Markus Riester
| Snapshot Date: 2025-11-17 13:40 -0500 (Mon, 17 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 2025-11-18 11:40 -0500 (Tue, 18 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" | 4826 |
| lconway | macOS 12.7.6 Monterey | x86_64 | R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" | 4561 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4562 |
| 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 | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the PureCN package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PureCN.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: PureCN |
| Version: 2.17.0 |
| 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: 2025-11-17 22:49:08 -0500 (Mon, 17 Nov 2025) |
| EndedAt: 2025-11-17 22:55:44 -0500 (Mon, 17 Nov 2025) |
| EllapsedTime: 396.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: PureCN.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PureCN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PureCN_2.17.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/PureCN.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PureCN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PureCN’ version ‘2.17.0’
* checking package namespace information ... OK
* checking package dependencies ... INFO
Package which this enhances but not available for checking: ‘genomicsdb’
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘PureCN’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
callAmplificationsInLowPurity 15.321 0.148 18.175
segmentationPSCBS 14.506 0.174 15.647
filterIntervals 8.854 0.148 10.065
runAbsoluteCN 6.711 0.125 7.260
annotateTargets 5.981 0.236 6.508
segmentationHclust 5.720 0.103 6.347
* 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 [2025-11-17 22:53:07] Attempted adding gene symbols to intervals. Heuristics have been used to pick symbols for overlapping genes.
WARN [2025-11-17 22:53:07] Chromosome naming style of txdb file (UCSC) was different from interval file (Ensembl).
WARN [2025-11-17 22:53:12] Attempted adding gene symbols to intervals. Heuristics have been used to pick symbols for overlapping genes.
FATAL [2025-11-17 22:53:13] tumor.coverage.file and interval.file do not align.
FATAL [2025-11-17 22:53:13]
FATAL [2025-11-17 22:53:13] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:53:13] parameters (PureCN 2.17.0).
WARN [2025-11-17 22:53:13] Cannot find all contig lengths while exporting interval file.
INFO [2025-11-17 22:53:14] Processing seq1:1-21 (1/3)...
INFO [2025-11-17 22:53:14] Processing seq1:1227-1247 (2/3)...
INFO [2025-11-17 22:53:15] Processing seq2:594-614 (3/3)...
WARN [2025-11-17 22:53:15] Large potential mis-calibration of on- and off-target log2 ratios: 0.26
FATAL [2025-11-17 22:53:15] Need either f or purity and ploidy.
FATAL [2025-11-17 22:53:15]
FATAL [2025-11-17 22:53:15] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:53:15] parameters (PureCN 2.17.0).
FATAL [2025-11-17 22:53:15] f not in expected range.
FATAL [2025-11-17 22:53:15]
FATAL [2025-11-17 22:53:15] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:53:15] parameters (PureCN 2.17.0).
FATAL [2025-11-17 22:53:15] coverage not in expected range (>=2)
FATAL [2025-11-17 22:53:15]
FATAL [2025-11-17 22:53:15] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:53:15] parameters (PureCN 2.17.0).
FATAL [2025-11-17 22:53:15] purity not in expected range.
FATAL [2025-11-17 22:53:15]
FATAL [2025-11-17 22:53:15] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:53:15] parameters (PureCN 2.17.0).
FATAL [2025-11-17 22:53:15] ploidy not in expected range.
FATAL [2025-11-17 22:53:15]
FATAL [2025-11-17 22:53:15] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:53:15] parameters (PureCN 2.17.0).
FATAL [2025-11-17 22:53:15] cell.fraction not in expected range.
FATAL [2025-11-17 22:53:15]
FATAL [2025-11-17 22:53:15] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:53:15] parameters (PureCN 2.17.0).
INFO [2025-11-17 22:53:16] 576 on-target bins with low coverage in all samples.
WARN [2025-11-17 22:53:16] You are likely not using the correct baits file!
WARN [2025-11-17 22:53:16] Allosome coverage missing, cannot determine sex.
WARN [2025-11-17 22:53:16] Allosome coverage missing, cannot determine sex.
INFO [2025-11-17 22:53:16] Processing on-target regions...
INFO [2025-11-17 22:53:16] Removing 930 intervals with low coverage in normalDB.
INFO [2025-11-17 22:53:16] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2025-11-17 22:53:17] Tumor/normal noise ratio: 19.041
WARN [2025-11-17 22:53:17] Extensive noise in tumor compared to normals.
INFO [2025-11-17 22:53:34] Tumor/normal noise ratio: 19.041
WARN [2025-11-17 22:53:34] Extensive noise in tumor compared to normals.
INFO [2025-11-17 22:53:36] Using BiocParallel for parallel optimization.
FATAL [2025-11-17 22:53:41] pvalue.cutoff not within expected range or format.
FATAL [2025-11-17 22:53:41]
FATAL [2025-11-17 22:53:41] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:53:41] parameters (PureCN 2.17.0).
FATAL [2025-11-17 22:53:41] pvalue.cutoff not within expected range or format.
FATAL [2025-11-17 22:53:41]
FATAL [2025-11-17 22:53:41] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:53:41] parameters (PureCN 2.17.0).
FATAL [2025-11-17 22:53:41] percentile.cutoff not in expected range (0 to 100).
FATAL [2025-11-17 22:53:41]
FATAL [2025-11-17 22:53:41] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:53:41] parameters (PureCN 2.17.0).
FATAL [2025-11-17 22:53:41] percentile.cutoff not in expected range (0 to 100).
FATAL [2025-11-17 22:53:41]
FATAL [2025-11-17 22:53:41] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:53:41] parameters (PureCN 2.17.0).
FATAL [2025-11-17 22:53:41] purity not within expected range or format.
FATAL [2025-11-17 22:53:41]
FATAL [2025-11-17 22:53:41] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:53:41] parameters (PureCN 2.17.0).
FATAL [2025-11-17 22:53:41] purity not within expected range or format.
FATAL [2025-11-17 22:53:41]
FATAL [2025-11-17 22:53:41] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:53:41] parameters (PureCN 2.17.0).
INFO [2025-11-17 22:53:42] ------------------------------------------------------------
INFO [2025-11-17 22:53:42] PureCN 2.17.0
INFO [2025-11-17 22:53:42] ------------------------------------------------------------
INFO [2025-11-17 22:53:42] Loading coverage files...
INFO [2025-11-17 22:53:42] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-11-17 22:53:42] Allosome coverage missing, cannot determine sex.
WARN [2025-11-17 22:53:42] Allosome coverage missing, cannot determine sex.
INFO [2025-11-17 22:53:42] Removing 228 intervals with missing log.ratio.
INFO [2025-11-17 22:53:42] Removing 22 small (< 5bp) intervals.
INFO [2025-11-17 22:53:42] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-11-17 22:53:42] No normalDB provided. Provide one for better results.
INFO [2025-11-17 22:53:42] Removing 1724 low count (< 100 total reads) intervals.
INFO [2025-11-17 22:53:42] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-11-17 22:53:42] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-11-17 22:53:42] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-11-17 22:53:42] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-11-17 22:53:42] Loading VCF...
INFO [2025-11-17 22:53:42] Found 127 variants in VCF file.
INFO [2025-11-17 22:53:42] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-11-17 22:53:42] LIB-02240e4 is tumor in VCF file.
INFO [2025-11-17 22:53:42] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-11-17 22:53:42] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-11-17 22:53:42] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-11-17 22:53:42] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-11-17 22:53:42] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-11-17 22:53:42] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-11-17 22:53:42] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding).
INFO [2025-11-17 22:53:42] 1.2% of targets contain variants.
INFO [2025-11-17 22:53:42] Removing 4 variants outside intervals.
INFO [2025-11-17 22:53:42] Found SOMATIC annotation in VCF.
INFO [2025-11-17 22:53:42] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-11-17 22:53:42] Found SOMATIC annotation in VCF. Setting mapping bias to 0.972.
INFO [2025-11-17 22:53:43] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-11-17 22:53:43] Sample sex: ?
INFO [2025-11-17 22:53:43] Segmenting data...
INFO [2025-11-17 22:53:43] Loading pre-computed boundaries for DNAcopy...
INFO [2025-11-17 22:53:43] Setting undo.SD parameter to 1.000000.
INFO [2025-11-17 22:53:43] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-11-17 22:53:43] Found 59 segments with median size of 17.67Mb.
INFO [2025-11-17 22:53:43] Using 121 variants.
INFO [2025-11-17 22:53:43] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-11-17 22:53:43] 2D-grid search of purity and ploidy...
INFO [2025-11-17 22:53:44] Local optima: 0.63/1.9, 0.5/2
INFO [2025-11-17 22:53:44] Testing local optimum 1/2 at purity 0.63 and total ploidy 1.90...
INFO [2025-11-17 22:53:44] Testing local optimum 2/2 at purity 0.50 and total ploidy 2.00...
INFO [2025-11-17 22:53:45] Skipping 1 solutions that converged to the same optima.
INFO [2025-11-17 22:53:45] Fitting variants with beta model for local optimum 1/2...
INFO [2025-11-17 22:53:45] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2025-11-17 22:53:46] Optimized purity: 0.65
INFO [2025-11-17 22:53:46] Done.
INFO [2025-11-17 22:53:46] ------------------------------------------------------------
INFO [2025-11-17 22:53:46] Estimating callable regions.
FATAL [2025-11-17 22:53:47] exclude not a GRanges object.
FATAL [2025-11-17 22:53:47]
FATAL [2025-11-17 22:53:47] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:53:47] parameters (PureCN 2.17.0).
FATAL [2025-11-17 22:53:47] callable not a GRanges object.
FATAL [2025-11-17 22:53:47]
FATAL [2025-11-17 22:53:47] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:53:47] parameters (PureCN 2.17.0).
WARN [2025-11-17 22:53:49] tumor.coverage.file and interval.file do not align.
INFO [2025-11-17 22:53:50] No Gene column in interval.file. You won't get gene-level calls.
FATAL [2025-11-17 22:53:50] No gc_bias column in interval.file.
FATAL [2025-11-17 22:53:50]
FATAL [2025-11-17 22:53:50] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:53:50] parameters (PureCN 2.17.0).
FATAL [2025-11-17 22:53:50] Provided coverage is zero, most likely due to a corrupt BAM file.
FATAL [2025-11-17 22:53:50]
FATAL [2025-11-17 22:53:50] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:53:50] parameters (PureCN 2.17.0).
INFO [2025-11-17 22:53:51] No reptiming column in interval.file.
INFO [2025-11-17 22:53:53] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2rjXjq/file1067a4c7efd4e.rds...
INFO [2025-11-17 22:53:53] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2rjXjq/file1067a4c7efd4e.rds...
INFO [2025-11-17 22:53:53] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2rjXjq/file1067a4c7efd4e.rds...
INFO [2025-11-17 22:53:53] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2rjXjq/file1067a4c7efd4e.rds...
INFO [2025-11-17 22:53:53] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2rjXjq/file1067a4c7efd4e.rds...
INFO [2025-11-17 22:53:53] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2rjXjq/file1067a4c7efd4e.rds...
FATAL [2025-11-17 22:53:53] Purity or Ploidy not numeric or in expected range.
FATAL [2025-11-17 22:53:53]
FATAL [2025-11-17 22:53:53] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:53:53] parameters (PureCN 2.17.0).
INFO [2025-11-17 22:53:53] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2rjXjq/file1067a4c7efd4e.rds...
INFO [2025-11-17 22:53:53] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2rjXjq/file1067a4c7efd4e.rds...
FATAL [2025-11-17 22:53:53] 'Failed' column in
FATAL [2025-11-17 22:53:53] /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2rjXjq/file1067a4c7efd4e.csv
FATAL [2025-11-17 22:53:53] not logical(1).
FATAL [2025-11-17 22:53:53]
FATAL [2025-11-17 22:53:53] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:53:53] parameters (PureCN 2.17.0).
INFO [2025-11-17 22:53:54] 576 on-target bins with low coverage in all samples.
WARN [2025-11-17 22:53:54] You are likely not using the correct baits file!
WARN [2025-11-17 22:53:54] Allosome coverage missing, cannot determine sex.
WARN [2025-11-17 22:53:54] Allosome coverage missing, cannot determine sex.
INFO [2025-11-17 22:53:54] Processing on-target regions...
INFO [2025-11-17 22:53:54] Removing 930 intervals with low coverage in normalDB.
INFO [2025-11-17 22:53:54] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2025-11-17 22:53:55] 576 on-target bins with low coverage in all samples.
WARN [2025-11-17 22:53:55] You are likely not using the correct baits file!
WARN [2025-11-17 22:53:55] Allosome coverage missing, cannot determine sex.
WARN [2025-11-17 22:53:55] Allosome coverage missing, cannot determine sex.
INFO [2025-11-17 22:53:55] Processing on-target regions...
INFO [2025-11-17 22:53:55] Removing 930 intervals with low coverage in normalDB.
INFO [2025-11-17 22:53:55] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2025-11-17 22:53:56] 576 on-target bins with low coverage in all samples.
WARN [2025-11-17 22:53:56] You are likely not using the correct baits file!
WARN [2025-11-17 22:53:56] Allosome coverage missing, cannot determine sex.
WARN [2025-11-17 22:53:56] Allosome coverage missing, cannot determine sex.
INFO [2025-11-17 22:53:56] Processing on-target regions...
INFO [2025-11-17 22:53:56] Removing 930 intervals with low coverage in normalDB.
INFO [2025-11-17 22:53:56] Removing 1 intervals with zero coverage in more than 3% of normalDB.
WARN [2025-11-17 22:53:57] Allosome coverage missing, cannot determine sex.
INFO [2025-11-17 22:53:57] Sample sex: NA
WARN [2025-11-17 22:53:57] Allosome coverage missing, cannot determine sex.
INFO [2025-11-17 22:53:57] Sample sex: NA
INFO [2025-11-17 22:53:57] 576 on-target bins with low coverage in all samples.
WARN [2025-11-17 22:53:57] You are likely not using the correct baits file!
WARN [2025-11-17 22:53:57] Allosome coverage missing, cannot determine sex.
WARN [2025-11-17 22:53:57] Allosome coverage missing, cannot determine sex.
FATAL [2025-11-17 22:53:57] Length of normal.coverage.files and sex different
FATAL [2025-11-17 22:53:57]
FATAL [2025-11-17 22:53:57] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:53:57] parameters (PureCN 2.17.0).
WARN [2025-11-17 22:53:59] Target intervals were not sorted.
INFO [2025-11-17 22:53:59] 560 on-target bins with low coverage in all samples.
WARN [2025-11-17 22:53:59] You are likely not using the correct baits file!
WARN [2025-11-17 22:53:59] Allosome coverage missing, cannot determine sex.
WARN [2025-11-17 22:53:59] Allosome coverage missing, cannot determine sex.
WARN [2025-11-17 22:53:59] Allosome coverage missing, cannot determine sex.
INFO [2025-11-17 22:53:59] Processing on-target regions...
INFO [2025-11-17 22:53:59] Removing 978 intervals with low coverage in normalDB.
INFO [2025-11-17 22:53:59] Removing 11 intervals with zero coverage in more than 3% of normalDB.
FATAL [2025-11-17 22:54:00] tumor.coverage.file and normalDB do not align.
FATAL [2025-11-17 22:54:00]
FATAL [2025-11-17 22:54:00] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:54:00] parameters (PureCN 2.17.0).
FATAL [2025-11-17 22:54:00] At least 2 normal.coverage.files required.
FATAL [2025-11-17 22:54:00]
FATAL [2025-11-17 22:54:00] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:54:00] parameters (PureCN 2.17.0).
INFO [2025-11-17 22:54:01] ------------------------------------------------------------
INFO [2025-11-17 22:54:01] PureCN 2.17.0
INFO [2025-11-17 22:54:01] ------------------------------------------------------------
INFO [2025-11-17 22:54:01] Loading coverage files...
INFO [2025-11-17 22:54:01] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-11-17 22:54:01] Allosome coverage missing, cannot determine sex.
WARN [2025-11-17 22:54:01] Allosome coverage missing, cannot determine sex.
INFO [2025-11-17 22:54:01] Removing 228 intervals with missing log.ratio.
FATAL [2025-11-17 22:54:01] normalDB incompatible with this PureCN version. Please re-run
FATAL [2025-11-17 22:54:01] NormalDB.R.
FATAL [2025-11-17 22:54:01]
FATAL [2025-11-17 22:54:01] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:54:01] parameters (PureCN 2.17.0).
FATAL [2025-11-17 22:54:01] normalDB incompatible with this PureCN version. Please re-run
FATAL [2025-11-17 22:54:01] NormalDB.R.
FATAL [2025-11-17 22:54:01]
FATAL [2025-11-17 22:54:01] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:54:01] parameters (PureCN 2.17.0).
FATAL [2025-11-17 22:54:01] normal.coverage.files with _coverage.txt and _loess.txt suffix
FATAL [2025-11-17 22:54:01] provided. Provide either only GC-normalized or raw coverage files!
FATAL [2025-11-17 22:54:01]
FATAL [2025-11-17 22:54:01] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:54:01] parameters (PureCN 2.17.0).
INFO [2025-11-17 22:54:01] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-11-17 22:54:01] Removing 19 low quality variants with non-offset BQ < 25.
INFO [2025-11-17 22:54:02] Base quality scores range from 24 to 35 (offset by 1)
INFO [2025-11-17 22:54:02] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS.
INFO [2025-11-17 22:54:02] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-11-17 22:54:02] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-11-17 22:54:02] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-11-17 22:54:02] Removing 19 low quality variants with non-offset BQ < 25.
INFO [2025-11-17 22:54:02] Base quality scores range from 24 to 35 (offset by 1)
INFO [2025-11-17 22:54:02] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS.
INFO [2025-11-17 22:54:03] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-11-17 22:54:03] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-11-17 22:54:03] Removing 6 blacklisted variants.
INFO [2025-11-17 22:54:03] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-11-17 22:54:03] Removing 19 low quality variants with non-offset BQ < 25.
INFO [2025-11-17 22:54:03] Base quality scores range from 24 to 35 (offset by 1)
INFO [2025-11-17 22:54:03] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS.
INFO [2025-11-17 22:54:03] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-11-17 22:54:03] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
WARN [2025-11-17 22:54:03] MuTect stats file lacks contig and position columns.
INFO [2025-11-17 22:54:03] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-11-17 22:54:03] Removing 19 low quality variants with non-offset BQ < 25.
INFO [2025-11-17 22:54:03] Base quality scores range from 24 to 35 (offset by 1)
INFO [2025-11-17 22:54:03] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS.
INFO [2025-11-17 22:54:03] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-11-17 22:54:03] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
WARN [2025-11-17 22:54:03] MuTect stats file and VCF file do not align perfectly. Will remove 2325 unmatched variants.
WARN [2025-11-17 22:54:03] MuTect stats file lacks failure_reasons column. Keeping all variants listed in stats file.
INFO [2025-11-17 22:54:03] Removing 0 non heterozygous (in matched normal) germline SNPs.
INFO [2025-11-17 22:54:03] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-11-17 22:54:03] Base quality scores range from 31 to 33 (offset by 1)
INFO [2025-11-17 22:54:03] Minimum number of supporting reads ranges from 3 to 4, depending on coverage and BQS.
INFO [2025-11-17 22:54:04] Removing 0 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-11-17 22:54:04] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-11-17 22:54:04] Base quality scores range from 7 to 35 (offset by 1)
INFO [2025-11-17 22:54:04] Minimum number of supporting reads ranges from 1 to 41, depending on coverage and BQS.
INFO [2025-11-17 22:54:04] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-11-17 22:54:04] Removing 49 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-11-17 22:54:04] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-11-17 22:54:04] Base quality scores range from 7 to 35 (offset by 1)
INFO [2025-11-17 22:54:04] Minimum number of supporting reads ranges from 1 to 41, depending on coverage and BQS.
INFO [2025-11-17 22:54:04] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-11-17 22:54:04] Removing 49 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-11-17 22:54:04] Removing 22 non heterozygous (in matched normal) germline SNPs.
WARN [2025-11-17 22:54:04] Many variants removed by min.base.quality (50) filter. You might want to lower the cutoff.
FATAL [2025-11-17 22:54:04] No variants passed filter BQ.
FATAL [2025-11-17 22:54:04]
FATAL [2025-11-17 22:54:04] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:54:04] parameters (PureCN 2.17.0).
INFO [2025-11-17 22:54:04] Found 11 variants in VCF file.
WARN [2025-11-17 22:54:04] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead.
INFO [2025-11-17 22:54:04] 1 (9.1%) variants annotated as likely germline (DB INFO flag).
INFO [2025-11-17 22:54:05] Found 11 variants in VCF file.
WARN [2025-11-17 22:54:05] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead.
INFO [2025-11-17 22:54:05] 1 (9.1%) variants annotated as likely germline (DB INFO flag).
INFO [2025-11-17 22:54:05] Found 11 variants in VCF file.
WARN [2025-11-17 22:54:05] vcf.file has no DB or POP_AF info field for membership in germline databases. Guessing it based on available dbSNP ID.
INFO [2025-11-17 22:54:05] 1 (9.1%) variants annotated as likely germline (DB INFO flag).
INFO [2025-11-17 22:54:06] Found 1000 variants in VCF file.
INFO [2025-11-17 22:54:06] Removing 2 triallelic sites.
WARN [2025-11-17 22:54:06] Having trouble guessing SOMATIC status...
WARN [2025-11-17 22:54:06] DP FORMAT field contains NAs. Removing 44 variants.
INFO [2025-11-17 22:54:06] 954 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-11-17 22:54:06] Found 12 variants in VCF file.
INFO [2025-11-17 22:54:06] Removing 1 triallelic sites.
WARN [2025-11-17 22:54:06] DP FORMAT field contains NAs. Removing 1 variants.
WARN [2025-11-17 22:54:06] vcf.file has no DB info field for membership in germline databases. Found and used somatic status instead.
INFO [2025-11-17 22:54:06] 8 (80.0%) variants annotated as likely germline (DB INFO flag).
WARN [2025-11-17 22:54:06] BQ FORMAT field contains NAs.
INFO [2025-11-17 22:54:07] Found 2331 variants in VCF file.
INFO [2025-11-17 22:54:07] 2282 (97.9%) variants annotated as likely germline (DB INFO flag).
INFO [2025-11-17 22:54:07] Found 2331 variants in VCF file.
INFO [2025-11-17 22:54:07] 2282 (97.9%) variants annotated as likely germline (DB INFO flag).
WARN [2025-11-17 22:54:07] Did not find base quality scores, will use global error rate of 0.0010 instead.
INFO [2025-11-17 22:54:07] Removing 21 low quality variants with non-offset BQ < 25.
INFO [2025-11-17 22:54:07] Base quality scores range from 24 to 35 (offset by 1)
INFO [2025-11-17 22:54:07] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-11-17 22:54:07] Removing 89 variants with AF < 0.030 or AF >= 0.970 or insufficient supporting reads or depth < 15.
INFO [2025-11-17 22:54:07] Found 2331 variants in VCF file.
INFO [2025-11-17 22:54:07] 2282 (97.9%) variants annotated as likely germline (DB INFO flag).
WARN [2025-11-17 22:54:07] BQ FORMAT field contains NAs.
WARN [2025-11-17 22:54:08] Allosome coverage missing, cannot determine sex.
WARN [2025-11-17 22:54:08] Allosome coverage missing, cannot determine sex.
INFO [2025-11-17 22:54:08] Mean coverages: chrX: 108.58, chrY: 108.58, chr1-22: 104.87.
INFO [2025-11-17 22:54:08] Mean coverages: chrX: 108.58, chrY: 2.17, chr1-22: 104.87.
INFO [2025-11-17 22:54:08] Mean coverages: chrX: 108.58, chrY: 5.17, chr1-22: 104.87.
INFO [2025-11-17 22:54:08] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-11-17 22:54:08] No germline variants in VCF.
FATAL [2025-11-17 22:54:08] No solution with id hello
FATAL [2025-11-17 22:54:08]
FATAL [2025-11-17 22:54:08] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:54:08] parameters (PureCN 2.17.0).
FATAL [2025-11-17 22:54:08] No solution with id 100
FATAL [2025-11-17 22:54:08]
FATAL [2025-11-17 22:54:08] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:54:08] parameters (PureCN 2.17.0).
FATAL [2025-11-17 22:54:09] all.data and w have different lengths.
FATAL [2025-11-17 22:54:09]
FATAL [2025-11-17 22:54:09] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:54:09] parameters (PureCN 2.17.0).
INFO [2025-11-17 22:54:09] Splitting 5 large targets to an average width of 400.
WARN [2025-11-17 22:54:09] No mappability scores provided.
WARN [2025-11-17 22:54:09] No reptiming scores provided.
INFO [2025-11-17 22:54:09] Calculating GC-content...
INFO [2025-11-17 22:54:09] Splitting 5 large targets to an average width of 400.
WARN [2025-11-17 22:54:09] No mappability scores provided.
WARN [2025-11-17 22:54:09] No reptiming scores provided.
INFO [2025-11-17 22:54:09] Calculating GC-content...
INFO [2025-11-17 22:54:09] Splitting 5 large targets to an average width of 400.
INFO [2025-11-17 22:54:09] Removing 1 targets overlapping with exclude.
WARN [2025-11-17 22:54:09] No mappability scores provided.
WARN [2025-11-17 22:54:09] No reptiming scores provided.
INFO [2025-11-17 22:54:09] Calculating GC-content...
WARN [2025-11-17 22:54:09] Found small target regions (< 100bp). Will resize them.
INFO [2025-11-17 22:54:09] Splitting 5 large targets to an average width of 400.
FATAL [2025-11-17 22:54:09] off.target.padding must be negative.
FATAL [2025-11-17 22:54:09]
FATAL [2025-11-17 22:54:09] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:54:09] parameters (PureCN 2.17.0).
FATAL [2025-11-17 22:54:09] Interval coordinates should start at 1, not at 0
FATAL [2025-11-17 22:54:09]
FATAL [2025-11-17 22:54:09] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:54:09] parameters (PureCN 2.17.0).
WARN [2025-11-17 22:54:09] Found small target regions (< 100bp). Will resize them.
INFO [2025-11-17 22:54:09] Splitting 5 large targets to an average width of 400.
FATAL [2025-11-17 22:54:09] No off-target regions after filtering for mappability and
FATAL [2025-11-17 22:54:09] off.target.padding
FATAL [2025-11-17 22:54:09]
FATAL [2025-11-17 22:54:09] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:54:09] parameters (PureCN 2.17.0).
WARN [2025-11-17 22:54:10] Found small target regions (< 100bp). Will resize them.
INFO [2025-11-17 22:54:10] Splitting 5 large targets to an average width of 400.
WARN [2025-11-17 22:54:10] No mappability scores provided.
INFO [2025-11-17 22:54:10] Calculating GC-content...
WARN [2025-11-17 22:54:10] Found small target regions (< 100bp). Will resize them.
INFO [2025-11-17 22:54:10] Averaging reptiming into bins of size 200...
INFO [2025-11-17 22:54:10] Splitting 5 large targets to an average width of 400.
WARN [2025-11-17 22:54:10] No mappability scores provided.
INFO [2025-11-17 22:54:10] Calculating GC-content...
WARN [2025-11-17 22:54:10] Found small target regions (< 100bp). Will resize them.
INFO [2025-11-17 22:54:10] Splitting 6 large targets to an average width of 200.
WARN [2025-11-17 22:54:10] No mappability scores provided.
WARN [2025-11-17 22:54:10] No reptiming scores provided.
INFO [2025-11-17 22:54:10] Calculating GC-content...
WARN [2025-11-17 22:54:10] Found small target regions (< 100bp). Will resize them.
INFO [2025-11-17 22:54:10] Splitting 5 large targets to an average width of 400.
WARN [2025-11-17 22:54:10] No mappability scores provided.
WARN [2025-11-17 22:54:10] No reptiming scores provided.
INFO [2025-11-17 22:54:10] Calculating GC-content...
INFO [2025-11-17 22:54:10] Splitting 5 large targets to an average width of 400.
INFO [2025-11-17 22:54:10] Tiling off-target regions to an average width of 200000.
WARN [2025-11-17 22:54:10] No mappability scores provided.
WARN [2025-11-17 22:54:10] No reptiming scores provided.
INFO [2025-11-17 22:54:10] Calculating GC-content...
WARN [2025-11-17 22:54:10] Intervals contain off-target regions. Will not change intervals.
WARN [2025-11-17 22:54:10] No mappability scores provided.
WARN [2025-11-17 22:54:10] No reptiming scores provided.
INFO [2025-11-17 22:54:10] Calculating GC-content...
INFO [2025-11-17 22:54:10] Splitting 5 large targets to an average width of 400.
WARN [2025-11-17 22:54:10] No reptiming scores provided.
INFO [2025-11-17 22:54:10] Calculating GC-content...
WARN [2025-11-17 22:54:10] Found small target regions (< 100bp). Will resize them.
INFO [2025-11-17 22:54:10] Splitting 5 large targets to an average width of 400.
WARN [2025-11-17 22:54:10] No reptiming scores provided.
INFO [2025-11-17 22:54:10] Calculating GC-content...
WARN [2025-11-17 22:54:11] Found small target regions (< 100bp). Will resize them.
INFO [2025-11-17 22:54:11] Splitting 5 large targets to an average width of 400.
WARN [2025-11-17 22:54:11] 1 intervals without mappability score (1 on-target).
INFO [2025-11-17 22:54:11] Removing 1 intervals with low mappability score (<0.60).
WARN [2025-11-17 22:54:11] No reptiming scores provided.
INFO [2025-11-17 22:54:11] Calculating GC-content...
WARN [2025-11-17 22:54:11] Found small target regions (< 100bp). Will resize them.
INFO [2025-11-17 22:54:11] Splitting 5 large targets to an average width of 400.
INFO [2025-11-17 22:54:11] Tiling off-target regions to an average width of 200000.
WARN [2025-11-17 22:54:11] No reptiming scores provided.
INFO [2025-11-17 22:54:11] Calculating GC-content...
INFO [2025-11-17 22:54:11] Splitting 5 large targets to an average width of 400.
WARN [2025-11-17 22:54:11] No mappability scores provided.
WARN [2025-11-17 22:54:11] No reptiming scores provided.
INFO [2025-11-17 22:54:11] Calculating GC-content...
WARN [2025-11-17 22:54:11] Chromosome naming style of interval file (Ensembl) was different from reference (UCSC).
INFO [2025-11-17 22:54:11] Splitting 5 large targets to an average width of 400.
WARN [2025-11-17 22:54:11] No mappability scores provided.
WARN [2025-11-17 22:54:11] No reptiming scores provided.
INFO [2025-11-17 22:54:11] Calculating GC-content...
FATAL [2025-11-17 22:54:11] Chromosome naming style of interval file unknown, should be UCSC.
FATAL [2025-11-17 22:54:11]
FATAL [2025-11-17 22:54:11] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:54:11] parameters (PureCN 2.17.0).
WARN [2025-11-17 22:54:12] Chromosome naming style of interval file (Ensembl) was different from reference (UCSC).
WARN [2025-11-17 22:54:12] Chromosome naming style of mappability file (Ensembl) was different from reference (UCSC).
INFO [2025-11-17 22:54:12] Splitting 5 large targets to an average width of 400.
WARN [2025-11-17 22:54:12] No reptiming scores provided.
INFO [2025-11-17 22:54:12] Calculating GC-content...
WARN [2025-11-17 22:54:12] Found small target regions (< 60bp). Will resize them.
INFO [2025-11-17 22:54:12] Splitting 5 large targets to an average width of 400.
WARN [2025-11-17 22:54:12] No mappability scores provided.
WARN [2025-11-17 22:54:12] No reptiming scores provided.
INFO [2025-11-17 22:54:12] Calculating GC-content...
WARN [2025-11-17 22:54:12] Found small target regions (< 60bp). Will drop them.
INFO [2025-11-17 22:54:12] Splitting 4 large targets to an average width of 400.
WARN [2025-11-17 22:54:12] No mappability scores provided.
WARN [2025-11-17 22:54:12] No reptiming scores provided.
INFO [2025-11-17 22:54:12] Calculating GC-content...
WARN [2025-11-17 22:54:12] Found small target regions (< 200bp). Will resize them.
INFO [2025-11-17 22:54:12] Splitting 5 large targets to an average width of 400.
WARN [2025-11-17 22:54:12] No mappability scores provided.
WARN [2025-11-17 22:54:12] No reptiming scores provided.
INFO [2025-11-17 22:54:12] Calculating GC-content...
INFO [2025-11-17 22:54:12] Found 20 variants in VCF file.
INFO [2025-11-17 22:54:12] 20 (100.0%) variants annotated as likely germline (DB INFO flag).
WARN [2025-11-17 22:54:12] 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 [2025-11-17 22:54:12] Error reading AllelicCountsFile
FATAL [2025-11-17 22:54:12] /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/PureCN/extdata/example_allelic_counts_empty.tsv
FATAL [2025-11-17 22:54:12]
FATAL [2025-11-17 22:54:12] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:54:12] parameters (PureCN 2.17.0).
INFO [2025-11-17 22:54:12] Found 127 variants in VCF file.
INFO [2025-11-17 22:54:13] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
WARN [2025-11-17 22:54:13] Did not find base quality scores, will use global error rate of 0.0010 instead.
INFO [2025-11-17 22:54:13] ------------------------------------------------------------
INFO [2025-11-17 22:54:13] PureCN 2.17.0
INFO [2025-11-17 22:54:13] ------------------------------------------------------------
INFO [2025-11-17 22:54:13] Loading coverage files...
INFO [2025-11-17 22:54:13] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-11-17 22:54:13] Allosome coverage missing, cannot determine sex.
WARN [2025-11-17 22:54:13] Allosome coverage missing, cannot determine sex.
INFO [2025-11-17 22:54:13] Removing 228 intervals with missing log.ratio.
INFO [2025-11-17 22:54:13] Removing 22 small (< 5bp) intervals.
INFO [2025-11-17 22:54:13] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-11-17 22:54:13] No normalDB provided. Provide one for better results.
INFO [2025-11-17 22:54:13] Removing 1724 low count (< 100 total reads) intervals.
INFO [2025-11-17 22:54:13] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-11-17 22:54:13] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-11-17 22:54:13] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-11-17 22:54:13] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-11-17 22:54:13] Loading VCF...
INFO [2025-11-17 22:54:13] Found 127 variants in VCF file.
INFO [2025-11-17 22:54:13] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-11-17 22:54:13] LIB-02240e4 is tumor in VCF file.
INFO [2025-11-17 22:54:13] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-11-17 22:54:13] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-11-17 22:54:13] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-11-17 22:54:13] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-11-17 22:54:13] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-11-17 22:54:13] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-11-17 22:54:13] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding).
INFO [2025-11-17 22:54:13] 1.2% of targets contain variants.
INFO [2025-11-17 22:54:13] Removing 4 variants outside intervals.
INFO [2025-11-17 22:54:13] Found SOMATIC annotation in VCF.
INFO [2025-11-17 22:54:13] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-11-17 22:54:13] Found SOMATIC annotation in VCF. Setting mapping bias to 0.972.
INFO [2025-11-17 22:54:13] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-11-17 22:54:13] Sample sex: ?
INFO [2025-11-17 22:54:13] Segmenting data...
INFO [2025-11-17 22:54:14] Loading pre-computed boundaries for DNAcopy...
INFO [2025-11-17 22:54:14] Setting undo.SD parameter to 1.000000.
INFO [2025-11-17 22:54:14] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-11-17 22:54:14] Found 59 segments with median size of 17.67Mb.
INFO [2025-11-17 22:54:14] Using 121 variants.
INFO [2025-11-17 22:54:14] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-11-17 22:54:14] 2D-grid search of purity and ploidy...
INFO [2025-11-17 22:54:14] Local optima: 0.65/1.8, 0.52/2
INFO [2025-11-17 22:54:14] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2025-11-17 22:54:14] Testing local optimum 2/2 at purity 0.52 and total ploidy 2.00...
INFO [2025-11-17 22:54:15] Skipping 1 solutions that converged to the same optima.
INFO [2025-11-17 22:54:15] Fitting variants with beta model for local optimum 1/2...
INFO [2025-11-17 22:54:15] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2025-11-17 22:54:16] Optimized purity: 0.65
INFO [2025-11-17 22:54:16] Done.
INFO [2025-11-17 22:54:16] ------------------------------------------------------------
FATAL [2025-11-17 22:54:16] log.ratio NULL in .writeLogRatioFileGATK4
FATAL [2025-11-17 22:54:16]
FATAL [2025-11-17 22:54:16] This runtime error might be caused by invalid input data or parameters.
FATAL [2025-11-17 22:54:16] Please report bug (PureCN 2.17.0).
INFO [2025-11-17 22:54:16] Loaded provided segmentation file example_seg.txt (format DNAcopy).
INFO [2025-11-17 22:54:16] Re-centering provided segment means (offset -0.0033).
INFO [2025-11-17 22:54:16] Loaded provided segmentation file example_gatk4_modelfinal.seg.gz (format GATK4).
WARN [2025-11-17 22:54:16] Expecting numeric chromosome names in seg.file, assuming file is properly sorted.
INFO [2025-11-17 22:54:16] Re-centering provided segment means (offset -0.0037).
INFO [2025-11-17 22:54:17] 576 on-target bins with low coverage in all samples.
WARN [2025-11-17 22:54:17] You are likely not using the correct baits file!
WARN [2025-11-17 22:54:17] Allosome coverage missing, cannot determine sex.
WARN [2025-11-17 22:54:17] Allosome coverage missing, cannot determine sex.
INFO [2025-11-17 22:54:17] Processing on-target regions...
INFO [2025-11-17 22:54:17] Removing 930 intervals with low coverage in normalDB.
INFO [2025-11-17 22:54:17] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2025-11-17 22:54:18] ------------------------------------------------------------
INFO [2025-11-17 22:54:18] PureCN 2.17.0
INFO [2025-11-17 22:54:18] ------------------------------------------------------------
INFO [2025-11-17 22:54:18] Using BiocParallel for parallel optimization.
INFO [2025-11-17 22:54:18] Loading coverage files...
INFO [2025-11-17 22:54:18] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-11-17 22:54:18] Allosome coverage missing, cannot determine sex.
WARN [2025-11-17 22:54:18] Allosome coverage missing, cannot determine sex.
INFO [2025-11-17 22:54:18] Removing 228 intervals with missing log.ratio.
INFO [2025-11-17 22:54:18] Removing 705 intervals excluded in normalDB.
INFO [2025-11-17 22:54:18] normalDB provided. Setting minimum coverage for segmentation to 0.0015X.
INFO [2025-11-17 22:54:18] Removing 1066 low count (< 100 total reads) intervals.
INFO [2025-11-17 22:54:18] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-11-17 22:54:18] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-11-17 22:54:18] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-11-17 22:54:18] Sample sex: ?
INFO [2025-11-17 22:54:18] Segmenting data...
INFO [2025-11-17 22:54:18] Interval weights found, will use weighted CBS.
INFO [2025-11-17 22:54:18] Loading pre-computed boundaries for DNAcopy...
INFO [2025-11-17 22:54:18] Setting undo.SD parameter to 1.000000.
Setting multi-figure configuration
INFO [2025-11-17 22:54:19] Found 52 segments with median size of 29.35Mb.
INFO [2025-11-17 22:54:19] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-11-17 22:54:19] 2D-grid search of purity and ploidy...
INFO [2025-11-17 22:54:19] Local optima: 0.65/1.8, 0.52/2
INFO [2025-11-17 22:54:20] Skipping 1 solutions that converged to the same optima.
INFO [2025-11-17 22:54:20] Done.
INFO [2025-11-17 22:54:20] ------------------------------------------------------------
INFO [2025-11-17 22:54:20] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2rjXjq/file1067a5dfc8f9d.rds...
FATAL [2025-11-17 22:54:20] runAbsoluteCN was run without a VCF file.
FATAL [2025-11-17 22:54:20]
FATAL [2025-11-17 22:54:20] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:54:20] parameters (PureCN 2.17.0).
FATAL [2025-11-17 22:54:20] runAbsoluteCN was run without a VCF file.
FATAL [2025-11-17 22:54:20]
FATAL [2025-11-17 22:54:20] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:54:20] parameters (PureCN 2.17.0).
INFO [2025-11-17 22:54:20] ------------------------------------------------------------
INFO [2025-11-17 22:54:20] PureCN 2.17.0
INFO [2025-11-17 22:54:20] ------------------------------------------------------------
INFO [2025-11-17 22:54:20] Loading coverage files...
INFO [2025-11-17 22:54:20] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-11-17 22:54:20] Allosome coverage missing, cannot determine sex.
WARN [2025-11-17 22:54:20] Allosome coverage missing, cannot determine sex.
INFO [2025-11-17 22:54:20] Removing 228 intervals with missing log.ratio.
INFO [2025-11-17 22:54:20] Removing 705 intervals excluded in normalDB.
INFO [2025-11-17 22:54:20] normalDB provided. Setting minimum coverage for segmentation to 0.0015X.
INFO [2025-11-17 22:54:20] Removing 1066 low count (< 100 total reads) intervals.
INFO [2025-11-17 22:54:20] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-11-17 22:54:20] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-11-17 22:54:20] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-11-17 22:54:20] Sample sex: ?
INFO [2025-11-17 22:54:20] Segmenting data...
INFO [2025-11-17 22:54:20] Interval weights found, will use weighted PSCBS.
FATAL [2025-11-17 22:54:20] segmentationPSCBS requires VCF file.
FATAL [2025-11-17 22:54:20]
FATAL [2025-11-17 22:54:20] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:54:20] parameters (PureCN 2.17.0).
INFO [2025-11-17 22:54:23] ------------------------------------------------------------
INFO [2025-11-17 22:54:23] PureCN 2.17.0
INFO [2025-11-17 22:54:23] ------------------------------------------------------------
INFO [2025-11-17 22:54:23] Loading coverage files...
FATAL [2025-11-17 22:54:23] Need a normal coverage file if log.ratio and seg.file are not provided.
FATAL [2025-11-17 22:54:23]
FATAL [2025-11-17 22:54:23] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:54:23] parameters (PureCN 2.17.0).
INFO [2025-11-17 22:54:23] ------------------------------------------------------------
INFO [2025-11-17 22:54:23] PureCN 2.17.0
INFO [2025-11-17 22:54:23] ------------------------------------------------------------
FATAL [2025-11-17 22:54:23] min.ploidy or max.ploidy not within expected range.
FATAL [2025-11-17 22:54:23]
FATAL [2025-11-17 22:54:23] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:54:23] parameters (PureCN 2.17.0).
INFO [2025-11-17 22:54:23] ------------------------------------------------------------
INFO [2025-11-17 22:54:23] PureCN 2.17.0
INFO [2025-11-17 22:54:23] ------------------------------------------------------------
FATAL [2025-11-17 22:54:23] min.ploidy or max.ploidy not within expected range.
FATAL [2025-11-17 22:54:23]
FATAL [2025-11-17 22:54:23] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:54:23] parameters (PureCN 2.17.0).
INFO [2025-11-17 22:54:23] ------------------------------------------------------------
INFO [2025-11-17 22:54:23] PureCN 2.17.0
INFO [2025-11-17 22:54:23] ------------------------------------------------------------
INFO [2025-11-17 22:54:23] ------------------------------------------------------------
INFO [2025-11-17 22:54:23] PureCN 2.17.0
INFO [2025-11-17 22:54:23] ------------------------------------------------------------
INFO [2025-11-17 22:54:23] ------------------------------------------------------------
INFO [2025-11-17 22:54:23] PureCN 2.17.0
INFO [2025-11-17 22:54:23] ------------------------------------------------------------
FATAL [2025-11-17 22:54:23] test.num.copy not within expected range.
FATAL [2025-11-17 22:54:23]
FATAL [2025-11-17 22:54:23] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:54:23] parameters (PureCN 2.17.0).
INFO [2025-11-17 22:54:23] ------------------------------------------------------------
INFO [2025-11-17 22:54:23] PureCN 2.17.0
INFO [2025-11-17 22:54:23] ------------------------------------------------------------
WARN [2025-11-17 22:54:23] test.num.copy outside recommended range.
FATAL [2025-11-17 22:54:23] max.non.clonal not within expected range or format.
FATAL [2025-11-17 22:54:23]
FATAL [2025-11-17 22:54:23] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:54:23] parameters (PureCN 2.17.0).
INFO [2025-11-17 22:54:23] ------------------------------------------------------------
INFO [2025-11-17 22:54:23] PureCN 2.17.0
INFO [2025-11-17 22:54:23] ------------------------------------------------------------
WARN [2025-11-17 22:54:23] test.num.copy outside recommended range.
FATAL [2025-11-17 22:54:23] max.non.clonal not within expected range or format.
FATAL [2025-11-17 22:54:23]
FATAL [2025-11-17 22:54:23] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:54:23] parameters (PureCN 2.17.0).
INFO [2025-11-17 22:54:23] ------------------------------------------------------------
INFO [2025-11-17 22:54:23] PureCN 2.17.0
INFO [2025-11-17 22:54:23] ------------------------------------------------------------
FATAL [2025-11-17 22:54:23] test.purity not within expected range.
FATAL [2025-11-17 22:54:23]
FATAL [2025-11-17 22:54:23] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:54:23] parameters (PureCN 2.17.0).
INFO [2025-11-17 22:54:23] ------------------------------------------------------------
INFO [2025-11-17 22:54:23] PureCN 2.17.0
INFO [2025-11-17 22:54:23] ------------------------------------------------------------
INFO [2025-11-17 22:54:23] Loading coverage files...
FATAL [2025-11-17 22:54:23] Tumor and normal are identical. This won't give any meaningful results
FATAL [2025-11-17 22:54:23] and I'm stopping here.
FATAL [2025-11-17 22:54:23]
FATAL [2025-11-17 22:54:23] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:54:23] parameters (PureCN 2.17.0).
INFO [2025-11-17 22:54:23] ------------------------------------------------------------
INFO [2025-11-17 22:54:23] PureCN 2.17.0
INFO [2025-11-17 22:54:23] ------------------------------------------------------------
INFO [2025-11-17 22:54:23] Loading coverage files...
FATAL [2025-11-17 22:54:23] Length of log.ratio different from tumor coverage.
FATAL [2025-11-17 22:54:23]
FATAL [2025-11-17 22:54:23] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:54:23] parameters (PureCN 2.17.0).
INFO [2025-11-17 22:54:23] ------------------------------------------------------------
INFO [2025-11-17 22:54:23] PureCN 2.17.0
INFO [2025-11-17 22:54:23] ------------------------------------------------------------
FATAL [2025-11-17 22:54:23] prior.purity must have the same length as test.purity.
FATAL [2025-11-17 22:54:23]
FATAL [2025-11-17 22:54:23] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:54:23] parameters (PureCN 2.17.0).
INFO [2025-11-17 22:54:23] ------------------------------------------------------------
INFO [2025-11-17 22:54:23] PureCN 2.17.0
INFO [2025-11-17 22:54:23] ------------------------------------------------------------
FATAL [2025-11-17 22:54:23] min.gof not within expected range or format.
FATAL [2025-11-17 22:54:23]
FATAL [2025-11-17 22:54:23] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:54:23] parameters (PureCN 2.17.0).
INFO [2025-11-17 22:54:23] ------------------------------------------------------------
INFO [2025-11-17 22:54:23] PureCN 2.17.0
INFO [2025-11-17 22:54:23] ------------------------------------------------------------
FATAL [2025-11-17 22:54:23] prior.purity not within expected range or format.
FATAL [2025-11-17 22:54:23]
FATAL [2025-11-17 22:54:23] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:54:23] parameters (PureCN 2.17.0).
INFO [2025-11-17 22:54:23] ------------------------------------------------------------
INFO [2025-11-17 22:54:23] PureCN 2.17.0
INFO [2025-11-17 22:54:23] ------------------------------------------------------------
FATAL [2025-11-17 22:54:23] prior.purity must add to 1. Sum is 1.5
FATAL [2025-11-17 22:54:23]
FATAL [2025-11-17 22:54:23] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:54:23] parameters (PureCN 2.17.0).
INFO [2025-11-17 22:54:23] ------------------------------------------------------------
INFO [2025-11-17 22:54:23] PureCN 2.17.0
INFO [2025-11-17 22:54:23] ------------------------------------------------------------
FATAL [2025-11-17 22:54:23] max.homozygous.loss not within expected range or format.
FATAL [2025-11-17 22:54:23]
FATAL [2025-11-17 22:54:23] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:54:23] parameters (PureCN 2.17.0).
INFO [2025-11-17 22:54:23] ------------------------------------------------------------
INFO [2025-11-17 22:54:23] PureCN 2.17.0
INFO [2025-11-17 22:54:23] ------------------------------------------------------------
FATAL [2025-11-17 22:54:23] prior.K not within expected range or format.
FATAL [2025-11-17 22:54:23]
FATAL [2025-11-17 22:54:23] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:54:23] parameters (PureCN 2.17.0).
INFO [2025-11-17 22:54:23] ------------------------------------------------------------
INFO [2025-11-17 22:54:23] PureCN 2.17.0
INFO [2025-11-17 22:54:23] ------------------------------------------------------------
FATAL [2025-11-17 22:54:23] prior.contamination not within expected range or format.
FATAL [2025-11-17 22:54:23]
FATAL [2025-11-17 22:54:23] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:54:23] parameters (PureCN 2.17.0).
INFO [2025-11-17 22:54:23] ------------------------------------------------------------
INFO [2025-11-17 22:54:23] PureCN 2.17.0
INFO [2025-11-17 22:54:23] ------------------------------------------------------------
FATAL [2025-11-17 22:54:23] Iterations not in the expected range from 10 to 250.
FATAL [2025-11-17 22:54:23]
FATAL [2025-11-17 22:54:23] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:54:23] parameters (PureCN 2.17.0).
INFO [2025-11-17 22:54:23] ------------------------------------------------------------
INFO [2025-11-17 22:54:23] PureCN 2.17.0
INFO [2025-11-17 22:54:23] ------------------------------------------------------------
FATAL [2025-11-17 22:54:23] Iterations not in the expected range from 10 to 250.
FATAL [2025-11-17 22:54:23]
FATAL [2025-11-17 22:54:23] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:54:23] parameters (PureCN 2.17.0).
INFO [2025-11-17 22:54:23] ------------------------------------------------------------
INFO [2025-11-17 22:54:23] PureCN 2.17.0
INFO [2025-11-17 22:54:23] ------------------------------------------------------------
INFO [2025-11-17 22:54:23] Loading coverage files...
FATAL [2025-11-17 22:54:24] Missing tumor.coverage.file requires seg.file or log.ratio and
FATAL [2025-11-17 22:54:24] interval.file.
FATAL [2025-11-17 22:54:24]
FATAL [2025-11-17 22:54:24] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:54:24] parameters (PureCN 2.17.0).
INFO [2025-11-17 22:54:24] ------------------------------------------------------------
INFO [2025-11-17 22:54:24] PureCN 2.17.0
INFO [2025-11-17 22:54:24] ------------------------------------------------------------
INFO [2025-11-17 22:54:24] ------------------------------------------------------------
INFO [2025-11-17 22:54:24] PureCN 2.17.0
INFO [2025-11-17 22:54:24] ------------------------------------------------------------
INFO [2025-11-17 22:54:24] Loading coverage files...
FATAL [2025-11-17 22:54:24] Interval files in normal and tumor different.
FATAL [2025-11-17 22:54:24]
FATAL [2025-11-17 22:54:24] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:54:24] parameters (PureCN 2.17.0).
INFO [2025-11-17 22:54:24] ------------------------------------------------------------
INFO [2025-11-17 22:54:24] PureCN 2.17.0
INFO [2025-11-17 22:54:24] ------------------------------------------------------------
INFO [2025-11-17 22:54:24] Loading coverage files...
INFO [2025-11-17 22:54:24] Mean target coverages: 0X (tumor) 99X (normal).
WARN [2025-11-17 22:54:24] Large difference in coverage of tumor and normal.
FATAL [2025-11-17 22:54:24] No finite intervals.
FATAL [2025-11-17 22:54:24]
FATAL [2025-11-17 22:54:24] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:54:24] parameters (PureCN 2.17.0).
INFO [2025-11-17 22:54:24] ------------------------------------------------------------
INFO [2025-11-17 22:54:24] PureCN 2.17.0
INFO [2025-11-17 22:54:24] ------------------------------------------------------------
INFO [2025-11-17 22:54:24] Loading coverage files...
INFO [2025-11-17 22:54:24] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-11-17 22:54:25] Allosome coverage missing, cannot determine sex.
WARN [2025-11-17 22:54:25] Allosome coverage missing, cannot determine sex.
INFO [2025-11-17 22:54:25] Removing 228 intervals with missing log.ratio.
INFO [2025-11-17 22:54:25] Removing 22 small (< 5bp) intervals.
INFO [2025-11-17 22:54:25] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-11-17 22:54:25] No normalDB provided. Provide one for better results.
INFO [2025-11-17 22:54:25] Removing 1724 low count (< 100 total reads) intervals.
INFO [2025-11-17 22:54:25] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-11-17 22:54:25] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-11-17 22:54:25] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-11-17 22:54:25] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-11-17 22:54:25] Loading VCF...
INFO [2025-11-17 22:54:25] Found 127 variants in VCF file.
INFO [2025-11-17 22:54:25] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-11-17 22:54:25] LIB-02240e4 is tumor in VCF file.
INFO [2025-11-17 22:54:25] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-11-17 22:54:25] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-11-17 22:54:25] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-11-17 22:54:25] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-11-17 22:54:25] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-11-17 22:54:25] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
Error in FileForFormat(resource(con), fileFormat(con)) :
Format 'txt' unsupported
In addition: Warning messages:
1: In for (i in (1L:cols)[do]) { :
closing unused connection 4 (/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/PureCN/extdata/example_allelic_counts_empty.tsv)
2: In for (i in seq_len(n)) { :
closing unused connection 5 (/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2rjXjq/file1067a30e1dd77.tsv)
3: In for (i in seq_len(n)) { :
closing unused connection 4 (/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/PureCN/extdata/example_gatk4_denoised_cr.tsv.gz)
FATAL [2025-11-17 22:54:25] Could not import snp.blacklist
FATAL [2025-11-17 22:54:25] /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/PureCN/extdata/example_normal.txt.gz:Error
FATAL [2025-11-17 22:54:25] in FileForFormat(resource(con), fileFormat(con)) : Format 'txt'
FATAL [2025-11-17 22:54:25] unsupported
FATAL [2025-11-17 22:54:25]
FATAL [2025-11-17 22:54:25] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:54:25] parameters (PureCN 2.17.0).
INFO [2025-11-17 22:54:25] ------------------------------------------------------------
INFO [2025-11-17 22:54:25] PureCN 2.17.0
INFO [2025-11-17 22:54:25] ------------------------------------------------------------
INFO [2025-11-17 22:54:25] Loading coverage files...
INFO [2025-11-17 22:54:25] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-11-17 22:54:25] Allosome coverage missing, cannot determine sex.
WARN [2025-11-17 22:54:25] Allosome coverage missing, cannot determine sex.
INFO [2025-11-17 22:54:25] Removing 228 intervals with missing log.ratio.
INFO [2025-11-17 22:54:25] Removing 22 small (< 5bp) intervals.
INFO [2025-11-17 22:54:25] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-11-17 22:54:25] No normalDB provided. Provide one for better results.
INFO [2025-11-17 22:54:25] Removing 233 low coverage (< 15.0000X) intervals.
INFO [2025-11-17 22:54:25] Using 9547 intervals (9547 on-target, 0 off-target).
INFO [2025-11-17 22:54:25] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-11-17 22:54:25] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-11-17 22:54:25] Loading VCF...
INFO [2025-11-17 22:54:26] Found 127 variants in VCF file.
INFO [2025-11-17 22:54:26] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-11-17 22:54:26] LIB-02240e4 is tumor in VCF file.
INFO [2025-11-17 22:54:26] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-11-17 22:54:26] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-11-17 22:54:26] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-11-17 22:54:26] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-11-17 22:54:26] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-11-17 22:54:26] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-11-17 22:54:26] Total size of targeted genomic region: 1.63Mb (2.58Mb with 50bp padding).
INFO [2025-11-17 22:54:26] 1.0% of targets contain variants.
INFO [2025-11-17 22:54:26] Removing 2 variants outside intervals.
INFO [2025-11-17 22:54:26] Found SOMATIC annotation in VCF.
INFO [2025-11-17 22:54:26] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-11-17 22:54:26] Found SOMATIC annotation in VCF. Setting mapping bias to 0.973.
INFO [2025-11-17 22:54:26] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-11-17 22:54:26] Sample sex: ?
INFO [2025-11-17 22:54:26] Segmenting data...
INFO [2025-11-17 22:54:26] Loading pre-computed boundaries for DNAcopy...
INFO [2025-11-17 22:54:26] Setting undo.SD parameter to 1.000000.
INFO [2025-11-17 22:54:26] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-11-17 22:54:27] Found 54 segments with median size of 24.88Mb.
INFO [2025-11-17 22:54:27] Using 123 variants.
INFO [2025-11-17 22:54:27] Mean standard deviation of log-ratios: 0.37 (MAPD: 0.32)
INFO [2025-11-17 22:54:27] 2D-grid search of purity and ploidy...
INFO [2025-11-17 22:54:27] Local optima: 0.62/1.9, 0.3/1.9, 0.32/2
INFO [2025-11-17 22:54:27] Testing local optimum 1/3 at purity 0.62 and total ploidy 1.90...
INFO [2025-11-17 22:54:28] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-11-17 22:54:28] Recalibrating log-ratios...
INFO [2025-11-17 22:54:28] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-11-17 22:54:28] Recalibrating log-ratios...
INFO [2025-11-17 22:54:28] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-11-17 22:54:28] Recalibrating log-ratios...
INFO [2025-11-17 22:54:28] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-11-17 22:54:28] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-11-17 22:54:28] Recalibrating log-ratios...
INFO [2025-11-17 22:54:28] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-11-17 22:54:28] Recalibrating log-ratios...
INFO [2025-11-17 22:54:28] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-11-17 22:54:29] Recalibrating log-ratios...
INFO [2025-11-17 22:54:29] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-11-17 22:54:29] Skipping 1 solutions that converged to the same optima.
INFO [2025-11-17 22:54:29] Skipping 1 solutions exceeding max.non.clonal (0.20): 0.3/1.9 (purity/tumor ploidy)
INFO [2025-11-17 22:54:29] Fitting variants with beta model for local optimum 1/3...
INFO [2025-11-17 22:54:29] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01.
INFO [2025-11-17 22:54:30] Optimized purity: 0.65
INFO [2025-11-17 22:54:30] Done.
INFO [2025-11-17 22:54:30] ------------------------------------------------------------
INFO [2025-11-17 22:54:30] ------------------------------------------------------------
INFO [2025-11-17 22:54:30] PureCN 2.17.0
INFO [2025-11-17 22:54:30] ------------------------------------------------------------
INFO [2025-11-17 22:54:30] Loading coverage files...
INFO [2025-11-17 22:54:30] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-11-17 22:54:30] Allosome coverage missing, cannot determine sex.
WARN [2025-11-17 22:54:30] Allosome coverage missing, cannot determine sex.
INFO [2025-11-17 22:54:30] Removing 228 intervals with missing log.ratio.
INFO [2025-11-17 22:54:30] Removing 22 small (< 5bp) intervals.
INFO [2025-11-17 22:54:30] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-11-17 22:54:30] No normalDB provided. Provide one for better results.
INFO [2025-11-17 22:54:30] Removing 1724 low count (< 100 total reads) intervals.
INFO [2025-11-17 22:54:30] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-11-17 22:54:30] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-11-17 22:54:30] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-11-17 22:54:30] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-11-17 22:54:30] Loading VCF...
INFO [2025-11-17 22:54:30] Found 127 variants in VCF file.
WARN [2025-11-17 22:54:30] DP FORMAT field contains NAs. Removing 3 variants.
WARN [2025-11-17 22:54:30] DB INFO flag contains NAs
INFO [2025-11-17 22:54:30] 119 (96.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-11-17 22:54:30] LIB-02240e4 is tumor in VCF file.
INFO [2025-11-17 22:54:30] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-11-17 22:54:30] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-11-17 22:54:30] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-11-17 22:54:30] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-11-17 22:54:31] Removing 1 variants with AF < 0.030 or AF >= 0.970 or insufficient supporting reads or depth < 15.
INFO [2025-11-17 22:54:31] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding).
INFO [2025-11-17 22:54:31] 1.2% of targets contain variants.
INFO [2025-11-17 22:54:31] Setting somatic prior probabilities for likely germline hits to 0.000500 or to 0.500000 otherwise.
INFO [2025-11-17 22:54:31] Excluding 5 novel or poor quality variants from segmentation.
INFO [2025-11-17 22:54:31] Sample sex: ?
INFO [2025-11-17 22:54:31] Segmenting data...
INFO [2025-11-17 22:54:31] Loading pre-computed boundaries for DNAcopy...
INFO [2025-11-17 22:54:31] Setting undo.SD parameter to 1.000000.
Setting multi-figure configuration
INFO [2025-11-17 22:54:31] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-11-17 22:54:31] Found 59 segments with median size of 17.67Mb.
INFO [2025-11-17 22:54:31] Using 123 variants.
INFO [2025-11-17 22:54:31] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-11-17 22:54:31] 2D-grid search of purity and ploidy...
INFO [2025-11-17 22:54:32] Local optima: 0.62/1.9, 0.3/1.9, 0.32/2
INFO [2025-11-17 22:54:32] Testing local optimum 1/3 at purity 0.62 and total ploidy 1.90...
INFO [2025-11-17 22:54:32] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-11-17 22:54:32] Recalibrating log-ratios...
INFO [2025-11-17 22:54:32] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-11-17 22:54:32] Recalibrating log-ratios...
INFO [2025-11-17 22:54:32] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-11-17 22:54:33] Recalibrating log-ratios...
INFO [2025-11-17 22:54:33] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-11-17 22:54:33] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-11-17 22:54:33] Recalibrating log-ratios...
INFO [2025-11-17 22:54:33] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-11-17 22:54:33] Recalibrating log-ratios...
INFO [2025-11-17 22:54:33] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-11-17 22:54:33] Recalibrating log-ratios...
INFO [2025-11-17 22:54:33] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-11-17 22:54:33] Skipping 2 solutions exceeding max.non.clonal (0.20): 0.3/1.9, 0.35/1.61 (purity/tumor ploidy)
INFO [2025-11-17 22:54:33] Fitting variants with beta model for local optimum 1/3...
INFO [2025-11-17 22:54:33] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2025-11-17 22:54:34] Optimized purity: 0.65
INFO [2025-11-17 22:54:34] Done.
INFO [2025-11-17 22:54:34] ------------------------------------------------------------
INFO [2025-11-17 22:54:34] ------------------------------------------------------------
INFO [2025-11-17 22:54:34] PureCN 2.17.0
INFO [2025-11-17 22:54:34] ------------------------------------------------------------
INFO [2025-11-17 22:54:34] Loading coverage files...
INFO [2025-11-17 22:54:35] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-11-17 22:54:35] Allosome coverage missing, cannot determine sex.
WARN [2025-11-17 22:54:35] Allosome coverage missing, cannot determine sex.
INFO [2025-11-17 22:54:35] No Gene column in interval.file. You won't get gene-level calls.
INFO [2025-11-17 22:54:35] Removing 228 intervals with missing log.ratio.
INFO [2025-11-17 22:54:35] Removing 15 low/high GC targets.
INFO [2025-11-17 22:54:35] Removing 21 small (< 5bp) intervals.
INFO [2025-11-17 22:54:35] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-11-17 22:54:35] No normalDB provided. Provide one for better results.
INFO [2025-11-17 22:54:35] Removing 1718 low count (< 100 total reads) intervals.
INFO [2025-11-17 22:54:35] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-11-17 22:54:35] Removing 36 low mappability intervals.
INFO [2025-11-17 22:54:35] Using 8006 intervals (8006 on-target, 0 off-target).
INFO [2025-11-17 22:54:35] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-11-17 22:54:35] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio).
INFO [2025-11-17 22:54:35] Loading VCF...
INFO [2025-11-17 22:54:35] Found 127 variants in VCF file.
INFO [2025-11-17 22:54:35] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-11-17 22:54:35] LIB-02240e4 is tumor in VCF file.
INFO [2025-11-17 22:54:35] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-11-17 22:54:35] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-11-17 22:54:35] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-11-17 22:54:35] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-11-17 22:54:35] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-11-17 22:54:35] Removing 1 variants with AF < 0.030 or AF >= Inf or insufficient supporting reads or depth < 15.
INFO [2025-11-17 22:54:35] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding).
INFO [2025-11-17 22:54:35] 1.2% of targets contain variants.
INFO [2025-11-17 22:54:35] Removing 11 variants outside intervals.
INFO [2025-11-17 22:54:35] Found SOMATIC annotation in VCF.
INFO [2025-11-17 22:54:35] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-11-17 22:54:36] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970.
INFO [2025-11-17 22:54:36] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-11-17 22:54:36] Sample sex: ?
INFO [2025-11-17 22:54:36] Segmenting data...
INFO [2025-11-17 22:54:36] MAPD of 114 allelic fractions: 0.14 (0.15 adjusted).
INFO [2025-11-17 22:54:36] Using unweighted PSCBS.
INFO [2025-11-17 22:54:36] Setting undo.SD parameter to 1.000000.
INFO [2025-11-17 22:54:47] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-11-17 22:54:47] Found 72 segments with median size of 27.25Mb.
INFO [2025-11-17 22:54:47] Using 114 variants.
INFO [2025-11-17 22:54:47] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-11-17 22:54:47] 2D-grid search of purity and ploidy...
INFO [2025-11-17 22:54:47] Local optima: 0.65/1.8, 0.38/2.2
INFO [2025-11-17 22:54:47] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2025-11-17 22:54:48] Recalibrating log-ratios...
INFO [2025-11-17 22:54:48] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2025-11-17 22:54:48] Recalibrating log-ratios...
INFO [2025-11-17 22:54:48] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2025-11-17 22:54:48] Recalibrating log-ratios...
INFO [2025-11-17 22:54:48] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2025-11-17 22:54:48] Testing local optimum 2/2 at purity 0.38 and total ploidy 2.20...
INFO [2025-11-17 22:54:49] Skipping 1 solutions exceeding max.non.clonal (0.20): 0.65/2.05 (purity/tumor ploidy)
INFO [2025-11-17 22:54:49] Fitting variants with beta model for local optimum 2/2...
INFO [2025-11-17 22:54:49] Fitting variants for purity 0.40, tumor ploidy 2.55 and contamination 0.01.
INFO [2025-11-17 22:54:50] Optimized purity: 0.40
INFO [2025-11-17 22:54:50] Done.
INFO [2025-11-17 22:54:50] ------------------------------------------------------------
FATAL [2025-11-17 22:54:50] This function requires gene-level calls. Please add a column 'Gene'
FATAL [2025-11-17 22:54:50] containing gene symbols to the interval.file.
FATAL [2025-11-17 22:54:50]
FATAL [2025-11-17 22:54:50] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:54:50] parameters (PureCN 2.17.0).
INFO [2025-11-17 22:54:50] ------------------------------------------------------------
INFO [2025-11-17 22:54:50] PureCN 2.17.0
INFO [2025-11-17 22:54:50] ------------------------------------------------------------
INFO [2025-11-17 22:54:50] Loading coverage files...
INFO [2025-11-17 22:54:51] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-11-17 22:54:51] Allosome coverage missing, cannot determine sex.
WARN [2025-11-17 22:54:51] Allosome coverage missing, cannot determine sex.
INFO [2025-11-17 22:54:51] Removing 228 intervals with missing log.ratio.
INFO [2025-11-17 22:54:51] Removing 22 small (< 5bp) intervals.
INFO [2025-11-17 22:54:51] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-11-17 22:54:51] No normalDB provided. Provide one for better results.
INFO [2025-11-17 22:54:51] Removing 1724 low count (< 100 total reads) intervals.
INFO [2025-11-17 22:54:51] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-11-17 22:54:51] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-11-17 22:54:51] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-11-17 22:54:51] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-11-17 22:54:51] Loading VCF...
INFO [2025-11-17 22:54:51] Found 127 variants in VCF file.
INFO [2025-11-17 22:54:51] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
FATAL [2025-11-17 22:54:51] Different chromosome names in coverage and VCF.
FATAL [2025-11-17 22:54:51]
FATAL [2025-11-17 22:54:51] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:54:51] parameters (PureCN 2.17.0).
INFO [2025-11-17 22:54:51] ------------------------------------------------------------
INFO [2025-11-17 22:54:51] PureCN 2.17.0
INFO [2025-11-17 22:54:51] ------------------------------------------------------------
INFO [2025-11-17 22:54:51] Loading coverage files...
INFO [2025-11-17 22:54:51] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-11-17 22:54:51] Allosome coverage missing, cannot determine sex.
WARN [2025-11-17 22:54:51] Allosome coverage missing, cannot determine sex.
FATAL [2025-11-17 22:54:51] tumor.coverage.file and interval.file do not align.
FATAL [2025-11-17 22:54:51]
FATAL [2025-11-17 22:54:51] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:54:51] parameters (PureCN 2.17.0).
INFO [2025-11-17 22:54:51] ------------------------------------------------------------
INFO [2025-11-17 22:54:51] PureCN 2.17.0
INFO [2025-11-17 22:54:51] ------------------------------------------------------------
INFO [2025-11-17 22:54:51] Loading coverage files...
INFO [2025-11-17 22:54:51] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-11-17 22:54:51] Allosome coverage missing, cannot determine sex.
WARN [2025-11-17 22:54:51] Allosome coverage missing, cannot determine sex.
INFO [2025-11-17 22:54:52] Removing 228 intervals with missing log.ratio.
INFO [2025-11-17 22:54:52] Removing 15 low/high GC targets.
INFO [2025-11-17 22:54:52] Removing 21 small (< 5bp) intervals.
INFO [2025-11-17 22:54:52] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-11-17 22:54:52] No normalDB provided. Provide one for better results.
INFO [2025-11-17 22:54:52] Removing 1718 low count (< 100 total reads) intervals.
INFO [2025-11-17 22:54:52] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-11-17 22:54:52] Removing 36 low mappability intervals.
INFO [2025-11-17 22:54:52] Using 8006 intervals (8006 on-target, 0 off-target).
INFO [2025-11-17 22:54:52] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-11-17 22:54:52] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio).
INFO [2025-11-17 22:54:52] Loading VCF...
INFO [2025-11-17 22:54:52] Found 127 variants in VCF file.
INFO [2025-11-17 22:54:52] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-11-17 22:54:52] LIB-02240e4 is tumor in VCF file.
INFO [2025-11-17 22:54:52] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-11-17 22:54:52] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-11-17 22:54:52] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-11-17 22:54:52] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-11-17 22:54:52] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-11-17 22:54:52] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-11-17 22:54:52] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding).
INFO [2025-11-17 22:54:52] 1.2% of targets contain variants.
INFO [2025-11-17 22:54:52] Removing 11 variants outside intervals.
INFO [2025-11-17 22:54:52] Found SOMATIC annotation in VCF.
INFO [2025-11-17 22:54:52] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-11-17 22:54:52] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970.
INFO [2025-11-17 22:54:52] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-11-17 22:54:52] Sample sex: ?
INFO [2025-11-17 22:54:52] Segmenting data...
INFO [2025-11-17 22:54:52] Loading pre-computed boundaries for DNAcopy...
INFO [2025-11-17 22:54:52] Setting undo.SD parameter to 1.000000.
INFO [2025-11-17 22:54:53] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-11-17 22:54:53] Found 59 segments with median size of 17.67Mb.
INFO [2025-11-17 22:54:53] Using 114 variants.
INFO [2025-11-17 22:54:53] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-11-17 22:54:53] 2D-grid search of purity and ploidy...
INFO [2025-11-17 22:54:53] Local optima: 0.63/1.9
INFO [2025-11-17 22:54:53] Testing local optimum 1/1 at purity 0.63 and total ploidy 1.90...
INFO [2025-11-17 22:54:53] Fitting variants with beta model for local optimum 1/1...
INFO [2025-11-17 22:54:54] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2025-11-17 22:54:55] Optimized purity: 0.65
INFO [2025-11-17 22:54:55] Done.
INFO [2025-11-17 22:54:55] ------------------------------------------------------------
INFO [2025-11-17 22:54:55] ------------------------------------------------------------
INFO [2025-11-17 22:54:55] PureCN 2.17.0
INFO [2025-11-17 22:54:55] ------------------------------------------------------------
INFO [2025-11-17 22:54:55] Loading coverage files...
INFO [2025-11-17 22:54:55] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-11-17 22:54:55] Allosome coverage missing, cannot determine sex.
WARN [2025-11-17 22:54:55] Allosome coverage missing, cannot determine sex.
INFO [2025-11-17 22:54:55] Removing 228 intervals with missing log.ratio.
INFO [2025-11-17 22:54:55] Removing 15 low/high GC targets.
INFO [2025-11-17 22:54:55] Removing 21 small (< 5bp) intervals.
INFO [2025-11-17 22:54:55] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-11-17 22:54:55] No normalDB provided. Provide one for better results.
INFO [2025-11-17 22:54:55] Removing 1718 low count (< 100 total reads) intervals.
INFO [2025-11-17 22:54:55] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-11-17 22:54:55] Removing 36 low mappability intervals.
INFO [2025-11-17 22:54:55] Using 8006 intervals (8006 on-target, 0 off-target).
INFO [2025-11-17 22:54:55] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-11-17 22:54:55] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio).
INFO [2025-11-17 22:54:55] Loading VCF...
INFO [2025-11-17 22:54:55] Found 127 variants in VCF file.
INFO [2025-11-17 22:54:55] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-11-17 22:54:55] LIB-02240e4 is tumor in VCF file.
INFO [2025-11-17 22:54:55] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-11-17 22:54:55] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-11-17 22:54:55] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-11-17 22:54:55] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-11-17 22:54:55] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-11-17 22:54:55] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-11-17 22:54:55] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding).
INFO [2025-11-17 22:54:55] 1.2% of targets contain variants.
INFO [2025-11-17 22:54:55] Removing 11 variants outside intervals.
INFO [2025-11-17 22:54:56] Found SOMATIC annotation in VCF.
INFO [2025-11-17 22:54:56] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-11-17 22:54:56] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970.
INFO [2025-11-17 22:54:56] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-11-17 22:54:56] Sample sex: ?
INFO [2025-11-17 22:54:56] Segmenting data...
INFO [2025-11-17 22:54:56] Loading pre-computed boundaries for DNAcopy...
INFO [2025-11-17 22:54:56] Setting undo.SD parameter to 1.000000.
INFO [2025-11-17 22:54:56] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-11-17 22:54:56] Found 59 segments with median size of 17.67Mb.
INFO [2025-11-17 22:54:56] Using 114 variants.
INFO [2025-11-17 22:54:56] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-11-17 22:54:56] 2D-grid search of purity and ploidy...
INFO [2025-11-17 22:54:56] Local optima: 0.63/1.9
INFO [2025-11-17 22:54:56] Testing local optimum 1/1 at purity 0.63 and total ploidy 1.90...
INFO [2025-11-17 22:54:57] Fitting variants with beta model for local optimum 1/1...
WARN [2025-11-17 22:54:57] Some gene symbols found on multiple chromosomes. Use of approved symbols suggested.
INFO [2025-11-17 22:54:57] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2025-11-17 22:54:58] Optimized purity: 0.65
INFO [2025-11-17 22:54:58] Done.
INFO [2025-11-17 22:54:58] ------------------------------------------------------------
FATAL [2025-11-17 22:54:58] chr1 not valid chromosome name(s). Valid names are:
FATAL [2025-11-17 22:54:58] 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22
FATAL [2025-11-17 22:54:58]
FATAL [2025-11-17 22:54:58] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:54:58] parameters (PureCN 2.17.0).
INFO [2025-11-17 22:54:58] ------------------------------------------------------------
INFO [2025-11-17 22:54:58] PureCN 2.17.0
INFO [2025-11-17 22:54:58] ------------------------------------------------------------
INFO [2025-11-17 22:54:58] Loading coverage files...
WARN [2025-11-17 22:54:58] Provided sampleid (Sample2) does not match Sample1 found in segmentation.
WARN [2025-11-17 22:54:58] Allosome coverage missing, cannot determine sex.
WARN [2025-11-17 22:54:58] Allosome coverage missing, cannot determine sex.
INFO [2025-11-17 22:54:58] Removing 10 intervals with missing log.ratio.
INFO [2025-11-17 22:54:58] Using 10039 intervals (10039 on-target, 0 off-target).
INFO [2025-11-17 22:54:58] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-11-17 22:54:58] Loading VCF...
INFO [2025-11-17 22:54:58] Found 127 variants in VCF file.
INFO [2025-11-17 22:54:58] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-11-17 22:54:58] LIB-02240e4 is tumor in VCF file.
INFO [2025-11-17 22:54:58] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-11-17 22:54:58] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-11-17 22:54:58] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-11-17 22:54:58] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-11-17 22:54:58] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-11-17 22:54:58] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-11-17 22:54:58] Total size of targeted genomic region: 1.71Mb (2.70Mb with 50bp padding).
INFO [2025-11-17 22:54:59] 1.0% of targets contain variants.
INFO [2025-11-17 22:54:59] Removing 0 variants outside intervals.
INFO [2025-11-17 22:54:59] Found SOMATIC annotation in VCF.
INFO [2025-11-17 22:54:59] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-11-17 22:54:59] Found SOMATIC annotation in VCF. Setting mapping bias to 0.976.
INFO [2025-11-17 22:54:59] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-11-17 22:54:59] Sample sex: ?
INFO [2025-11-17 22:54:59] Segmenting data...
INFO [2025-11-17 22:54:59] Loaded provided segmentation file example_seg.txt (format DNAcopy).
WARN [2025-11-17 22:54:59] Provided sampleid (Sample2) does not match Sample1 found in segmentation.
INFO [2025-11-17 22:54:59] Re-centering provided segment means (offset -0.0033).
INFO [2025-11-17 22:54:59] Loading pre-computed boundaries for DNAcopy...
INFO [2025-11-17 22:54:59] Setting undo.SD parameter to 0.000000.
Setting multi-figure configuration
INFO [2025-11-17 22:54:59] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-11-17 22:54:59] Found 54 segments with median size of 24.88Mb.
INFO [2025-11-17 22:54:59] Using 125 variants.
INFO [2025-11-17 22:54:59] Mean standard deviation of log-ratios: 0.40 (MAPD: 0.00)
INFO [2025-11-17 22:54:59] 2D-grid search of purity and ploidy...
INFO [2025-11-17 22:54:59] Local optima: 0.6/1.9
INFO [2025-11-17 22:54:59] Testing local optimum 1/1 at purity 0.60 and total ploidy 1.90...
INFO [2025-11-17 22:55:00] Fitting variants with beta model for local optimum 1/1...
INFO [2025-11-17 22:55:00] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01.
INFO [2025-11-17 22:55:01] Optimized purity: 0.65
INFO [2025-11-17 22:55:01] Done.
INFO [2025-11-17 22:55:01] ------------------------------------------------------------
WARN [2025-11-17 22:55:01] Allosome coverage missing, cannot determine sex.
WARN [2025-11-17 22:55:01] Allosome coverage missing, cannot determine sex.
Setting multi-figure configuration
FATAL [2025-11-17 22:55:04] Segmentation file expected with colnames ID, chrom, loc.start, loc.end,
FATAL [2025-11-17 22:55:04] num.mark, seg.mean
FATAL [2025-11-17 22:55:04]
FATAL [2025-11-17 22:55:04] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:55:04] parameters (PureCN 2.17.0).
FATAL [2025-11-17 22:55:04] seg.file contains multiple samples and sampleid missing.
FATAL [2025-11-17 22:55:04]
FATAL [2025-11-17 22:55:04] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:55:04] parameters (PureCN 2.17.0).
FATAL [2025-11-17 22:55:04] seg.file contains multiple samples and sampleid does not match any.
FATAL [2025-11-17 22:55:04]
FATAL [2025-11-17 22:55:04] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:55:04] parameters (PureCN 2.17.0).
WARN [2025-11-17 22:55:04] Allosome coverage missing, cannot determine sex.
WARN [2025-11-17 22:55:04] Allosome coverage missing, cannot determine sex.
WARN [2025-11-17 22:55:08] Allosome coverage missing, cannot determine sex.
WARN [2025-11-17 22:55:08] Allosome coverage missing, cannot determine sex.
WARN [2025-11-17 22:55:08] Provided sampleid (example_tumor.txt.gz) does not match Sample1 found in segmentation.
WARN [2025-11-17 22:55:09] Allosome coverage missing, cannot determine sex.
WARN [2025-11-17 22:55:09] Allosome coverage missing, cannot determine sex.
WARN [2025-11-17 22:55:10] No normalDB provided. Provide one for better results.
WARN [2025-11-17 22:55:12] Allosome coverage missing, cannot determine sex.
WARN [2025-11-17 22:55:12] Allosome coverage missing, cannot determine sex.
WARN [2025-11-17 22:55:13] Provided sampleid (Sample.1) does not match Sample1 found in segmentation.
Setting multi-figure configuration
WARN [2025-11-17 22:55:16] Allosome coverage missing, cannot determine sex.
WARN [2025-11-17 22:55:16] Allosome coverage missing, cannot determine sex.
WARN [2025-11-17 22:55:16] No normalDB provided. Provide one for better results.
WARN [2025-11-17 22:55:16] Sampleid looks like a normal in VCF, not like a tumor.
WARN [2025-11-17 22:55:19] Allosome coverage missing, cannot determine sex.
WARN [2025-11-17 22:55:19] Allosome coverage missing, cannot determine sex.
FATAL [2025-11-17 22:55:19] normalDB not a valid normalDB object. Use createNormalDatabase to
FATAL [2025-11-17 22:55:19] create one.
FATAL [2025-11-17 22:55:19]
FATAL [2025-11-17 22:55:19] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:55:19] parameters (PureCN 2.17.0).
WARN [2025-11-17 22:55:19] You are likely not using the correct baits file!
WARN [2025-11-17 22:55:19] Allosome coverage missing, cannot determine sex.
WARN [2025-11-17 22:55:19] Allosome coverage missing, cannot determine sex.
WARN [2025-11-17 22:55:20] Allosome coverage missing, cannot determine sex.
WARN [2025-11-17 22:55:20] Allosome coverage missing, cannot determine sex.
FATAL [2025-11-17 22:55:20] normalDB appears to be empty.
FATAL [2025-11-17 22:55:20]
FATAL [2025-11-17 22:55:20] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:55:20] parameters (PureCN 2.17.0).
WARN [2025-11-17 22:55:20] Allosome coverage missing, cannot determine sex.
WARN [2025-11-17 22:55:20] Allosome coverage missing, cannot determine sex.
WARN [2025-11-17 22:55:21] Intervals in coverage and interval.file have conflicting on/off-target annotation.
WARN [2025-11-17 22:55:25] Allosome coverage missing, cannot determine sex.
WARN [2025-11-17 22:55:25] Allosome coverage missing, cannot determine sex.
FATAL [2025-11-17 22:55:25] Seqlevels missing in provided segmentation: 6
FATAL [2025-11-17 22:55:25]
FATAL [2025-11-17 22:55:25] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:55:25] parameters (PureCN 2.17.0).
sh: gatk: command not found
WARN [2025-11-17 22:55:26] Cannot find gatk binary in path.
WARN [2025-11-17 22:55:26] Allosome coverage missing, cannot determine sex.
WARN [2025-11-17 22:55:26] Allosome coverage missing, cannot determine sex.
WARN [2025-11-17 22:55:26] No normalDB provided. Provide one for better results.
FATAL [2025-11-17 22:55:26] segmentationHclust requires an input segmentation.
FATAL [2025-11-17 22:55:26]
FATAL [2025-11-17 22:55:26] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:55:26] parameters (PureCN 2.17.0).
WARN [2025-11-17 22:55:26] Allosome coverage missing, cannot determine sex.
WARN [2025-11-17 22:55:26] Allosome coverage missing, cannot determine sex.
WARN [2025-11-17 22:55:26] No normalDB provided. Provide one for better results.
FATAL [2025-11-17 22:55:36] The normal.panel.vcf.file contains only a single sample.
FATAL [2025-11-17 22:55:36]
FATAL [2025-11-17 22:55:36] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:55:36] parameters (PureCN 2.17.0).
FATAL [2025-11-17 22:55:36] mapping.bias.file must be a file with *.rds suffix.
FATAL [2025-11-17 22:55:36]
FATAL [2025-11-17 22:55:36] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:55:36] parameters (PureCN 2.17.0).
Failed with error: 'there is no package called 'genomicsdb''
FATAL [2025-11-17 22:55:37] min.normals (0) must be >= 1.
FATAL [2025-11-17 22:55:37]
FATAL [2025-11-17 22:55:37] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:55:37] parameters (PureCN 2.17.0).
FATAL [2025-11-17 22:55:37] min.normals (10) cannot be larger than min.normals.assign.betafit (3).
FATAL [2025-11-17 22:55:37]
FATAL [2025-11-17 22:55:37] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:55:37] parameters (PureCN 2.17.0).
FATAL [2025-11-17 22:55:37] min.normals.assign.betafit (10) cannot be larger than
FATAL [2025-11-17 22:55:37] min.normals.betafit (7).
FATAL [2025-11-17 22:55:37]
FATAL [2025-11-17 22:55:37] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:55:37] parameters (PureCN 2.17.0).
FATAL [2025-11-17 22:55:37] min.normals.betafit (20) cannot be larger than
FATAL [2025-11-17 22:55:37] min.normals.position.specific.fit (10).
FATAL [2025-11-17 22:55:37]
FATAL [2025-11-17 22:55:37] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:55:37] parameters (PureCN 2.17.0).
FATAL [2025-11-17 22:55:37] min.betafit.rho not within expected range or format.
FATAL [2025-11-17 22:55:37]
FATAL [2025-11-17 22:55:37] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:55:37] parameters (PureCN 2.17.0).
FATAL [2025-11-17 22:55:37] max.betafit.rho not within expected range or format.
FATAL [2025-11-17 22:55:37]
FATAL [2025-11-17 22:55:37] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:55:37] parameters (PureCN 2.17.0).
FATAL [2025-11-17 22:55:37] min.betafit.rho (0.9) cannot be larger than max.betafit.rho (0.2).
FATAL [2025-11-17 22:55:37]
FATAL [2025-11-17 22:55:37] This is most likely a user error due to invalid input data or
FATAL [2025-11-17 22:55:37] 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
162.144 5.821 163.717
PureCN.Rcheck/PureCN-Ex.timings
| name | user | system | elapsed | |
| adjustLogRatio | 0.858 | 0.014 | 0.936 | |
| annotateTargets | 5.981 | 0.236 | 6.508 | |
| bootstrapResults | 0.208 | 0.020 | 0.252 | |
| calculateBamCoverageByInterval | 0.078 | 0.003 | 0.087 | |
| calculateLogRatio | 0.346 | 0.014 | 0.399 | |
| calculateMappingBiasGatk4 | 0 | 0 | 0 | |
| calculateMappingBiasVcf | 0.721 | 0.025 | 0.805 | |
| calculatePowerDetectSomatic | 0.646 | 0.005 | 0.672 | |
| calculateTangentNormal | 1.377 | 0.026 | 1.526 | |
| callAlterations | 0.057 | 0.002 | 0.066 | |
| callAlterationsFromSegmentation | 0.869 | 0.016 | 0.941 | |
| callAmplificationsInLowPurity | 15.321 | 0.148 | 18.175 | |
| callCIN | 0.119 | 0.003 | 0.133 | |
| callLOH | 0.077 | 0.002 | 0.083 | |
| callMutationBurden | 0.629 | 0.018 | 0.735 | |
| centromeres | 0.000 | 0.001 | 0.003 | |
| correctCoverageBias | 0.668 | 0.015 | 0.728 | |
| createCurationFile | 0.158 | 0.005 | 0.178 | |
| createNormalDatabase | 1.069 | 0.014 | 1.227 | |
| filterIntervals | 8.854 | 0.148 | 10.065 | |
| filterVcfBasic | 0.266 | 0.002 | 0.317 | |
| filterVcfMuTect | 0.271 | 0.002 | 0.303 | |
| filterVcfMuTect2 | 0.245 | 0.004 | 0.263 | |
| findFocal | 4.497 | 0.047 | 4.865 | |
| findHighQualitySNPs | 0.566 | 0.011 | 0.619 | |
| getSexFromCoverage | 0.120 | 0.004 | 0.141 | |
| getSexFromVcf | 0.103 | 0.003 | 0.124 | |
| plotAbs | 0.098 | 0.004 | 0.116 | |
| poolCoverage | 0.223 | 0.009 | 0.263 | |
| predictSomatic | 0.192 | 0.005 | 0.211 | |
| preprocessIntervals | 0.240 | 0.003 | 0.288 | |
| processMultipleSamples | 0.957 | 0.020 | 1.096 | |
| readAllelicCountsFile | 0.209 | 0.000 | 0.236 | |
| readCoverageFile | 0.102 | 0.004 | 0.120 | |
| readCurationFile | 0.090 | 0.003 | 0.108 | |
| readIntervalFile | 0.071 | 0.002 | 0.074 | |
| readLogRatioFile | 0.014 | 0.000 | 0.015 | |
| readSegmentationFile | 0.003 | 0.001 | 0.004 | |
| runAbsoluteCN | 6.711 | 0.125 | 7.260 | |
| segmentationCBS | 3.129 | 0.038 | 3.339 | |
| segmentationGATK4 | 0.001 | 0.001 | 0.001 | |
| segmentationHclust | 5.720 | 0.103 | 6.347 | |
| segmentationPSCBS | 14.506 | 0.174 | 15.647 | |
| setMappingBiasVcf | 0.113 | 0.003 | 0.122 | |
| setPriorVcf | 0.133 | 0.004 | 0.145 | |