Markus Riester
| Snapshot Date: 2025-11-18 13:40 -0500 (Tue, 18 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 2025-11-19 10:14 -0500 (Wed, 19 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" | 4827 |
| lconway | macOS 12.7.6 Monterey | x86_64 | R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" | 4600 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4564 |
| 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: 2025-11-18 21:58:01 -0500 (Tue, 18 Nov 2025) |
| EndedAt: 2025-11-18 22:04:30 -0500 (Tue, 18 Nov 2025) |
| EllapsedTime: 389.2 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 15.270 0.175 16.982
segmentationPSCBS 14.471 0.198 15.252
filterIntervals 8.426 0.149 8.966
runAbsoluteCN 6.353 0.122 6.902
segmentationHclust 5.660 0.105 5.954
annotateTargets 5.441 0.222 5.796
* 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 [2025-11-18 22:01:56] Attempted adding gene symbols to intervals. Heuristics have been used to pick symbols for overlapping genes.
WARN [2025-11-18 22:01:56] Chromosome naming style of txdb file (UCSC) was different from interval file (Ensembl).
WARN [2025-11-18 22:02:01] Attempted adding gene symbols to intervals. Heuristics have been used to pick symbols for overlapping genes.
FATAL [2025-11-18 22:02:02] tumor.coverage.file and interval.file do not align.
FATAL [2025-11-18 22:02:02]
FATAL [2025-11-18 22:02:02] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:02:02] parameters (PureCN 2.17.0).
WARN [2025-11-18 22:02:02] Cannot find all contig lengths while exporting interval file.
INFO [2025-11-18 22:02:02] Processing seq1:1-21 (1/3)...
INFO [2025-11-18 22:02:03] Processing seq1:1227-1247 (2/3)...
INFO [2025-11-18 22:02:03] Processing seq2:594-614 (3/3)...
WARN [2025-11-18 22:02:04] Large potential mis-calibration of on- and off-target log2 ratios: 0.26
FATAL [2025-11-18 22:02:04] Need either f or purity and ploidy.
FATAL [2025-11-18 22:02:04]
FATAL [2025-11-18 22:02:04] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:02:04] parameters (PureCN 2.17.0).
FATAL [2025-11-18 22:02:04] f not in expected range.
FATAL [2025-11-18 22:02:04]
FATAL [2025-11-18 22:02:04] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:02:04] parameters (PureCN 2.17.0).
FATAL [2025-11-18 22:02:04] coverage not in expected range (>=2)
FATAL [2025-11-18 22:02:04]
FATAL [2025-11-18 22:02:04] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:02:04] parameters (PureCN 2.17.0).
FATAL [2025-11-18 22:02:04] purity not in expected range.
FATAL [2025-11-18 22:02:04]
FATAL [2025-11-18 22:02:04] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:02:04] parameters (PureCN 2.17.0).
FATAL [2025-11-18 22:02:04] ploidy not in expected range.
FATAL [2025-11-18 22:02:04]
FATAL [2025-11-18 22:02:04] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:02:04] parameters (PureCN 2.17.0).
FATAL [2025-11-18 22:02:04] cell.fraction not in expected range.
FATAL [2025-11-18 22:02:04]
FATAL [2025-11-18 22:02:04] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:02:04] parameters (PureCN 2.17.0).
INFO [2025-11-18 22:02:05] 576 on-target bins with low coverage in all samples.
WARN [2025-11-18 22:02:05] You are likely not using the correct baits file!
WARN [2025-11-18 22:02:05] Allosome coverage missing, cannot determine sex.
WARN [2025-11-18 22:02:05] Allosome coverage missing, cannot determine sex.
INFO [2025-11-18 22:02:05] Processing on-target regions...
INFO [2025-11-18 22:02:05] Removing 930 intervals with low coverage in normalDB.
INFO [2025-11-18 22:02:05] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2025-11-18 22:02:06] Tumor/normal noise ratio: 19.041
WARN [2025-11-18 22:02:06] Extensive noise in tumor compared to normals.
INFO [2025-11-18 22:02:22] Tumor/normal noise ratio: 19.041
WARN [2025-11-18 22:02:22] Extensive noise in tumor compared to normals.
INFO [2025-11-18 22:02:24] Using BiocParallel for parallel optimization.
FATAL [2025-11-18 22:02:30] pvalue.cutoff not within expected range or format.
FATAL [2025-11-18 22:02:30]
FATAL [2025-11-18 22:02:30] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:02:30] parameters (PureCN 2.17.0).
FATAL [2025-11-18 22:02:30] pvalue.cutoff not within expected range or format.
FATAL [2025-11-18 22:02:30]
FATAL [2025-11-18 22:02:30] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:02:30] parameters (PureCN 2.17.0).
FATAL [2025-11-18 22:02:30] percentile.cutoff not in expected range (0 to 100).
FATAL [2025-11-18 22:02:30]
FATAL [2025-11-18 22:02:30] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:02:30] parameters (PureCN 2.17.0).
FATAL [2025-11-18 22:02:30] percentile.cutoff not in expected range (0 to 100).
FATAL [2025-11-18 22:02:30]
FATAL [2025-11-18 22:02:30] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:02:30] parameters (PureCN 2.17.0).
FATAL [2025-11-18 22:02:30] purity not within expected range or format.
FATAL [2025-11-18 22:02:30]
FATAL [2025-11-18 22:02:30] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:02:30] parameters (PureCN 2.17.0).
FATAL [2025-11-18 22:02:30] purity not within expected range or format.
FATAL [2025-11-18 22:02:30]
FATAL [2025-11-18 22:02:30] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:02:30] parameters (PureCN 2.17.0).
INFO [2025-11-18 22:02:31] ------------------------------------------------------------
INFO [2025-11-18 22:02:31] PureCN 2.17.0
INFO [2025-11-18 22:02:31] ------------------------------------------------------------
INFO [2025-11-18 22:02:31] Loading coverage files...
INFO [2025-11-18 22:02:31] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-11-18 22:02:31] Allosome coverage missing, cannot determine sex.
WARN [2025-11-18 22:02:31] Allosome coverage missing, cannot determine sex.
INFO [2025-11-18 22:02:31] Removing 228 intervals with missing log.ratio.
INFO [2025-11-18 22:02:31] Removing 22 small (< 5bp) intervals.
INFO [2025-11-18 22:02:31] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-11-18 22:02:31] No normalDB provided. Provide one for better results.
INFO [2025-11-18 22:02:31] Removing 1724 low count (< 100 total reads) intervals.
INFO [2025-11-18 22:02:31] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-11-18 22:02:31] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-11-18 22:02:31] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-11-18 22:02:31] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-11-18 22:02:31] Loading VCF...
INFO [2025-11-18 22:02:31] Found 127 variants in VCF file.
INFO [2025-11-18 22:02:31] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-11-18 22:02:31] LIB-02240e4 is tumor in VCF file.
INFO [2025-11-18 22:02:31] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-11-18 22:02:31] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-11-18 22:02:31] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-11-18 22:02:31] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-11-18 22:02:31] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-11-18 22:02:31] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-11-18 22:02:31] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding).
INFO [2025-11-18 22:02:31] 1.2% of targets contain variants.
INFO [2025-11-18 22:02:31] Removing 4 variants outside intervals.
INFO [2025-11-18 22:02:31] Found SOMATIC annotation in VCF.
INFO [2025-11-18 22:02:31] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-11-18 22:02:31] Found SOMATIC annotation in VCF. Setting mapping bias to 0.972.
INFO [2025-11-18 22:02:31] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-11-18 22:02:31] Sample sex: ?
INFO [2025-11-18 22:02:31] Segmenting data...
INFO [2025-11-18 22:02:31] Loading pre-computed boundaries for DNAcopy...
INFO [2025-11-18 22:02:31] Setting undo.SD parameter to 1.000000.
INFO [2025-11-18 22:02:32] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-11-18 22:02:32] Found 59 segments with median size of 17.67Mb.
INFO [2025-11-18 22:02:32] Using 121 variants.
INFO [2025-11-18 22:02:32] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-11-18 22:02:32] 2D-grid search of purity and ploidy...
INFO [2025-11-18 22:02:32] Local optima: 0.63/1.9, 0.5/2
INFO [2025-11-18 22:02:32] Testing local optimum 1/2 at purity 0.63 and total ploidy 1.90...
INFO [2025-11-18 22:02:33] Testing local optimum 2/2 at purity 0.50 and total ploidy 2.00...
INFO [2025-11-18 22:02:33] Skipping 1 solutions that converged to the same optima.
INFO [2025-11-18 22:02:33] Fitting variants with beta model for local optimum 1/2...
INFO [2025-11-18 22:02:33] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2025-11-18 22:02:34] Optimized purity: 0.65
INFO [2025-11-18 22:02:34] Done.
INFO [2025-11-18 22:02:34] ------------------------------------------------------------
INFO [2025-11-18 22:02:34] Estimating callable regions.
FATAL [2025-11-18 22:02:35] exclude not a GRanges object.
FATAL [2025-11-18 22:02:35]
FATAL [2025-11-18 22:02:35] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:02:35] parameters (PureCN 2.17.0).
FATAL [2025-11-18 22:02:35] callable not a GRanges object.
FATAL [2025-11-18 22:02:35]
FATAL [2025-11-18 22:02:35] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:02:35] parameters (PureCN 2.17.0).
WARN [2025-11-18 22:02:38] tumor.coverage.file and interval.file do not align.
INFO [2025-11-18 22:02:38] No Gene column in interval.file. You won't get gene-level calls.
FATAL [2025-11-18 22:02:39] No gc_bias column in interval.file.
FATAL [2025-11-18 22:02:39]
FATAL [2025-11-18 22:02:39] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:02:39] parameters (PureCN 2.17.0).
FATAL [2025-11-18 22:02:39] Provided coverage is zero, most likely due to a corrupt BAM file.
FATAL [2025-11-18 22:02:39]
FATAL [2025-11-18 22:02:39] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:02:39] parameters (PureCN 2.17.0).
INFO [2025-11-18 22:02:40] No reptiming column in interval.file.
INFO [2025-11-18 22:02:41] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpVqWITm/file10b0e160e8f62.rds...
INFO [2025-11-18 22:02:41] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpVqWITm/file10b0e160e8f62.rds...
INFO [2025-11-18 22:02:41] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpVqWITm/file10b0e160e8f62.rds...
INFO [2025-11-18 22:02:42] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpVqWITm/file10b0e160e8f62.rds...
INFO [2025-11-18 22:02:42] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpVqWITm/file10b0e160e8f62.rds...
INFO [2025-11-18 22:02:42] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpVqWITm/file10b0e160e8f62.rds...
FATAL [2025-11-18 22:02:42] Purity or Ploidy not numeric or in expected range.
FATAL [2025-11-18 22:02:42]
FATAL [2025-11-18 22:02:42] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:02:42] parameters (PureCN 2.17.0).
INFO [2025-11-18 22:02:42] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpVqWITm/file10b0e160e8f62.rds...
INFO [2025-11-18 22:02:42] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpVqWITm/file10b0e160e8f62.rds...
FATAL [2025-11-18 22:02:42] 'Failed' column in
FATAL [2025-11-18 22:02:42] /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpVqWITm/file10b0e160e8f62.csv
FATAL [2025-11-18 22:02:42] not logical(1).
FATAL [2025-11-18 22:02:42]
FATAL [2025-11-18 22:02:42] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:02:42] parameters (PureCN 2.17.0).
INFO [2025-11-18 22:02:42] 576 on-target bins with low coverage in all samples.
WARN [2025-11-18 22:02:42] You are likely not using the correct baits file!
WARN [2025-11-18 22:02:42] Allosome coverage missing, cannot determine sex.
WARN [2025-11-18 22:02:42] Allosome coverage missing, cannot determine sex.
INFO [2025-11-18 22:02:42] Processing on-target regions...
INFO [2025-11-18 22:02:42] Removing 930 intervals with low coverage in normalDB.
INFO [2025-11-18 22:02:42] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2025-11-18 22:02:44] 576 on-target bins with low coverage in all samples.
WARN [2025-11-18 22:02:44] You are likely not using the correct baits file!
WARN [2025-11-18 22:02:44] Allosome coverage missing, cannot determine sex.
WARN [2025-11-18 22:02:44] Allosome coverage missing, cannot determine sex.
INFO [2025-11-18 22:02:44] Processing on-target regions...
INFO [2025-11-18 22:02:44] Removing 930 intervals with low coverage in normalDB.
INFO [2025-11-18 22:02:44] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2025-11-18 22:02:45] 576 on-target bins with low coverage in all samples.
WARN [2025-11-18 22:02:45] You are likely not using the correct baits file!
WARN [2025-11-18 22:02:45] Allosome coverage missing, cannot determine sex.
WARN [2025-11-18 22:02:45] Allosome coverage missing, cannot determine sex.
INFO [2025-11-18 22:02:45] Processing on-target regions...
INFO [2025-11-18 22:02:45] Removing 930 intervals with low coverage in normalDB.
INFO [2025-11-18 22:02:45] Removing 1 intervals with zero coverage in more than 3% of normalDB.
WARN [2025-11-18 22:02:45] Allosome coverage missing, cannot determine sex.
INFO [2025-11-18 22:02:45] Sample sex: NA
WARN [2025-11-18 22:02:45] Allosome coverage missing, cannot determine sex.
INFO [2025-11-18 22:02:45] Sample sex: NA
INFO [2025-11-18 22:02:46] 576 on-target bins with low coverage in all samples.
WARN [2025-11-18 22:02:46] You are likely not using the correct baits file!
WARN [2025-11-18 22:02:46] Allosome coverage missing, cannot determine sex.
WARN [2025-11-18 22:02:46] Allosome coverage missing, cannot determine sex.
FATAL [2025-11-18 22:02:46] Length of normal.coverage.files and sex different
FATAL [2025-11-18 22:02:46]
FATAL [2025-11-18 22:02:46] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:02:46] parameters (PureCN 2.17.0).
WARN [2025-11-18 22:02:48] Target intervals were not sorted.
INFO [2025-11-18 22:02:48] 560 on-target bins with low coverage in all samples.
WARN [2025-11-18 22:02:48] You are likely not using the correct baits file!
WARN [2025-11-18 22:02:48] Allosome coverage missing, cannot determine sex.
WARN [2025-11-18 22:02:48] Allosome coverage missing, cannot determine sex.
WARN [2025-11-18 22:02:48] Allosome coverage missing, cannot determine sex.
INFO [2025-11-18 22:02:48] Processing on-target regions...
INFO [2025-11-18 22:02:48] Removing 978 intervals with low coverage in normalDB.
INFO [2025-11-18 22:02:48] Removing 11 intervals with zero coverage in more than 3% of normalDB.
FATAL [2025-11-18 22:02:49] tumor.coverage.file and normalDB do not align.
FATAL [2025-11-18 22:02:49]
FATAL [2025-11-18 22:02:49] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:02:49] parameters (PureCN 2.17.0).
FATAL [2025-11-18 22:02:49] At least 2 normal.coverage.files required.
FATAL [2025-11-18 22:02:49]
FATAL [2025-11-18 22:02:49] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:02:49] parameters (PureCN 2.17.0).
INFO [2025-11-18 22:02:50] ------------------------------------------------------------
INFO [2025-11-18 22:02:50] PureCN 2.17.0
INFO [2025-11-18 22:02:50] ------------------------------------------------------------
INFO [2025-11-18 22:02:50] Loading coverage files...
INFO [2025-11-18 22:02:50] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-11-18 22:02:50] Allosome coverage missing, cannot determine sex.
WARN [2025-11-18 22:02:50] Allosome coverage missing, cannot determine sex.
INFO [2025-11-18 22:02:50] Removing 228 intervals with missing log.ratio.
FATAL [2025-11-18 22:02:50] normalDB incompatible with this PureCN version. Please re-run
FATAL [2025-11-18 22:02:50] NormalDB.R.
FATAL [2025-11-18 22:02:50]
FATAL [2025-11-18 22:02:50] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:02:50] parameters (PureCN 2.17.0).
FATAL [2025-11-18 22:02:50] normalDB incompatible with this PureCN version. Please re-run
FATAL [2025-11-18 22:02:50] NormalDB.R.
FATAL [2025-11-18 22:02:50]
FATAL [2025-11-18 22:02:50] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:02:50] parameters (PureCN 2.17.0).
FATAL [2025-11-18 22:02:50] normal.coverage.files with _coverage.txt and _loess.txt suffix
FATAL [2025-11-18 22:02:50] provided. Provide either only GC-normalized or raw coverage files!
FATAL [2025-11-18 22:02:50]
FATAL [2025-11-18 22:02:50] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:02:50] parameters (PureCN 2.17.0).
INFO [2025-11-18 22:02:50] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-11-18 22:02:50] Removing 19 low quality variants with non-offset BQ < 25.
INFO [2025-11-18 22:02:50] Base quality scores range from 24 to 35 (offset by 1)
INFO [2025-11-18 22:02:50] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS.
INFO [2025-11-18 22:02:51] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-11-18 22:02:51] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-11-18 22:02:51] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-11-18 22:02:51] Removing 19 low quality variants with non-offset BQ < 25.
INFO [2025-11-18 22:02:51] Base quality scores range from 24 to 35 (offset by 1)
INFO [2025-11-18 22:02:51] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS.
INFO [2025-11-18 22:02:52] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-11-18 22:02:52] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-11-18 22:02:52] Removing 6 blacklisted variants.
INFO [2025-11-18 22:02:52] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-11-18 22:02:52] Removing 19 low quality variants with non-offset BQ < 25.
INFO [2025-11-18 22:02:52] Base quality scores range from 24 to 35 (offset by 1)
INFO [2025-11-18 22:02:52] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS.
INFO [2025-11-18 22:02:52] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-11-18 22:02:52] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
WARN [2025-11-18 22:02:52] MuTect stats file lacks contig and position columns.
INFO [2025-11-18 22:02:52] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-11-18 22:02:52] Removing 19 low quality variants with non-offset BQ < 25.
INFO [2025-11-18 22:02:52] Base quality scores range from 24 to 35 (offset by 1)
INFO [2025-11-18 22:02:52] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS.
INFO [2025-11-18 22:02:52] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-11-18 22:02:52] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
WARN [2025-11-18 22:02:52] MuTect stats file and VCF file do not align perfectly. Will remove 2325 unmatched variants.
WARN [2025-11-18 22:02:52] MuTect stats file lacks failure_reasons column. Keeping all variants listed in stats file.
INFO [2025-11-18 22:02:52] Removing 0 non heterozygous (in matched normal) germline SNPs.
INFO [2025-11-18 22:02:52] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-11-18 22:02:52] Base quality scores range from 31 to 33 (offset by 1)
INFO [2025-11-18 22:02:52] Minimum number of supporting reads ranges from 3 to 4, depending on coverage and BQS.
INFO [2025-11-18 22:02:53] Removing 0 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-11-18 22:02:53] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-11-18 22:02:53] Base quality scores range from 7 to 35 (offset by 1)
INFO [2025-11-18 22:02:53] Minimum number of supporting reads ranges from 1 to 41, depending on coverage and BQS.
INFO [2025-11-18 22:02:53] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-11-18 22:02:53] Removing 49 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-11-18 22:02:53] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-11-18 22:02:53] Base quality scores range from 7 to 35 (offset by 1)
INFO [2025-11-18 22:02:53] Minimum number of supporting reads ranges from 1 to 41, depending on coverage and BQS.
INFO [2025-11-18 22:02:53] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-11-18 22:02:53] Removing 49 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-11-18 22:02:53] Removing 22 non heterozygous (in matched normal) germline SNPs.
WARN [2025-11-18 22:02:53] Many variants removed by min.base.quality (50) filter. You might want to lower the cutoff.
FATAL [2025-11-18 22:02:53] No variants passed filter BQ.
FATAL [2025-11-18 22:02:53]
FATAL [2025-11-18 22:02:53] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:02:53] parameters (PureCN 2.17.0).
INFO [2025-11-18 22:02:53] Found 11 variants in VCF file.
WARN [2025-11-18 22:02:53] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead.
INFO [2025-11-18 22:02:53] 1 (9.1%) variants annotated as likely germline (DB INFO flag).
INFO [2025-11-18 22:02:54] Found 11 variants in VCF file.
WARN [2025-11-18 22:02:54] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead.
INFO [2025-11-18 22:02:54] 1 (9.1%) variants annotated as likely germline (DB INFO flag).
INFO [2025-11-18 22:02:54] Found 11 variants in VCF file.
WARN [2025-11-18 22:02:54] vcf.file has no DB or POP_AF info field for membership in germline databases. Guessing it based on available dbSNP ID.
INFO [2025-11-18 22:02:54] 1 (9.1%) variants annotated as likely germline (DB INFO flag).
INFO [2025-11-18 22:02:55] Found 1000 variants in VCF file.
INFO [2025-11-18 22:02:55] Removing 2 triallelic sites.
WARN [2025-11-18 22:02:55] Having trouble guessing SOMATIC status...
WARN [2025-11-18 22:02:55] DP FORMAT field contains NAs. Removing 44 variants.
INFO [2025-11-18 22:02:55] 954 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-11-18 22:02:55] Found 12 variants in VCF file.
INFO [2025-11-18 22:02:55] Removing 1 triallelic sites.
WARN [2025-11-18 22:02:55] DP FORMAT field contains NAs. Removing 1 variants.
WARN [2025-11-18 22:02:55] vcf.file has no DB info field for membership in germline databases. Found and used somatic status instead.
INFO [2025-11-18 22:02:55] 8 (80.0%) variants annotated as likely germline (DB INFO flag).
WARN [2025-11-18 22:02:55] BQ FORMAT field contains NAs.
INFO [2025-11-18 22:02:56] Found 2331 variants in VCF file.
INFO [2025-11-18 22:02:56] 2282 (97.9%) variants annotated as likely germline (DB INFO flag).
INFO [2025-11-18 22:02:56] Found 2331 variants in VCF file.
INFO [2025-11-18 22:02:56] 2282 (97.9%) variants annotated as likely germline (DB INFO flag).
WARN [2025-11-18 22:02:56] Did not find base quality scores, will use global error rate of 0.0010 instead.
INFO [2025-11-18 22:02:56] Removing 21 low quality variants with non-offset BQ < 25.
INFO [2025-11-18 22:02:56] Base quality scores range from 24 to 35 (offset by 1)
INFO [2025-11-18 22:02:56] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-11-18 22:02:56] Removing 89 variants with AF < 0.030 or AF >= 0.970 or insufficient supporting reads or depth < 15.
INFO [2025-11-18 22:02:56] Found 2331 variants in VCF file.
INFO [2025-11-18 22:02:56] 2282 (97.9%) variants annotated as likely germline (DB INFO flag).
WARN [2025-11-18 22:02:56] BQ FORMAT field contains NAs.
WARN [2025-11-18 22:02:57] Allosome coverage missing, cannot determine sex.
WARN [2025-11-18 22:02:57] Allosome coverage missing, cannot determine sex.
INFO [2025-11-18 22:02:57] Mean coverages: chrX: 108.58, chrY: 108.58, chr1-22: 104.87.
INFO [2025-11-18 22:02:57] Mean coverages: chrX: 108.58, chrY: 2.17, chr1-22: 104.87.
INFO [2025-11-18 22:02:57] Mean coverages: chrX: 108.58, chrY: 5.17, chr1-22: 104.87.
INFO [2025-11-18 22:02:57] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-11-18 22:02:57] No germline variants in VCF.
FATAL [2025-11-18 22:02:57] No solution with id hello
FATAL [2025-11-18 22:02:57]
FATAL [2025-11-18 22:02:57] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:02:57] parameters (PureCN 2.17.0).
FATAL [2025-11-18 22:02:57] No solution with id 100
FATAL [2025-11-18 22:02:57]
FATAL [2025-11-18 22:02:57] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:02:57] parameters (PureCN 2.17.0).
FATAL [2025-11-18 22:02:58] all.data and w have different lengths.
FATAL [2025-11-18 22:02:58]
FATAL [2025-11-18 22:02:58] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:02:58] parameters (PureCN 2.17.0).
INFO [2025-11-18 22:02:58] Splitting 5 large targets to an average width of 400.
WARN [2025-11-18 22:02:58] No mappability scores provided.
WARN [2025-11-18 22:02:58] No reptiming scores provided.
INFO [2025-11-18 22:02:58] Calculating GC-content...
INFO [2025-11-18 22:02:58] Splitting 5 large targets to an average width of 400.
WARN [2025-11-18 22:02:58] No mappability scores provided.
WARN [2025-11-18 22:02:58] No reptiming scores provided.
INFO [2025-11-18 22:02:58] Calculating GC-content...
INFO [2025-11-18 22:02:58] Splitting 5 large targets to an average width of 400.
INFO [2025-11-18 22:02:58] Removing 1 targets overlapping with exclude.
WARN [2025-11-18 22:02:58] No mappability scores provided.
WARN [2025-11-18 22:02:58] No reptiming scores provided.
INFO [2025-11-18 22:02:58] Calculating GC-content...
WARN [2025-11-18 22:02:58] Found small target regions (< 100bp). Will resize them.
INFO [2025-11-18 22:02:58] Splitting 5 large targets to an average width of 400.
FATAL [2025-11-18 22:02:58] off.target.padding must be negative.
FATAL [2025-11-18 22:02:58]
FATAL [2025-11-18 22:02:58] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:02:58] parameters (PureCN 2.17.0).
FATAL [2025-11-18 22:02:58] Interval coordinates should start at 1, not at 0
FATAL [2025-11-18 22:02:58]
FATAL [2025-11-18 22:02:58] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:02:58] parameters (PureCN 2.17.0).
WARN [2025-11-18 22:02:58] Found small target regions (< 100bp). Will resize them.
INFO [2025-11-18 22:02:58] Splitting 5 large targets to an average width of 400.
FATAL [2025-11-18 22:02:59] No off-target regions after filtering for mappability and
FATAL [2025-11-18 22:02:59] off.target.padding
FATAL [2025-11-18 22:02:59]
FATAL [2025-11-18 22:02:59] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:02:59] parameters (PureCN 2.17.0).
WARN [2025-11-18 22:02:59] Found small target regions (< 100bp). Will resize them.
INFO [2025-11-18 22:02:59] Splitting 5 large targets to an average width of 400.
WARN [2025-11-18 22:02:59] No mappability scores provided.
INFO [2025-11-18 22:02:59] Calculating GC-content...
WARN [2025-11-18 22:02:59] Found small target regions (< 100bp). Will resize them.
INFO [2025-11-18 22:02:59] Averaging reptiming into bins of size 200...
INFO [2025-11-18 22:02:59] Splitting 5 large targets to an average width of 400.
WARN [2025-11-18 22:02:59] No mappability scores provided.
INFO [2025-11-18 22:02:59] Calculating GC-content...
WARN [2025-11-18 22:02:59] Found small target regions (< 100bp). Will resize them.
INFO [2025-11-18 22:02:59] Splitting 6 large targets to an average width of 200.
WARN [2025-11-18 22:02:59] No mappability scores provided.
WARN [2025-11-18 22:02:59] No reptiming scores provided.
INFO [2025-11-18 22:02:59] Calculating GC-content...
WARN [2025-11-18 22:02:59] Found small target regions (< 100bp). Will resize them.
INFO [2025-11-18 22:02:59] Splitting 5 large targets to an average width of 400.
WARN [2025-11-18 22:02:59] No mappability scores provided.
WARN [2025-11-18 22:02:59] No reptiming scores provided.
INFO [2025-11-18 22:02:59] Calculating GC-content...
INFO [2025-11-18 22:02:59] Splitting 5 large targets to an average width of 400.
INFO [2025-11-18 22:02:59] Tiling off-target regions to an average width of 200000.
WARN [2025-11-18 22:02:59] No mappability scores provided.
WARN [2025-11-18 22:02:59] No reptiming scores provided.
INFO [2025-11-18 22:02:59] Calculating GC-content...
WARN [2025-11-18 22:02:59] Intervals contain off-target regions. Will not change intervals.
WARN [2025-11-18 22:02:59] No mappability scores provided.
WARN [2025-11-18 22:02:59] No reptiming scores provided.
INFO [2025-11-18 22:02:59] Calculating GC-content...
INFO [2025-11-18 22:02:59] Splitting 5 large targets to an average width of 400.
WARN [2025-11-18 22:02:59] No reptiming scores provided.
INFO [2025-11-18 22:02:59] Calculating GC-content...
WARN [2025-11-18 22:02:59] Found small target regions (< 100bp). Will resize them.
INFO [2025-11-18 22:02:59] Splitting 5 large targets to an average width of 400.
WARN [2025-11-18 22:02:59] No reptiming scores provided.
INFO [2025-11-18 22:02:59] Calculating GC-content...
WARN [2025-11-18 22:03:00] Found small target regions (< 100bp). Will resize them.
INFO [2025-11-18 22:03:00] Splitting 5 large targets to an average width of 400.
WARN [2025-11-18 22:03:00] 1 intervals without mappability score (1 on-target).
INFO [2025-11-18 22:03:00] Removing 1 intervals with low mappability score (<0.60).
WARN [2025-11-18 22:03:00] No reptiming scores provided.
INFO [2025-11-18 22:03:00] Calculating GC-content...
WARN [2025-11-18 22:03:00] Found small target regions (< 100bp). Will resize them.
INFO [2025-11-18 22:03:00] Splitting 5 large targets to an average width of 400.
INFO [2025-11-18 22:03:00] Tiling off-target regions to an average width of 200000.
WARN [2025-11-18 22:03:00] No reptiming scores provided.
INFO [2025-11-18 22:03:00] Calculating GC-content...
INFO [2025-11-18 22:03:00] Splitting 5 large targets to an average width of 400.
WARN [2025-11-18 22:03:00] No mappability scores provided.
WARN [2025-11-18 22:03:00] No reptiming scores provided.
INFO [2025-11-18 22:03:00] Calculating GC-content...
WARN [2025-11-18 22:03:00] Chromosome naming style of interval file (Ensembl) was different from reference (UCSC).
INFO [2025-11-18 22:03:00] Splitting 5 large targets to an average width of 400.
WARN [2025-11-18 22:03:00] No mappability scores provided.
WARN [2025-11-18 22:03:00] No reptiming scores provided.
INFO [2025-11-18 22:03:00] Calculating GC-content...
FATAL [2025-11-18 22:03:00] Chromosome naming style of interval file unknown, should be UCSC.
FATAL [2025-11-18 22:03:00]
FATAL [2025-11-18 22:03:00] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:03:00] parameters (PureCN 2.17.0).
WARN [2025-11-18 22:03:01] Chromosome naming style of interval file (Ensembl) was different from reference (UCSC).
WARN [2025-11-18 22:03:01] Chromosome naming style of mappability file (Ensembl) was different from reference (UCSC).
INFO [2025-11-18 22:03:01] Splitting 5 large targets to an average width of 400.
WARN [2025-11-18 22:03:01] No reptiming scores provided.
INFO [2025-11-18 22:03:01] Calculating GC-content...
WARN [2025-11-18 22:03:01] Found small target regions (< 60bp). Will resize them.
INFO [2025-11-18 22:03:01] Splitting 5 large targets to an average width of 400.
WARN [2025-11-18 22:03:01] No mappability scores provided.
WARN [2025-11-18 22:03:01] No reptiming scores provided.
INFO [2025-11-18 22:03:01] Calculating GC-content...
WARN [2025-11-18 22:03:01] Found small target regions (< 60bp). Will drop them.
INFO [2025-11-18 22:03:01] Splitting 4 large targets to an average width of 400.
WARN [2025-11-18 22:03:01] No mappability scores provided.
WARN [2025-11-18 22:03:01] No reptiming scores provided.
INFO [2025-11-18 22:03:01] Calculating GC-content...
WARN [2025-11-18 22:03:01] Found small target regions (< 200bp). Will resize them.
INFO [2025-11-18 22:03:01] Splitting 5 large targets to an average width of 400.
WARN [2025-11-18 22:03:01] No mappability scores provided.
WARN [2025-11-18 22:03:01] No reptiming scores provided.
INFO [2025-11-18 22:03:01] Calculating GC-content...
INFO [2025-11-18 22:03:01] Found 20 variants in VCF file.
INFO [2025-11-18 22:03:01] 20 (100.0%) variants annotated as likely germline (DB INFO flag).
WARN [2025-11-18 22:03:01] 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 [2025-11-18 22:03:01] Error reading AllelicCountsFile
FATAL [2025-11-18 22:03:01] /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/PureCN/extdata/example_allelic_counts_empty.tsv
FATAL [2025-11-18 22:03:01]
FATAL [2025-11-18 22:03:01] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:03:01] parameters (PureCN 2.17.0).
INFO [2025-11-18 22:03:01] Found 127 variants in VCF file.
INFO [2025-11-18 22:03:02] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
WARN [2025-11-18 22:03:02] Did not find base quality scores, will use global error rate of 0.0010 instead.
INFO [2025-11-18 22:03:02] ------------------------------------------------------------
INFO [2025-11-18 22:03:02] PureCN 2.17.0
INFO [2025-11-18 22:03:02] ------------------------------------------------------------
INFO [2025-11-18 22:03:02] Loading coverage files...
INFO [2025-11-18 22:03:02] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-11-18 22:03:02] Allosome coverage missing, cannot determine sex.
WARN [2025-11-18 22:03:02] Allosome coverage missing, cannot determine sex.
INFO [2025-11-18 22:03:02] Removing 228 intervals with missing log.ratio.
INFO [2025-11-18 22:03:02] Removing 22 small (< 5bp) intervals.
INFO [2025-11-18 22:03:02] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-11-18 22:03:02] No normalDB provided. Provide one for better results.
INFO [2025-11-18 22:03:02] Removing 1724 low count (< 100 total reads) intervals.
INFO [2025-11-18 22:03:02] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-11-18 22:03:02] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-11-18 22:03:02] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-11-18 22:03:02] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-11-18 22:03:02] Loading VCF...
INFO [2025-11-18 22:03:02] Found 127 variants in VCF file.
INFO [2025-11-18 22:03:02] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-11-18 22:03:02] LIB-02240e4 is tumor in VCF file.
INFO [2025-11-18 22:03:02] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-11-18 22:03:02] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-11-18 22:03:02] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-11-18 22:03:02] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-11-18 22:03:02] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-11-18 22:03:02] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-11-18 22:03:02] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding).
INFO [2025-11-18 22:03:02] 1.2% of targets contain variants.
INFO [2025-11-18 22:03:02] Removing 4 variants outside intervals.
INFO [2025-11-18 22:03:02] Found SOMATIC annotation in VCF.
INFO [2025-11-18 22:03:02] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-11-18 22:03:02] Found SOMATIC annotation in VCF. Setting mapping bias to 0.972.
INFO [2025-11-18 22:03:02] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-11-18 22:03:02] Sample sex: ?
INFO [2025-11-18 22:03:02] Segmenting data...
INFO [2025-11-18 22:03:02] Loading pre-computed boundaries for DNAcopy...
INFO [2025-11-18 22:03:02] Setting undo.SD parameter to 1.000000.
INFO [2025-11-18 22:03:03] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-11-18 22:03:03] Found 59 segments with median size of 17.67Mb.
INFO [2025-11-18 22:03:03] Using 121 variants.
INFO [2025-11-18 22:03:03] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-11-18 22:03:03] 2D-grid search of purity and ploidy...
INFO [2025-11-18 22:03:03] Local optima: 0.65/1.8, 0.52/2
INFO [2025-11-18 22:03:03] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2025-11-18 22:03:03] Testing local optimum 2/2 at purity 0.52 and total ploidy 2.00...
INFO [2025-11-18 22:03:04] Skipping 1 solutions that converged to the same optima.
INFO [2025-11-18 22:03:04] Fitting variants with beta model for local optimum 1/2...
INFO [2025-11-18 22:03:04] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2025-11-18 22:03:05] Optimized purity: 0.65
INFO [2025-11-18 22:03:05] Done.
INFO [2025-11-18 22:03:05] ------------------------------------------------------------
FATAL [2025-11-18 22:03:05] log.ratio NULL in .writeLogRatioFileGATK4
FATAL [2025-11-18 22:03:05]
FATAL [2025-11-18 22:03:05] This runtime error might be caused by invalid input data or parameters.
FATAL [2025-11-18 22:03:05] Please report bug (PureCN 2.17.0).
INFO [2025-11-18 22:03:05] Loaded provided segmentation file example_seg.txt (format DNAcopy).
INFO [2025-11-18 22:03:05] Re-centering provided segment means (offset -0.0033).
INFO [2025-11-18 22:03:05] Loaded provided segmentation file example_gatk4_modelfinal.seg.gz (format GATK4).
WARN [2025-11-18 22:03:05] Expecting numeric chromosome names in seg.file, assuming file is properly sorted.
INFO [2025-11-18 22:03:05] Re-centering provided segment means (offset -0.0037).
INFO [2025-11-18 22:03:06] 576 on-target bins with low coverage in all samples.
WARN [2025-11-18 22:03:06] You are likely not using the correct baits file!
WARN [2025-11-18 22:03:06] Allosome coverage missing, cannot determine sex.
WARN [2025-11-18 22:03:06] Allosome coverage missing, cannot determine sex.
INFO [2025-11-18 22:03:06] Processing on-target regions...
INFO [2025-11-18 22:03:06] Removing 930 intervals with low coverage in normalDB.
INFO [2025-11-18 22:03:06] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2025-11-18 22:03:07] ------------------------------------------------------------
INFO [2025-11-18 22:03:07] PureCN 2.17.0
INFO [2025-11-18 22:03:07] ------------------------------------------------------------
INFO [2025-11-18 22:03:07] Using BiocParallel for parallel optimization.
INFO [2025-11-18 22:03:07] Loading coverage files...
INFO [2025-11-18 22:03:07] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-11-18 22:03:07] Allosome coverage missing, cannot determine sex.
WARN [2025-11-18 22:03:07] Allosome coverage missing, cannot determine sex.
INFO [2025-11-18 22:03:07] Removing 228 intervals with missing log.ratio.
INFO [2025-11-18 22:03:07] Removing 705 intervals excluded in normalDB.
INFO [2025-11-18 22:03:07] normalDB provided. Setting minimum coverage for segmentation to 0.0015X.
INFO [2025-11-18 22:03:07] Removing 1066 low count (< 100 total reads) intervals.
INFO [2025-11-18 22:03:07] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-11-18 22:03:07] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-11-18 22:03:07] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-11-18 22:03:07] Sample sex: ?
INFO [2025-11-18 22:03:07] Segmenting data...
INFO [2025-11-18 22:03:07] Interval weights found, will use weighted CBS.
INFO [2025-11-18 22:03:07] Loading pre-computed boundaries for DNAcopy...
INFO [2025-11-18 22:03:07] Setting undo.SD parameter to 1.000000.
Setting multi-figure configuration
INFO [2025-11-18 22:03:08] Found 52 segments with median size of 29.35Mb.
INFO [2025-11-18 22:03:08] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-11-18 22:03:08] 2D-grid search of purity and ploidy...
INFO [2025-11-18 22:03:08] Local optima: 0.65/1.8, 0.52/2
INFO [2025-11-18 22:03:09] Skipping 1 solutions that converged to the same optima.
INFO [2025-11-18 22:03:09] Done.
INFO [2025-11-18 22:03:09] ------------------------------------------------------------
INFO [2025-11-18 22:03:09] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpVqWITm/file10b0e8677186.rds...
FATAL [2025-11-18 22:03:09] runAbsoluteCN was run without a VCF file.
FATAL [2025-11-18 22:03:09]
FATAL [2025-11-18 22:03:09] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:03:09] parameters (PureCN 2.17.0).
FATAL [2025-11-18 22:03:09] runAbsoluteCN was run without a VCF file.
FATAL [2025-11-18 22:03:09]
FATAL [2025-11-18 22:03:09] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:03:09] parameters (PureCN 2.17.0).
INFO [2025-11-18 22:03:09] ------------------------------------------------------------
INFO [2025-11-18 22:03:09] PureCN 2.17.0
INFO [2025-11-18 22:03:09] ------------------------------------------------------------
INFO [2025-11-18 22:03:09] Loading coverage files...
INFO [2025-11-18 22:03:09] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-11-18 22:03:09] Allosome coverage missing, cannot determine sex.
WARN [2025-11-18 22:03:09] Allosome coverage missing, cannot determine sex.
INFO [2025-11-18 22:03:09] Removing 228 intervals with missing log.ratio.
INFO [2025-11-18 22:03:09] Removing 705 intervals excluded in normalDB.
INFO [2025-11-18 22:03:09] normalDB provided. Setting minimum coverage for segmentation to 0.0015X.
INFO [2025-11-18 22:03:09] Removing 1066 low count (< 100 total reads) intervals.
INFO [2025-11-18 22:03:09] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-11-18 22:03:09] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-11-18 22:03:09] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-11-18 22:03:09] Sample sex: ?
INFO [2025-11-18 22:03:09] Segmenting data...
INFO [2025-11-18 22:03:09] Interval weights found, will use weighted PSCBS.
FATAL [2025-11-18 22:03:09] segmentationPSCBS requires VCF file.
FATAL [2025-11-18 22:03:09]
FATAL [2025-11-18 22:03:09] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:03:09] parameters (PureCN 2.17.0).
INFO [2025-11-18 22:03:12] ------------------------------------------------------------
INFO [2025-11-18 22:03:12] PureCN 2.17.0
INFO [2025-11-18 22:03:12] ------------------------------------------------------------
INFO [2025-11-18 22:03:12] Loading coverage files...
FATAL [2025-11-18 22:03:12] Need a normal coverage file if log.ratio and seg.file are not provided.
FATAL [2025-11-18 22:03:12]
FATAL [2025-11-18 22:03:12] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:03:12] parameters (PureCN 2.17.0).
INFO [2025-11-18 22:03:12] ------------------------------------------------------------
INFO [2025-11-18 22:03:12] PureCN 2.17.0
INFO [2025-11-18 22:03:12] ------------------------------------------------------------
FATAL [2025-11-18 22:03:12] min.ploidy or max.ploidy not within expected range.
FATAL [2025-11-18 22:03:12]
FATAL [2025-11-18 22:03:12] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:03:12] parameters (PureCN 2.17.0).
INFO [2025-11-18 22:03:12] ------------------------------------------------------------
INFO [2025-11-18 22:03:12] PureCN 2.17.0
INFO [2025-11-18 22:03:12] ------------------------------------------------------------
FATAL [2025-11-18 22:03:12] min.ploidy or max.ploidy not within expected range.
FATAL [2025-11-18 22:03:12]
FATAL [2025-11-18 22:03:12] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:03:12] parameters (PureCN 2.17.0).
INFO [2025-11-18 22:03:12] ------------------------------------------------------------
INFO [2025-11-18 22:03:12] PureCN 2.17.0
INFO [2025-11-18 22:03:12] ------------------------------------------------------------
INFO [2025-11-18 22:03:12] ------------------------------------------------------------
INFO [2025-11-18 22:03:12] PureCN 2.17.0
INFO [2025-11-18 22:03:12] ------------------------------------------------------------
INFO [2025-11-18 22:03:12] ------------------------------------------------------------
INFO [2025-11-18 22:03:12] PureCN 2.17.0
INFO [2025-11-18 22:03:12] ------------------------------------------------------------
FATAL [2025-11-18 22:03:12] test.num.copy not within expected range.
FATAL [2025-11-18 22:03:12]
FATAL [2025-11-18 22:03:12] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:03:12] parameters (PureCN 2.17.0).
INFO [2025-11-18 22:03:12] ------------------------------------------------------------
INFO [2025-11-18 22:03:12] PureCN 2.17.0
INFO [2025-11-18 22:03:12] ------------------------------------------------------------
WARN [2025-11-18 22:03:12] test.num.copy outside recommended range.
FATAL [2025-11-18 22:03:12] max.non.clonal not within expected range or format.
FATAL [2025-11-18 22:03:12]
FATAL [2025-11-18 22:03:12] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:03:12] parameters (PureCN 2.17.0).
INFO [2025-11-18 22:03:12] ------------------------------------------------------------
INFO [2025-11-18 22:03:12] PureCN 2.17.0
INFO [2025-11-18 22:03:12] ------------------------------------------------------------
WARN [2025-11-18 22:03:12] test.num.copy outside recommended range.
FATAL [2025-11-18 22:03:12] max.non.clonal not within expected range or format.
FATAL [2025-11-18 22:03:12]
FATAL [2025-11-18 22:03:12] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:03:12] parameters (PureCN 2.17.0).
INFO [2025-11-18 22:03:12] ------------------------------------------------------------
INFO [2025-11-18 22:03:12] PureCN 2.17.0
INFO [2025-11-18 22:03:12] ------------------------------------------------------------
FATAL [2025-11-18 22:03:12] test.purity not within expected range.
FATAL [2025-11-18 22:03:12]
FATAL [2025-11-18 22:03:12] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:03:12] parameters (PureCN 2.17.0).
INFO [2025-11-18 22:03:12] ------------------------------------------------------------
INFO [2025-11-18 22:03:12] PureCN 2.17.0
INFO [2025-11-18 22:03:12] ------------------------------------------------------------
INFO [2025-11-18 22:03:12] Loading coverage files...
FATAL [2025-11-18 22:03:12] Tumor and normal are identical. This won't give any meaningful results
FATAL [2025-11-18 22:03:12] and I'm stopping here.
FATAL [2025-11-18 22:03:12]
FATAL [2025-11-18 22:03:12] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:03:12] parameters (PureCN 2.17.0).
INFO [2025-11-18 22:03:12] ------------------------------------------------------------
INFO [2025-11-18 22:03:12] PureCN 2.17.0
INFO [2025-11-18 22:03:12] ------------------------------------------------------------
INFO [2025-11-18 22:03:12] Loading coverage files...
FATAL [2025-11-18 22:03:12] Length of log.ratio different from tumor coverage.
FATAL [2025-11-18 22:03:12]
FATAL [2025-11-18 22:03:12] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:03:12] parameters (PureCN 2.17.0).
INFO [2025-11-18 22:03:12] ------------------------------------------------------------
INFO [2025-11-18 22:03:12] PureCN 2.17.0
INFO [2025-11-18 22:03:12] ------------------------------------------------------------
FATAL [2025-11-18 22:03:12] prior.purity must have the same length as test.purity.
FATAL [2025-11-18 22:03:12]
FATAL [2025-11-18 22:03:12] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:03:12] parameters (PureCN 2.17.0).
INFO [2025-11-18 22:03:12] ------------------------------------------------------------
INFO [2025-11-18 22:03:12] PureCN 2.17.0
INFO [2025-11-18 22:03:12] ------------------------------------------------------------
FATAL [2025-11-18 22:03:12] min.gof not within expected range or format.
FATAL [2025-11-18 22:03:12]
FATAL [2025-11-18 22:03:12] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:03:12] parameters (PureCN 2.17.0).
INFO [2025-11-18 22:03:12] ------------------------------------------------------------
INFO [2025-11-18 22:03:12] PureCN 2.17.0
INFO [2025-11-18 22:03:12] ------------------------------------------------------------
FATAL [2025-11-18 22:03:12] prior.purity not within expected range or format.
FATAL [2025-11-18 22:03:12]
FATAL [2025-11-18 22:03:12] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:03:12] parameters (PureCN 2.17.0).
INFO [2025-11-18 22:03:12] ------------------------------------------------------------
INFO [2025-11-18 22:03:12] PureCN 2.17.0
INFO [2025-11-18 22:03:12] ------------------------------------------------------------
FATAL [2025-11-18 22:03:12] prior.purity must add to 1. Sum is 1.5
FATAL [2025-11-18 22:03:12]
FATAL [2025-11-18 22:03:12] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:03:12] parameters (PureCN 2.17.0).
INFO [2025-11-18 22:03:12] ------------------------------------------------------------
INFO [2025-11-18 22:03:12] PureCN 2.17.0
INFO [2025-11-18 22:03:12] ------------------------------------------------------------
FATAL [2025-11-18 22:03:12] max.homozygous.loss not within expected range or format.
FATAL [2025-11-18 22:03:12]
FATAL [2025-11-18 22:03:12] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:03:12] parameters (PureCN 2.17.0).
INFO [2025-11-18 22:03:12] ------------------------------------------------------------
INFO [2025-11-18 22:03:12] PureCN 2.17.0
INFO [2025-11-18 22:03:12] ------------------------------------------------------------
FATAL [2025-11-18 22:03:12] prior.K not within expected range or format.
FATAL [2025-11-18 22:03:12]
FATAL [2025-11-18 22:03:12] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:03:12] parameters (PureCN 2.17.0).
INFO [2025-11-18 22:03:12] ------------------------------------------------------------
INFO [2025-11-18 22:03:12] PureCN 2.17.0
INFO [2025-11-18 22:03:12] ------------------------------------------------------------
FATAL [2025-11-18 22:03:12] prior.contamination not within expected range or format.
FATAL [2025-11-18 22:03:12]
FATAL [2025-11-18 22:03:12] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:03:12] parameters (PureCN 2.17.0).
INFO [2025-11-18 22:03:12] ------------------------------------------------------------
INFO [2025-11-18 22:03:12] PureCN 2.17.0
INFO [2025-11-18 22:03:12] ------------------------------------------------------------
FATAL [2025-11-18 22:03:12] Iterations not in the expected range from 10 to 250.
FATAL [2025-11-18 22:03:12]
FATAL [2025-11-18 22:03:12] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:03:12] parameters (PureCN 2.17.0).
INFO [2025-11-18 22:03:12] ------------------------------------------------------------
INFO [2025-11-18 22:03:12] PureCN 2.17.0
INFO [2025-11-18 22:03:12] ------------------------------------------------------------
FATAL [2025-11-18 22:03:12] Iterations not in the expected range from 10 to 250.
FATAL [2025-11-18 22:03:12]
FATAL [2025-11-18 22:03:12] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:03:12] parameters (PureCN 2.17.0).
INFO [2025-11-18 22:03:12] ------------------------------------------------------------
INFO [2025-11-18 22:03:12] PureCN 2.17.0
INFO [2025-11-18 22:03:12] ------------------------------------------------------------
INFO [2025-11-18 22:03:12] Loading coverage files...
FATAL [2025-11-18 22:03:12] Missing tumor.coverage.file requires seg.file or log.ratio and
FATAL [2025-11-18 22:03:12] interval.file.
FATAL [2025-11-18 22:03:12]
FATAL [2025-11-18 22:03:12] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:03:12] parameters (PureCN 2.17.0).
INFO [2025-11-18 22:03:12] ------------------------------------------------------------
INFO [2025-11-18 22:03:12] PureCN 2.17.0
INFO [2025-11-18 22:03:12] ------------------------------------------------------------
INFO [2025-11-18 22:03:13] ------------------------------------------------------------
INFO [2025-11-18 22:03:13] PureCN 2.17.0
INFO [2025-11-18 22:03:13] ------------------------------------------------------------
INFO [2025-11-18 22:03:13] Loading coverage files...
FATAL [2025-11-18 22:03:13] Interval files in normal and tumor different.
FATAL [2025-11-18 22:03:13]
FATAL [2025-11-18 22:03:13] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:03:13] parameters (PureCN 2.17.0).
INFO [2025-11-18 22:03:13] ------------------------------------------------------------
INFO [2025-11-18 22:03:13] PureCN 2.17.0
INFO [2025-11-18 22:03:13] ------------------------------------------------------------
INFO [2025-11-18 22:03:13] Loading coverage files...
INFO [2025-11-18 22:03:13] Mean target coverages: 0X (tumor) 99X (normal).
WARN [2025-11-18 22:03:13] Large difference in coverage of tumor and normal.
FATAL [2025-11-18 22:03:13] No finite intervals.
FATAL [2025-11-18 22:03:13]
FATAL [2025-11-18 22:03:13] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:03:13] parameters (PureCN 2.17.0).
INFO [2025-11-18 22:03:13] ------------------------------------------------------------
INFO [2025-11-18 22:03:13] PureCN 2.17.0
INFO [2025-11-18 22:03:13] ------------------------------------------------------------
INFO [2025-11-18 22:03:13] Loading coverage files...
INFO [2025-11-18 22:03:13] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-11-18 22:03:13] Allosome coverage missing, cannot determine sex.
WARN [2025-11-18 22:03:13] Allosome coverage missing, cannot determine sex.
INFO [2025-11-18 22:03:13] Removing 228 intervals with missing log.ratio.
INFO [2025-11-18 22:03:13] Removing 22 small (< 5bp) intervals.
INFO [2025-11-18 22:03:13] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-11-18 22:03:13] No normalDB provided. Provide one for better results.
INFO [2025-11-18 22:03:13] Removing 1724 low count (< 100 total reads) intervals.
INFO [2025-11-18 22:03:13] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-11-18 22:03:13] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-11-18 22:03:13] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-11-18 22:03:13] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-11-18 22:03:13] Loading VCF...
INFO [2025-11-18 22:03:13] Found 127 variants in VCF file.
INFO [2025-11-18 22:03:14] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-11-18 22:03:14] LIB-02240e4 is tumor in VCF file.
INFO [2025-11-18 22:03:14] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-11-18 22:03:14] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-11-18 22:03:14] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-11-18 22:03:14] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-11-18 22:03:14] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-11-18 22:03:14] 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//RtmpVqWITm/file10b0e2800f046.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 [2025-11-18 22:03:14] Could not import snp.blacklist
FATAL [2025-11-18 22:03:14] /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/PureCN/extdata/example_normal.txt.gz:Error
FATAL [2025-11-18 22:03:14] in FileForFormat(resource(con), fileFormat(con)) : Format 'txt'
FATAL [2025-11-18 22:03:14] unsupported
FATAL [2025-11-18 22:03:14]
FATAL [2025-11-18 22:03:14] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:03:14] parameters (PureCN 2.17.0).
INFO [2025-11-18 22:03:14] ------------------------------------------------------------
INFO [2025-11-18 22:03:14] PureCN 2.17.0
INFO [2025-11-18 22:03:14] ------------------------------------------------------------
INFO [2025-11-18 22:03:14] Loading coverage files...
INFO [2025-11-18 22:03:14] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-11-18 22:03:14] Allosome coverage missing, cannot determine sex.
WARN [2025-11-18 22:03:14] Allosome coverage missing, cannot determine sex.
INFO [2025-11-18 22:03:14] Removing 228 intervals with missing log.ratio.
INFO [2025-11-18 22:03:14] Removing 22 small (< 5bp) intervals.
INFO [2025-11-18 22:03:14] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-11-18 22:03:14] No normalDB provided. Provide one for better results.
INFO [2025-11-18 22:03:14] Removing 233 low coverage (< 15.0000X) intervals.
INFO [2025-11-18 22:03:14] Using 9547 intervals (9547 on-target, 0 off-target).
INFO [2025-11-18 22:03:14] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-11-18 22:03:14] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-11-18 22:03:14] Loading VCF...
INFO [2025-11-18 22:03:14] Found 127 variants in VCF file.
INFO [2025-11-18 22:03:14] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-11-18 22:03:14] LIB-02240e4 is tumor in VCF file.
INFO [2025-11-18 22:03:14] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-11-18 22:03:14] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-11-18 22:03:14] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-11-18 22:03:14] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-11-18 22:03:14] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-11-18 22:03:15] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-11-18 22:03:15] Total size of targeted genomic region: 1.63Mb (2.58Mb with 50bp padding).
INFO [2025-11-18 22:03:15] 1.0% of targets contain variants.
INFO [2025-11-18 22:03:15] Removing 2 variants outside intervals.
INFO [2025-11-18 22:03:15] Found SOMATIC annotation in VCF.
INFO [2025-11-18 22:03:15] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-11-18 22:03:15] Found SOMATIC annotation in VCF. Setting mapping bias to 0.973.
INFO [2025-11-18 22:03:15] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-11-18 22:03:15] Sample sex: ?
INFO [2025-11-18 22:03:15] Segmenting data...
INFO [2025-11-18 22:03:15] Loading pre-computed boundaries for DNAcopy...
INFO [2025-11-18 22:03:15] Setting undo.SD parameter to 1.000000.
INFO [2025-11-18 22:03:15] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-11-18 22:03:15] Found 54 segments with median size of 24.88Mb.
INFO [2025-11-18 22:03:15] Using 123 variants.
INFO [2025-11-18 22:03:15] Mean standard deviation of log-ratios: 0.37 (MAPD: 0.32)
INFO [2025-11-18 22:03:15] 2D-grid search of purity and ploidy...
INFO [2025-11-18 22:03:16] Local optima: 0.62/1.9, 0.3/1.9, 0.32/2
INFO [2025-11-18 22:03:16] Testing local optimum 1/3 at purity 0.62 and total ploidy 1.90...
INFO [2025-11-18 22:03:16] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-11-18 22:03:16] Recalibrating log-ratios...
INFO [2025-11-18 22:03:16] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-11-18 22:03:16] Recalibrating log-ratios...
INFO [2025-11-18 22:03:16] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-11-18 22:03:17] Recalibrating log-ratios...
INFO [2025-11-18 22:03:17] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-11-18 22:03:17] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-11-18 22:03:17] Recalibrating log-ratios...
INFO [2025-11-18 22:03:17] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-11-18 22:03:17] Recalibrating log-ratios...
INFO [2025-11-18 22:03:17] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-11-18 22:03:17] Recalibrating log-ratios...
INFO [2025-11-18 22:03:17] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-11-18 22:03:17] Skipping 1 solutions that converged to the same optima.
INFO [2025-11-18 22:03:17] Skipping 1 solutions exceeding max.non.clonal (0.20): 0.3/1.9 (purity/tumor ploidy)
INFO [2025-11-18 22:03:17] Fitting variants with beta model for local optimum 1/3...
INFO [2025-11-18 22:03:17] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01.
INFO [2025-11-18 22:03:18] Optimized purity: 0.65
INFO [2025-11-18 22:03:18] Done.
INFO [2025-11-18 22:03:18] ------------------------------------------------------------
INFO [2025-11-18 22:03:18] ------------------------------------------------------------
INFO [2025-11-18 22:03:18] PureCN 2.17.0
INFO [2025-11-18 22:03:18] ------------------------------------------------------------
INFO [2025-11-18 22:03:18] Loading coverage files...
INFO [2025-11-18 22:03:18] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-11-18 22:03:19] Allosome coverage missing, cannot determine sex.
WARN [2025-11-18 22:03:19] Allosome coverage missing, cannot determine sex.
INFO [2025-11-18 22:03:19] Removing 228 intervals with missing log.ratio.
INFO [2025-11-18 22:03:19] Removing 22 small (< 5bp) intervals.
INFO [2025-11-18 22:03:19] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-11-18 22:03:19] No normalDB provided. Provide one for better results.
INFO [2025-11-18 22:03:19] Removing 1724 low count (< 100 total reads) intervals.
INFO [2025-11-18 22:03:19] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-11-18 22:03:19] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-11-18 22:03:19] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-11-18 22:03:19] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-11-18 22:03:19] Loading VCF...
INFO [2025-11-18 22:03:19] Found 127 variants in VCF file.
WARN [2025-11-18 22:03:19] DP FORMAT field contains NAs. Removing 3 variants.
WARN [2025-11-18 22:03:19] DB INFO flag contains NAs
INFO [2025-11-18 22:03:19] 119 (96.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-11-18 22:03:19] LIB-02240e4 is tumor in VCF file.
INFO [2025-11-18 22:03:19] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-11-18 22:03:19] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-11-18 22:03:19] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-11-18 22:03:19] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-11-18 22:03:19] Removing 1 variants with AF < 0.030 or AF >= 0.970 or insufficient supporting reads or depth < 15.
INFO [2025-11-18 22:03:19] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding).
INFO [2025-11-18 22:03:19] 1.2% of targets contain variants.
INFO [2025-11-18 22:03:19] Setting somatic prior probabilities for likely germline hits to 0.000500 or to 0.500000 otherwise.
INFO [2025-11-18 22:03:19] Excluding 5 novel or poor quality variants from segmentation.
INFO [2025-11-18 22:03:19] Sample sex: ?
INFO [2025-11-18 22:03:19] Segmenting data...
INFO [2025-11-18 22:03:19] Loading pre-computed boundaries for DNAcopy...
INFO [2025-11-18 22:03:19] Setting undo.SD parameter to 1.000000.
Setting multi-figure configuration
INFO [2025-11-18 22:03:20] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-11-18 22:03:20] Found 59 segments with median size of 17.67Mb.
INFO [2025-11-18 22:03:20] Using 123 variants.
INFO [2025-11-18 22:03:20] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-11-18 22:03:20] 2D-grid search of purity and ploidy...
INFO [2025-11-18 22:03:20] Local optima: 0.62/1.9, 0.3/1.9, 0.32/2
INFO [2025-11-18 22:03:20] Testing local optimum 1/3 at purity 0.62 and total ploidy 1.90...
INFO [2025-11-18 22:03:20] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-11-18 22:03:20] Recalibrating log-ratios...
INFO [2025-11-18 22:03:20] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-11-18 22:03:20] Recalibrating log-ratios...
INFO [2025-11-18 22:03:20] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-11-18 22:03:21] Recalibrating log-ratios...
INFO [2025-11-18 22:03:21] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-11-18 22:03:21] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-11-18 22:03:21] Recalibrating log-ratios...
INFO [2025-11-18 22:03:21] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-11-18 22:03:21] Recalibrating log-ratios...
INFO [2025-11-18 22:03:21] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-11-18 22:03:21] Recalibrating log-ratios...
INFO [2025-11-18 22:03:21] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-11-18 22:03:21] Skipping 2 solutions exceeding max.non.clonal (0.20): 0.3/1.9, 0.35/1.61 (purity/tumor ploidy)
INFO [2025-11-18 22:03:21] Fitting variants with beta model for local optimum 1/3...
INFO [2025-11-18 22:03:21] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2025-11-18 22:03:22] Optimized purity: 0.65
INFO [2025-11-18 22:03:22] Done.
INFO [2025-11-18 22:03:22] ------------------------------------------------------------
INFO [2025-11-18 22:03:22] ------------------------------------------------------------
INFO [2025-11-18 22:03:22] PureCN 2.17.0
INFO [2025-11-18 22:03:22] ------------------------------------------------------------
INFO [2025-11-18 22:03:22] Loading coverage files...
INFO [2025-11-18 22:03:23] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-11-18 22:03:23] Allosome coverage missing, cannot determine sex.
WARN [2025-11-18 22:03:23] Allosome coverage missing, cannot determine sex.
INFO [2025-11-18 22:03:23] No Gene column in interval.file. You won't get gene-level calls.
INFO [2025-11-18 22:03:23] Removing 228 intervals with missing log.ratio.
INFO [2025-11-18 22:03:23] Removing 15 low/high GC targets.
INFO [2025-11-18 22:03:23] Removing 21 small (< 5bp) intervals.
INFO [2025-11-18 22:03:23] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-11-18 22:03:23] No normalDB provided. Provide one for better results.
INFO [2025-11-18 22:03:23] Removing 1718 low count (< 100 total reads) intervals.
INFO [2025-11-18 22:03:23] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-11-18 22:03:23] Removing 36 low mappability intervals.
INFO [2025-11-18 22:03:23] Using 8006 intervals (8006 on-target, 0 off-target).
INFO [2025-11-18 22:03:23] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-11-18 22:03:23] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio).
INFO [2025-11-18 22:03:23] Loading VCF...
INFO [2025-11-18 22:03:23] Found 127 variants in VCF file.
INFO [2025-11-18 22:03:23] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-11-18 22:03:23] LIB-02240e4 is tumor in VCF file.
INFO [2025-11-18 22:03:23] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-11-18 22:03:23] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-11-18 22:03:23] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-11-18 22:03:23] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-11-18 22:03:23] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-11-18 22:03:23] Removing 1 variants with AF < 0.030 or AF >= Inf or insufficient supporting reads or depth < 15.
INFO [2025-11-18 22:03:23] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding).
INFO [2025-11-18 22:03:23] 1.2% of targets contain variants.
INFO [2025-11-18 22:03:23] Removing 11 variants outside intervals.
INFO [2025-11-18 22:03:23] Found SOMATIC annotation in VCF.
INFO [2025-11-18 22:03:23] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-11-18 22:03:23] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970.
INFO [2025-11-18 22:03:23] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-11-18 22:03:23] Sample sex: ?
INFO [2025-11-18 22:03:23] Segmenting data...
INFO [2025-11-18 22:03:23] MAPD of 114 allelic fractions: 0.14 (0.15 adjusted).
INFO [2025-11-18 22:03:23] Using unweighted PSCBS.
INFO [2025-11-18 22:03:23] Setting undo.SD parameter to 1.000000.
INFO [2025-11-18 22:03:35] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-11-18 22:03:35] Found 72 segments with median size of 27.25Mb.
INFO [2025-11-18 22:03:35] Using 114 variants.
INFO [2025-11-18 22:03:35] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-11-18 22:03:35] 2D-grid search of purity and ploidy...
INFO [2025-11-18 22:03:35] Local optima: 0.65/1.8, 0.38/2.2
INFO [2025-11-18 22:03:35] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2025-11-18 22:03:35] Recalibrating log-ratios...
INFO [2025-11-18 22:03:35] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2025-11-18 22:03:35] Recalibrating log-ratios...
INFO [2025-11-18 22:03:35] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2025-11-18 22:03:35] Recalibrating log-ratios...
INFO [2025-11-18 22:03:35] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2025-11-18 22:03:36] Testing local optimum 2/2 at purity 0.38 and total ploidy 2.20...
INFO [2025-11-18 22:03:36] Skipping 1 solutions exceeding max.non.clonal (0.20): 0.65/2.05 (purity/tumor ploidy)
INFO [2025-11-18 22:03:36] Fitting variants with beta model for local optimum 2/2...
INFO [2025-11-18 22:03:36] Fitting variants for purity 0.40, tumor ploidy 2.55 and contamination 0.01.
INFO [2025-11-18 22:03:37] Optimized purity: 0.40
INFO [2025-11-18 22:03:37] Done.
INFO [2025-11-18 22:03:37] ------------------------------------------------------------
FATAL [2025-11-18 22:03:37] This function requires gene-level calls. Please add a column 'Gene'
FATAL [2025-11-18 22:03:37] containing gene symbols to the interval.file.
FATAL [2025-11-18 22:03:37]
FATAL [2025-11-18 22:03:37] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:03:37] parameters (PureCN 2.17.0).
INFO [2025-11-18 22:03:38] ------------------------------------------------------------
INFO [2025-11-18 22:03:38] PureCN 2.17.0
INFO [2025-11-18 22:03:38] ------------------------------------------------------------
INFO [2025-11-18 22:03:38] Loading coverage files...
INFO [2025-11-18 22:03:38] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-11-18 22:03:38] Allosome coverage missing, cannot determine sex.
WARN [2025-11-18 22:03:38] Allosome coverage missing, cannot determine sex.
INFO [2025-11-18 22:03:38] Removing 228 intervals with missing log.ratio.
INFO [2025-11-18 22:03:38] Removing 22 small (< 5bp) intervals.
INFO [2025-11-18 22:03:38] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-11-18 22:03:38] No normalDB provided. Provide one for better results.
INFO [2025-11-18 22:03:38] Removing 1724 low count (< 100 total reads) intervals.
INFO [2025-11-18 22:03:38] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-11-18 22:03:38] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-11-18 22:03:38] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-11-18 22:03:38] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-11-18 22:03:38] Loading VCF...
INFO [2025-11-18 22:03:38] Found 127 variants in VCF file.
INFO [2025-11-18 22:03:38] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
FATAL [2025-11-18 22:03:38] Different chromosome names in coverage and VCF.
FATAL [2025-11-18 22:03:38]
FATAL [2025-11-18 22:03:38] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:03:38] parameters (PureCN 2.17.0).
INFO [2025-11-18 22:03:38] ------------------------------------------------------------
INFO [2025-11-18 22:03:38] PureCN 2.17.0
INFO [2025-11-18 22:03:38] ------------------------------------------------------------
INFO [2025-11-18 22:03:38] Loading coverage files...
INFO [2025-11-18 22:03:38] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-11-18 22:03:38] Allosome coverage missing, cannot determine sex.
WARN [2025-11-18 22:03:38] Allosome coverage missing, cannot determine sex.
FATAL [2025-11-18 22:03:39] tumor.coverage.file and interval.file do not align.
FATAL [2025-11-18 22:03:39]
FATAL [2025-11-18 22:03:39] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:03:39] parameters (PureCN 2.17.0).
INFO [2025-11-18 22:03:39] ------------------------------------------------------------
INFO [2025-11-18 22:03:39] PureCN 2.17.0
INFO [2025-11-18 22:03:39] ------------------------------------------------------------
INFO [2025-11-18 22:03:39] Loading coverage files...
INFO [2025-11-18 22:03:39] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-11-18 22:03:39] Allosome coverage missing, cannot determine sex.
WARN [2025-11-18 22:03:39] Allosome coverage missing, cannot determine sex.
INFO [2025-11-18 22:03:39] Removing 228 intervals with missing log.ratio.
INFO [2025-11-18 22:03:39] Removing 15 low/high GC targets.
INFO [2025-11-18 22:03:39] Removing 21 small (< 5bp) intervals.
INFO [2025-11-18 22:03:39] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-11-18 22:03:39] No normalDB provided. Provide one for better results.
INFO [2025-11-18 22:03:39] Removing 1718 low count (< 100 total reads) intervals.
INFO [2025-11-18 22:03:39] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-11-18 22:03:39] Removing 36 low mappability intervals.
INFO [2025-11-18 22:03:39] Using 8006 intervals (8006 on-target, 0 off-target).
INFO [2025-11-18 22:03:39] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-11-18 22:03:39] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio).
INFO [2025-11-18 22:03:39] Loading VCF...
INFO [2025-11-18 22:03:39] Found 127 variants in VCF file.
INFO [2025-11-18 22:03:39] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-11-18 22:03:39] LIB-02240e4 is tumor in VCF file.
INFO [2025-11-18 22:03:39] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-11-18 22:03:39] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-11-18 22:03:39] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-11-18 22:03:39] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-11-18 22:03:39] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-11-18 22:03:40] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-11-18 22:03:40] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding).
INFO [2025-11-18 22:03:40] 1.2% of targets contain variants.
INFO [2025-11-18 22:03:40] Removing 11 variants outside intervals.
INFO [2025-11-18 22:03:40] Found SOMATIC annotation in VCF.
INFO [2025-11-18 22:03:40] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-11-18 22:03:40] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970.
INFO [2025-11-18 22:03:40] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-11-18 22:03:40] Sample sex: ?
INFO [2025-11-18 22:03:40] Segmenting data...
INFO [2025-11-18 22:03:40] Loading pre-computed boundaries for DNAcopy...
INFO [2025-11-18 22:03:40] Setting undo.SD parameter to 1.000000.
INFO [2025-11-18 22:03:40] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-11-18 22:03:40] Found 59 segments with median size of 17.67Mb.
INFO [2025-11-18 22:03:40] Using 114 variants.
INFO [2025-11-18 22:03:40] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-11-18 22:03:40] 2D-grid search of purity and ploidy...
INFO [2025-11-18 22:03:41] Local optima: 0.63/1.9
INFO [2025-11-18 22:03:41] Testing local optimum 1/1 at purity 0.63 and total ploidy 1.90...
INFO [2025-11-18 22:03:41] Fitting variants with beta model for local optimum 1/1...
INFO [2025-11-18 22:03:41] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2025-11-18 22:03:42] Optimized purity: 0.65
INFO [2025-11-18 22:03:42] Done.
INFO [2025-11-18 22:03:42] ------------------------------------------------------------
INFO [2025-11-18 22:03:42] ------------------------------------------------------------
INFO [2025-11-18 22:03:42] PureCN 2.17.0
INFO [2025-11-18 22:03:42] ------------------------------------------------------------
INFO [2025-11-18 22:03:42] Loading coverage files...
INFO [2025-11-18 22:03:42] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-11-18 22:03:42] Allosome coverage missing, cannot determine sex.
WARN [2025-11-18 22:03:42] Allosome coverage missing, cannot determine sex.
INFO [2025-11-18 22:03:42] Removing 228 intervals with missing log.ratio.
INFO [2025-11-18 22:03:42] Removing 15 low/high GC targets.
INFO [2025-11-18 22:03:42] Removing 21 small (< 5bp) intervals.
INFO [2025-11-18 22:03:42] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-11-18 22:03:42] No normalDB provided. Provide one for better results.
INFO [2025-11-18 22:03:42] Removing 1718 low count (< 100 total reads) intervals.
INFO [2025-11-18 22:03:42] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-11-18 22:03:42] Removing 36 low mappability intervals.
INFO [2025-11-18 22:03:42] Using 8006 intervals (8006 on-target, 0 off-target).
INFO [2025-11-18 22:03:42] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-11-18 22:03:42] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio).
INFO [2025-11-18 22:03:42] Loading VCF...
INFO [2025-11-18 22:03:42] Found 127 variants in VCF file.
INFO [2025-11-18 22:03:42] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-11-18 22:03:42] LIB-02240e4 is tumor in VCF file.
INFO [2025-11-18 22:03:43] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-11-18 22:03:43] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-11-18 22:03:43] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-11-18 22:03:43] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-11-18 22:03:43] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-11-18 22:03:43] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-11-18 22:03:43] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding).
INFO [2025-11-18 22:03:43] 1.2% of targets contain variants.
INFO [2025-11-18 22:03:43] Removing 11 variants outside intervals.
INFO [2025-11-18 22:03:43] Found SOMATIC annotation in VCF.
INFO [2025-11-18 22:03:43] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-11-18 22:03:43] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970.
INFO [2025-11-18 22:03:43] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-11-18 22:03:43] Sample sex: ?
INFO [2025-11-18 22:03:43] Segmenting data...
INFO [2025-11-18 22:03:43] Loading pre-computed boundaries for DNAcopy...
INFO [2025-11-18 22:03:43] Setting undo.SD parameter to 1.000000.
INFO [2025-11-18 22:03:43] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-11-18 22:03:43] Found 59 segments with median size of 17.67Mb.
INFO [2025-11-18 22:03:43] Using 114 variants.
INFO [2025-11-18 22:03:43] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-11-18 22:03:43] 2D-grid search of purity and ploidy...
INFO [2025-11-18 22:03:44] Local optima: 0.63/1.9
INFO [2025-11-18 22:03:44] Testing local optimum 1/1 at purity 0.63 and total ploidy 1.90...
INFO [2025-11-18 22:03:44] Fitting variants with beta model for local optimum 1/1...
WARN [2025-11-18 22:03:44] Some gene symbols found on multiple chromosomes. Use of approved symbols suggested.
INFO [2025-11-18 22:03:44] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2025-11-18 22:03:45] Optimized purity: 0.65
INFO [2025-11-18 22:03:45] Done.
INFO [2025-11-18 22:03:45] ------------------------------------------------------------
FATAL [2025-11-18 22:03:45] chr1 not valid chromosome name(s). Valid names are:
FATAL [2025-11-18 22:03:45] 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22
FATAL [2025-11-18 22:03:45]
FATAL [2025-11-18 22:03:45] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:03:45] parameters (PureCN 2.17.0).
INFO [2025-11-18 22:03:45] ------------------------------------------------------------
INFO [2025-11-18 22:03:45] PureCN 2.17.0
INFO [2025-11-18 22:03:45] ------------------------------------------------------------
INFO [2025-11-18 22:03:45] Loading coverage files...
WARN [2025-11-18 22:03:45] Provided sampleid (Sample2) does not match Sample1 found in segmentation.
WARN [2025-11-18 22:03:45] Allosome coverage missing, cannot determine sex.
WARN [2025-11-18 22:03:45] Allosome coverage missing, cannot determine sex.
INFO [2025-11-18 22:03:45] Removing 10 intervals with missing log.ratio.
INFO [2025-11-18 22:03:45] Using 10039 intervals (10039 on-target, 0 off-target).
INFO [2025-11-18 22:03:45] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-11-18 22:03:45] Loading VCF...
INFO [2025-11-18 22:03:45] Found 127 variants in VCF file.
INFO [2025-11-18 22:03:46] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-11-18 22:03:46] LIB-02240e4 is tumor in VCF file.
INFO [2025-11-18 22:03:46] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-11-18 22:03:46] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-11-18 22:03:46] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-11-18 22:03:46] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-11-18 22:03:46] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-11-18 22:03:46] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-11-18 22:03:46] Total size of targeted genomic region: 1.71Mb (2.70Mb with 50bp padding).
INFO [2025-11-18 22:03:46] 1.0% of targets contain variants.
INFO [2025-11-18 22:03:46] Removing 0 variants outside intervals.
INFO [2025-11-18 22:03:46] Found SOMATIC annotation in VCF.
INFO [2025-11-18 22:03:46] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-11-18 22:03:46] Found SOMATIC annotation in VCF. Setting mapping bias to 0.976.
INFO [2025-11-18 22:03:46] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-11-18 22:03:46] Sample sex: ?
INFO [2025-11-18 22:03:46] Segmenting data...
INFO [2025-11-18 22:03:46] Loaded provided segmentation file example_seg.txt (format DNAcopy).
WARN [2025-11-18 22:03:46] Provided sampleid (Sample2) does not match Sample1 found in segmentation.
INFO [2025-11-18 22:03:46] Re-centering provided segment means (offset -0.0033).
INFO [2025-11-18 22:03:46] Loading pre-computed boundaries for DNAcopy...
INFO [2025-11-18 22:03:46] Setting undo.SD parameter to 0.000000.
Setting multi-figure configuration
INFO [2025-11-18 22:03:46] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-11-18 22:03:46] Found 54 segments with median size of 24.88Mb.
INFO [2025-11-18 22:03:46] Using 125 variants.
INFO [2025-11-18 22:03:46] Mean standard deviation of log-ratios: 0.40 (MAPD: 0.00)
INFO [2025-11-18 22:03:46] 2D-grid search of purity and ploidy...
INFO [2025-11-18 22:03:47] Local optima: 0.6/1.9
INFO [2025-11-18 22:03:47] Testing local optimum 1/1 at purity 0.60 and total ploidy 1.90...
INFO [2025-11-18 22:03:47] Fitting variants with beta model for local optimum 1/1...
INFO [2025-11-18 22:03:47] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01.
INFO [2025-11-18 22:03:48] Optimized purity: 0.65
INFO [2025-11-18 22:03:48] Done.
INFO [2025-11-18 22:03:48] ------------------------------------------------------------
WARN [2025-11-18 22:03:48] Allosome coverage missing, cannot determine sex.
WARN [2025-11-18 22:03:48] Allosome coverage missing, cannot determine sex.
Setting multi-figure configuration
FATAL [2025-11-18 22:03:51] Segmentation file expected with colnames ID, chrom, loc.start, loc.end,
FATAL [2025-11-18 22:03:51] num.mark, seg.mean
FATAL [2025-11-18 22:03:51]
FATAL [2025-11-18 22:03:51] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:03:51] parameters (PureCN 2.17.0).
FATAL [2025-11-18 22:03:51] seg.file contains multiple samples and sampleid missing.
FATAL [2025-11-18 22:03:51]
FATAL [2025-11-18 22:03:51] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:03:51] parameters (PureCN 2.17.0).
FATAL [2025-11-18 22:03:51] seg.file contains multiple samples and sampleid does not match any.
FATAL [2025-11-18 22:03:51]
FATAL [2025-11-18 22:03:51] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:03:51] parameters (PureCN 2.17.0).
WARN [2025-11-18 22:03:51] Allosome coverage missing, cannot determine sex.
WARN [2025-11-18 22:03:51] Allosome coverage missing, cannot determine sex.
WARN [2025-11-18 22:03:55] Allosome coverage missing, cannot determine sex.
WARN [2025-11-18 22:03:55] Allosome coverage missing, cannot determine sex.
WARN [2025-11-18 22:03:55] Provided sampleid (example_tumor.txt.gz) does not match Sample1 found in segmentation.
WARN [2025-11-18 22:03:56] Allosome coverage missing, cannot determine sex.
WARN [2025-11-18 22:03:56] Allosome coverage missing, cannot determine sex.
WARN [2025-11-18 22:03:57] No normalDB provided. Provide one for better results.
WARN [2025-11-18 22:03:59] Allosome coverage missing, cannot determine sex.
WARN [2025-11-18 22:03:59] Allosome coverage missing, cannot determine sex.
WARN [2025-11-18 22:04:00] Provided sampleid (Sample.1) does not match Sample1 found in segmentation.
Setting multi-figure configuration
WARN [2025-11-18 22:04:03] Allosome coverage missing, cannot determine sex.
WARN [2025-11-18 22:04:03] Allosome coverage missing, cannot determine sex.
WARN [2025-11-18 22:04:03] No normalDB provided. Provide one for better results.
WARN [2025-11-18 22:04:03] Sampleid looks like a normal in VCF, not like a tumor.
WARN [2025-11-18 22:04:05] Allosome coverage missing, cannot determine sex.
WARN [2025-11-18 22:04:05] Allosome coverage missing, cannot determine sex.
FATAL [2025-11-18 22:04:05] normalDB not a valid normalDB object. Use createNormalDatabase to
FATAL [2025-11-18 22:04:05] create one.
FATAL [2025-11-18 22:04:05]
FATAL [2025-11-18 22:04:05] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:04:05] parameters (PureCN 2.17.0).
WARN [2025-11-18 22:04:06] You are likely not using the correct baits file!
WARN [2025-11-18 22:04:06] Allosome coverage missing, cannot determine sex.
WARN [2025-11-18 22:04:06] Allosome coverage missing, cannot determine sex.
WARN [2025-11-18 22:04:07] Allosome coverage missing, cannot determine sex.
WARN [2025-11-18 22:04:07] Allosome coverage missing, cannot determine sex.
FATAL [2025-11-18 22:04:07] normalDB appears to be empty.
FATAL [2025-11-18 22:04:07]
FATAL [2025-11-18 22:04:07] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:04:07] parameters (PureCN 2.17.0).
WARN [2025-11-18 22:04:07] Allosome coverage missing, cannot determine sex.
WARN [2025-11-18 22:04:07] Allosome coverage missing, cannot determine sex.
WARN [2025-11-18 22:04:07] Intervals in coverage and interval.file have conflicting on/off-target annotation.
WARN [2025-11-18 22:04:11] Allosome coverage missing, cannot determine sex.
WARN [2025-11-18 22:04:11] Allosome coverage missing, cannot determine sex.
FATAL [2025-11-18 22:04:11] Seqlevels missing in provided segmentation: 6
FATAL [2025-11-18 22:04:11]
FATAL [2025-11-18 22:04:11] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:04:11] parameters (PureCN 2.17.0).
sh: gatk: command not found
WARN [2025-11-18 22:04:12] Cannot find gatk binary in path.
WARN [2025-11-18 22:04:12] Allosome coverage missing, cannot determine sex.
WARN [2025-11-18 22:04:12] Allosome coverage missing, cannot determine sex.
WARN [2025-11-18 22:04:12] No normalDB provided. Provide one for better results.
FATAL [2025-11-18 22:04:13] segmentationHclust requires an input segmentation.
FATAL [2025-11-18 22:04:13]
FATAL [2025-11-18 22:04:13] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:04:13] parameters (PureCN 2.17.0).
WARN [2025-11-18 22:04:13] Allosome coverage missing, cannot determine sex.
WARN [2025-11-18 22:04:13] Allosome coverage missing, cannot determine sex.
WARN [2025-11-18 22:04:13] No normalDB provided. Provide one for better results.
FATAL [2025-11-18 22:04:23] The normal.panel.vcf.file contains only a single sample.
FATAL [2025-11-18 22:04:23]
FATAL [2025-11-18 22:04:23] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:04:23] parameters (PureCN 2.17.0).
FATAL [2025-11-18 22:04:23] mapping.bias.file must be a file with *.rds suffix.
FATAL [2025-11-18 22:04:23]
FATAL [2025-11-18 22:04:23] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:04:23] parameters (PureCN 2.17.0).
Failed with error: 'there is no package called 'genomicsdb''
FATAL [2025-11-18 22:04:24] min.normals (0) must be >= 1.
FATAL [2025-11-18 22:04:24]
FATAL [2025-11-18 22:04:24] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:04:24] parameters (PureCN 2.17.0).
FATAL [2025-11-18 22:04:24] min.normals (10) cannot be larger than min.normals.assign.betafit (3).
FATAL [2025-11-18 22:04:24]
FATAL [2025-11-18 22:04:24] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:04:24] parameters (PureCN 2.17.0).
FATAL [2025-11-18 22:04:24] min.normals.assign.betafit (10) cannot be larger than
FATAL [2025-11-18 22:04:24] min.normals.betafit (7).
FATAL [2025-11-18 22:04:24]
FATAL [2025-11-18 22:04:24] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:04:24] parameters (PureCN 2.17.0).
FATAL [2025-11-18 22:04:24] min.normals.betafit (20) cannot be larger than
FATAL [2025-11-18 22:04:24] min.normals.position.specific.fit (10).
FATAL [2025-11-18 22:04:24]
FATAL [2025-11-18 22:04:24] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:04:24] parameters (PureCN 2.17.0).
FATAL [2025-11-18 22:04:24] min.betafit.rho not within expected range or format.
FATAL [2025-11-18 22:04:24]
FATAL [2025-11-18 22:04:24] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:04:24] parameters (PureCN 2.17.0).
FATAL [2025-11-18 22:04:24] max.betafit.rho not within expected range or format.
FATAL [2025-11-18 22:04:24]
FATAL [2025-11-18 22:04:24] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:04:24] parameters (PureCN 2.17.0).
FATAL [2025-11-18 22:04:24] min.betafit.rho (0.9) cannot be larger than max.betafit.rho (0.2).
FATAL [2025-11-18 22:04:24]
FATAL [2025-11-18 22:04:24] This is most likely a user error due to invalid input data or
FATAL [2025-11-18 22:04:24] parameters (PureCN 2.17.0).
[ FAIL 0 | WARN 12 | SKIP 2 | PASS 405 ]
══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• gatk binary > 4.1.7.0 required (1): 'test_segmentation.R:25:4'
• genomicsdb required (1): 'test_setMappingBiasVcf.R:45:5'
[ FAIL 0 | WARN 12 | SKIP 2 | PASS 405 ]
>
> proc.time()
user system elapsed
161.578 5.639 161.654
PureCN.Rcheck/PureCN-Ex.timings
| name | user | system | elapsed | |
| adjustLogRatio | 0.899 | 0.015 | 0.960 | |
| annotateTargets | 5.441 | 0.222 | 5.796 | |
| bootstrapResults | 0.220 | 0.017 | 0.239 | |
| calculateBamCoverageByInterval | 0.080 | 0.004 | 0.088 | |
| calculateLogRatio | 0.359 | 0.025 | 0.415 | |
| calculateMappingBiasGatk4 | 0 | 0 | 0 | |
| calculateMappingBiasVcf | 0.735 | 0.031 | 0.842 | |
| calculatePowerDetectSomatic | 0.656 | 0.005 | 0.683 | |
| calculateTangentNormal | 1.320 | 0.027 | 1.379 | |
| callAlterations | 0.056 | 0.003 | 0.060 | |
| callAlterationsFromSegmentation | 0.637 | 0.016 | 0.678 | |
| callAmplificationsInLowPurity | 15.270 | 0.175 | 16.982 | |
| callCIN | 0.116 | 0.003 | 0.131 | |
| callLOH | 0.081 | 0.002 | 0.093 | |
| callMutationBurden | 0.641 | 0.020 | 0.707 | |
| centromeres | 0.001 | 0.002 | 0.003 | |
| correctCoverageBias | 0.700 | 0.018 | 0.761 | |
| createCurationFile | 0.154 | 0.005 | 0.169 | |
| createNormalDatabase | 1.050 | 0.017 | 1.110 | |
| filterIntervals | 8.426 | 0.149 | 8.966 | |
| filterVcfBasic | 0.280 | 0.004 | 0.299 | |
| filterVcfMuTect | 0.268 | 0.004 | 0.284 | |
| filterVcfMuTect2 | 0.243 | 0.002 | 0.256 | |
| findFocal | 4.481 | 0.049 | 4.829 | |
| findHighQualitySNPs | 0.581 | 0.009 | 0.624 | |
| getSexFromCoverage | 0.126 | 0.008 | 0.150 | |
| getSexFromVcf | 0.109 | 0.006 | 0.130 | |
| plotAbs | 0.090 | 0.004 | 0.095 | |
| poolCoverage | 0.236 | 0.011 | 0.292 | |
| predictSomatic | 0.198 | 0.004 | 0.206 | |
| preprocessIntervals | 0.244 | 0.005 | 0.284 | |
| processMultipleSamples | 0.921 | 0.020 | 1.067 | |
| readAllelicCountsFile | 0.207 | 0.001 | 0.233 | |
| readCoverageFile | 0.106 | 0.005 | 0.129 | |
| readCurationFile | 0.094 | 0.003 | 0.121 | |
| readIntervalFile | 0.068 | 0.002 | 0.082 | |
| readLogRatioFile | 0.012 | 0.000 | 0.015 | |
| readSegmentationFile | 0.003 | 0.001 | 0.003 | |
| runAbsoluteCN | 6.353 | 0.122 | 6.902 | |
| segmentationCBS | 3.140 | 0.040 | 3.225 | |
| segmentationGATK4 | 0.001 | 0.001 | 0.002 | |
| segmentationHclust | 5.660 | 0.105 | 5.954 | |
| segmentationPSCBS | 14.471 | 0.198 | 15.252 | |
| setMappingBiasVcf | 0.107 | 0.003 | 0.112 | |
| setPriorVcf | 0.121 | 0.003 | 0.125 | |