotation in VCF.
INFO [2025-11-13 22:00:41] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-11-13 22:00:41] Found SOMATIC annotation in VCF. Setting mapping bias to 0.976.
INFO [2025-11-13 22:00:41] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-11-13 22:00:41] Sample sex: ?
INFO [2025-11-13 22:00:41] Segmenting data...
INFO [2025-11-13 22:00:41] Loaded provided segmentation file example_seg.txt (format DNAcopy).
WARN [2025-11-13 22:00:41] Provided sampleid (Sample2) does not match Sample1 found in segmentation.
INFO [2025-11-13 22:00:41] Re-centering provided segment means (offset -0.0033).
INFO [2025-11-13 22:00:41] Loading pre-computed boundaries for DNAcopy...
INFO [2025-11-13 22:00:41] Setting undo.SD parameter to 0.000000.
Setting multi-figure configuration
INFO [2025-11-13 22:00:41] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-11-13 22:00:41] Found 54 segments with median size of 24.88Mb.
INFO [2025-11-13 22:00:42] Using 125 variants.
INFO [2025-11-13 22:00:42] Mean standard deviation of log-ratios: 0.40 (MAPD: 0.00)
INFO [2025-11-13 22:00:42] 2D-grid search of purity and ploidy...
INFO [2025-11-13 22:00:42] Local optima: 0.6/1.9
INFO [2025-11-13 22:00:42] Testing local optimum 1/1 at purity 0.60 and total ploidy 1.90...
INFO [2025-11-13 22:00:42] Fitting variants with beta model for local optimum 1/1...
INFO [2025-11-13 22:00:42] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01.
INFO [2025-11-13 22:00:43] Optimized purity: 0.65
INFO [2025-11-13 22:00:43] Done.
INFO [2025-11-13 22:00:43] ------------------------------------------------------------
WARN [2025-11-13 22:00:43] Allosome coverage missing, cannot determine sex.
WARN [2025-11-13 22:00:43] Allosome coverage missing, cannot determine sex.
Setting multi-figure configuration
FATAL [2025-11-13 22:00:46] Segmentation file expected with colnames ID, chrom, loc.start, loc.end,
FATAL [2025-11-13 22:00:46] num.mark, seg.mean
FATAL [2025-11-13 22:00:46]
FATAL [2025-11-13 22:00:46] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 22:00:46] parameters (PureCN 2.17.0).
FATAL [2025-11-13 22:00:46] seg.file contains multiple samples and sampleid missing.
FATAL [2025-11-13 22:00:46]
FATAL [2025-11-13 22:00:46] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 22:00:46] parameters (PureCN 2.17.0).
FATAL [2025-11-13 22:00:46] seg.file contains multiple samples and sampleid does not match any.
FATAL [2025-11-13 22:00:46]
FATAL [2025-11-13 22:00:46] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 22:00:46] parameters (PureCN 2.17.0).
WARN [2025-11-13 22:00:46] Allosome coverage missing, cannot determine sex.
WARN [2025-11-13 22:00:46] Allosome coverage missing, cannot determine sex.
WARN [2025-11-13 22:00:49] Allosome coverage missing, cannot determine sex.
WARN [2025-11-13 22:00:49] Allosome coverage missing, cannot determine sex.
WARN [2025-11-13 22:00:49] Provided sampleid (example_tumor.txt.gz) does not match Sample1 found in segmentation.
WARN [2025-11-13 22:00:51] Allosome coverage missing, cannot determine sex.
WARN [2025-11-13 22:00:51] Allosome coverage missing, cannot determine sex.
WARN [2025-11-13 22:00:51] No normalDB provided. Provide one for better results.
WARN [2025-11-13 22:00:54] Allosome coverage missing, cannot determine sex.
WARN [2025-11-13 22:00:54] Allosome coverage missing, cannot determine sex.
WARN [2025-11-13 22:00:55] Provided sampleid (Sample.1) does not match Sample1 found in segmentation.
Setting multi-figure configuration
WARN [2025-11-13 22:00:57] Allosome coverage missing, cannot determine sex.
WARN [2025-11-13 22:00:57] Allosome coverage missing, cannot determine sex.
WARN [2025-11-13 22:00:57] No normalDB provided. Provide one for better results.
WARN [2025-11-13 22:00:58] Sampleid looks like a normal in VCF, not like a tumor.
WARN [2025-11-13 22:01:00] Allosome coverage missing, cannot determine sex.
WARN [2025-11-13 22:01:00] Allosome coverage missing, cannot determine sex.
FATAL [2025-11-13 22:01:00] normalDB not a valid normalDB object. Use createNormalDatabase to
FATAL [2025-11-13 22:01:00] create one.
FATAL [2025-11-13 22:01:00]
FATAL [2025-11-13 22:01:00] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 22:01:00] parameters (PureCN 2.17.0).
WARN [2025-11-13 22:01:00] You are likely not using the correct baits file!
WARN [2025-11-13 22:01:00] Allosome coverage missing, cannot determine sex.
WARN [2025-11-13 22:01:00] Allosome coverage missing, cannot determine sex.
WARN [2025-11-13 22:01:01] Allosome coverage missing, cannot determine sex.
WARN [2025-11-13 22:01:01] Allosome coverage missing, cannot determine sex.
FATAL [2025-11-13 22:01:01] normalDB appears to be empty.
FATAL [2025-11-13 22:01:01]
FATAL [2025-11-13 22:01:01] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 22:01:01] parameters (PureCN 2.17.0).
WARN [2025-11-13 22:01:02] Allosome coverage missing, cannot determine sex.
WARN [2025-11-13 22:01:02] Allosome coverage missing, cannot determine sex.
WARN [2025-11-13 22:01:02] Intervals in coverage and interval.file have conflicting on/off-target annotation.
WARN [2025-11-13 22:01:06] Allosome coverage missing, cannot determine sex.
WARN [2025-11-13 22:01:06] Allosome coverage missing, cannot determine sex.
FATAL [2025-11-13 22:01:06] Seqlevels missing in provided segmentation: 6
FATAL [2025-11-13 22:01:06]
FATAL [2025-11-13 22:01:06] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 22:01:06] parameters (PureCN 2.17.0).
sh: gatk: command not found
WARN [2025-11-13 22:01:07] Cannot find gatk binary in path.
WARN [2025-11-13 22:01:07] Allosome coverage missing, cannot determine sex.
WARN [2025-11-13 22:01:07] Allosome coverage missing, cannot determine sex.
WARN [2025-11-13 22:01:07] No normalDB provided. Provide one for better results.
FATAL [2025-11-13 22:01:07] segmentationHclust requires an input segmentation.
FATAL [2025-11-13 22:01:07]
FATAL [2025-11-13 22:01:07] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 22:01:07] parameters (PureCN 2.17.0).
WARN [2025-11-13 22:01:07] Allosome coverage missing, cannot determine sex.
WARN [2025-11-13 22:01:07] Allosome coverage missing, cannot determine sex.
WARN [2025-11-13 22:01:07] No normalDB provided. Provide one for better results.
FATAL [2025-11-13 22:01:17] The normal.panel.vcf.file contains only a single sample.
FATAL [2025-11-13 22:01:17]
FATAL [2025-11-13 22:01:17] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 22:01:17] parameters (PureCN 2.17.0).
FATAL [2025-11-13 22:01:18] mapping.bias.file must be a file with *.rds suffix.
FATAL [2025-11-13 22:01:18]
FATAL [2025-11-13 22:01:18] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 22:01:18] parameters (PureCN 2.17.0).
Failed with error: 'there is no package called 'genomicsdb''
FATAL [2025-11-13 22:01:18] min.normals (0) must be >= 1.
FATAL [2025-11-13 22:01:18]
FATAL [2025-11-13 22:01:18] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 22:01:18] parameters (PureCN 2.17.0).
FATAL [2025-11-13 22:01:18] min.normals (10) cannot be larger than min.normals.assign.betafit (3).
FATAL [2025-11-13 22:01:18]
FATAL [2025-11-13 22:01:18] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 22:01:18] parameters (PureCN 2.17.0).
FATAL [2025-11-13 22:01:18] min.normals.assign.betafit (10) cannot be larger than
FATAL [2025-11-13 22:01:18] min.normals.betafit (7).
FATAL [2025-11-13 22:01:18]
FATAL [2025-11-13 22:01:18] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 22:01:18] parameters (PureCN 2.17.0).
FATAL [2025-11-13 22:01:18] min.normals.betafit (20) cannot be larger than
FATAL [2025-11-13 22:01:18] min.normals.position.specific.fit (10).
FATAL [2025-11-13 22:01:18]
FATAL [2025-11-13 22:01:18] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 22:01:18] parameters (PureCN 2.17.0).
FATAL [2025-11-13 22:01:18] min.betafit.rho not within expected range or format.
FATAL [2025-11-13 22:01:18]
FATAL [2025-11-13 22:01:18] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 22:01:18] parameters (PureCN 2.17.0).
FATAL [2025-11-13 22:01:18] max.betafit.rho not within expected range or format.
FATAL [2025-11-13 22:01:18]
FATAL [2025-11-13 22:01:18] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 22:01:18] parameters (PureCN 2.17.0).
FATAL [2025-11-13 22:01:18] min.betafit.rho (0.9) cannot be larger than max.betafit.rho (0.2).
FATAL [2025-11-13 22:01:18]
FATAL [2025-11-13 22:01:18] This is most likely a user error due to invalid input data or
FATAL [2025-11-13 22:01:18] parameters (PureCN 2.17.0).
[ FAIL 0 | WARN 12 | SKIP 2 | PASS 405 ]
══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• gatk binary > 4.1.7.0 required (1): 'test_segmentation.R:25:4'
• genomicsdb required (1): 'test_setMappingBiasVcf.R:45:5'
[ FAIL 0 | WARN 12 | SKIP 2 | PASS 405 ]
>
> proc.time()
user system elapsed
161.501 5.548 159.954
PureCN.Rcheck/PureCN-Ex.timings
| name | user | system | elapsed | |
| adjustLogRatio | 0.882 | 0.016 | 0.973 | |
| annotateTargets | 5.644 | 0.223 | 6.066 | |
| bootstrapResults | 0.213 | 0.020 | 0.264 | |
| calculateBamCoverageByInterval | 0.080 | 0.002 | 0.085 | |
| calculateLogRatio | 0.360 | 0.018 | 0.409 | |
| calculateMappingBiasGatk4 | 0.000 | 0.000 | 0.001 | |
| calculateMappingBiasVcf | 0.748 | 0.027 | 0.809 | |
| calculatePowerDetectSomatic | 0.559 | 0.002 | 0.563 | |
| calculateTangentNormal | 1.248 | 0.025 | 1.376 | |
| callAlterations | 0.058 | 0.002 | 0.063 | |
| callAlterationsFromSegmentation | 0.670 | 0.013 | 0.796 | |
| callAmplificationsInLowPurity | 15.188 | 0.155 | 16.326 | |
| callCIN | 0.116 | 0.003 | 0.119 | |
| callLOH | 0.080 | 0.002 | 0.091 | |
| callMutationBurden | 0.662 | 0.014 | 0.694 | |
| centromeres | 0.000 | 0.001 | 0.002 | |
| correctCoverageBias | 0.698 | 0.014 | 0.724 | |
| createCurationFile | 0.162 | 0.004 | 0.168 | |
| createNormalDatabase | 1.048 | 0.014 | 1.098 | |
| filterIntervals | 8.379 | 0.153 | 8.822 | |
| filterVcfBasic | 0.269 | 0.005 | 0.297 | |
| filterVcfMuTect | 0.269 | 0.005 | 0.291 | |
| filterVcfMuTect2 | 0.258 | 0.003 | 0.279 | |
| findFocal | 4.475 | 0.055 | 4.773 | |
| findHighQualitySNPs | 0.596 | 0.004 | 0.619 | |
| getSexFromCoverage | 0.098 | 0.004 | 0.108 | |
| getSexFromVcf | 0.103 | 0.004 | 0.115 | |
| plotAbs | 0.092 | 0.004 | 0.106 | |
| poolCoverage | 0.242 | 0.012 | 0.262 | |
| predictSomatic | 0.178 | 0.002 | 0.191 | |
| preprocessIntervals | 0.260 | 0.006 | 0.271 | |
| processMultipleSamples | 0.880 | 0.015 | 0.929 | |
| readAllelicCountsFile | 0.220 | 0.001 | 0.243 | |
| readCoverageFile | 0.098 | 0.004 | 0.112 | |
| readCurationFile | 0.093 | 0.004 | 0.107 | |
| readIntervalFile | 0.067 | 0.003 | 0.069 | |
| readLogRatioFile | 0.011 | 0.000 | 0.012 | |
| readSegmentationFile | 0.003 | 0.001 | 0.004 | |
| runAbsoluteCN | 6.375 | 0.121 | 6.827 | |
| segmentationCBS | 3.078 | 0.028 | 3.249 | |
| segmentationGATK4 | 0.001 | 0.000 | 0.001 | |
| segmentationHclust | 5.757 | 0.113 | 6.086 | |
| segmentationPSCBS | 14.324 | 0.164 | 15.033 | |
| setMappingBiasVcf | 0.133 | 0.003 | 0.138 | |
| setPriorVcf | 0.105 | 0.003 | 0.111 | |