Markus Riester
| Snapshot Date: 2025-01-03 13:40 -0500 (Fri, 03 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/PureCN |
| git_branch: devel |
| git_last_commit: cb8d0f6 |
| git_last_commit_date: 2024-10-29 10:10:26 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-04 11:45 -0500 (Sat, 04 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4756 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4475 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4435 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4390 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4383 |
| 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 1608/2275 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| PureCN 2.13.0 (landing page) Markus Riester
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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: 2.13.0 |
| 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_2.13.0.tar.gz |
| StartedAt: 2025-01-03 20:53:42 -0500 (Fri, 03 Jan 2025) |
| EndedAt: 2025-01-03 20:58:53 -0500 (Fri, 03 Jan 2025) |
| EllapsedTime: 310.8 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_2.13.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/PureCN.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PureCN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PureCN’ version ‘2.13.0’
* checking package namespace information ... OK
* checking package dependencies ... INFO
Package which this enhances but not available for checking: ‘genomicsdb’
* 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 12.414 0.173 12.603
segmentationPSCBS 8.515 0.133 8.662
filterIntervals 7.007 0.162 7.212
runAbsoluteCN 6.155 0.112 6.273
segmentationHclust 5.055 0.123 5.212
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
PureCN.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PureCN ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘PureCN’ ... ** 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) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 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: GenomeInfoDb
Loading required package: S4Vectors
Loading required package: stats4
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: GenomicRanges
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 [2025-01-03 20:56:47] Attempted adding gene symbols to intervals. Heuristics have been used to pick symbols for overlapping genes.
WARN [2025-01-03 20:56:47] Chromosome naming style of txdb file (UCSC) was different from interval file (Ensembl).
WARN [2025-01-03 20:56:49] Attempted adding gene symbols to intervals. Heuristics have been used to pick symbols for overlapping genes.
FATAL [2025-01-03 20:56:50] tumor.coverage.file and interval.file do not align.
FATAL [2025-01-03 20:56:50]
FATAL [2025-01-03 20:56:50] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:56:50] parameters (PureCN 2.13.0).
WARN [2025-01-03 20:56:50] Cannot find all contig lengths while exporting interval file.
INFO [2025-01-03 20:56:51] Processing seq1:1-21 (1/3)...
INFO [2025-01-03 20:56:51] Processing seq1:1227-1247 (2/3)...
INFO [2025-01-03 20:56:51] Processing seq2:594-614 (3/3)...
WARN [2025-01-03 20:56:51] Large potential mis-calibration of on- and off-target log2 ratios: 0.26
FATAL [2025-01-03 20:56:51] Need either f or purity and ploidy.
FATAL [2025-01-03 20:56:51]
FATAL [2025-01-03 20:56:51] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:56:51] parameters (PureCN 2.13.0).
FATAL [2025-01-03 20:56:51] f not in expected range.
FATAL [2025-01-03 20:56:51]
FATAL [2025-01-03 20:56:51] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:56:51] parameters (PureCN 2.13.0).
FATAL [2025-01-03 20:56:51] coverage not in expected range (>=2)
FATAL [2025-01-03 20:56:51]
FATAL [2025-01-03 20:56:51] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:56:51] parameters (PureCN 2.13.0).
FATAL [2025-01-03 20:56:51] purity not in expected range.
FATAL [2025-01-03 20:56:51]
FATAL [2025-01-03 20:56:51] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:56:51] parameters (PureCN 2.13.0).
FATAL [2025-01-03 20:56:51] ploidy not in expected range.
FATAL [2025-01-03 20:56:51]
FATAL [2025-01-03 20:56:51] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:56:51] parameters (PureCN 2.13.0).
FATAL [2025-01-03 20:56:51] cell.fraction not in expected range.
FATAL [2025-01-03 20:56:51]
FATAL [2025-01-03 20:56:51] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:56:51] parameters (PureCN 2.13.0).
INFO [2025-01-03 20:56:52] 576 on-target bins with low coverage in all samples.
WARN [2025-01-03 20:56:52] You are likely not using the correct baits file!
WARN [2025-01-03 20:56:52] Allosome coverage missing, cannot determine sex.
WARN [2025-01-03 20:56:52] Allosome coverage missing, cannot determine sex.
INFO [2025-01-03 20:56:52] Processing on-target regions...
INFO [2025-01-03 20:56:52] Removing 930 intervals with low coverage in normalDB.
INFO [2025-01-03 20:56:52] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2025-01-03 20:56:53] Tumor/normal noise ratio: 19.041
WARN [2025-01-03 20:56:53] Extensive noise in tumor compared to normals.
INFO [2025-01-03 20:57:07] Tumor/normal noise ratio: 19.041
WARN [2025-01-03 20:57:07] Extensive noise in tumor compared to normals.
INFO [2025-01-03 20:57:09] Using BiocParallel for parallel optimization.
FATAL [2025-01-03 20:57:13] pvalue.cutoff not within expected range or format.
FATAL [2025-01-03 20:57:13]
FATAL [2025-01-03 20:57:13] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:13] parameters (PureCN 2.13.0).
FATAL [2025-01-03 20:57:13] pvalue.cutoff not within expected range or format.
FATAL [2025-01-03 20:57:13]
FATAL [2025-01-03 20:57:13] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:13] parameters (PureCN 2.13.0).
FATAL [2025-01-03 20:57:13] percentile.cutoff not in expected range (0 to 100).
FATAL [2025-01-03 20:57:13]
FATAL [2025-01-03 20:57:13] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:13] parameters (PureCN 2.13.0).
FATAL [2025-01-03 20:57:13] percentile.cutoff not in expected range (0 to 100).
FATAL [2025-01-03 20:57:13]
FATAL [2025-01-03 20:57:13] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:13] parameters (PureCN 2.13.0).
FATAL [2025-01-03 20:57:13] purity not within expected range or format.
FATAL [2025-01-03 20:57:13]
FATAL [2025-01-03 20:57:13] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:13] parameters (PureCN 2.13.0).
FATAL [2025-01-03 20:57:13] purity not within expected range or format.
FATAL [2025-01-03 20:57:13]
FATAL [2025-01-03 20:57:13] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:13] parameters (PureCN 2.13.0).
INFO [2025-01-03 20:57:14] ------------------------------------------------------------
INFO [2025-01-03 20:57:14] PureCN 2.13.0
INFO [2025-01-03 20:57:14] ------------------------------------------------------------
INFO [2025-01-03 20:57:14] Loading coverage files...
INFO [2025-01-03 20:57:14] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-01-03 20:57:14] Allosome coverage missing, cannot determine sex.
WARN [2025-01-03 20:57:14] Allosome coverage missing, cannot determine sex.
INFO [2025-01-03 20:57:14] Removing 228 intervals with missing log.ratio.
INFO [2025-01-03 20:57:14] Removing 22 small (< 5bp) intervals.
INFO [2025-01-03 20:57:14] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-01-03 20:57:14] No normalDB provided. Provide one for better results.
INFO [2025-01-03 20:57:14] Removing 1724 low count (< 100 total reads) intervals.
INFO [2025-01-03 20:57:14] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-01-03 20:57:14] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-01-03 20:57:14] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-01-03 20:57:14] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-01-03 20:57:14] Loading VCF...
INFO [2025-01-03 20:57:14] Found 127 variants in VCF file.
INFO [2025-01-03 20:57:14] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-01-03 20:57:14] LIB-02240e4 is tumor in VCF file.
INFO [2025-01-03 20:57:14] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-01-03 20:57:14] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-01-03 20:57:14] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-01-03 20:57:14] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-01-03 20:57:14] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-01-03 20:57:14] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-01-03 20:57:14] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding).
INFO [2025-01-03 20:57:14] 1.2% of targets contain variants.
INFO [2025-01-03 20:57:14] Removing 4 variants outside intervals.
INFO [2025-01-03 20:57:14] Found SOMATIC annotation in VCF.
INFO [2025-01-03 20:57:14] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-01-03 20:57:14] Found SOMATIC annotation in VCF. Setting mapping bias to 0.972.
INFO [2025-01-03 20:57:14] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-01-03 20:57:14] Sample sex: ?
INFO [2025-01-03 20:57:14] Segmenting data...
INFO [2025-01-03 20:57:14] Loading pre-computed boundaries for DNAcopy...
INFO [2025-01-03 20:57:14] Setting undo.SD parameter to 1.000000.
INFO [2025-01-03 20:57:15] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-01-03 20:57:15] Found 59 segments with median size of 17.67Mb.
INFO [2025-01-03 20:57:15] Using 121 variants.
INFO [2025-01-03 20:57:15] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-01-03 20:57:15] 2D-grid search of purity and ploidy...
INFO [2025-01-03 20:57:15] Local optima: 0.63/1.9, 0.5/2
INFO [2025-01-03 20:57:15] Testing local optimum 1/2 at purity 0.63 and total ploidy 1.90...
INFO [2025-01-03 20:57:16] Testing local optimum 2/2 at purity 0.50 and total ploidy 2.00...
INFO [2025-01-03 20:57:16] Skipping 1 solutions that converged to the same optima.
INFO [2025-01-03 20:57:16] Fitting variants with beta model for local optimum 1/2...
INFO [2025-01-03 20:57:16] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2025-01-03 20:57:17] Optimized purity: 0.65
INFO [2025-01-03 20:57:17] Done.
INFO [2025-01-03 20:57:17] ------------------------------------------------------------
INFO [2025-01-03 20:57:17] Estimating callable regions.
FATAL [2025-01-03 20:57:18] exclude not a GRanges object.
FATAL [2025-01-03 20:57:18]
FATAL [2025-01-03 20:57:18] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:18] parameters (PureCN 2.13.0).
FATAL [2025-01-03 20:57:18] callable not a GRanges object.
FATAL [2025-01-03 20:57:18]
FATAL [2025-01-03 20:57:18] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:18] parameters (PureCN 2.13.0).
WARN [2025-01-03 20:57:20] tumor.coverage.file and interval.file do not align.
INFO [2025-01-03 20:57:21] No Gene column in interval.file. You won't get gene-level calls.
FATAL [2025-01-03 20:57:21] No gc_bias column in interval.file.
FATAL [2025-01-03 20:57:21]
FATAL [2025-01-03 20:57:21] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:21] parameters (PureCN 2.13.0).
FATAL [2025-01-03 20:57:21] Provided coverage is zero, most likely due to a corrupt BAM file.
FATAL [2025-01-03 20:57:21]
FATAL [2025-01-03 20:57:21] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:21] parameters (PureCN 2.13.0).
INFO [2025-01-03 20:57:22] No reptiming column in interval.file.
INFO [2025-01-03 20:57:23] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpc1zcDQ/fileb57a402a92d7.rds...
INFO [2025-01-03 20:57:23] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpc1zcDQ/fileb57a402a92d7.rds...
INFO [2025-01-03 20:57:23] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpc1zcDQ/fileb57a402a92d7.rds...
INFO [2025-01-03 20:57:23] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpc1zcDQ/fileb57a402a92d7.rds...
INFO [2025-01-03 20:57:24] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpc1zcDQ/fileb57a402a92d7.rds...
INFO [2025-01-03 20:57:24] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpc1zcDQ/fileb57a402a92d7.rds...
FATAL [2025-01-03 20:57:24] Purity or Ploidy not numeric or in expected range.
FATAL [2025-01-03 20:57:24]
FATAL [2025-01-03 20:57:24] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:24] parameters (PureCN 2.13.0).
INFO [2025-01-03 20:57:24] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpc1zcDQ/fileb57a402a92d7.rds...
INFO [2025-01-03 20:57:24] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpc1zcDQ/fileb57a402a92d7.rds...
FATAL [2025-01-03 20:57:24] 'Failed' column in
FATAL [2025-01-03 20:57:24] /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpc1zcDQ/fileb57a402a92d7.csv
FATAL [2025-01-03 20:57:24] not logical(1).
FATAL [2025-01-03 20:57:24]
FATAL [2025-01-03 20:57:24] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:24] parameters (PureCN 2.13.0).
INFO [2025-01-03 20:57:25] 576 on-target bins with low coverage in all samples.
WARN [2025-01-03 20:57:25] You are likely not using the correct baits file!
WARN [2025-01-03 20:57:25] Allosome coverage missing, cannot determine sex.
WARN [2025-01-03 20:57:25] Allosome coverage missing, cannot determine sex.
INFO [2025-01-03 20:57:25] Processing on-target regions...
INFO [2025-01-03 20:57:25] Removing 930 intervals with low coverage in normalDB.
INFO [2025-01-03 20:57:25] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2025-01-03 20:57:26] 576 on-target bins with low coverage in all samples.
WARN [2025-01-03 20:57:26] You are likely not using the correct baits file!
WARN [2025-01-03 20:57:26] Allosome coverage missing, cannot determine sex.
WARN [2025-01-03 20:57:26] Allosome coverage missing, cannot determine sex.
INFO [2025-01-03 20:57:26] Processing on-target regions...
INFO [2025-01-03 20:57:26] Removing 930 intervals with low coverage in normalDB.
INFO [2025-01-03 20:57:26] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2025-01-03 20:57:27] 576 on-target bins with low coverage in all samples.
WARN [2025-01-03 20:57:27] You are likely not using the correct baits file!
WARN [2025-01-03 20:57:27] Allosome coverage missing, cannot determine sex.
WARN [2025-01-03 20:57:27] Allosome coverage missing, cannot determine sex.
INFO [2025-01-03 20:57:27] Processing on-target regions...
INFO [2025-01-03 20:57:27] Removing 930 intervals with low coverage in normalDB.
INFO [2025-01-03 20:57:27] Removing 1 intervals with zero coverage in more than 3% of normalDB.
WARN [2025-01-03 20:57:27] Allosome coverage missing, cannot determine sex.
INFO [2025-01-03 20:57:27] Sample sex: NA
WARN [2025-01-03 20:57:27] Allosome coverage missing, cannot determine sex.
INFO [2025-01-03 20:57:27] Sample sex: NA
INFO [2025-01-03 20:57:27] 576 on-target bins with low coverage in all samples.
WARN [2025-01-03 20:57:27] You are likely not using the correct baits file!
WARN [2025-01-03 20:57:27] Allosome coverage missing, cannot determine sex.
WARN [2025-01-03 20:57:27] Allosome coverage missing, cannot determine sex.
FATAL [2025-01-03 20:57:27] Length of normal.coverage.files and sex different
FATAL [2025-01-03 20:57:27]
FATAL [2025-01-03 20:57:27] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:27] parameters (PureCN 2.13.0).
WARN [2025-01-03 20:57:29] Target intervals were not sorted.
INFO [2025-01-03 20:57:29] 560 on-target bins with low coverage in all samples.
WARN [2025-01-03 20:57:29] You are likely not using the correct baits file!
WARN [2025-01-03 20:57:29] Allosome coverage missing, cannot determine sex.
WARN [2025-01-03 20:57:29] Allosome coverage missing, cannot determine sex.
WARN [2025-01-03 20:57:29] Allosome coverage missing, cannot determine sex.
INFO [2025-01-03 20:57:29] Processing on-target regions...
INFO [2025-01-03 20:57:29] Removing 978 intervals with low coverage in normalDB.
INFO [2025-01-03 20:57:29] Removing 11 intervals with zero coverage in more than 3% of normalDB.
FATAL [2025-01-03 20:57:30] tumor.coverage.file and normalDB do not align.
FATAL [2025-01-03 20:57:30]
FATAL [2025-01-03 20:57:30] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:30] parameters (PureCN 2.13.0).
FATAL [2025-01-03 20:57:30] At least 2 normal.coverage.files required.
FATAL [2025-01-03 20:57:30]
FATAL [2025-01-03 20:57:30] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:30] parameters (PureCN 2.13.0).
INFO [2025-01-03 20:57:31] ------------------------------------------------------------
INFO [2025-01-03 20:57:31] PureCN 2.13.0
INFO [2025-01-03 20:57:31] ------------------------------------------------------------
INFO [2025-01-03 20:57:31] Loading coverage files...
INFO [2025-01-03 20:57:31] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-01-03 20:57:31] Allosome coverage missing, cannot determine sex.
WARN [2025-01-03 20:57:31] Allosome coverage missing, cannot determine sex.
INFO [2025-01-03 20:57:31] Removing 228 intervals with missing log.ratio.
FATAL [2025-01-03 20:57:31] normalDB incompatible with this PureCN version. Please re-run
FATAL [2025-01-03 20:57:31] NormalDB.R.
FATAL [2025-01-03 20:57:31]
FATAL [2025-01-03 20:57:31] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:31] parameters (PureCN 2.13.0).
FATAL [2025-01-03 20:57:31] normalDB incompatible with this PureCN version. Please re-run
FATAL [2025-01-03 20:57:31] NormalDB.R.
FATAL [2025-01-03 20:57:31]
FATAL [2025-01-03 20:57:31] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:31] parameters (PureCN 2.13.0).
FATAL [2025-01-03 20:57:31] normal.coverage.files with _coverage.txt and _loess.txt suffix
FATAL [2025-01-03 20:57:31] provided. Provide either only GC-normalized or raw coverage files!
FATAL [2025-01-03 20:57:31]
FATAL [2025-01-03 20:57:31] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:31] parameters (PureCN 2.13.0).
INFO [2025-01-03 20:57:31] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-01-03 20:57:31] Removing 19 low quality variants with non-offset BQ < 25.
INFO [2025-01-03 20:57:31] Base quality scores range from 24 to 35 (offset by 1)
INFO [2025-01-03 20:57:31] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS.
INFO [2025-01-03 20:57:31] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-01-03 20:57:31] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-01-03 20:57:31] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-01-03 20:57:31] Removing 19 low quality variants with non-offset BQ < 25.
INFO [2025-01-03 20:57:31] Base quality scores range from 24 to 35 (offset by 1)
INFO [2025-01-03 20:57:31] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS.
INFO [2025-01-03 20:57:32] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-01-03 20:57:32] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-01-03 20:57:32] Removing 6 blacklisted variants.
INFO [2025-01-03 20:57:32] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-01-03 20:57:32] Removing 19 low quality variants with non-offset BQ < 25.
INFO [2025-01-03 20:57:32] Base quality scores range from 24 to 35 (offset by 1)
INFO [2025-01-03 20:57:32] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS.
INFO [2025-01-03 20:57:32] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-01-03 20:57:32] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
WARN [2025-01-03 20:57:32] MuTect stats file lacks contig and position columns.
INFO [2025-01-03 20:57:32] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-01-03 20:57:32] Removing 19 low quality variants with non-offset BQ < 25.
INFO [2025-01-03 20:57:32] Base quality scores range from 24 to 35 (offset by 1)
INFO [2025-01-03 20:57:32] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS.
INFO [2025-01-03 20:57:32] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-01-03 20:57:32] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
WARN [2025-01-03 20:57:32] MuTect stats file and VCF file do not align perfectly. Will remove 2325 unmatched variants.
WARN [2025-01-03 20:57:32] MuTect stats file lacks failure_reasons column. Keeping all variants listed in stats file.
INFO [2025-01-03 20:57:32] Removing 0 non heterozygous (in matched normal) germline SNPs.
INFO [2025-01-03 20:57:32] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-01-03 20:57:32] Base quality scores range from 31 to 33 (offset by 1)
INFO [2025-01-03 20:57:32] Minimum number of supporting reads ranges from 3 to 4, depending on coverage and BQS.
INFO [2025-01-03 20:57:32] Removing 0 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-01-03 20:57:32] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-01-03 20:57:32] Base quality scores range from 7 to 35 (offset by 1)
INFO [2025-01-03 20:57:32] Minimum number of supporting reads ranges from 1 to 41, depending on coverage and BQS.
INFO [2025-01-03 20:57:32] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-01-03 20:57:32] Removing 49 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-01-03 20:57:33] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-01-03 20:57:33] Base quality scores range from 7 to 35 (offset by 1)
INFO [2025-01-03 20:57:33] Minimum number of supporting reads ranges from 1 to 41, depending on coverage and BQS.
INFO [2025-01-03 20:57:33] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-01-03 20:57:33] Removing 49 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-01-03 20:57:33] Removing 22 non heterozygous (in matched normal) germline SNPs.
WARN [2025-01-03 20:57:33] Many variants removed by min.base.quality (50) filter. You might want to lower the cutoff.
FATAL [2025-01-03 20:57:33] No variants passed filter BQ.
FATAL [2025-01-03 20:57:33]
FATAL [2025-01-03 20:57:33] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:33] parameters (PureCN 2.13.0).
INFO [2025-01-03 20:57:33] Found 11 variants in VCF file.
WARN [2025-01-03 20:57:33] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead.
INFO [2025-01-03 20:57:33] 1 (9.1%) variants annotated as likely germline (DB INFO flag).
INFO [2025-01-03 20:57:34] Found 11 variants in VCF file.
WARN [2025-01-03 20:57:34] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead.
INFO [2025-01-03 20:57:34] 1 (9.1%) variants annotated as likely germline (DB INFO flag).
INFO [2025-01-03 20:57:34] Found 11 variants in VCF file.
WARN [2025-01-03 20:57:34] vcf.file has no DB or POP_AF info field for membership in germline databases. Guessing it based on available dbSNP ID.
INFO [2025-01-03 20:57:34] 1 (9.1%) variants annotated as likely germline (DB INFO flag).
INFO [2025-01-03 20:57:34] Found 1000 variants in VCF file.
INFO [2025-01-03 20:57:34] Removing 2 triallelic sites.
WARN [2025-01-03 20:57:34] Having trouble guessing SOMATIC status...
WARN [2025-01-03 20:57:34] DP FORMAT field contains NAs. Removing 44 variants.
INFO [2025-01-03 20:57:34] 954 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-01-03 20:57:35] Found 12 variants in VCF file.
INFO [2025-01-03 20:57:35] Removing 1 triallelic sites.
WARN [2025-01-03 20:57:35] DP FORMAT field contains NAs. Removing 1 variants.
WARN [2025-01-03 20:57:35] vcf.file has no DB info field for membership in germline databases. Found and used somatic status instead.
INFO [2025-01-03 20:57:35] 8 (80.0%) variants annotated as likely germline (DB INFO flag).
WARN [2025-01-03 20:57:35] BQ FORMAT field contains NAs.
INFO [2025-01-03 20:57:35] Found 2331 variants in VCF file.
INFO [2025-01-03 20:57:35] 2282 (97.9%) variants annotated as likely germline (DB INFO flag).
INFO [2025-01-03 20:57:35] Found 2331 variants in VCF file.
INFO [2025-01-03 20:57:35] 2282 (97.9%) variants annotated as likely germline (DB INFO flag).
WARN [2025-01-03 20:57:35] Did not find base quality scores, will use global error rate of 0.0010 instead.
INFO [2025-01-03 20:57:35] Removing 21 low quality variants with non-offset BQ < 25.
INFO [2025-01-03 20:57:35] Base quality scores range from 24 to 35 (offset by 1)
INFO [2025-01-03 20:57:35] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-01-03 20:57:35] Removing 89 variants with AF < 0.030 or AF >= 0.970 or insufficient supporting reads or depth < 15.
INFO [2025-01-03 20:57:35] Found 2331 variants in VCF file.
INFO [2025-01-03 20:57:35] 2282 (97.9%) variants annotated as likely germline (DB INFO flag).
WARN [2025-01-03 20:57:35] BQ FORMAT field contains NAs.
WARN [2025-01-03 20:57:36] Allosome coverage missing, cannot determine sex.
WARN [2025-01-03 20:57:36] Allosome coverage missing, cannot determine sex.
INFO [2025-01-03 20:57:36] Mean coverages: chrX: 108.58, chrY: 108.58, chr1-22: 104.87.
INFO [2025-01-03 20:57:36] Mean coverages: chrX: 108.58, chrY: 2.17, chr1-22: 104.87.
INFO [2025-01-03 20:57:36] Mean coverages: chrX: 108.58, chrY: 5.17, chr1-22: 104.87.
INFO [2025-01-03 20:57:36] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-01-03 20:57:36] No germline variants in VCF.
FATAL [2025-01-03 20:57:36] No solution with id hello
FATAL [2025-01-03 20:57:36]
FATAL [2025-01-03 20:57:36] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:36] parameters (PureCN 2.13.0).
FATAL [2025-01-03 20:57:36] No solution with id 100
FATAL [2025-01-03 20:57:36]
FATAL [2025-01-03 20:57:36] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:36] parameters (PureCN 2.13.0).
FATAL [2025-01-03 20:57:37] all.data and w have different lengths.
FATAL [2025-01-03 20:57:37]
FATAL [2025-01-03 20:57:37] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:37] parameters (PureCN 2.13.0).
INFO [2025-01-03 20:57:37] Splitting 5 large targets to an average width of 400.
WARN [2025-01-03 20:57:37] No mappability scores provided.
WARN [2025-01-03 20:57:37] No reptiming scores provided.
INFO [2025-01-03 20:57:37] Calculating GC-content...
INFO [2025-01-03 20:57:37] Splitting 5 large targets to an average width of 400.
WARN [2025-01-03 20:57:37] No mappability scores provided.
WARN [2025-01-03 20:57:37] No reptiming scores provided.
INFO [2025-01-03 20:57:37] Calculating GC-content...
INFO [2025-01-03 20:57:37] Splitting 5 large targets to an average width of 400.
INFO [2025-01-03 20:57:37] Removing 1 targets overlapping with exclude.
WARN [2025-01-03 20:57:37] No mappability scores provided.
WARN [2025-01-03 20:57:37] No reptiming scores provided.
INFO [2025-01-03 20:57:37] Calculating GC-content...
WARN [2025-01-03 20:57:37] Found small target regions (< 100bp). Will resize them.
INFO [2025-01-03 20:57:37] Splitting 5 large targets to an average width of 400.
FATAL [2025-01-03 20:57:37] off.target.padding must be negative.
FATAL [2025-01-03 20:57:37]
FATAL [2025-01-03 20:57:37] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:37] parameters (PureCN 2.13.0).
FATAL [2025-01-03 20:57:37] Interval coordinates should start at 1, not at 0
FATAL [2025-01-03 20:57:37]
FATAL [2025-01-03 20:57:37] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:37] parameters (PureCN 2.13.0).
WARN [2025-01-03 20:57:37] Found small target regions (< 100bp). Will resize them.
INFO [2025-01-03 20:57:37] Splitting 5 large targets to an average width of 400.
FATAL [2025-01-03 20:57:37] No off-target regions after filtering for mappability and
FATAL [2025-01-03 20:57:37] off.target.padding
FATAL [2025-01-03 20:57:37]
FATAL [2025-01-03 20:57:37] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:37] parameters (PureCN 2.13.0).
WARN [2025-01-03 20:57:37] Found small target regions (< 100bp). Will resize them.
INFO [2025-01-03 20:57:37] Splitting 5 large targets to an average width of 400.
WARN [2025-01-03 20:57:37] No mappability scores provided.
INFO [2025-01-03 20:57:37] Calculating GC-content...
WARN [2025-01-03 20:57:37] Found small target regions (< 100bp). Will resize them.
INFO [2025-01-03 20:57:37] Averaging reptiming into bins of size 200...
INFO [2025-01-03 20:57:37] Splitting 5 large targets to an average width of 400.
WARN [2025-01-03 20:57:37] No mappability scores provided.
INFO [2025-01-03 20:57:38] Calculating GC-content...
WARN [2025-01-03 20:57:38] Found small target regions (< 100bp). Will resize them.
INFO [2025-01-03 20:57:38] Splitting 6 large targets to an average width of 200.
WARN [2025-01-03 20:57:38] No mappability scores provided.
WARN [2025-01-03 20:57:38] No reptiming scores provided.
INFO [2025-01-03 20:57:38] Calculating GC-content...
WARN [2025-01-03 20:57:38] Found small target regions (< 100bp). Will resize them.
INFO [2025-01-03 20:57:38] Splitting 5 large targets to an average width of 400.
WARN [2025-01-03 20:57:38] No mappability scores provided.
WARN [2025-01-03 20:57:38] No reptiming scores provided.
INFO [2025-01-03 20:57:38] Calculating GC-content...
INFO [2025-01-03 20:57:38] Splitting 5 large targets to an average width of 400.
INFO [2025-01-03 20:57:38] Tiling off-target regions to an average width of 200000.
WARN [2025-01-03 20:57:38] No mappability scores provided.
WARN [2025-01-03 20:57:38] No reptiming scores provided.
INFO [2025-01-03 20:57:38] Calculating GC-content...
WARN [2025-01-03 20:57:38] Intervals contain off-target regions. Will not change intervals.
WARN [2025-01-03 20:57:38] No mappability scores provided.
WARN [2025-01-03 20:57:38] No reptiming scores provided.
INFO [2025-01-03 20:57:38] Calculating GC-content...
INFO [2025-01-03 20:57:38] Splitting 5 large targets to an average width of 400.
WARN [2025-01-03 20:57:38] No reptiming scores provided.
INFO [2025-01-03 20:57:38] Calculating GC-content...
WARN [2025-01-03 20:57:38] Found small target regions (< 100bp). Will resize them.
INFO [2025-01-03 20:57:38] Splitting 5 large targets to an average width of 400.
WARN [2025-01-03 20:57:38] No reptiming scores provided.
INFO [2025-01-03 20:57:38] Calculating GC-content...
WARN [2025-01-03 20:57:38] Found small target regions (< 100bp). Will resize them.
INFO [2025-01-03 20:57:38] Splitting 5 large targets to an average width of 400.
WARN [2025-01-03 20:57:38] 1 intervals without mappability score (1 on-target).
INFO [2025-01-03 20:57:38] Removing 1 intervals with low mappability score (<0.60).
WARN [2025-01-03 20:57:38] No reptiming scores provided.
INFO [2025-01-03 20:57:38] Calculating GC-content...
WARN [2025-01-03 20:57:38] Found small target regions (< 100bp). Will resize them.
INFO [2025-01-03 20:57:39] Splitting 5 large targets to an average width of 400.
INFO [2025-01-03 20:57:39] Tiling off-target regions to an average width of 200000.
WARN [2025-01-03 20:57:39] No reptiming scores provided.
INFO [2025-01-03 20:57:39] Calculating GC-content...
INFO [2025-01-03 20:57:39] Splitting 5 large targets to an average width of 400.
WARN [2025-01-03 20:57:39] No mappability scores provided.
WARN [2025-01-03 20:57:39] No reptiming scores provided.
INFO [2025-01-03 20:57:39] Calculating GC-content...
WARN [2025-01-03 20:57:39] Chromosome naming style of interval file (Ensembl) was different from reference (UCSC).
INFO [2025-01-03 20:57:39] Splitting 5 large targets to an average width of 400.
WARN [2025-01-03 20:57:39] No mappability scores provided.
WARN [2025-01-03 20:57:39] No reptiming scores provided.
INFO [2025-01-03 20:57:39] Calculating GC-content...
FATAL [2025-01-03 20:57:39] Chromosome naming style of interval file unknown, should be UCSC.
FATAL [2025-01-03 20:57:39]
FATAL [2025-01-03 20:57:39] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:39] parameters (PureCN 2.13.0).
WARN [2025-01-03 20:57:39] Chromosome naming style of interval file (Ensembl) was different from reference (UCSC).
WARN [2025-01-03 20:57:39] Chromosome naming style of mappability file (Ensembl) was different from reference (UCSC).
INFO [2025-01-03 20:57:39] Splitting 5 large targets to an average width of 400.
WARN [2025-01-03 20:57:39] No reptiming scores provided.
INFO [2025-01-03 20:57:39] Calculating GC-content...
WARN [2025-01-03 20:57:39] Found small target regions (< 60bp). Will resize them.
INFO [2025-01-03 20:57:39] Splitting 5 large targets to an average width of 400.
WARN [2025-01-03 20:57:39] No mappability scores provided.
WARN [2025-01-03 20:57:39] No reptiming scores provided.
INFO [2025-01-03 20:57:39] Calculating GC-content...
WARN [2025-01-03 20:57:39] Found small target regions (< 60bp). Will drop them.
INFO [2025-01-03 20:57:39] Splitting 4 large targets to an average width of 400.
WARN [2025-01-03 20:57:39] No mappability scores provided.
WARN [2025-01-03 20:57:39] No reptiming scores provided.
INFO [2025-01-03 20:57:39] Calculating GC-content...
WARN [2025-01-03 20:57:39] Found small target regions (< 200bp). Will resize them.
INFO [2025-01-03 20:57:39] Splitting 5 large targets to an average width of 400.
WARN [2025-01-03 20:57:39] No mappability scores provided.
WARN [2025-01-03 20:57:39] No reptiming scores provided.
INFO [2025-01-03 20:57:39] Calculating GC-content...
INFO [2025-01-03 20:57:40] Found 20 variants in VCF file.
INFO [2025-01-03 20:57:40] 20 (100.0%) variants annotated as likely germline (DB INFO flag).
WARN [2025-01-03 20:57:40] Did not find base quality scores, will use global error rate of 0.0010 instead.
INFO [2025-01-03 20:57:40] Found 127 variants in VCF file.
INFO [2025-01-03 20:57:40] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
WARN [2025-01-03 20:57:40] Did not find base quality scores, will use global error rate of 0.0010 instead.
INFO [2025-01-03 20:57:40] ------------------------------------------------------------
INFO [2025-01-03 20:57:40] PureCN 2.13.0
INFO [2025-01-03 20:57:40] ------------------------------------------------------------
INFO [2025-01-03 20:57:40] Loading coverage files...
INFO [2025-01-03 20:57:40] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-01-03 20:57:40] Allosome coverage missing, cannot determine sex.
WARN [2025-01-03 20:57:40] Allosome coverage missing, cannot determine sex.
INFO [2025-01-03 20:57:40] Removing 228 intervals with missing log.ratio.
INFO [2025-01-03 20:57:40] Removing 22 small (< 5bp) intervals.
INFO [2025-01-03 20:57:40] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-01-03 20:57:40] No normalDB provided. Provide one for better results.
INFO [2025-01-03 20:57:40] Removing 1724 low count (< 100 total reads) intervals.
INFO [2025-01-03 20:57:40] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-01-03 20:57:40] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-01-03 20:57:40] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-01-03 20:57:40] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-01-03 20:57:40] Loading VCF...
INFO [2025-01-03 20:57:40] Found 127 variants in VCF file.
INFO [2025-01-03 20:57:40] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-01-03 20:57:40] LIB-02240e4 is tumor in VCF file.
INFO [2025-01-03 20:57:40] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-01-03 20:57:40] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-01-03 20:57:41] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-01-03 20:57:41] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-01-03 20:57:41] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-01-03 20:57:41] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-01-03 20:57:41] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding).
INFO [2025-01-03 20:57:41] 1.2% of targets contain variants.
INFO [2025-01-03 20:57:41] Removing 4 variants outside intervals.
INFO [2025-01-03 20:57:41] Found SOMATIC annotation in VCF.
INFO [2025-01-03 20:57:41] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-01-03 20:57:41] Found SOMATIC annotation in VCF. Setting mapping bias to 0.972.
INFO [2025-01-03 20:57:41] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-01-03 20:57:41] Sample sex: ?
INFO [2025-01-03 20:57:41] Segmenting data...
INFO [2025-01-03 20:57:41] Loading pre-computed boundaries for DNAcopy...
INFO [2025-01-03 20:57:41] Setting undo.SD parameter to 1.000000.
INFO [2025-01-03 20:57:41] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-01-03 20:57:41] Found 59 segments with median size of 17.67Mb.
INFO [2025-01-03 20:57:41] Using 121 variants.
INFO [2025-01-03 20:57:41] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-01-03 20:57:41] 2D-grid search of purity and ploidy...
INFO [2025-01-03 20:57:41] Local optima: 0.65/1.8, 0.52/2
INFO [2025-01-03 20:57:41] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2025-01-03 20:57:42] Testing local optimum 2/2 at purity 0.52 and total ploidy 2.00...
INFO [2025-01-03 20:57:42] Skipping 1 solutions that converged to the same optima.
INFO [2025-01-03 20:57:42] Fitting variants with beta model for local optimum 1/2...
INFO [2025-01-03 20:57:42] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2025-01-03 20:57:43] Optimized purity: 0.65
INFO [2025-01-03 20:57:43] Done.
INFO [2025-01-03 20:57:43] ------------------------------------------------------------
FATAL [2025-01-03 20:57:44] log.ratio NULL in .writeLogRatioFileGATK4
FATAL [2025-01-03 20:57:44]
FATAL [2025-01-03 20:57:44] This runtime error might be caused by invalid input data or parameters.
FATAL [2025-01-03 20:57:44] Please report bug (PureCN 2.13.0).
INFO [2025-01-03 20:57:44] Loaded provided segmentation file example_seg.txt (format DNAcopy).
INFO [2025-01-03 20:57:44] Re-centering provided segment means (offset -0.0033).
INFO [2025-01-03 20:57:44] Loaded provided segmentation file example_gatk4_modelfinal.seg.gz (format GATK4).
WARN [2025-01-03 20:57:44] Expecting numeric chromosome names in seg.file, assuming file is properly sorted.
INFO [2025-01-03 20:57:44] Re-centering provided segment means (offset -0.0037).
INFO [2025-01-03 20:57:44] 576 on-target bins with low coverage in all samples.
WARN [2025-01-03 20:57:44] You are likely not using the correct baits file!
WARN [2025-01-03 20:57:44] Allosome coverage missing, cannot determine sex.
WARN [2025-01-03 20:57:44] Allosome coverage missing, cannot determine sex.
INFO [2025-01-03 20:57:44] Processing on-target regions...
INFO [2025-01-03 20:57:44] Removing 930 intervals with low coverage in normalDB.
INFO [2025-01-03 20:57:44] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2025-01-03 20:57:45] ------------------------------------------------------------
INFO [2025-01-03 20:57:45] PureCN 2.13.0
INFO [2025-01-03 20:57:45] ------------------------------------------------------------
INFO [2025-01-03 20:57:45] Using BiocParallel for parallel optimization.
INFO [2025-01-03 20:57:45] Loading coverage files...
INFO [2025-01-03 20:57:45] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-01-03 20:57:45] Allosome coverage missing, cannot determine sex.
WARN [2025-01-03 20:57:45] Allosome coverage missing, cannot determine sex.
INFO [2025-01-03 20:57:45] Removing 228 intervals with missing log.ratio.
INFO [2025-01-03 20:57:45] Removing 705 intervals excluded in normalDB.
INFO [2025-01-03 20:57:45] normalDB provided. Setting minimum coverage for segmentation to 0.0015X.
INFO [2025-01-03 20:57:45] Removing 1066 low count (< 100 total reads) intervals.
INFO [2025-01-03 20:57:45] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-01-03 20:57:45] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-01-03 20:57:45] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-01-03 20:57:45] Sample sex: ?
INFO [2025-01-03 20:57:45] Segmenting data...
INFO [2025-01-03 20:57:45] Interval weights found, will use weighted CBS.
INFO [2025-01-03 20:57:45] Loading pre-computed boundaries for DNAcopy...
INFO [2025-01-03 20:57:45] Setting undo.SD parameter to 1.000000.
Setting multi-figure configuration
INFO [2025-01-03 20:57:46] Found 52 segments with median size of 29.35Mb.
INFO [2025-01-03 20:57:46] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-01-03 20:57:46] 2D-grid search of purity and ploidy...
INFO [2025-01-03 20:57:46] Local optima: 0.65/1.8, 0.52/2
INFO [2025-01-03 20:57:46] Skipping 1 solutions that converged to the same optima.
INFO [2025-01-03 20:57:46] Done.
INFO [2025-01-03 20:57:46] ------------------------------------------------------------
INFO [2025-01-03 20:57:46] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpc1zcDQ/fileb57a433b023e.rds...
FATAL [2025-01-03 20:57:46] runAbsoluteCN was run without a VCF file.
FATAL [2025-01-03 20:57:46]
FATAL [2025-01-03 20:57:46] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:46] parameters (PureCN 2.13.0).
FATAL [2025-01-03 20:57:46] runAbsoluteCN was run without a VCF file.
FATAL [2025-01-03 20:57:46]
FATAL [2025-01-03 20:57:46] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:46] parameters (PureCN 2.13.0).
INFO [2025-01-03 20:57:46] ------------------------------------------------------------
INFO [2025-01-03 20:57:46] PureCN 2.13.0
INFO [2025-01-03 20:57:46] ------------------------------------------------------------
INFO [2025-01-03 20:57:46] Loading coverage files...
INFO [2025-01-03 20:57:47] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-01-03 20:57:47] Allosome coverage missing, cannot determine sex.
WARN [2025-01-03 20:57:47] Allosome coverage missing, cannot determine sex.
INFO [2025-01-03 20:57:47] Removing 228 intervals with missing log.ratio.
INFO [2025-01-03 20:57:47] Removing 705 intervals excluded in normalDB.
INFO [2025-01-03 20:57:47] normalDB provided. Setting minimum coverage for segmentation to 0.0015X.
INFO [2025-01-03 20:57:47] Removing 1066 low count (< 100 total reads) intervals.
INFO [2025-01-03 20:57:47] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-01-03 20:57:47] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-01-03 20:57:47] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-01-03 20:57:47] Sample sex: ?
INFO [2025-01-03 20:57:47] Segmenting data...
INFO [2025-01-03 20:57:47] Interval weights found, will use weighted PSCBS.
FATAL [2025-01-03 20:57:47] segmentationPSCBS requires VCF file.
FATAL [2025-01-03 20:57:47]
FATAL [2025-01-03 20:57:47] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:47] parameters (PureCN 2.13.0).
INFO [2025-01-03 20:57:49] ------------------------------------------------------------
INFO [2025-01-03 20:57:49] PureCN 2.13.0
INFO [2025-01-03 20:57:49] ------------------------------------------------------------
INFO [2025-01-03 20:57:49] Loading coverage files...
FATAL [2025-01-03 20:57:49] Need a normal coverage file if log.ratio and seg.file are not provided.
FATAL [2025-01-03 20:57:49]
FATAL [2025-01-03 20:57:49] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:49] parameters (PureCN 2.13.0).
INFO [2025-01-03 20:57:49] ------------------------------------------------------------
INFO [2025-01-03 20:57:49] PureCN 2.13.0
INFO [2025-01-03 20:57:49] ------------------------------------------------------------
FATAL [2025-01-03 20:57:49] min.ploidy or max.ploidy not within expected range.
FATAL [2025-01-03 20:57:49]
FATAL [2025-01-03 20:57:49] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:49] parameters (PureCN 2.13.0).
INFO [2025-01-03 20:57:49] ------------------------------------------------------------
INFO [2025-01-03 20:57:49] PureCN 2.13.0
INFO [2025-01-03 20:57:49] ------------------------------------------------------------
FATAL [2025-01-03 20:57:49] min.ploidy or max.ploidy not within expected range.
FATAL [2025-01-03 20:57:49]
FATAL [2025-01-03 20:57:49] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:49] parameters (PureCN 2.13.0).
INFO [2025-01-03 20:57:49] ------------------------------------------------------------
INFO [2025-01-03 20:57:49] PureCN 2.13.0
INFO [2025-01-03 20:57:49] ------------------------------------------------------------
INFO [2025-01-03 20:57:49] ------------------------------------------------------------
INFO [2025-01-03 20:57:49] PureCN 2.13.0
INFO [2025-01-03 20:57:49] ------------------------------------------------------------
INFO [2025-01-03 20:57:49] ------------------------------------------------------------
INFO [2025-01-03 20:57:49] PureCN 2.13.0
INFO [2025-01-03 20:57:49] ------------------------------------------------------------
FATAL [2025-01-03 20:57:49] test.num.copy not within expected range.
FATAL [2025-01-03 20:57:49]
FATAL [2025-01-03 20:57:49] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:49] parameters (PureCN 2.13.0).
INFO [2025-01-03 20:57:49] ------------------------------------------------------------
INFO [2025-01-03 20:57:49] PureCN 2.13.0
INFO [2025-01-03 20:57:49] ------------------------------------------------------------
WARN [2025-01-03 20:57:49] test.num.copy outside recommended range.
FATAL [2025-01-03 20:57:49] max.non.clonal not within expected range or format.
FATAL [2025-01-03 20:57:49]
FATAL [2025-01-03 20:57:49] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:49] parameters (PureCN 2.13.0).
INFO [2025-01-03 20:57:49] ------------------------------------------------------------
INFO [2025-01-03 20:57:49] PureCN 2.13.0
INFO [2025-01-03 20:57:49] ------------------------------------------------------------
WARN [2025-01-03 20:57:49] test.num.copy outside recommended range.
FATAL [2025-01-03 20:57:49] max.non.clonal not within expected range or format.
FATAL [2025-01-03 20:57:49]
FATAL [2025-01-03 20:57:49] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:49] parameters (PureCN 2.13.0).
INFO [2025-01-03 20:57:49] ------------------------------------------------------------
INFO [2025-01-03 20:57:49] PureCN 2.13.0
INFO [2025-01-03 20:57:49] ------------------------------------------------------------
FATAL [2025-01-03 20:57:49] test.purity not within expected range.
FATAL [2025-01-03 20:57:49]
FATAL [2025-01-03 20:57:49] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:49] parameters (PureCN 2.13.0).
INFO [2025-01-03 20:57:49] ------------------------------------------------------------
INFO [2025-01-03 20:57:49] PureCN 2.13.0
INFO [2025-01-03 20:57:49] ------------------------------------------------------------
INFO [2025-01-03 20:57:49] Loading coverage files...
FATAL [2025-01-03 20:57:49] Tumor and normal are identical. This won't give any meaningful results
FATAL [2025-01-03 20:57:49] and I'm stopping here.
FATAL [2025-01-03 20:57:49]
FATAL [2025-01-03 20:57:49] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:49] parameters (PureCN 2.13.0).
INFO [2025-01-03 20:57:49] ------------------------------------------------------------
INFO [2025-01-03 20:57:49] PureCN 2.13.0
INFO [2025-01-03 20:57:49] ------------------------------------------------------------
INFO [2025-01-03 20:57:49] Loading coverage files...
FATAL [2025-01-03 20:57:49] Length of log.ratio different from tumor coverage.
FATAL [2025-01-03 20:57:49]
FATAL [2025-01-03 20:57:49] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:49] parameters (PureCN 2.13.0).
INFO [2025-01-03 20:57:49] ------------------------------------------------------------
INFO [2025-01-03 20:57:49] PureCN 2.13.0
INFO [2025-01-03 20:57:49] ------------------------------------------------------------
FATAL [2025-01-03 20:57:49] prior.purity must have the same length as test.purity.
FATAL [2025-01-03 20:57:49]
FATAL [2025-01-03 20:57:49] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:49] parameters (PureCN 2.13.0).
INFO [2025-01-03 20:57:49] ------------------------------------------------------------
INFO [2025-01-03 20:57:49] PureCN 2.13.0
INFO [2025-01-03 20:57:49] ------------------------------------------------------------
FATAL [2025-01-03 20:57:49] min.gof not within expected range or format.
FATAL [2025-01-03 20:57:49]
FATAL [2025-01-03 20:57:49] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:49] parameters (PureCN 2.13.0).
INFO [2025-01-03 20:57:49] ------------------------------------------------------------
INFO [2025-01-03 20:57:49] PureCN 2.13.0
INFO [2025-01-03 20:57:49] ------------------------------------------------------------
FATAL [2025-01-03 20:57:49] prior.purity not within expected range or format.
FATAL [2025-01-03 20:57:49]
FATAL [2025-01-03 20:57:49] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:49] parameters (PureCN 2.13.0).
INFO [2025-01-03 20:57:49] ------------------------------------------------------------
INFO [2025-01-03 20:57:49] PureCN 2.13.0
INFO [2025-01-03 20:57:49] ------------------------------------------------------------
FATAL [2025-01-03 20:57:49] prior.purity must add to 1. Sum is 1.5
FATAL [2025-01-03 20:57:49]
FATAL [2025-01-03 20:57:49] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:49] parameters (PureCN 2.13.0).
INFO [2025-01-03 20:57:49] ------------------------------------------------------------
INFO [2025-01-03 20:57:49] PureCN 2.13.0
INFO [2025-01-03 20:57:49] ------------------------------------------------------------
FATAL [2025-01-03 20:57:49] max.homozygous.loss not within expected range or format.
FATAL [2025-01-03 20:57:49]
FATAL [2025-01-03 20:57:49] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:49] parameters (PureCN 2.13.0).
INFO [2025-01-03 20:57:49] ------------------------------------------------------------
INFO [2025-01-03 20:57:49] PureCN 2.13.0
INFO [2025-01-03 20:57:49] ------------------------------------------------------------
FATAL [2025-01-03 20:57:49] prior.K not within expected range or format.
FATAL [2025-01-03 20:57:49]
FATAL [2025-01-03 20:57:49] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:49] parameters (PureCN 2.13.0).
INFO [2025-01-03 20:57:49] ------------------------------------------------------------
INFO [2025-01-03 20:57:49] PureCN 2.13.0
INFO [2025-01-03 20:57:49] ------------------------------------------------------------
FATAL [2025-01-03 20:57:49] prior.contamination not within expected range or format.
FATAL [2025-01-03 20:57:49]
FATAL [2025-01-03 20:57:49] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:49] parameters (PureCN 2.13.0).
INFO [2025-01-03 20:57:49] ------------------------------------------------------------
INFO [2025-01-03 20:57:49] PureCN 2.13.0
INFO [2025-01-03 20:57:49] ------------------------------------------------------------
FATAL [2025-01-03 20:57:49] Iterations not in the expected range from 10 to 250.
FATAL [2025-01-03 20:57:49]
FATAL [2025-01-03 20:57:49] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:49] parameters (PureCN 2.13.0).
INFO [2025-01-03 20:57:49] ------------------------------------------------------------
INFO [2025-01-03 20:57:49] PureCN 2.13.0
INFO [2025-01-03 20:57:49] ------------------------------------------------------------
FATAL [2025-01-03 20:57:49] Iterations not in the expected range from 10 to 250.
FATAL [2025-01-03 20:57:49]
FATAL [2025-01-03 20:57:49] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:49] parameters (PureCN 2.13.0).
INFO [2025-01-03 20:57:49] ------------------------------------------------------------
INFO [2025-01-03 20:57:49] PureCN 2.13.0
INFO [2025-01-03 20:57:49] ------------------------------------------------------------
INFO [2025-01-03 20:57:49] Loading coverage files...
FATAL [2025-01-03 20:57:50] Missing tumor.coverage.file requires seg.file or log.ratio and
FATAL [2025-01-03 20:57:50] interval.file.
FATAL [2025-01-03 20:57:50]
FATAL [2025-01-03 20:57:50] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:50] parameters (PureCN 2.13.0).
INFO [2025-01-03 20:57:50] ------------------------------------------------------------
INFO [2025-01-03 20:57:50] PureCN 2.13.0
INFO [2025-01-03 20:57:50] ------------------------------------------------------------
INFO [2025-01-03 20:57:50] ------------------------------------------------------------
INFO [2025-01-03 20:57:50] PureCN 2.13.0
INFO [2025-01-03 20:57:50] ------------------------------------------------------------
INFO [2025-01-03 20:57:50] Loading coverage files...
FATAL [2025-01-03 20:57:50] Interval files in normal and tumor different.
FATAL [2025-01-03 20:57:50]
FATAL [2025-01-03 20:57:50] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:50] parameters (PureCN 2.13.0).
INFO [2025-01-03 20:57:50] ------------------------------------------------------------
INFO [2025-01-03 20:57:50] PureCN 2.13.0
INFO [2025-01-03 20:57:50] ------------------------------------------------------------
INFO [2025-01-03 20:57:50] Loading coverage files...
INFO [2025-01-03 20:57:50] Mean target coverages: 0X (tumor) 99X (normal).
WARN [2025-01-03 20:57:50] Large difference in coverage of tumor and normal.
FATAL [2025-01-03 20:57:50] No finite intervals.
FATAL [2025-01-03 20:57:50]
FATAL [2025-01-03 20:57:50] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:50] parameters (PureCN 2.13.0).
INFO [2025-01-03 20:57:50] ------------------------------------------------------------
INFO [2025-01-03 20:57:50] PureCN 2.13.0
INFO [2025-01-03 20:57:50] ------------------------------------------------------------
INFO [2025-01-03 20:57:50] Loading coverage files...
INFO [2025-01-03 20:57:50] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-01-03 20:57:50] Allosome coverage missing, cannot determine sex.
WARN [2025-01-03 20:57:50] Allosome coverage missing, cannot determine sex.
INFO [2025-01-03 20:57:50] Removing 228 intervals with missing log.ratio.
INFO [2025-01-03 20:57:50] Removing 22 small (< 5bp) intervals.
INFO [2025-01-03 20:57:50] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-01-03 20:57:50] No normalDB provided. Provide one for better results.
INFO [2025-01-03 20:57:50] Removing 1724 low count (< 100 total reads) intervals.
INFO [2025-01-03 20:57:50] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-01-03 20:57:50] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-01-03 20:57:50] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-01-03 20:57:50] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-01-03 20:57:50] Loading VCF...
INFO [2025-01-03 20:57:50] Found 127 variants in VCF file.
INFO [2025-01-03 20:57:50] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-01-03 20:57:50] LIB-02240e4 is tumor in VCF file.
INFO [2025-01-03 20:57:51] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-01-03 20:57:51] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-01-03 20:57:51] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-01-03 20:57:51] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-01-03 20:57:51] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-01-03 20:57:51] 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 list(...) :
closing unused connection 5 (/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpc1zcDQ/fileb57a489cbc9.tsv)
2: In list(...) :
closing unused connection 4 (/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/PureCN/extdata/example_gatk4_denoised_cr.tsv.gz)
FATAL [2025-01-03 20:57:51] Could not import snp.blacklist
FATAL [2025-01-03 20:57:51] /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/PureCN/extdata/example_normal.txt.gz:Error
FATAL [2025-01-03 20:57:51] in FileForFormat(resource(con), fileFormat(con)) : Format 'txt'
FATAL [2025-01-03 20:57:51] unsupported
FATAL [2025-01-03 20:57:51]
FATAL [2025-01-03 20:57:51] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:57:51] parameters (PureCN 2.13.0).
INFO [2025-01-03 20:57:51] ------------------------------------------------------------
INFO [2025-01-03 20:57:51] PureCN 2.13.0
INFO [2025-01-03 20:57:51] ------------------------------------------------------------
INFO [2025-01-03 20:57:51] Loading coverage files...
INFO [2025-01-03 20:57:51] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-01-03 20:57:51] Allosome coverage missing, cannot determine sex.
WARN [2025-01-03 20:57:51] Allosome coverage missing, cannot determine sex.
INFO [2025-01-03 20:57:51] Removing 228 intervals with missing log.ratio.
INFO [2025-01-03 20:57:51] Removing 22 small (< 5bp) intervals.
INFO [2025-01-03 20:57:51] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-01-03 20:57:51] No normalDB provided. Provide one for better results.
INFO [2025-01-03 20:57:51] Removing 233 low coverage (< 15.0000X) intervals.
INFO [2025-01-03 20:57:51] Using 9547 intervals (9547 on-target, 0 off-target).
INFO [2025-01-03 20:57:51] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-01-03 20:57:51] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-01-03 20:57:51] Loading VCF...
INFO [2025-01-03 20:57:51] Found 127 variants in VCF file.
INFO [2025-01-03 20:57:51] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-01-03 20:57:51] LIB-02240e4 is tumor in VCF file.
INFO [2025-01-03 20:57:51] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-01-03 20:57:51] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-01-03 20:57:51] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-01-03 20:57:51] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-01-03 20:57:51] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-01-03 20:57:51] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-01-03 20:57:51] Total size of targeted genomic region: 1.63Mb (2.58Mb with 50bp padding).
INFO [2025-01-03 20:57:51] 1.0% of targets contain variants.
INFO [2025-01-03 20:57:51] Removing 2 variants outside intervals.
INFO [2025-01-03 20:57:51] Found SOMATIC annotation in VCF.
INFO [2025-01-03 20:57:51] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-01-03 20:57:51] Found SOMATIC annotation in VCF. Setting mapping bias to 0.973.
INFO [2025-01-03 20:57:51] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-01-03 20:57:51] Sample sex: ?
INFO [2025-01-03 20:57:51] Segmenting data...
INFO [2025-01-03 20:57:52] Loading pre-computed boundaries for DNAcopy...
INFO [2025-01-03 20:57:52] Setting undo.SD parameter to 1.000000.
INFO [2025-01-03 20:57:52] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-01-03 20:57:52] Found 54 segments with median size of 24.88Mb.
INFO [2025-01-03 20:57:52] Using 123 variants.
INFO [2025-01-03 20:57:52] Mean standard deviation of log-ratios: 0.37 (MAPD: 0.32)
INFO [2025-01-03 20:57:52] 2D-grid search of purity and ploidy...
INFO [2025-01-03 20:57:52] Local optima: 0.62/1.9, 0.3/1.9, 0.32/2
INFO [2025-01-03 20:57:52] Testing local optimum 1/3 at purity 0.62 and total ploidy 1.90...
INFO [2025-01-03 20:57:53] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-01-03 20:57:53] Recalibrating log-ratios...
INFO [2025-01-03 20:57:53] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-01-03 20:57:53] Recalibrating log-ratios...
INFO [2025-01-03 20:57:53] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-01-03 20:57:53] Recalibrating log-ratios...
INFO [2025-01-03 20:57:53] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-01-03 20:57:53] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-01-03 20:57:53] Recalibrating log-ratios...
INFO [2025-01-03 20:57:53] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-01-03 20:57:53] Recalibrating log-ratios...
INFO [2025-01-03 20:57:53] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-01-03 20:57:54] Recalibrating log-ratios...
INFO [2025-01-03 20:57:54] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-01-03 20:57:54] Skipping 1 solutions that converged to the same optima.
INFO [2025-01-03 20:57:54] Skipping 1 solutions exceeding max.non.clonal (0.20): 0.3/1.9 (purity/tumor ploidy)
INFO [2025-01-03 20:57:54] Fitting variants with beta model for local optimum 1/3...
INFO [2025-01-03 20:57:54] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01.
INFO [2025-01-03 20:57:55] Optimized purity: 0.65
INFO [2025-01-03 20:57:55] Done.
INFO [2025-01-03 20:57:55] ------------------------------------------------------------
INFO [2025-01-03 20:57:55] ------------------------------------------------------------
INFO [2025-01-03 20:57:55] PureCN 2.13.0
INFO [2025-01-03 20:57:55] ------------------------------------------------------------
INFO [2025-01-03 20:57:55] Loading coverage files...
INFO [2025-01-03 20:57:55] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-01-03 20:57:55] Allosome coverage missing, cannot determine sex.
WARN [2025-01-03 20:57:55] Allosome coverage missing, cannot determine sex.
INFO [2025-01-03 20:57:55] Removing 228 intervals with missing log.ratio.
INFO [2025-01-03 20:57:55] Removing 22 small (< 5bp) intervals.
INFO [2025-01-03 20:57:55] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-01-03 20:57:55] No normalDB provided. Provide one for better results.
INFO [2025-01-03 20:57:55] Removing 1724 low count (< 100 total reads) intervals.
INFO [2025-01-03 20:57:55] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-01-03 20:57:55] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-01-03 20:57:55] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-01-03 20:57:55] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-01-03 20:57:55] Loading VCF...
INFO [2025-01-03 20:57:55] Found 127 variants in VCF file.
WARN [2025-01-03 20:57:55] DP FORMAT field contains NAs. Removing 3 variants.
WARN [2025-01-03 20:57:55] DB INFO flag contains NAs
INFO [2025-01-03 20:57:55] 119 (96.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-01-03 20:57:55] LIB-02240e4 is tumor in VCF file.
INFO [2025-01-03 20:57:55] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-01-03 20:57:55] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-01-03 20:57:55] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-01-03 20:57:55] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-01-03 20:57:55] Removing 1 variants with AF < 0.030 or AF >= 0.970 or insufficient supporting reads or depth < 15.
INFO [2025-01-03 20:57:55] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding).
INFO [2025-01-03 20:57:55] 1.2% of targets contain variants.
INFO [2025-01-03 20:57:55] Setting somatic prior probabilities for likely germline hits to 0.000500 or to 0.500000 otherwise.
INFO [2025-01-03 20:57:55] Excluding 5 novel or poor quality variants from segmentation.
INFO [2025-01-03 20:57:55] Sample sex: ?
INFO [2025-01-03 20:57:55] Segmenting data...
INFO [2025-01-03 20:57:55] Loading pre-computed boundaries for DNAcopy...
INFO [2025-01-03 20:57:55] Setting undo.SD parameter to 1.000000.
Setting multi-figure configuration
INFO [2025-01-03 20:57:56] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-01-03 20:57:56] Found 59 segments with median size of 17.67Mb.
INFO [2025-01-03 20:57:56] Using 123 variants.
INFO [2025-01-03 20:57:56] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-01-03 20:57:56] 2D-grid search of purity and ploidy...
INFO [2025-01-03 20:57:56] Local optima: 0.62/1.9, 0.3/1.9, 0.32/2
INFO [2025-01-03 20:57:56] Testing local optimum 1/3 at purity 0.62 and total ploidy 1.90...
INFO [2025-01-03 20:57:57] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-01-03 20:57:57] Recalibrating log-ratios...
INFO [2025-01-03 20:57:57] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-01-03 20:57:57] Recalibrating log-ratios...
INFO [2025-01-03 20:57:57] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-01-03 20:57:57] Recalibrating log-ratios...
INFO [2025-01-03 20:57:57] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-01-03 20:57:57] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-01-03 20:57:57] Recalibrating log-ratios...
INFO [2025-01-03 20:57:57] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-01-03 20:57:57] Recalibrating log-ratios...
INFO [2025-01-03 20:57:57] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-01-03 20:57:57] Recalibrating log-ratios...
INFO [2025-01-03 20:57:57] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-01-03 20:57:57] Skipping 2 solutions exceeding max.non.clonal (0.20): 0.3/1.9, 0.35/1.61 (purity/tumor ploidy)
INFO [2025-01-03 20:57:57] Fitting variants with beta model for local optimum 1/3...
INFO [2025-01-03 20:57:57] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2025-01-03 20:57:58] Optimized purity: 0.65
INFO [2025-01-03 20:57:58] Done.
INFO [2025-01-03 20:57:58] ------------------------------------------------------------
INFO [2025-01-03 20:57:58] ------------------------------------------------------------
INFO [2025-01-03 20:57:58] PureCN 2.13.0
INFO [2025-01-03 20:57:58] ------------------------------------------------------------
INFO [2025-01-03 20:57:58] Loading coverage files...
INFO [2025-01-03 20:57:59] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-01-03 20:57:59] Allosome coverage missing, cannot determine sex.
WARN [2025-01-03 20:57:59] Allosome coverage missing, cannot determine sex.
INFO [2025-01-03 20:57:59] No Gene column in interval.file. You won't get gene-level calls.
INFO [2025-01-03 20:57:59] Removing 228 intervals with missing log.ratio.
INFO [2025-01-03 20:57:59] Removing 15 low/high GC targets.
INFO [2025-01-03 20:57:59] Removing 21 small (< 5bp) intervals.
INFO [2025-01-03 20:57:59] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-01-03 20:57:59] No normalDB provided. Provide one for better results.
INFO [2025-01-03 20:57:59] Removing 1718 low count (< 100 total reads) intervals.
INFO [2025-01-03 20:57:59] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-01-03 20:57:59] Removing 36 low mappability intervals.
INFO [2025-01-03 20:57:59] Using 8006 intervals (8006 on-target, 0 off-target).
INFO [2025-01-03 20:57:59] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-01-03 20:57:59] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio).
INFO [2025-01-03 20:57:59] Loading VCF...
INFO [2025-01-03 20:57:59] Found 127 variants in VCF file.
INFO [2025-01-03 20:57:59] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-01-03 20:57:59] LIB-02240e4 is tumor in VCF file.
INFO [2025-01-03 20:57:59] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-01-03 20:57:59] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-01-03 20:57:59] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-01-03 20:57:59] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-01-03 20:57:59] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-01-03 20:57:59] Removing 1 variants with AF < 0.030 or AF >= Inf or insufficient supporting reads or depth < 15.
INFO [2025-01-03 20:57:59] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding).
INFO [2025-01-03 20:57:59] 1.2% of targets contain variants.
INFO [2025-01-03 20:57:59] Removing 11 variants outside intervals.
INFO [2025-01-03 20:57:59] Found SOMATIC annotation in VCF.
INFO [2025-01-03 20:57:59] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-01-03 20:57:59] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970.
INFO [2025-01-03 20:57:59] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-01-03 20:57:59] Sample sex: ?
INFO [2025-01-03 20:57:59] Segmenting data...
INFO [2025-01-03 20:57:59] MAPD of 114 allelic fractions: 0.14 (0.15 adjusted).
INFO [2025-01-03 20:57:59] Using unweighted PSCBS.
INFO [2025-01-03 20:58:00] Setting undo.SD parameter to 1.000000.
INFO [2025-01-03 20:58:05] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-01-03 20:58:05] Found 71 segments with median size of 27.72Mb.
INFO [2025-01-03 20:58:05] Using 114 variants.
INFO [2025-01-03 20:58:05] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-01-03 20:58:05] 2D-grid search of purity and ploidy...
INFO [2025-01-03 20:58:05] Local optima: 0.65/1.8, 0.38/2.2
INFO [2025-01-03 20:58:05] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2025-01-03 20:58:05] Recalibrating log-ratios...
INFO [2025-01-03 20:58:05] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2025-01-03 20:58:05] Recalibrating log-ratios...
INFO [2025-01-03 20:58:05] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2025-01-03 20:58:05] Recalibrating log-ratios...
INFO [2025-01-03 20:58:05] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2025-01-03 20:58:06] Testing local optimum 2/2 at purity 0.38 and total ploidy 2.20...
INFO [2025-01-03 20:58:06] Skipping 1 solutions exceeding max.non.clonal (0.20): 0.65/2.04 (purity/tumor ploidy)
INFO [2025-01-03 20:58:06] Fitting variants with beta model for local optimum 2/2...
INFO [2025-01-03 20:58:06] Fitting variants for purity 0.40, tumor ploidy 2.53 and contamination 0.01.
INFO [2025-01-03 20:58:07] Optimized purity: 0.40
INFO [2025-01-03 20:58:07] Done.
INFO [2025-01-03 20:58:07] ------------------------------------------------------------
FATAL [2025-01-03 20:58:07] This function requires gene-level calls. Please add a column 'Gene'
FATAL [2025-01-03 20:58:07] containing gene symbols to the interval.file.
FATAL [2025-01-03 20:58:07]
FATAL [2025-01-03 20:58:07] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:58:07] parameters (PureCN 2.13.0).
INFO [2025-01-03 20:58:08] ------------------------------------------------------------
INFO [2025-01-03 20:58:08] PureCN 2.13.0
INFO [2025-01-03 20:58:08] ------------------------------------------------------------
INFO [2025-01-03 20:58:08] Loading coverage files...
INFO [2025-01-03 20:58:08] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-01-03 20:58:08] Allosome coverage missing, cannot determine sex.
WARN [2025-01-03 20:58:08] Allosome coverage missing, cannot determine sex.
INFO [2025-01-03 20:58:08] Removing 228 intervals with missing log.ratio.
INFO [2025-01-03 20:58:08] Removing 22 small (< 5bp) intervals.
INFO [2025-01-03 20:58:08] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-01-03 20:58:08] No normalDB provided. Provide one for better results.
INFO [2025-01-03 20:58:08] Removing 1724 low count (< 100 total reads) intervals.
INFO [2025-01-03 20:58:08] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-01-03 20:58:08] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-01-03 20:58:08] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-01-03 20:58:08] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-01-03 20:58:08] Loading VCF...
INFO [2025-01-03 20:58:08] Found 127 variants in VCF file.
INFO [2025-01-03 20:58:08] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
FATAL [2025-01-03 20:58:08] Different chromosome names in coverage and VCF.
FATAL [2025-01-03 20:58:08]
FATAL [2025-01-03 20:58:08] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:58:08] parameters (PureCN 2.13.0).
INFO [2025-01-03 20:58:08] ------------------------------------------------------------
INFO [2025-01-03 20:58:08] PureCN 2.13.0
INFO [2025-01-03 20:58:08] ------------------------------------------------------------
INFO [2025-01-03 20:58:08] Loading coverage files...
INFO [2025-01-03 20:58:08] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-01-03 20:58:08] Allosome coverage missing, cannot determine sex.
WARN [2025-01-03 20:58:08] Allosome coverage missing, cannot determine sex.
FATAL [2025-01-03 20:58:08] tumor.coverage.file and interval.file do not align.
FATAL [2025-01-03 20:58:08]
FATAL [2025-01-03 20:58:08] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:58:08] parameters (PureCN 2.13.0).
INFO [2025-01-03 20:58:08] ------------------------------------------------------------
INFO [2025-01-03 20:58:08] PureCN 2.13.0
INFO [2025-01-03 20:58:08] ------------------------------------------------------------
INFO [2025-01-03 20:58:08] Loading coverage files...
INFO [2025-01-03 20:58:08] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-01-03 20:58:08] Allosome coverage missing, cannot determine sex.
WARN [2025-01-03 20:58:08] Allosome coverage missing, cannot determine sex.
INFO [2025-01-03 20:58:09] Removing 228 intervals with missing log.ratio.
INFO [2025-01-03 20:58:09] Removing 15 low/high GC targets.
INFO [2025-01-03 20:58:09] Removing 21 small (< 5bp) intervals.
INFO [2025-01-03 20:58:09] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-01-03 20:58:09] No normalDB provided. Provide one for better results.
INFO [2025-01-03 20:58:09] Removing 1718 low count (< 100 total reads) intervals.
INFO [2025-01-03 20:58:09] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-01-03 20:58:09] Removing 36 low mappability intervals.
INFO [2025-01-03 20:58:09] Using 8006 intervals (8006 on-target, 0 off-target).
INFO [2025-01-03 20:58:09] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-01-03 20:58:09] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio).
INFO [2025-01-03 20:58:09] Loading VCF...
INFO [2025-01-03 20:58:09] Found 127 variants in VCF file.
INFO [2025-01-03 20:58:09] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-01-03 20:58:09] LIB-02240e4 is tumor in VCF file.
INFO [2025-01-03 20:58:09] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-01-03 20:58:09] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-01-03 20:58:09] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-01-03 20:58:09] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-01-03 20:58:09] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-01-03 20:58:09] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-01-03 20:58:09] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding).
INFO [2025-01-03 20:58:09] 1.2% of targets contain variants.
INFO [2025-01-03 20:58:09] Removing 11 variants outside intervals.
INFO [2025-01-03 20:58:09] Found SOMATIC annotation in VCF.
INFO [2025-01-03 20:58:09] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-01-03 20:58:09] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970.
INFO [2025-01-03 20:58:09] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-01-03 20:58:09] Sample sex: ?
INFO [2025-01-03 20:58:09] Segmenting data...
INFO [2025-01-03 20:58:09] Loading pre-computed boundaries for DNAcopy...
INFO [2025-01-03 20:58:09] Setting undo.SD parameter to 1.000000.
INFO [2025-01-03 20:58:10] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-01-03 20:58:10] Found 59 segments with median size of 17.67Mb.
INFO [2025-01-03 20:58:10] Using 114 variants.
INFO [2025-01-03 20:58:10] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-01-03 20:58:10] 2D-grid search of purity and ploidy...
INFO [2025-01-03 20:58:10] Local optima: 0.63/1.9
INFO [2025-01-03 20:58:10] Testing local optimum 1/1 at purity 0.63 and total ploidy 1.90...
INFO [2025-01-03 20:58:10] Fitting variants with beta model for local optimum 1/1...
INFO [2025-01-03 20:58:10] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2025-01-03 20:58:11] Optimized purity: 0.65
INFO [2025-01-03 20:58:11] Done.
INFO [2025-01-03 20:58:11] ------------------------------------------------------------
INFO [2025-01-03 20:58:11] ------------------------------------------------------------
INFO [2025-01-03 20:58:11] PureCN 2.13.0
INFO [2025-01-03 20:58:11] ------------------------------------------------------------
INFO [2025-01-03 20:58:11] Loading coverage files...
INFO [2025-01-03 20:58:11] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-01-03 20:58:11] Allosome coverage missing, cannot determine sex.
WARN [2025-01-03 20:58:11] Allosome coverage missing, cannot determine sex.
INFO [2025-01-03 20:58:12] Removing 228 intervals with missing log.ratio.
INFO [2025-01-03 20:58:12] Removing 15 low/high GC targets.
INFO [2025-01-03 20:58:12] Removing 21 small (< 5bp) intervals.
INFO [2025-01-03 20:58:12] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-01-03 20:58:12] No normalDB provided. Provide one for better results.
INFO [2025-01-03 20:58:12] Removing 1718 low count (< 100 total reads) intervals.
INFO [2025-01-03 20:58:12] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-01-03 20:58:12] Removing 36 low mappability intervals.
INFO [2025-01-03 20:58:12] Using 8006 intervals (8006 on-target, 0 off-target).
INFO [2025-01-03 20:58:12] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-01-03 20:58:12] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio).
INFO [2025-01-03 20:58:12] Loading VCF...
INFO [2025-01-03 20:58:12] Found 127 variants in VCF file.
INFO [2025-01-03 20:58:12] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-01-03 20:58:12] LIB-02240e4 is tumor in VCF file.
INFO [2025-01-03 20:58:12] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-01-03 20:58:12] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-01-03 20:58:12] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-01-03 20:58:12] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-01-03 20:58:12] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-01-03 20:58:12] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-01-03 20:58:12] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding).
INFO [2025-01-03 20:58:12] 1.2% of targets contain variants.
INFO [2025-01-03 20:58:12] Removing 11 variants outside intervals.
INFO [2025-01-03 20:58:12] Found SOMATIC annotation in VCF.
INFO [2025-01-03 20:58:12] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-01-03 20:58:12] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970.
INFO [2025-01-03 20:58:12] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-01-03 20:58:12] Sample sex: ?
INFO [2025-01-03 20:58:12] Segmenting data...
INFO [2025-01-03 20:58:12] Loading pre-computed boundaries for DNAcopy...
INFO [2025-01-03 20:58:12] Setting undo.SD parameter to 1.000000.
INFO [2025-01-03 20:58:13] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-01-03 20:58:13] Found 59 segments with median size of 17.67Mb.
INFO [2025-01-03 20:58:13] Using 114 variants.
INFO [2025-01-03 20:58:13] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-01-03 20:58:13] 2D-grid search of purity and ploidy...
INFO [2025-01-03 20:58:13] Local optima: 0.63/1.9
INFO [2025-01-03 20:58:13] Testing local optimum 1/1 at purity 0.63 and total ploidy 1.90...
INFO [2025-01-03 20:58:13] Fitting variants with beta model for local optimum 1/1...
WARN [2025-01-03 20:58:13] Some gene symbols found on multiple chromosomes. Use of approved symbols suggested.
INFO [2025-01-03 20:58:13] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2025-01-03 20:58:14] Optimized purity: 0.65
INFO [2025-01-03 20:58:14] Done.
INFO [2025-01-03 20:58:14] ------------------------------------------------------------
FATAL [2025-01-03 20:58:14] chr1 not valid chromosome name(s). Valid names are:
FATAL [2025-01-03 20:58:14] 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22
FATAL [2025-01-03 20:58:14]
FATAL [2025-01-03 20:58:14] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:58:14] parameters (PureCN 2.13.0).
INFO [2025-01-03 20:58:14] ------------------------------------------------------------
INFO [2025-01-03 20:58:14] PureCN 2.13.0
INFO [2025-01-03 20:58:14] ------------------------------------------------------------
INFO [2025-01-03 20:58:14] Loading coverage files...
WARN [2025-01-03 20:58:15] Provided sampleid (Sample2) does not match Sample1 found in segmentation.
WARN [2025-01-03 20:58:15] Allosome coverage missing, cannot determine sex.
WARN [2025-01-03 20:58:15] Allosome coverage missing, cannot determine sex.
INFO [2025-01-03 20:58:15] Removing 10 intervals with missing log.ratio.
INFO [2025-01-03 20:58:15] Using 10039 intervals (10039 on-target, 0 off-target).
INFO [2025-01-03 20:58:15] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-01-03 20:58:15] Loading VCF...
INFO [2025-01-03 20:58:15] Found 127 variants in VCF file.
INFO [2025-01-03 20:58:15] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-01-03 20:58:15] LIB-02240e4 is tumor in VCF file.
INFO [2025-01-03 20:58:15] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-01-03 20:58:15] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-01-03 20:58:15] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-01-03 20:58:15] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-01-03 20:58:15] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-01-03 20:58:15] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-01-03 20:58:15] Total size of targeted genomic region: 1.71Mb (2.70Mb with 50bp padding).
INFO [2025-01-03 20:58:15] 1.0% of targets contain variants.
INFO [2025-01-03 20:58:15] Removing 0 variants outside intervals.
INFO [2025-01-03 20:58:15] Found SOMATIC annotation in VCF.
INFO [2025-01-03 20:58:15] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-01-03 20:58:15] Found SOMATIC annotation in VCF. Setting mapping bias to 0.976.
INFO [2025-01-03 20:58:15] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-01-03 20:58:15] Sample sex: ?
INFO [2025-01-03 20:58:15] Segmenting data...
INFO [2025-01-03 20:58:15] Loaded provided segmentation file example_seg.txt (format DNAcopy).
WARN [2025-01-03 20:58:15] Provided sampleid (Sample2) does not match Sample1 found in segmentation.
INFO [2025-01-03 20:58:15] Re-centering provided segment means (offset -0.0033).
INFO [2025-01-03 20:58:15] Loading pre-computed boundaries for DNAcopy...
INFO [2025-01-03 20:58:15] Setting undo.SD parameter to 0.000000.
Setting multi-figure configuration
INFO [2025-01-03 20:58:15] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-01-03 20:58:15] Found 54 segments with median size of 24.88Mb.
INFO [2025-01-03 20:58:15] Using 125 variants.
INFO [2025-01-03 20:58:15] Mean standard deviation of log-ratios: 0.40 (MAPD: 0.00)
INFO [2025-01-03 20:58:15] 2D-grid search of purity and ploidy...
INFO [2025-01-03 20:58:16] Local optima: 0.6/1.9
INFO [2025-01-03 20:58:16] Testing local optimum 1/1 at purity 0.60 and total ploidy 1.90...
INFO [2025-01-03 20:58:16] Fitting variants with beta model for local optimum 1/1...
INFO [2025-01-03 20:58:16] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01.
INFO [2025-01-03 20:58:17] Optimized purity: 0.65
INFO [2025-01-03 20:58:17] Done.
INFO [2025-01-03 20:58:17] ------------------------------------------------------------
WARN [2025-01-03 20:58:17] Allosome coverage missing, cannot determine sex.
WARN [2025-01-03 20:58:17] Allosome coverage missing, cannot determine sex.
Setting multi-figure configuration
FATAL [2025-01-03 20:58:20] Segmentation file expected with colnames ID, chrom, loc.start, loc.end,
FATAL [2025-01-03 20:58:20] num.mark, seg.mean
FATAL [2025-01-03 20:58:20]
FATAL [2025-01-03 20:58:20] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:58:20] parameters (PureCN 2.13.0).
FATAL [2025-01-03 20:58:20] seg.file contains multiple samples and sampleid missing.
FATAL [2025-01-03 20:58:20]
FATAL [2025-01-03 20:58:20] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:58:20] parameters (PureCN 2.13.0).
FATAL [2025-01-03 20:58:20] seg.file contains multiple samples and sampleid does not match any.
FATAL [2025-01-03 20:58:20]
FATAL [2025-01-03 20:58:20] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:58:20] parameters (PureCN 2.13.0).
WARN [2025-01-03 20:58:20] Allosome coverage missing, cannot determine sex.
WARN [2025-01-03 20:58:20] Allosome coverage missing, cannot determine sex.
WARN [2025-01-03 20:58:23] Allosome coverage missing, cannot determine sex.
WARN [2025-01-03 20:58:23] Allosome coverage missing, cannot determine sex.
WARN [2025-01-03 20:58:23] Provided sampleid (example_tumor.txt.gz) does not match Sample1 found in segmentation.
WARN [2025-01-03 20:58:24] Allosome coverage missing, cannot determine sex.
WARN [2025-01-03 20:58:24] Allosome coverage missing, cannot determine sex.
WARN [2025-01-03 20:58:25] No normalDB provided. Provide one for better results.
WARN [2025-01-03 20:58:27] Allosome coverage missing, cannot determine sex.
WARN [2025-01-03 20:58:27] Allosome coverage missing, cannot determine sex.
WARN [2025-01-03 20:58:28] Provided sampleid (Sample.1) does not match Sample1 found in segmentation.
Setting multi-figure configuration
WARN [2025-01-03 20:58:31] Allosome coverage missing, cannot determine sex.
WARN [2025-01-03 20:58:31] Allosome coverage missing, cannot determine sex.
WARN [2025-01-03 20:58:31] No normalDB provided. Provide one for better results.
WARN [2025-01-03 20:58:31] Sampleid looks like a normal in VCF, not like a tumor.
WARN [2025-01-03 20:58:33] Allosome coverage missing, cannot determine sex.
WARN [2025-01-03 20:58:33] Allosome coverage missing, cannot determine sex.
FATAL [2025-01-03 20:58:33] normalDB not a valid normalDB object. Use createNormalDatabase to
FATAL [2025-01-03 20:58:33] create one.
FATAL [2025-01-03 20:58:33]
FATAL [2025-01-03 20:58:33] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:58:33] parameters (PureCN 2.13.0).
WARN [2025-01-03 20:58:33] You are likely not using the correct baits file!
WARN [2025-01-03 20:58:33] Allosome coverage missing, cannot determine sex.
WARN [2025-01-03 20:58:33] Allosome coverage missing, cannot determine sex.
WARN [2025-01-03 20:58:34] Allosome coverage missing, cannot determine sex.
WARN [2025-01-03 20:58:34] Allosome coverage missing, cannot determine sex.
FATAL [2025-01-03 20:58:34] normalDB appears to be empty.
FATAL [2025-01-03 20:58:34]
FATAL [2025-01-03 20:58:34] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:58:34] parameters (PureCN 2.13.0).
WARN [2025-01-03 20:58:35] Allosome coverage missing, cannot determine sex.
WARN [2025-01-03 20:58:35] Allosome coverage missing, cannot determine sex.
WARN [2025-01-03 20:58:35] Intervals in coverage and interval.file have conflicting on/off-target annotation.
WARN [2025-01-03 20:58:38] Allosome coverage missing, cannot determine sex.
WARN [2025-01-03 20:58:38] Allosome coverage missing, cannot determine sex.
FATAL [2025-01-03 20:58:38] Seqlevels missing in provided segmentation: 6
FATAL [2025-01-03 20:58:38]
FATAL [2025-01-03 20:58:38] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:58:38] parameters (PureCN 2.13.0).
sh: gatk: command not found
WARN [2025-01-03 20:58:39] Cannot find gatk binary in path.
WARN [2025-01-03 20:58:39] Allosome coverage missing, cannot determine sex.
WARN [2025-01-03 20:58:39] Allosome coverage missing, cannot determine sex.
WARN [2025-01-03 20:58:39] No normalDB provided. Provide one for better results.
FATAL [2025-01-03 20:58:39] segmentationHclust requires an input segmentation.
FATAL [2025-01-03 20:58:39]
FATAL [2025-01-03 20:58:39] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:58:39] parameters (PureCN 2.13.0).
WARN [2025-01-03 20:58:39] Allosome coverage missing, cannot determine sex.
WARN [2025-01-03 20:58:39] Allosome coverage missing, cannot determine sex.
WARN [2025-01-03 20:58:39] No normalDB provided. Provide one for better results.
FATAL [2025-01-03 20:58:48] The normal.panel.vcf.file contains only a single sample.
FATAL [2025-01-03 20:58:48]
FATAL [2025-01-03 20:58:48] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:58:48] parameters (PureCN 2.13.0).
FATAL [2025-01-03 20:58:48] mapping.bias.file must be a file with *.rds suffix.
FATAL [2025-01-03 20:58:48]
FATAL [2025-01-03 20:58:48] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:58:48] parameters (PureCN 2.13.0).
Failed with error: 'there is no package called 'genomicsdb''
FATAL [2025-01-03 20:58:49] min.normals (0) must be >= 1.
FATAL [2025-01-03 20:58:49]
FATAL [2025-01-03 20:58:49] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:58:49] parameters (PureCN 2.13.0).
FATAL [2025-01-03 20:58:49] min.normals (10) cannot be larger than min.normals.assign.betafit (3).
FATAL [2025-01-03 20:58:49]
FATAL [2025-01-03 20:58:49] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:58:49] parameters (PureCN 2.13.0).
FATAL [2025-01-03 20:58:49] min.normals.assign.betafit (10) cannot be larger than
FATAL [2025-01-03 20:58:49] min.normals.betafit (7).
FATAL [2025-01-03 20:58:49]
FATAL [2025-01-03 20:58:49] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:58:49] parameters (PureCN 2.13.0).
FATAL [2025-01-03 20:58:49] min.normals.betafit (20) cannot be larger than
FATAL [2025-01-03 20:58:49] min.normals.position.specific.fit (10).
FATAL [2025-01-03 20:58:49]
FATAL [2025-01-03 20:58:49] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:58:49] parameters (PureCN 2.13.0).
FATAL [2025-01-03 20:58:49] min.betafit.rho not within expected range or format.
FATAL [2025-01-03 20:58:49]
FATAL [2025-01-03 20:58:49] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:58:49] parameters (PureCN 2.13.0).
FATAL [2025-01-03 20:58:49] max.betafit.rho not within expected range or format.
FATAL [2025-01-03 20:58:49]
FATAL [2025-01-03 20:58:49] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:58:49] parameters (PureCN 2.13.0).
FATAL [2025-01-03 20:58:49] min.betafit.rho (0.9) cannot be larger than max.betafit.rho (0.2).
FATAL [2025-01-03 20:58:49]
FATAL [2025-01-03 20:58:49] This is most likely a user error due to invalid input data or
FATAL [2025-01-03 20:58:49] parameters (PureCN 2.13.0).
[ FAIL 0 | WARN 13 | SKIP 2 | PASS 404 ]
══ 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 13 | SKIP 2 | PASS 404 ]
>
> proc.time()
user system elapsed
136.566 5.203 130.563
PureCN.Rcheck/PureCN-Ex.timings
| name | user | system | elapsed | |
| adjustLogRatio | 0.874 | 0.015 | 0.945 | |
| annotateTargets | 2.498 | 0.104 | 2.632 | |
| bootstrapResults | 0.200 | 0.019 | 0.219 | |
| calculateBamCoverageByInterval | 0.068 | 0.002 | 0.070 | |
| calculateLogRatio | 0.249 | 0.016 | 0.266 | |
| calculateMappingBiasGatk4 | 0 | 0 | 0 | |
| calculateMappingBiasVcf | 0.639 | 0.020 | 0.660 | |
| calculatePowerDetectSomatic | 0.926 | 0.006 | 0.931 | |
| calculateTangentNormal | 0.977 | 0.022 | 1.000 | |
| callAlterations | 0.058 | 0.003 | 0.060 | |
| callAlterationsFromSegmentation | 0.502 | 0.014 | 0.517 | |
| callAmplificationsInLowPurity | 12.414 | 0.173 | 12.603 | |
| callCIN | 0.088 | 0.002 | 0.089 | |
| callLOH | 0.078 | 0.002 | 0.081 | |
| callMutationBurden | 0.564 | 0.017 | 0.582 | |
| centromeres | 0.001 | 0.001 | 0.001 | |
| correctCoverageBias | 0.560 | 0.017 | 0.577 | |
| createCurationFile | 0.154 | 0.003 | 0.158 | |
| createNormalDatabase | 0.864 | 0.025 | 0.890 | |
| filterIntervals | 7.007 | 0.162 | 7.212 | |
| filterVcfBasic | 0.220 | 0.003 | 0.223 | |
| filterVcfMuTect | 0.206 | 0.004 | 0.209 | |
| filterVcfMuTect2 | 0.225 | 0.005 | 0.231 | |
| findFocal | 3.644 | 0.049 | 3.702 | |
| getSexFromCoverage | 0.10 | 0.01 | 0.11 | |
| getSexFromVcf | 0.107 | 0.005 | 0.112 | |
| plotAbs | 0.090 | 0.003 | 0.095 | |
| poolCoverage | 0.225 | 0.011 | 0.237 | |
| predictSomatic | 0.172 | 0.002 | 0.175 | |
| preprocessIntervals | 0.216 | 0.004 | 0.230 | |
| processMultipleSamples | 0.891 | 0.017 | 0.913 | |
| readAllelicCountsFile | 0.202 | 0.001 | 0.203 | |
| readCoverageFile | 0.087 | 0.003 | 0.090 | |
| readCurationFile | 0.092 | 0.003 | 0.094 | |
| readIntervalFile | 0.077 | 0.002 | 0.079 | |
| readLogRatioFile | 0.009 | 0.000 | 0.010 | |
| readSegmentationFile | 0.002 | 0.000 | 0.004 | |
| runAbsoluteCN | 6.155 | 0.112 | 6.273 | |
| segmentationCBS | 2.706 | 0.023 | 2.730 | |
| segmentationGATK4 | 0.001 | 0.000 | 0.002 | |
| segmentationHclust | 5.055 | 0.123 | 5.212 | |
| segmentationPSCBS | 8.515 | 0.133 | 8.662 | |
| setMappingBiasVcf | 0.105 | 0.004 | 0.108 | |
| setPriorVcf | 0.091 | 0.003 | 0.093 | |