Markus Riester
| Snapshot Date: 2025-03-24 13:40 -0400 (Mon, 24 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/PureCN |
| git_branch: devel |
| git_last_commit: 88754b2 |
| git_last_commit_date: 2025-03-20 12:07:34 -0400 (Thu, 20 Mar 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-03-25 11:46 -0400 (Tue, 25 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" | 4782 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4552 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4581 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4533 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4463 |
| 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 1633/2315 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| PureCN 2.13.2 (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 24.03 LTS) / 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: 2.13.2 |
| 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_2.13.2.tar.gz |
| StartedAt: 2025-03-24 20:51:57 -0400 (Mon, 24 Mar 2025) |
| EndedAt: 2025-03-24 20:57:08 -0400 (Mon, 24 Mar 2025) |
| EllapsedTime: 310.9 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_2.13.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/PureCN.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* 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 ‘2.13.2’
* 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 12.911 0.212 12.948
segmentationPSCBS 8.767 0.161 8.950
filterIntervals 7.486 0.177 7.293
runAbsoluteCN 6.100 0.128 6.259
segmentationHclust 4.990 0.094 5.111
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
PureCN.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PureCN ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘PureCN’ ... ** this is package ‘PureCN’ version ‘2.13.2’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (PureCN)
PureCN.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(PureCN)
Loading required package: DNAcopy
Loading required package: VariantAnnotation
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: 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 [2025-03-24 20:55:02] Attempted adding gene symbols to intervals. Heuristics have been used to pick symbols for overlapping genes.
WARN [2025-03-24 20:55:02] Chromosome naming style of txdb file (UCSC) was different from interval file (Ensembl).
WARN [2025-03-24 20:55:04] Attempted adding gene symbols to intervals. Heuristics have been used to pick symbols for overlapping genes.
FATAL [2025-03-24 20:55:05] tumor.coverage.file and interval.file do not align.
FATAL [2025-03-24 20:55:05]
FATAL [2025-03-24 20:55:05] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:55:05] parameters (PureCN 2.13.2).
WARN [2025-03-24 20:55:05] Cannot find all contig lengths while exporting interval file.
INFO [2025-03-24 20:55:05] Processing seq1:1-21 (1/3)...
INFO [2025-03-24 20:55:05] Processing seq1:1227-1247 (2/3)...
INFO [2025-03-24 20:55:06] Processing seq2:594-614 (3/3)...
WARN [2025-03-24 20:55:06] Large potential mis-calibration of on- and off-target log2 ratios: 0.26
FATAL [2025-03-24 20:55:06] Need either f or purity and ploidy.
FATAL [2025-03-24 20:55:06]
FATAL [2025-03-24 20:55:06] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:55:06] parameters (PureCN 2.13.2).
FATAL [2025-03-24 20:55:06] f not in expected range.
FATAL [2025-03-24 20:55:06]
FATAL [2025-03-24 20:55:06] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:55:06] parameters (PureCN 2.13.2).
FATAL [2025-03-24 20:55:06] coverage not in expected range (>=2)
FATAL [2025-03-24 20:55:06]
FATAL [2025-03-24 20:55:06] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:55:06] parameters (PureCN 2.13.2).
FATAL [2025-03-24 20:55:06] purity not in expected range.
FATAL [2025-03-24 20:55:06]
FATAL [2025-03-24 20:55:06] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:55:06] parameters (PureCN 2.13.2).
FATAL [2025-03-24 20:55:06] ploidy not in expected range.
FATAL [2025-03-24 20:55:06]
FATAL [2025-03-24 20:55:06] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:55:06] parameters (PureCN 2.13.2).
FATAL [2025-03-24 20:55:06] cell.fraction not in expected range.
FATAL [2025-03-24 20:55:06]
FATAL [2025-03-24 20:55:06] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:55:06] parameters (PureCN 2.13.2).
INFO [2025-03-24 20:55:07] 576 on-target bins with low coverage in all samples.
WARN [2025-03-24 20:55:07] You are likely not using the correct baits file!
WARN [2025-03-24 20:55:07] Allosome coverage missing, cannot determine sex.
WARN [2025-03-24 20:55:07] Allosome coverage missing, cannot determine sex.
INFO [2025-03-24 20:55:07] Processing on-target regions...
INFO [2025-03-24 20:55:07] Removing 930 intervals with low coverage in normalDB.
INFO [2025-03-24 20:55:07] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2025-03-24 20:55:08] Tumor/normal noise ratio: 19.041
WARN [2025-03-24 20:55:08] Extensive noise in tumor compared to normals.
INFO [2025-03-24 20:55:22] Tumor/normal noise ratio: 19.041
WARN [2025-03-24 20:55:22] Extensive noise in tumor compared to normals.
INFO [2025-03-24 20:55:24] Using BiocParallel for parallel optimization.
FATAL [2025-03-24 20:55:28] pvalue.cutoff not within expected range or format.
FATAL [2025-03-24 20:55:28]
FATAL [2025-03-24 20:55:28] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:55:28] parameters (PureCN 2.13.2).
FATAL [2025-03-24 20:55:28] pvalue.cutoff not within expected range or format.
FATAL [2025-03-24 20:55:28]
FATAL [2025-03-24 20:55:28] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:55:28] parameters (PureCN 2.13.2).
FATAL [2025-03-24 20:55:28] percentile.cutoff not in expected range (0 to 100).
FATAL [2025-03-24 20:55:28]
FATAL [2025-03-24 20:55:28] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:55:28] parameters (PureCN 2.13.2).
FATAL [2025-03-24 20:55:28] percentile.cutoff not in expected range (0 to 100).
FATAL [2025-03-24 20:55:28]
FATAL [2025-03-24 20:55:28] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:55:28] parameters (PureCN 2.13.2).
FATAL [2025-03-24 20:55:28] purity not within expected range or format.
FATAL [2025-03-24 20:55:28]
FATAL [2025-03-24 20:55:28] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:55:28] parameters (PureCN 2.13.2).
FATAL [2025-03-24 20:55:28] purity not within expected range or format.
FATAL [2025-03-24 20:55:28]
FATAL [2025-03-24 20:55:28] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:55:28] parameters (PureCN 2.13.2).
INFO [2025-03-24 20:55:29] ------------------------------------------------------------
INFO [2025-03-24 20:55:29] PureCN 2.13.2
INFO [2025-03-24 20:55:29] ------------------------------------------------------------
INFO [2025-03-24 20:55:29] Loading coverage files...
INFO [2025-03-24 20:55:29] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-03-24 20:55:29] Allosome coverage missing, cannot determine sex.
WARN [2025-03-24 20:55:29] Allosome coverage missing, cannot determine sex.
INFO [2025-03-24 20:55:29] Removing 228 intervals with missing log.ratio.
INFO [2025-03-24 20:55:29] Removing 22 small (< 5bp) intervals.
INFO [2025-03-24 20:55:29] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-03-24 20:55:29] No normalDB provided. Provide one for better results.
INFO [2025-03-24 20:55:29] Removing 1724 low count (< 100 total reads) intervals.
INFO [2025-03-24 20:55:29] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-03-24 20:55:29] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-03-24 20:55:29] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-03-24 20:55:29] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-03-24 20:55:29] Loading VCF...
INFO [2025-03-24 20:55:29] Found 127 variants in VCF file.
INFO [2025-03-24 20:55:29] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-03-24 20:55:29] LIB-02240e4 is tumor in VCF file.
INFO [2025-03-24 20:55:29] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-03-24 20:55:29] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-03-24 20:55:29] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-03-24 20:55:29] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-03-24 20:55:29] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-03-24 20:55:29] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-03-24 20:55:29] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding).
INFO [2025-03-24 20:55:29] 1.2% of targets contain variants.
INFO [2025-03-24 20:55:29] Removing 4 variants outside intervals.
INFO [2025-03-24 20:55:29] Found SOMATIC annotation in VCF.
INFO [2025-03-24 20:55:29] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-03-24 20:55:29] Found SOMATIC annotation in VCF. Setting mapping bias to 0.972.
INFO [2025-03-24 20:55:29] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-03-24 20:55:29] Sample sex: ?
INFO [2025-03-24 20:55:29] Segmenting data...
INFO [2025-03-24 20:55:29] Loading pre-computed boundaries for DNAcopy...
INFO [2025-03-24 20:55:29] Setting undo.SD parameter to 1.000000.
INFO [2025-03-24 20:55:30] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-03-24 20:55:30] Found 59 segments with median size of 17.67Mb.
INFO [2025-03-24 20:55:30] Using 121 variants.
INFO [2025-03-24 20:55:30] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-03-24 20:55:30] 2D-grid search of purity and ploidy...
INFO [2025-03-24 20:55:30] Local optima: 0.63/1.9, 0.5/2
INFO [2025-03-24 20:55:30] Testing local optimum 1/2 at purity 0.63 and total ploidy 1.90...
INFO [2025-03-24 20:55:31] Testing local optimum 2/2 at purity 0.50 and total ploidy 2.00...
INFO [2025-03-24 20:55:31] Skipping 1 solutions that converged to the same optima.
INFO [2025-03-24 20:55:31] Fitting variants with beta model for local optimum 1/2...
INFO [2025-03-24 20:55:31] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2025-03-24 20:55:32] Optimized purity: 0.65
INFO [2025-03-24 20:55:32] Done.
INFO [2025-03-24 20:55:32] ------------------------------------------------------------
INFO [2025-03-24 20:55:32] Estimating callable regions.
FATAL [2025-03-24 20:55:33] exclude not a GRanges object.
FATAL [2025-03-24 20:55:33]
FATAL [2025-03-24 20:55:33] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:55:33] parameters (PureCN 2.13.2).
FATAL [2025-03-24 20:55:33] callable not a GRanges object.
FATAL [2025-03-24 20:55:33]
FATAL [2025-03-24 20:55:33] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:55:33] parameters (PureCN 2.13.2).
WARN [2025-03-24 20:55:35] tumor.coverage.file and interval.file do not align.
INFO [2025-03-24 20:55:36] No Gene column in interval.file. You won't get gene-level calls.
FATAL [2025-03-24 20:55:36] No gc_bias column in interval.file.
FATAL [2025-03-24 20:55:36]
FATAL [2025-03-24 20:55:36] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:55:36] parameters (PureCN 2.13.2).
FATAL [2025-03-24 20:55:36] Provided coverage is zero, most likely due to a corrupt BAM file.
FATAL [2025-03-24 20:55:36]
FATAL [2025-03-24 20:55:36] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:55:36] parameters (PureCN 2.13.2).
INFO [2025-03-24 20:55:37] No reptiming column in interval.file.
INFO [2025-03-24 20:55:38] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpKtTX4g/filed7e67a030a9f.rds...
INFO [2025-03-24 20:55:38] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpKtTX4g/filed7e67a030a9f.rds...
INFO [2025-03-24 20:55:38] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpKtTX4g/filed7e67a030a9f.rds...
INFO [2025-03-24 20:55:38] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpKtTX4g/filed7e67a030a9f.rds...
INFO [2025-03-24 20:55:38] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpKtTX4g/filed7e67a030a9f.rds...
INFO [2025-03-24 20:55:38] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpKtTX4g/filed7e67a030a9f.rds...
FATAL [2025-03-24 20:55:38] Purity or Ploidy not numeric or in expected range.
FATAL [2025-03-24 20:55:38]
FATAL [2025-03-24 20:55:38] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:55:38] parameters (PureCN 2.13.2).
INFO [2025-03-24 20:55:38] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpKtTX4g/filed7e67a030a9f.rds...
INFO [2025-03-24 20:55:39] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpKtTX4g/filed7e67a030a9f.rds...
FATAL [2025-03-24 20:55:39] 'Failed' column in
FATAL [2025-03-24 20:55:39] /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpKtTX4g/filed7e67a030a9f.csv
FATAL [2025-03-24 20:55:39] not logical(1).
FATAL [2025-03-24 20:55:39]
FATAL [2025-03-24 20:55:39] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:55:39] parameters (PureCN 2.13.2).
INFO [2025-03-24 20:55:39] 576 on-target bins with low coverage in all samples.
WARN [2025-03-24 20:55:39] You are likely not using the correct baits file!
WARN [2025-03-24 20:55:39] Allosome coverage missing, cannot determine sex.
WARN [2025-03-24 20:55:39] Allosome coverage missing, cannot determine sex.
INFO [2025-03-24 20:55:39] Processing on-target regions...
INFO [2025-03-24 20:55:39] Removing 930 intervals with low coverage in normalDB.
INFO [2025-03-24 20:55:39] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2025-03-24 20:55:41] 576 on-target bins with low coverage in all samples.
WARN [2025-03-24 20:55:41] You are likely not using the correct baits file!
WARN [2025-03-24 20:55:41] Allosome coverage missing, cannot determine sex.
WARN [2025-03-24 20:55:41] Allosome coverage missing, cannot determine sex.
INFO [2025-03-24 20:55:41] Processing on-target regions...
INFO [2025-03-24 20:55:41] Removing 930 intervals with low coverage in normalDB.
INFO [2025-03-24 20:55:41] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2025-03-24 20:55:42] 576 on-target bins with low coverage in all samples.
WARN [2025-03-24 20:55:42] You are likely not using the correct baits file!
WARN [2025-03-24 20:55:42] Allosome coverage missing, cannot determine sex.
WARN [2025-03-24 20:55:42] Allosome coverage missing, cannot determine sex.
INFO [2025-03-24 20:55:42] Processing on-target regions...
INFO [2025-03-24 20:55:42] Removing 930 intervals with low coverage in normalDB.
INFO [2025-03-24 20:55:42] Removing 1 intervals with zero coverage in more than 3% of normalDB.
WARN [2025-03-24 20:55:42] Allosome coverage missing, cannot determine sex.
INFO [2025-03-24 20:55:42] Sample sex: NA
WARN [2025-03-24 20:55:42] Allosome coverage missing, cannot determine sex.
INFO [2025-03-24 20:55:42] Sample sex: NA
INFO [2025-03-24 20:55:42] 576 on-target bins with low coverage in all samples.
WARN [2025-03-24 20:55:42] You are likely not using the correct baits file!
WARN [2025-03-24 20:55:42] Allosome coverage missing, cannot determine sex.
WARN [2025-03-24 20:55:42] Allosome coverage missing, cannot determine sex.
FATAL [2025-03-24 20:55:42] Length of normal.coverage.files and sex different
FATAL [2025-03-24 20:55:42]
FATAL [2025-03-24 20:55:42] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:55:42] parameters (PureCN 2.13.2).
WARN [2025-03-24 20:55:44] Target intervals were not sorted.
INFO [2025-03-24 20:55:44] 560 on-target bins with low coverage in all samples.
WARN [2025-03-24 20:55:44] You are likely not using the correct baits file!
WARN [2025-03-24 20:55:44] Allosome coverage missing, cannot determine sex.
WARN [2025-03-24 20:55:44] Allosome coverage missing, cannot determine sex.
WARN [2025-03-24 20:55:44] Allosome coverage missing, cannot determine sex.
INFO [2025-03-24 20:55:44] Processing on-target regions...
INFO [2025-03-24 20:55:44] Removing 978 intervals with low coverage in normalDB.
INFO [2025-03-24 20:55:44] Removing 11 intervals with zero coverage in more than 3% of normalDB.
FATAL [2025-03-24 20:55:45] tumor.coverage.file and normalDB do not align.
FATAL [2025-03-24 20:55:45]
FATAL [2025-03-24 20:55:45] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:55:45] parameters (PureCN 2.13.2).
FATAL [2025-03-24 20:55:45] At least 2 normal.coverage.files required.
FATAL [2025-03-24 20:55:45]
FATAL [2025-03-24 20:55:45] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:55:45] parameters (PureCN 2.13.2).
INFO [2025-03-24 20:55:46] ------------------------------------------------------------
INFO [2025-03-24 20:55:46] PureCN 2.13.2
INFO [2025-03-24 20:55:46] ------------------------------------------------------------
INFO [2025-03-24 20:55:46] Loading coverage files...
INFO [2025-03-24 20:55:46] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-03-24 20:55:46] Allosome coverage missing, cannot determine sex.
WARN [2025-03-24 20:55:46] Allosome coverage missing, cannot determine sex.
INFO [2025-03-24 20:55:46] Removing 228 intervals with missing log.ratio.
FATAL [2025-03-24 20:55:46] normalDB incompatible with this PureCN version. Please re-run
FATAL [2025-03-24 20:55:46] NormalDB.R.
FATAL [2025-03-24 20:55:46]
FATAL [2025-03-24 20:55:46] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:55:46] parameters (PureCN 2.13.2).
FATAL [2025-03-24 20:55:46] normalDB incompatible with this PureCN version. Please re-run
FATAL [2025-03-24 20:55:46] NormalDB.R.
FATAL [2025-03-24 20:55:46]
FATAL [2025-03-24 20:55:46] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:55:46] parameters (PureCN 2.13.2).
FATAL [2025-03-24 20:55:46] normal.coverage.files with _coverage.txt and _loess.txt suffix
FATAL [2025-03-24 20:55:46] provided. Provide either only GC-normalized or raw coverage files!
FATAL [2025-03-24 20:55:46]
FATAL [2025-03-24 20:55:46] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:55:46] parameters (PureCN 2.13.2).
INFO [2025-03-24 20:55:46] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-03-24 20:55:46] Removing 19 low quality variants with non-offset BQ < 25.
INFO [2025-03-24 20:55:46] Base quality scores range from 24 to 35 (offset by 1)
INFO [2025-03-24 20:55:46] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS.
INFO [2025-03-24 20:55:46] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-03-24 20:55:46] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-03-24 20:55:46] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-03-24 20:55:46] Removing 19 low quality variants with non-offset BQ < 25.
INFO [2025-03-24 20:55:46] Base quality scores range from 24 to 35 (offset by 1)
INFO [2025-03-24 20:55:46] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS.
INFO [2025-03-24 20:55:46] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-03-24 20:55:46] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-03-24 20:55:47] Removing 6 blacklisted variants.
INFO [2025-03-24 20:55:47] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-03-24 20:55:47] Removing 19 low quality variants with non-offset BQ < 25.
INFO [2025-03-24 20:55:47] Base quality scores range from 24 to 35 (offset by 1)
INFO [2025-03-24 20:55:47] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS.
INFO [2025-03-24 20:55:47] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-03-24 20:55:47] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
WARN [2025-03-24 20:55:47] MuTect stats file lacks contig and position columns.
INFO [2025-03-24 20:55:47] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-03-24 20:55:47] Removing 19 low quality variants with non-offset BQ < 25.
INFO [2025-03-24 20:55:47] Base quality scores range from 24 to 35 (offset by 1)
INFO [2025-03-24 20:55:47] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS.
INFO [2025-03-24 20:55:47] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-03-24 20:55:47] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
WARN [2025-03-24 20:55:47] MuTect stats file and VCF file do not align perfectly. Will remove 2325 unmatched variants.
WARN [2025-03-24 20:55:47] MuTect stats file lacks failure_reasons column. Keeping all variants listed in stats file.
INFO [2025-03-24 20:55:47] Removing 0 non heterozygous (in matched normal) germline SNPs.
INFO [2025-03-24 20:55:47] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-03-24 20:55:47] Base quality scores range from 31 to 33 (offset by 1)
INFO [2025-03-24 20:55:47] Minimum number of supporting reads ranges from 3 to 4, depending on coverage and BQS.
INFO [2025-03-24 20:55:47] Removing 0 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-03-24 20:55:47] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-03-24 20:55:47] Base quality scores range from 7 to 35 (offset by 1)
INFO [2025-03-24 20:55:47] Minimum number of supporting reads ranges from 1 to 41, depending on coverage and BQS.
INFO [2025-03-24 20:55:47] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-03-24 20:55:47] Removing 49 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-03-24 20:55:47] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2025-03-24 20:55:47] Base quality scores range from 7 to 35 (offset by 1)
INFO [2025-03-24 20:55:48] Minimum number of supporting reads ranges from 1 to 41, depending on coverage and BQS.
INFO [2025-03-24 20:55:48] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-03-24 20:55:48] Removing 49 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-03-24 20:55:48] Removing 22 non heterozygous (in matched normal) germline SNPs.
WARN [2025-03-24 20:55:48] Many variants removed by min.base.quality (50) filter. You might want to lower the cutoff.
FATAL [2025-03-24 20:55:48] No variants passed filter BQ.
FATAL [2025-03-24 20:55:48]
FATAL [2025-03-24 20:55:48] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:55:48] parameters (PureCN 2.13.2).
INFO [2025-03-24 20:55:48] Found 11 variants in VCF file.
WARN [2025-03-24 20:55:48] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead.
INFO [2025-03-24 20:55:48] 1 (9.1%) variants annotated as likely germline (DB INFO flag).
INFO [2025-03-24 20:55:48] Found 11 variants in VCF file.
WARN [2025-03-24 20:55:49] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead.
INFO [2025-03-24 20:55:49] 1 (9.1%) variants annotated as likely germline (DB INFO flag).
INFO [2025-03-24 20:55:49] Found 11 variants in VCF file.
WARN [2025-03-24 20:55:49] vcf.file has no DB or POP_AF info field for membership in germline databases. Guessing it based on available dbSNP ID.
INFO [2025-03-24 20:55:49] 1 (9.1%) variants annotated as likely germline (DB INFO flag).
INFO [2025-03-24 20:55:49] Found 1000 variants in VCF file.
INFO [2025-03-24 20:55:49] Removing 2 triallelic sites.
WARN [2025-03-24 20:55:49] Having trouble guessing SOMATIC status...
WARN [2025-03-24 20:55:49] DP FORMAT field contains NAs. Removing 44 variants.
INFO [2025-03-24 20:55:49] 954 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-03-24 20:55:50] Found 12 variants in VCF file.
INFO [2025-03-24 20:55:50] Removing 1 triallelic sites.
WARN [2025-03-24 20:55:50] DP FORMAT field contains NAs. Removing 1 variants.
WARN [2025-03-24 20:55:50] vcf.file has no DB info field for membership in germline databases. Found and used somatic status instead.
INFO [2025-03-24 20:55:50] 8 (80.0%) variants annotated as likely germline (DB INFO flag).
WARN [2025-03-24 20:55:50] BQ FORMAT field contains NAs.
INFO [2025-03-24 20:55:50] Found 2331 variants in VCF file.
INFO [2025-03-24 20:55:50] 2282 (97.9%) variants annotated as likely germline (DB INFO flag).
INFO [2025-03-24 20:55:50] Found 2331 variants in VCF file.
INFO [2025-03-24 20:55:50] 2282 (97.9%) variants annotated as likely germline (DB INFO flag).
WARN [2025-03-24 20:55:50] Did not find base quality scores, will use global error rate of 0.0010 instead.
INFO [2025-03-24 20:55:50] Removing 21 low quality variants with non-offset BQ < 25.
INFO [2025-03-24 20:55:50] Base quality scores range from 24 to 35 (offset by 1)
INFO [2025-03-24 20:55:50] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-03-24 20:55:50] Removing 89 variants with AF < 0.030 or AF >= 0.970 or insufficient supporting reads or depth < 15.
INFO [2025-03-24 20:55:50] Found 2331 variants in VCF file.
INFO [2025-03-24 20:55:50] 2282 (97.9%) variants annotated as likely germline (DB INFO flag).
WARN [2025-03-24 20:55:50] BQ FORMAT field contains NAs.
WARN [2025-03-24 20:55:51] Allosome coverage missing, cannot determine sex.
WARN [2025-03-24 20:55:51] Allosome coverage missing, cannot determine sex.
INFO [2025-03-24 20:55:51] Mean coverages: chrX: 108.58, chrY: 108.58, chr1-22: 104.87.
INFO [2025-03-24 20:55:51] Mean coverages: chrX: 108.58, chrY: 2.17, chr1-22: 104.87.
INFO [2025-03-24 20:55:51] Mean coverages: chrX: 108.58, chrY: 5.17, chr1-22: 104.87.
INFO [2025-03-24 20:55:51] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-03-24 20:55:51] No germline variants in VCF.
FATAL [2025-03-24 20:55:51] No solution with id hello
FATAL [2025-03-24 20:55:51]
FATAL [2025-03-24 20:55:51] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:55:51] parameters (PureCN 2.13.2).
FATAL [2025-03-24 20:55:51] No solution with id 100
FATAL [2025-03-24 20:55:51]
FATAL [2025-03-24 20:55:51] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:55:51] parameters (PureCN 2.13.2).
FATAL [2025-03-24 20:55:52] all.data and w have different lengths.
FATAL [2025-03-24 20:55:52]
FATAL [2025-03-24 20:55:52] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:55:52] parameters (PureCN 2.13.2).
INFO [2025-03-24 20:55:52] Splitting 5 large targets to an average width of 400.
WARN [2025-03-24 20:55:52] No mappability scores provided.
WARN [2025-03-24 20:55:52] No reptiming scores provided.
INFO [2025-03-24 20:55:52] Calculating GC-content...
INFO [2025-03-24 20:55:52] Splitting 5 large targets to an average width of 400.
WARN [2025-03-24 20:55:52] No mappability scores provided.
WARN [2025-03-24 20:55:52] No reptiming scores provided.
INFO [2025-03-24 20:55:52] Calculating GC-content...
INFO [2025-03-24 20:55:52] Splitting 5 large targets to an average width of 400.
INFO [2025-03-24 20:55:52] Removing 1 targets overlapping with exclude.
WARN [2025-03-24 20:55:52] No mappability scores provided.
WARN [2025-03-24 20:55:52] No reptiming scores provided.
INFO [2025-03-24 20:55:52] Calculating GC-content...
WARN [2025-03-24 20:55:52] Found small target regions (< 100bp). Will resize them.
INFO [2025-03-24 20:55:52] Splitting 5 large targets to an average width of 400.
FATAL [2025-03-24 20:55:52] off.target.padding must be negative.
FATAL [2025-03-24 20:55:52]
FATAL [2025-03-24 20:55:52] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:55:52] parameters (PureCN 2.13.2).
FATAL [2025-03-24 20:55:52] Interval coordinates should start at 1, not at 0
FATAL [2025-03-24 20:55:52]
FATAL [2025-03-24 20:55:52] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:55:52] parameters (PureCN 2.13.2).
WARN [2025-03-24 20:55:52] Found small target regions (< 100bp). Will resize them.
INFO [2025-03-24 20:55:52] Splitting 5 large targets to an average width of 400.
FATAL [2025-03-24 20:55:52] No off-target regions after filtering for mappability and
FATAL [2025-03-24 20:55:52] off.target.padding
FATAL [2025-03-24 20:55:52]
FATAL [2025-03-24 20:55:52] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:55:52] parameters (PureCN 2.13.2).
WARN [2025-03-24 20:55:52] Found small target regions (< 100bp). Will resize them.
INFO [2025-03-24 20:55:52] Splitting 5 large targets to an average width of 400.
WARN [2025-03-24 20:55:52] No mappability scores provided.
INFO [2025-03-24 20:55:52] Calculating GC-content...
WARN [2025-03-24 20:55:52] Found small target regions (< 100bp). Will resize them.
INFO [2025-03-24 20:55:52] Averaging reptiming into bins of size 200...
INFO [2025-03-24 20:55:52] Splitting 5 large targets to an average width of 400.
WARN [2025-03-24 20:55:52] No mappability scores provided.
INFO [2025-03-24 20:55:53] Calculating GC-content...
WARN [2025-03-24 20:55:53] Found small target regions (< 100bp). Will resize them.
INFO [2025-03-24 20:55:53] Splitting 6 large targets to an average width of 200.
WARN [2025-03-24 20:55:53] No mappability scores provided.
WARN [2025-03-24 20:55:53] No reptiming scores provided.
INFO [2025-03-24 20:55:53] Calculating GC-content...
WARN [2025-03-24 20:55:53] Found small target regions (< 100bp). Will resize them.
INFO [2025-03-24 20:55:53] Splitting 5 large targets to an average width of 400.
WARN [2025-03-24 20:55:53] No mappability scores provided.
WARN [2025-03-24 20:55:53] No reptiming scores provided.
INFO [2025-03-24 20:55:53] Calculating GC-content...
INFO [2025-03-24 20:55:53] Splitting 5 large targets to an average width of 400.
INFO [2025-03-24 20:55:53] Tiling off-target regions to an average width of 200000.
WARN [2025-03-24 20:55:53] No mappability scores provided.
WARN [2025-03-24 20:55:53] No reptiming scores provided.
INFO [2025-03-24 20:55:53] Calculating GC-content...
WARN [2025-03-24 20:55:53] Intervals contain off-target regions. Will not change intervals.
WARN [2025-03-24 20:55:53] No mappability scores provided.
WARN [2025-03-24 20:55:53] No reptiming scores provided.
INFO [2025-03-24 20:55:53] Calculating GC-content...
INFO [2025-03-24 20:55:53] Splitting 5 large targets to an average width of 400.
WARN [2025-03-24 20:55:53] No reptiming scores provided.
INFO [2025-03-24 20:55:53] Calculating GC-content...
WARN [2025-03-24 20:55:53] Found small target regions (< 100bp). Will resize them.
INFO [2025-03-24 20:55:53] Splitting 5 large targets to an average width of 400.
WARN [2025-03-24 20:55:53] No reptiming scores provided.
INFO [2025-03-24 20:55:53] Calculating GC-content...
WARN [2025-03-24 20:55:53] Found small target regions (< 100bp). Will resize them.
INFO [2025-03-24 20:55:53] Splitting 5 large targets to an average width of 400.
WARN [2025-03-24 20:55:54] 1 intervals without mappability score (1 on-target).
INFO [2025-03-24 20:55:54] Removing 1 intervals with low mappability score (<0.60).
WARN [2025-03-24 20:55:54] No reptiming scores provided.
INFO [2025-03-24 20:55:54] Calculating GC-content...
WARN [2025-03-24 20:55:54] Found small target regions (< 100bp). Will resize them.
INFO [2025-03-24 20:55:54] Splitting 5 large targets to an average width of 400.
INFO [2025-03-24 20:55:54] Tiling off-target regions to an average width of 200000.
WARN [2025-03-24 20:55:54] No reptiming scores provided.
INFO [2025-03-24 20:55:54] Calculating GC-content...
INFO [2025-03-24 20:55:54] Splitting 5 large targets to an average width of 400.
WARN [2025-03-24 20:55:54] No mappability scores provided.
WARN [2025-03-24 20:55:54] No reptiming scores provided.
INFO [2025-03-24 20:55:54] Calculating GC-content...
WARN [2025-03-24 20:55:54] Chromosome naming style of interval file (Ensembl) was different from reference (UCSC).
INFO [2025-03-24 20:55:54] Splitting 5 large targets to an average width of 400.
WARN [2025-03-24 20:55:54] No mappability scores provided.
WARN [2025-03-24 20:55:54] No reptiming scores provided.
INFO [2025-03-24 20:55:54] Calculating GC-content...
FATAL [2025-03-24 20:55:54] Chromosome naming style of interval file unknown, should be UCSC.
FATAL [2025-03-24 20:55:54]
FATAL [2025-03-24 20:55:54] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:55:54] parameters (PureCN 2.13.2).
WARN [2025-03-24 20:55:54] Chromosome naming style of interval file (Ensembl) was different from reference (UCSC).
WARN [2025-03-24 20:55:54] Chromosome naming style of mappability file (Ensembl) was different from reference (UCSC).
INFO [2025-03-24 20:55:54] Splitting 5 large targets to an average width of 400.
WARN [2025-03-24 20:55:54] No reptiming scores provided.
INFO [2025-03-24 20:55:54] Calculating GC-content...
WARN [2025-03-24 20:55:54] Found small target regions (< 60bp). Will resize them.
INFO [2025-03-24 20:55:54] Splitting 5 large targets to an average width of 400.
WARN [2025-03-24 20:55:54] No mappability scores provided.
WARN [2025-03-24 20:55:54] No reptiming scores provided.
INFO [2025-03-24 20:55:54] Calculating GC-content...
WARN [2025-03-24 20:55:54] Found small target regions (< 60bp). Will drop them.
INFO [2025-03-24 20:55:54] Splitting 4 large targets to an average width of 400.
WARN [2025-03-24 20:55:54] No mappability scores provided.
WARN [2025-03-24 20:55:54] No reptiming scores provided.
INFO [2025-03-24 20:55:54] Calculating GC-content...
WARN [2025-03-24 20:55:54] Found small target regions (< 200bp). Will resize them.
INFO [2025-03-24 20:55:54] Splitting 5 large targets to an average width of 400.
WARN [2025-03-24 20:55:54] No mappability scores provided.
WARN [2025-03-24 20:55:54] No reptiming scores provided.
INFO [2025-03-24 20:55:54] Calculating GC-content...
INFO [2025-03-24 20:55:55] Found 20 variants in VCF file.
INFO [2025-03-24 20:55:55] 20 (100.0%) variants annotated as likely germline (DB INFO flag).
WARN [2025-03-24 20:55:55] Did not find base quality scores, will use global error rate of 0.0010 instead.
Error in read.table(file = file, header = header, sep = sep, quote = quote, :
no lines available in input
FATAL [2025-03-24 20:55:55] Error reading AllelicCountsFile
FATAL [2025-03-24 20:55:55] /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/PureCN/extdata/example_allelic_counts_empty.tsv
FATAL [2025-03-24 20:55:55]
FATAL [2025-03-24 20:55:55] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:55:55] parameters (PureCN 2.13.2).
INFO [2025-03-24 20:55:55] Found 127 variants in VCF file.
INFO [2025-03-24 20:55:55] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
WARN [2025-03-24 20:55:55] Did not find base quality scores, will use global error rate of 0.0010 instead.
INFO [2025-03-24 20:55:55] ------------------------------------------------------------
INFO [2025-03-24 20:55:55] PureCN 2.13.2
INFO [2025-03-24 20:55:55] ------------------------------------------------------------
INFO [2025-03-24 20:55:55] Loading coverage files...
INFO [2025-03-24 20:55:55] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-03-24 20:55:55] Allosome coverage missing, cannot determine sex.
WARN [2025-03-24 20:55:55] Allosome coverage missing, cannot determine sex.
INFO [2025-03-24 20:55:55] Removing 228 intervals with missing log.ratio.
INFO [2025-03-24 20:55:55] Removing 22 small (< 5bp) intervals.
INFO [2025-03-24 20:55:55] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-03-24 20:55:55] No normalDB provided. Provide one for better results.
INFO [2025-03-24 20:55:55] Removing 1724 low count (< 100 total reads) intervals.
INFO [2025-03-24 20:55:55] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-03-24 20:55:55] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-03-24 20:55:55] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-03-24 20:55:55] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-03-24 20:55:55] Loading VCF...
INFO [2025-03-24 20:55:55] Found 127 variants in VCF file.
INFO [2025-03-24 20:55:55] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-03-24 20:55:55] LIB-02240e4 is tumor in VCF file.
INFO [2025-03-24 20:55:55] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-03-24 20:55:55] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-03-24 20:55:55] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-03-24 20:55:55] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-03-24 20:55:55] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-03-24 20:55:56] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-03-24 20:55:56] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding).
INFO [2025-03-24 20:55:56] 1.2% of targets contain variants.
INFO [2025-03-24 20:55:56] Removing 4 variants outside intervals.
INFO [2025-03-24 20:55:56] Found SOMATIC annotation in VCF.
INFO [2025-03-24 20:55:56] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-03-24 20:55:56] Found SOMATIC annotation in VCF. Setting mapping bias to 0.972.
INFO [2025-03-24 20:55:56] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-03-24 20:55:56] Sample sex: ?
INFO [2025-03-24 20:55:56] Segmenting data...
INFO [2025-03-24 20:55:56] Loading pre-computed boundaries for DNAcopy...
INFO [2025-03-24 20:55:56] Setting undo.SD parameter to 1.000000.
INFO [2025-03-24 20:55:56] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-03-24 20:55:56] Found 59 segments with median size of 17.67Mb.
INFO [2025-03-24 20:55:56] Using 121 variants.
INFO [2025-03-24 20:55:56] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-03-24 20:55:56] 2D-grid search of purity and ploidy...
INFO [2025-03-24 20:55:56] Local optima: 0.65/1.8, 0.52/2
INFO [2025-03-24 20:55:56] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2025-03-24 20:55:57] Testing local optimum 2/2 at purity 0.52 and total ploidy 2.00...
INFO [2025-03-24 20:55:57] Skipping 1 solutions that converged to the same optima.
INFO [2025-03-24 20:55:57] Fitting variants with beta model for local optimum 1/2...
INFO [2025-03-24 20:55:57] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2025-03-24 20:55:58] Optimized purity: 0.65
INFO [2025-03-24 20:55:58] Done.
INFO [2025-03-24 20:55:58] ------------------------------------------------------------
FATAL [2025-03-24 20:55:58] log.ratio NULL in .writeLogRatioFileGATK4
FATAL [2025-03-24 20:55:58]
FATAL [2025-03-24 20:55:58] This runtime error might be caused by invalid input data or parameters.
FATAL [2025-03-24 20:55:58] Please report bug (PureCN 2.13.2).
INFO [2025-03-24 20:55:58] Loaded provided segmentation file example_seg.txt (format DNAcopy).
INFO [2025-03-24 20:55:58] Re-centering provided segment means (offset -0.0033).
INFO [2025-03-24 20:55:58] Loaded provided segmentation file example_gatk4_modelfinal.seg.gz (format GATK4).
WARN [2025-03-24 20:55:58] Expecting numeric chromosome names in seg.file, assuming file is properly sorted.
INFO [2025-03-24 20:55:58] Re-centering provided segment means (offset -0.0037).
INFO [2025-03-24 20:55:59] 576 on-target bins with low coverage in all samples.
WARN [2025-03-24 20:55:59] You are likely not using the correct baits file!
WARN [2025-03-24 20:55:59] Allosome coverage missing, cannot determine sex.
WARN [2025-03-24 20:55:59] Allosome coverage missing, cannot determine sex.
INFO [2025-03-24 20:55:59] Processing on-target regions...
INFO [2025-03-24 20:55:59] Removing 930 intervals with low coverage in normalDB.
INFO [2025-03-24 20:55:59] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2025-03-24 20:55:59] ------------------------------------------------------------
INFO [2025-03-24 20:55:59] PureCN 2.13.2
INFO [2025-03-24 20:55:59] ------------------------------------------------------------
INFO [2025-03-24 20:55:59] Using BiocParallel for parallel optimization.
INFO [2025-03-24 20:55:59] Loading coverage files...
INFO [2025-03-24 20:55:59] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-03-24 20:56:00] Allosome coverage missing, cannot determine sex.
WARN [2025-03-24 20:56:00] Allosome coverage missing, cannot determine sex.
INFO [2025-03-24 20:56:00] Removing 228 intervals with missing log.ratio.
INFO [2025-03-24 20:56:00] Removing 705 intervals excluded in normalDB.
INFO [2025-03-24 20:56:00] normalDB provided. Setting minimum coverage for segmentation to 0.0015X.
INFO [2025-03-24 20:56:00] Removing 1066 low count (< 100 total reads) intervals.
INFO [2025-03-24 20:56:00] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-03-24 20:56:00] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-03-24 20:56:00] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-03-24 20:56:00] Sample sex: ?
INFO [2025-03-24 20:56:00] Segmenting data...
INFO [2025-03-24 20:56:00] Interval weights found, will use weighted CBS.
INFO [2025-03-24 20:56:00] Loading pre-computed boundaries for DNAcopy...
INFO [2025-03-24 20:56:00] Setting undo.SD parameter to 1.000000.
Setting multi-figure configuration
INFO [2025-03-24 20:56:00] Found 52 segments with median size of 29.35Mb.
INFO [2025-03-24 20:56:00] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-03-24 20:56:00] 2D-grid search of purity and ploidy...
INFO [2025-03-24 20:56:00] Local optima: 0.65/1.8, 0.52/2
INFO [2025-03-24 20:56:01] Skipping 1 solutions that converged to the same optima.
INFO [2025-03-24 20:56:01] Done.
INFO [2025-03-24 20:56:01] ------------------------------------------------------------
INFO [2025-03-24 20:56:01] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpKtTX4g/filed7e62939523c.rds...
FATAL [2025-03-24 20:56:01] runAbsoluteCN was run without a VCF file.
FATAL [2025-03-24 20:56:01]
FATAL [2025-03-24 20:56:01] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:56:01] parameters (PureCN 2.13.2).
FATAL [2025-03-24 20:56:01] runAbsoluteCN was run without a VCF file.
FATAL [2025-03-24 20:56:01]
FATAL [2025-03-24 20:56:01] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:56:01] parameters (PureCN 2.13.2).
INFO [2025-03-24 20:56:01] ------------------------------------------------------------
INFO [2025-03-24 20:56:01] PureCN 2.13.2
INFO [2025-03-24 20:56:01] ------------------------------------------------------------
INFO [2025-03-24 20:56:01] Loading coverage files...
INFO [2025-03-24 20:56:01] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-03-24 20:56:01] Allosome coverage missing, cannot determine sex.
WARN [2025-03-24 20:56:01] Allosome coverage missing, cannot determine sex.
INFO [2025-03-24 20:56:01] Removing 228 intervals with missing log.ratio.
INFO [2025-03-24 20:56:01] Removing 705 intervals excluded in normalDB.
INFO [2025-03-24 20:56:01] normalDB provided. Setting minimum coverage for segmentation to 0.0015X.
INFO [2025-03-24 20:56:01] Removing 1066 low count (< 100 total reads) intervals.
INFO [2025-03-24 20:56:01] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-03-24 20:56:01] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-03-24 20:56:01] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-03-24 20:56:01] Sample sex: ?
INFO [2025-03-24 20:56:01] Segmenting data...
INFO [2025-03-24 20:56:01] Interval weights found, will use weighted PSCBS.
FATAL [2025-03-24 20:56:01] segmentationPSCBS requires VCF file.
FATAL [2025-03-24 20:56:01]
FATAL [2025-03-24 20:56:01] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:56:01] parameters (PureCN 2.13.2).
INFO [2025-03-24 20:56:04] ------------------------------------------------------------
INFO [2025-03-24 20:56:04] PureCN 2.13.2
INFO [2025-03-24 20:56:04] ------------------------------------------------------------
INFO [2025-03-24 20:56:04] Loading coverage files...
FATAL [2025-03-24 20:56:04] Need a normal coverage file if log.ratio and seg.file are not provided.
FATAL [2025-03-24 20:56:04]
FATAL [2025-03-24 20:56:04] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:56:04] parameters (PureCN 2.13.2).
INFO [2025-03-24 20:56:04] ------------------------------------------------------------
INFO [2025-03-24 20:56:04] PureCN 2.13.2
INFO [2025-03-24 20:56:04] ------------------------------------------------------------
FATAL [2025-03-24 20:56:04] min.ploidy or max.ploidy not within expected range.
FATAL [2025-03-24 20:56:04]
FATAL [2025-03-24 20:56:04] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:56:04] parameters (PureCN 2.13.2).
INFO [2025-03-24 20:56:04] ------------------------------------------------------------
INFO [2025-03-24 20:56:04] PureCN 2.13.2
INFO [2025-03-24 20:56:04] ------------------------------------------------------------
FATAL [2025-03-24 20:56:04] min.ploidy or max.ploidy not within expected range.
FATAL [2025-03-24 20:56:04]
FATAL [2025-03-24 20:56:04] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:56:04] parameters (PureCN 2.13.2).
INFO [2025-03-24 20:56:04] ------------------------------------------------------------
INFO [2025-03-24 20:56:04] PureCN 2.13.2
INFO [2025-03-24 20:56:04] ------------------------------------------------------------
INFO [2025-03-24 20:56:04] ------------------------------------------------------------
INFO [2025-03-24 20:56:04] PureCN 2.13.2
INFO [2025-03-24 20:56:04] ------------------------------------------------------------
INFO [2025-03-24 20:56:04] ------------------------------------------------------------
INFO [2025-03-24 20:56:04] PureCN 2.13.2
INFO [2025-03-24 20:56:04] ------------------------------------------------------------
FATAL [2025-03-24 20:56:04] test.num.copy not within expected range.
FATAL [2025-03-24 20:56:04]
FATAL [2025-03-24 20:56:04] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:56:04] parameters (PureCN 2.13.2).
INFO [2025-03-24 20:56:04] ------------------------------------------------------------
INFO [2025-03-24 20:56:04] PureCN 2.13.2
INFO [2025-03-24 20:56:04] ------------------------------------------------------------
WARN [2025-03-24 20:56:04] test.num.copy outside recommended range.
FATAL [2025-03-24 20:56:04] max.non.clonal not within expected range or format.
FATAL [2025-03-24 20:56:04]
FATAL [2025-03-24 20:56:04] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:56:04] parameters (PureCN 2.13.2).
INFO [2025-03-24 20:56:04] ------------------------------------------------------------
INFO [2025-03-24 20:56:04] PureCN 2.13.2
INFO [2025-03-24 20:56:04] ------------------------------------------------------------
WARN [2025-03-24 20:56:04] test.num.copy outside recommended range.
FATAL [2025-03-24 20:56:04] max.non.clonal not within expected range or format.
FATAL [2025-03-24 20:56:04]
FATAL [2025-03-24 20:56:04] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:56:04] parameters (PureCN 2.13.2).
INFO [2025-03-24 20:56:04] ------------------------------------------------------------
INFO [2025-03-24 20:56:04] PureCN 2.13.2
INFO [2025-03-24 20:56:04] ------------------------------------------------------------
FATAL [2025-03-24 20:56:04] test.purity not within expected range.
FATAL [2025-03-24 20:56:04]
FATAL [2025-03-24 20:56:04] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:56:04] parameters (PureCN 2.13.2).
INFO [2025-03-24 20:56:04] ------------------------------------------------------------
INFO [2025-03-24 20:56:04] PureCN 2.13.2
INFO [2025-03-24 20:56:04] ------------------------------------------------------------
INFO [2025-03-24 20:56:04] Loading coverage files...
FATAL [2025-03-24 20:56:04] Tumor and normal are identical. This won't give any meaningful results
FATAL [2025-03-24 20:56:04] and I'm stopping here.
FATAL [2025-03-24 20:56:04]
FATAL [2025-03-24 20:56:04] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:56:04] parameters (PureCN 2.13.2).
INFO [2025-03-24 20:56:04] ------------------------------------------------------------
INFO [2025-03-24 20:56:04] PureCN 2.13.2
INFO [2025-03-24 20:56:04] ------------------------------------------------------------
INFO [2025-03-24 20:56:04] Loading coverage files...
FATAL [2025-03-24 20:56:04] Length of log.ratio different from tumor coverage.
FATAL [2025-03-24 20:56:04]
FATAL [2025-03-24 20:56:04] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:56:04] parameters (PureCN 2.13.2).
INFO [2025-03-24 20:56:04] ------------------------------------------------------------
INFO [2025-03-24 20:56:04] PureCN 2.13.2
INFO [2025-03-24 20:56:04] ------------------------------------------------------------
FATAL [2025-03-24 20:56:04] prior.purity must have the same length as test.purity.
FATAL [2025-03-24 20:56:04]
FATAL [2025-03-24 20:56:04] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:56:04] parameters (PureCN 2.13.2).
INFO [2025-03-24 20:56:04] ------------------------------------------------------------
INFO [2025-03-24 20:56:04] PureCN 2.13.2
INFO [2025-03-24 20:56:04] ------------------------------------------------------------
FATAL [2025-03-24 20:56:04] min.gof not within expected range or format.
FATAL [2025-03-24 20:56:04]
FATAL [2025-03-24 20:56:04] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:56:04] parameters (PureCN 2.13.2).
INFO [2025-03-24 20:56:04] ------------------------------------------------------------
INFO [2025-03-24 20:56:04] PureCN 2.13.2
INFO [2025-03-24 20:56:04] ------------------------------------------------------------
FATAL [2025-03-24 20:56:04] prior.purity not within expected range or format.
FATAL [2025-03-24 20:56:04]
FATAL [2025-03-24 20:56:04] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:56:04] parameters (PureCN 2.13.2).
INFO [2025-03-24 20:56:04] ------------------------------------------------------------
INFO [2025-03-24 20:56:04] PureCN 2.13.2
INFO [2025-03-24 20:56:04] ------------------------------------------------------------
FATAL [2025-03-24 20:56:04] prior.purity must add to 1. Sum is 1.5
FATAL [2025-03-24 20:56:04]
FATAL [2025-03-24 20:56:04] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:56:04] parameters (PureCN 2.13.2).
INFO [2025-03-24 20:56:04] ------------------------------------------------------------
INFO [2025-03-24 20:56:04] PureCN 2.13.2
INFO [2025-03-24 20:56:04] ------------------------------------------------------------
FATAL [2025-03-24 20:56:04] max.homozygous.loss not within expected range or format.
FATAL [2025-03-24 20:56:04]
FATAL [2025-03-24 20:56:04] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:56:04] parameters (PureCN 2.13.2).
INFO [2025-03-24 20:56:04] ------------------------------------------------------------
INFO [2025-03-24 20:56:04] PureCN 2.13.2
INFO [2025-03-24 20:56:04] ------------------------------------------------------------
FATAL [2025-03-24 20:56:04] prior.K not within expected range or format.
FATAL [2025-03-24 20:56:04]
FATAL [2025-03-24 20:56:04] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:56:04] parameters (PureCN 2.13.2).
INFO [2025-03-24 20:56:04] ------------------------------------------------------------
INFO [2025-03-24 20:56:04] PureCN 2.13.2
INFO [2025-03-24 20:56:04] ------------------------------------------------------------
FATAL [2025-03-24 20:56:04] prior.contamination not within expected range or format.
FATAL [2025-03-24 20:56:04]
FATAL [2025-03-24 20:56:04] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:56:04] parameters (PureCN 2.13.2).
INFO [2025-03-24 20:56:04] ------------------------------------------------------------
INFO [2025-03-24 20:56:04] PureCN 2.13.2
INFO [2025-03-24 20:56:04] ------------------------------------------------------------
FATAL [2025-03-24 20:56:04] Iterations not in the expected range from 10 to 250.
FATAL [2025-03-24 20:56:04]
FATAL [2025-03-24 20:56:04] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:56:04] parameters (PureCN 2.13.2).
INFO [2025-03-24 20:56:04] ------------------------------------------------------------
INFO [2025-03-24 20:56:04] PureCN 2.13.2
INFO [2025-03-24 20:56:04] ------------------------------------------------------------
FATAL [2025-03-24 20:56:04] Iterations not in the expected range from 10 to 250.
FATAL [2025-03-24 20:56:04]
FATAL [2025-03-24 20:56:04] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:56:04] parameters (PureCN 2.13.2).
INFO [2025-03-24 20:56:04] ------------------------------------------------------------
INFO [2025-03-24 20:56:04] PureCN 2.13.2
INFO [2025-03-24 20:56:04] ------------------------------------------------------------
INFO [2025-03-24 20:56:04] Loading coverage files...
FATAL [2025-03-24 20:56:04] Missing tumor.coverage.file requires seg.file or log.ratio and
FATAL [2025-03-24 20:56:04] interval.file.
FATAL [2025-03-24 20:56:04]
FATAL [2025-03-24 20:56:04] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:56:04] parameters (PureCN 2.13.2).
INFO [2025-03-24 20:56:04] ------------------------------------------------------------
INFO [2025-03-24 20:56:04] PureCN 2.13.2
INFO [2025-03-24 20:56:04] ------------------------------------------------------------
INFO [2025-03-24 20:56:04] ------------------------------------------------------------
INFO [2025-03-24 20:56:04] PureCN 2.13.2
INFO [2025-03-24 20:56:04] ------------------------------------------------------------
INFO [2025-03-24 20:56:04] Loading coverage files...
FATAL [2025-03-24 20:56:05] Interval files in normal and tumor different.
FATAL [2025-03-24 20:56:05]
FATAL [2025-03-24 20:56:05] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:56:05] parameters (PureCN 2.13.2).
INFO [2025-03-24 20:56:05] ------------------------------------------------------------
INFO [2025-03-24 20:56:05] PureCN 2.13.2
INFO [2025-03-24 20:56:05] ------------------------------------------------------------
INFO [2025-03-24 20:56:05] Loading coverage files...
INFO [2025-03-24 20:56:05] Mean target coverages: 0X (tumor) 99X (normal).
WARN [2025-03-24 20:56:05] Large difference in coverage of tumor and normal.
FATAL [2025-03-24 20:56:05] No finite intervals.
FATAL [2025-03-24 20:56:05]
FATAL [2025-03-24 20:56:05] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:56:05] parameters (PureCN 2.13.2).
INFO [2025-03-24 20:56:05] ------------------------------------------------------------
INFO [2025-03-24 20:56:05] PureCN 2.13.2
INFO [2025-03-24 20:56:05] ------------------------------------------------------------
INFO [2025-03-24 20:56:05] Loading coverage files...
INFO [2025-03-24 20:56:05] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-03-24 20:56:05] Allosome coverage missing, cannot determine sex.
WARN [2025-03-24 20:56:05] Allosome coverage missing, cannot determine sex.
INFO [2025-03-24 20:56:05] Removing 228 intervals with missing log.ratio.
INFO [2025-03-24 20:56:05] Removing 22 small (< 5bp) intervals.
INFO [2025-03-24 20:56:05] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-03-24 20:56:05] No normalDB provided. Provide one for better results.
INFO [2025-03-24 20:56:05] Removing 1724 low count (< 100 total reads) intervals.
INFO [2025-03-24 20:56:05] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-03-24 20:56:05] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-03-24 20:56:05] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-03-24 20:56:05] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-03-24 20:56:05] Loading VCF...
INFO [2025-03-24 20:56:05] Found 127 variants in VCF file.
INFO [2025-03-24 20:56:05] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-03-24 20:56:05] LIB-02240e4 is tumor in VCF file.
INFO [2025-03-24 20:56:05] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-03-24 20:56:05] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-03-24 20:56:05] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-03-24 20:56:05] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-03-24 20:56:05] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-03-24 20:56:06] 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 .Internal(get0(x, envir, mode, inherits, ifnotfound)) :
closing unused connection 4 (/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/PureCN/extdata/example_allelic_counts_empty.tsv)
2: In for (i in seq_len(n)) { :
closing unused connection 5 (/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpKtTX4g/filed7e627d52368.tsv)
3: In for (i in seq_len(n)) { :
closing unused connection 4 (/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/PureCN/extdata/example_gatk4_denoised_cr.tsv.gz)
FATAL [2025-03-24 20:56:06] Could not import snp.blacklist
FATAL [2025-03-24 20:56:06] /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/PureCN/extdata/example_normal.txt.gz:Error
FATAL [2025-03-24 20:56:06] in FileForFormat(resource(con), fileFormat(con)) : Format 'txt'
FATAL [2025-03-24 20:56:06] unsupported
FATAL [2025-03-24 20:56:06]
FATAL [2025-03-24 20:56:06] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:56:06] parameters (PureCN 2.13.2).
INFO [2025-03-24 20:56:06] ------------------------------------------------------------
INFO [2025-03-24 20:56:06] PureCN 2.13.2
INFO [2025-03-24 20:56:06] ------------------------------------------------------------
INFO [2025-03-24 20:56:06] Loading coverage files...
INFO [2025-03-24 20:56:06] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-03-24 20:56:06] Allosome coverage missing, cannot determine sex.
WARN [2025-03-24 20:56:06] Allosome coverage missing, cannot determine sex.
INFO [2025-03-24 20:56:06] Removing 228 intervals with missing log.ratio.
INFO [2025-03-24 20:56:06] Removing 22 small (< 5bp) intervals.
INFO [2025-03-24 20:56:06] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-03-24 20:56:06] No normalDB provided. Provide one for better results.
INFO [2025-03-24 20:56:06] Removing 233 low coverage (< 15.0000X) intervals.
INFO [2025-03-24 20:56:06] Using 9547 intervals (9547 on-target, 0 off-target).
INFO [2025-03-24 20:56:06] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-03-24 20:56:06] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-03-24 20:56:06] Loading VCF...
INFO [2025-03-24 20:56:06] Found 127 variants in VCF file.
INFO [2025-03-24 20:56:06] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-03-24 20:56:06] LIB-02240e4 is tumor in VCF file.
INFO [2025-03-24 20:56:06] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-03-24 20:56:06] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-03-24 20:56:06] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-03-24 20:56:06] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-03-24 20:56:06] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-03-24 20:56:06] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-03-24 20:56:06] Total size of targeted genomic region: 1.63Mb (2.58Mb with 50bp padding).
INFO [2025-03-24 20:56:06] 1.0% of targets contain variants.
INFO [2025-03-24 20:56:06] Removing 2 variants outside intervals.
INFO [2025-03-24 20:56:06] Found SOMATIC annotation in VCF.
INFO [2025-03-24 20:56:06] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-03-24 20:56:06] Found SOMATIC annotation in VCF. Setting mapping bias to 0.973.
INFO [2025-03-24 20:56:06] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-03-24 20:56:06] Sample sex: ?
INFO [2025-03-24 20:56:06] Segmenting data...
INFO [2025-03-24 20:56:06] Loading pre-computed boundaries for DNAcopy...
INFO [2025-03-24 20:56:06] Setting undo.SD parameter to 1.000000.
INFO [2025-03-24 20:56:07] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-03-24 20:56:07] Found 54 segments with median size of 24.88Mb.
INFO [2025-03-24 20:56:07] Using 123 variants.
INFO [2025-03-24 20:56:07] Mean standard deviation of log-ratios: 0.37 (MAPD: 0.32)
INFO [2025-03-24 20:56:07] 2D-grid search of purity and ploidy...
INFO [2025-03-24 20:56:07] Local optima: 0.62/1.9, 0.3/1.9, 0.32/2
INFO [2025-03-24 20:56:07] Testing local optimum 1/3 at purity 0.62 and total ploidy 1.90...
INFO [2025-03-24 20:56:08] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-03-24 20:56:08] Recalibrating log-ratios...
INFO [2025-03-24 20:56:08] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-03-24 20:56:08] Recalibrating log-ratios...
INFO [2025-03-24 20:56:08] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-03-24 20:56:08] Recalibrating log-ratios...
INFO [2025-03-24 20:56:08] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-03-24 20:56:08] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-03-24 20:56:08] Recalibrating log-ratios...
INFO [2025-03-24 20:56:08] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-03-24 20:56:08] Recalibrating log-ratios...
INFO [2025-03-24 20:56:08] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-03-24 20:56:08] Recalibrating log-ratios...
INFO [2025-03-24 20:56:08] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-03-24 20:56:08] Skipping 1 solutions that converged to the same optima.
INFO [2025-03-24 20:56:08] Skipping 1 solutions exceeding max.non.clonal (0.20): 0.3/1.9 (purity/tumor ploidy)
INFO [2025-03-24 20:56:08] Fitting variants with beta model for local optimum 1/3...
INFO [2025-03-24 20:56:08] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01.
INFO [2025-03-24 20:56:09] Optimized purity: 0.65
INFO [2025-03-24 20:56:09] Done.
INFO [2025-03-24 20:56:09] ------------------------------------------------------------
INFO [2025-03-24 20:56:09] ------------------------------------------------------------
INFO [2025-03-24 20:56:09] PureCN 2.13.2
INFO [2025-03-24 20:56:09] ------------------------------------------------------------
INFO [2025-03-24 20:56:09] Loading coverage files...
INFO [2025-03-24 20:56:10] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-03-24 20:56:10] Allosome coverage missing, cannot determine sex.
WARN [2025-03-24 20:56:10] Allosome coverage missing, cannot determine sex.
INFO [2025-03-24 20:56:10] Removing 228 intervals with missing log.ratio.
INFO [2025-03-24 20:56:10] Removing 22 small (< 5bp) intervals.
INFO [2025-03-24 20:56:10] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-03-24 20:56:10] No normalDB provided. Provide one for better results.
INFO [2025-03-24 20:56:10] Removing 1724 low count (< 100 total reads) intervals.
INFO [2025-03-24 20:56:10] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-03-24 20:56:10] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-03-24 20:56:10] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-03-24 20:56:10] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-03-24 20:56:10] Loading VCF...
INFO [2025-03-24 20:56:10] Found 127 variants in VCF file.
WARN [2025-03-24 20:56:10] DP FORMAT field contains NAs. Removing 3 variants.
WARN [2025-03-24 20:56:10] DB INFO flag contains NAs
INFO [2025-03-24 20:56:10] 119 (96.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-03-24 20:56:10] LIB-02240e4 is tumor in VCF file.
INFO [2025-03-24 20:56:10] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-03-24 20:56:10] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-03-24 20:56:10] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-03-24 20:56:10] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-03-24 20:56:10] Removing 1 variants with AF < 0.030 or AF >= 0.970 or insufficient supporting reads or depth < 15.
INFO [2025-03-24 20:56:10] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding).
INFO [2025-03-24 20:56:10] 1.2% of targets contain variants.
INFO [2025-03-24 20:56:10] Setting somatic prior probabilities for likely germline hits to 0.000500 or to 0.500000 otherwise.
INFO [2025-03-24 20:56:10] Excluding 5 novel or poor quality variants from segmentation.
INFO [2025-03-24 20:56:10] Sample sex: ?
INFO [2025-03-24 20:56:10] Segmenting data...
INFO [2025-03-24 20:56:10] Loading pre-computed boundaries for DNAcopy...
INFO [2025-03-24 20:56:10] Setting undo.SD parameter to 1.000000.
Setting multi-figure configuration
INFO [2025-03-24 20:56:11] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-03-24 20:56:11] Found 59 segments with median size of 17.67Mb.
INFO [2025-03-24 20:56:11] Using 123 variants.
INFO [2025-03-24 20:56:11] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-03-24 20:56:11] 2D-grid search of purity and ploidy...
INFO [2025-03-24 20:56:11] Local optima: 0.62/1.9, 0.3/1.9, 0.32/2
INFO [2025-03-24 20:56:11] Testing local optimum 1/3 at purity 0.62 and total ploidy 1.90...
INFO [2025-03-24 20:56:11] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-03-24 20:56:11] Recalibrating log-ratios...
INFO [2025-03-24 20:56:11] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-03-24 20:56:12] Recalibrating log-ratios...
INFO [2025-03-24 20:56:12] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-03-24 20:56:12] Recalibrating log-ratios...
INFO [2025-03-24 20:56:12] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2025-03-24 20:56:12] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-03-24 20:56:12] Recalibrating log-ratios...
INFO [2025-03-24 20:56:12] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-03-24 20:56:12] Recalibrating log-ratios...
INFO [2025-03-24 20:56:12] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-03-24 20:56:12] Recalibrating log-ratios...
INFO [2025-03-24 20:56:12] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2025-03-24 20:56:12] Skipping 2 solutions exceeding max.non.clonal (0.20): 0.3/1.9, 0.35/1.61 (purity/tumor ploidy)
INFO [2025-03-24 20:56:12] Fitting variants with beta model for local optimum 1/3...
INFO [2025-03-24 20:56:12] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2025-03-24 20:56:13] Optimized purity: 0.65
INFO [2025-03-24 20:56:13] Done.
INFO [2025-03-24 20:56:13] ------------------------------------------------------------
INFO [2025-03-24 20:56:13] ------------------------------------------------------------
INFO [2025-03-24 20:56:13] PureCN 2.13.2
INFO [2025-03-24 20:56:13] ------------------------------------------------------------
INFO [2025-03-24 20:56:13] Loading coverage files...
INFO [2025-03-24 20:56:13] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-03-24 20:56:13] Allosome coverage missing, cannot determine sex.
WARN [2025-03-24 20:56:13] Allosome coverage missing, cannot determine sex.
INFO [2025-03-24 20:56:13] No Gene column in interval.file. You won't get gene-level calls.
INFO [2025-03-24 20:56:14] Removing 228 intervals with missing log.ratio.
INFO [2025-03-24 20:56:14] Removing 15 low/high GC targets.
INFO [2025-03-24 20:56:14] Removing 21 small (< 5bp) intervals.
INFO [2025-03-24 20:56:14] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-03-24 20:56:14] No normalDB provided. Provide one for better results.
INFO [2025-03-24 20:56:14] Removing 1718 low count (< 100 total reads) intervals.
INFO [2025-03-24 20:56:14] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-03-24 20:56:14] Removing 36 low mappability intervals.
INFO [2025-03-24 20:56:14] Using 8006 intervals (8006 on-target, 0 off-target).
INFO [2025-03-24 20:56:14] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-03-24 20:56:14] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio).
INFO [2025-03-24 20:56:14] Loading VCF...
INFO [2025-03-24 20:56:14] Found 127 variants in VCF file.
INFO [2025-03-24 20:56:14] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-03-24 20:56:14] LIB-02240e4 is tumor in VCF file.
INFO [2025-03-24 20:56:14] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-03-24 20:56:14] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-03-24 20:56:14] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-03-24 20:56:14] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-03-24 20:56:14] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-03-24 20:56:14] Removing 1 variants with AF < 0.030 or AF >= Inf or insufficient supporting reads or depth < 15.
INFO [2025-03-24 20:56:14] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding).
INFO [2025-03-24 20:56:14] 1.2% of targets contain variants.
INFO [2025-03-24 20:56:14] Removing 11 variants outside intervals.
INFO [2025-03-24 20:56:14] Found SOMATIC annotation in VCF.
INFO [2025-03-24 20:56:14] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-03-24 20:56:14] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970.
INFO [2025-03-24 20:56:14] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-03-24 20:56:14] Sample sex: ?
INFO [2025-03-24 20:56:14] Segmenting data...
INFO [2025-03-24 20:56:14] MAPD of 114 allelic fractions: 0.14 (0.15 adjusted).
INFO [2025-03-24 20:56:14] Using unweighted PSCBS.
INFO [2025-03-24 20:56:14] Setting undo.SD parameter to 1.000000.
INFO [2025-03-24 20:56:20] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-03-24 20:56:20] Found 71 segments with median size of 27.72Mb.
INFO [2025-03-24 20:56:20] Using 114 variants.
INFO [2025-03-24 20:56:20] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-03-24 20:56:20] 2D-grid search of purity and ploidy...
INFO [2025-03-24 20:56:20] Local optima: 0.65/1.8, 0.38/2.2
INFO [2025-03-24 20:56:20] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2025-03-24 20:56:20] Recalibrating log-ratios...
INFO [2025-03-24 20:56:20] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2025-03-24 20:56:20] Recalibrating log-ratios...
INFO [2025-03-24 20:56:20] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2025-03-24 20:56:20] Recalibrating log-ratios...
INFO [2025-03-24 20:56:20] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2025-03-24 20:56:21] Testing local optimum 2/2 at purity 0.38 and total ploidy 2.20...
INFO [2025-03-24 20:56:21] Skipping 1 solutions exceeding max.non.clonal (0.20): 0.65/2.04 (purity/tumor ploidy)
INFO [2025-03-24 20:56:21] Fitting variants with beta model for local optimum 2/2...
INFO [2025-03-24 20:56:21] Fitting variants for purity 0.40, tumor ploidy 2.53 and contamination 0.01.
INFO [2025-03-24 20:56:22] Optimized purity: 0.40
INFO [2025-03-24 20:56:22] Done.
INFO [2025-03-24 20:56:22] ------------------------------------------------------------
FATAL [2025-03-24 20:56:22] This function requires gene-level calls. Please add a column 'Gene'
FATAL [2025-03-24 20:56:22] containing gene symbols to the interval.file.
FATAL [2025-03-24 20:56:22]
FATAL [2025-03-24 20:56:22] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:56:22] parameters (PureCN 2.13.2).
INFO [2025-03-24 20:56:23] ------------------------------------------------------------
INFO [2025-03-24 20:56:23] PureCN 2.13.2
INFO [2025-03-24 20:56:23] ------------------------------------------------------------
INFO [2025-03-24 20:56:23] Loading coverage files...
INFO [2025-03-24 20:56:23] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-03-24 20:56:23] Allosome coverage missing, cannot determine sex.
WARN [2025-03-24 20:56:23] Allosome coverage missing, cannot determine sex.
INFO [2025-03-24 20:56:23] Removing 228 intervals with missing log.ratio.
INFO [2025-03-24 20:56:23] Removing 22 small (< 5bp) intervals.
INFO [2025-03-24 20:56:23] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-03-24 20:56:23] No normalDB provided. Provide one for better results.
INFO [2025-03-24 20:56:23] Removing 1724 low count (< 100 total reads) intervals.
INFO [2025-03-24 20:56:23] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-03-24 20:56:23] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2025-03-24 20:56:23] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-03-24 20:56:23] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-03-24 20:56:23] Loading VCF...
INFO [2025-03-24 20:56:23] Found 127 variants in VCF file.
INFO [2025-03-24 20:56:23] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
FATAL [2025-03-24 20:56:23] Different chromosome names in coverage and VCF.
FATAL [2025-03-24 20:56:23]
FATAL [2025-03-24 20:56:23] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:56:23] parameters (PureCN 2.13.2).
INFO [2025-03-24 20:56:23] ------------------------------------------------------------
INFO [2025-03-24 20:56:23] PureCN 2.13.2
INFO [2025-03-24 20:56:23] ------------------------------------------------------------
INFO [2025-03-24 20:56:23] Loading coverage files...
INFO [2025-03-24 20:56:23] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-03-24 20:56:23] Allosome coverage missing, cannot determine sex.
WARN [2025-03-24 20:56:23] Allosome coverage missing, cannot determine sex.
FATAL [2025-03-24 20:56:23] tumor.coverage.file and interval.file do not align.
FATAL [2025-03-24 20:56:23]
FATAL [2025-03-24 20:56:23] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:56:23] parameters (PureCN 2.13.2).
INFO [2025-03-24 20:56:23] ------------------------------------------------------------
INFO [2025-03-24 20:56:23] PureCN 2.13.2
INFO [2025-03-24 20:56:23] ------------------------------------------------------------
INFO [2025-03-24 20:56:23] Loading coverage files...
INFO [2025-03-24 20:56:23] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-03-24 20:56:24] Allosome coverage missing, cannot determine sex.
WARN [2025-03-24 20:56:24] Allosome coverage missing, cannot determine sex.
INFO [2025-03-24 20:56:24] Removing 228 intervals with missing log.ratio.
INFO [2025-03-24 20:56:24] Removing 15 low/high GC targets.
INFO [2025-03-24 20:56:24] Removing 21 small (< 5bp) intervals.
INFO [2025-03-24 20:56:24] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-03-24 20:56:24] No normalDB provided. Provide one for better results.
INFO [2025-03-24 20:56:24] Removing 1718 low count (< 100 total reads) intervals.
INFO [2025-03-24 20:56:24] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-03-24 20:56:24] Removing 36 low mappability intervals.
INFO [2025-03-24 20:56:24] Using 8006 intervals (8006 on-target, 0 off-target).
INFO [2025-03-24 20:56:24] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-03-24 20:56:24] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio).
INFO [2025-03-24 20:56:24] Loading VCF...
INFO [2025-03-24 20:56:24] Found 127 variants in VCF file.
INFO [2025-03-24 20:56:24] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-03-24 20:56:24] LIB-02240e4 is tumor in VCF file.
INFO [2025-03-24 20:56:24] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-03-24 20:56:24] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-03-24 20:56:24] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-03-24 20:56:24] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-03-24 20:56:24] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-03-24 20:56:24] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-03-24 20:56:24] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding).
INFO [2025-03-24 20:56:24] 1.2% of targets contain variants.
INFO [2025-03-24 20:56:24] Removing 11 variants outside intervals.
INFO [2025-03-24 20:56:24] Found SOMATIC annotation in VCF.
INFO [2025-03-24 20:56:24] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-03-24 20:56:24] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970.
INFO [2025-03-24 20:56:24] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-03-24 20:56:24] Sample sex: ?
INFO [2025-03-24 20:56:24] Segmenting data...
INFO [2025-03-24 20:56:24] Loading pre-computed boundaries for DNAcopy...
INFO [2025-03-24 20:56:24] Setting undo.SD parameter to 1.000000.
INFO [2025-03-24 20:56:25] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-03-24 20:56:25] Found 59 segments with median size of 17.67Mb.
INFO [2025-03-24 20:56:25] Using 114 variants.
INFO [2025-03-24 20:56:25] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-03-24 20:56:25] 2D-grid search of purity and ploidy...
INFO [2025-03-24 20:56:25] Local optima: 0.63/1.9
INFO [2025-03-24 20:56:25] Testing local optimum 1/1 at purity 0.63 and total ploidy 1.90...
INFO [2025-03-24 20:56:25] Fitting variants with beta model for local optimum 1/1...
INFO [2025-03-24 20:56:25] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2025-03-24 20:56:26] Optimized purity: 0.65
INFO [2025-03-24 20:56:26] Done.
INFO [2025-03-24 20:56:26] ------------------------------------------------------------
INFO [2025-03-24 20:56:26] ------------------------------------------------------------
INFO [2025-03-24 20:56:26] PureCN 2.13.2
INFO [2025-03-24 20:56:26] ------------------------------------------------------------
INFO [2025-03-24 20:56:26] Loading coverage files...
INFO [2025-03-24 20:56:26] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2025-03-24 20:56:26] Allosome coverage missing, cannot determine sex.
WARN [2025-03-24 20:56:26] Allosome coverage missing, cannot determine sex.
INFO [2025-03-24 20:56:27] Removing 228 intervals with missing log.ratio.
INFO [2025-03-24 20:56:27] Removing 15 low/high GC targets.
INFO [2025-03-24 20:56:27] Removing 21 small (< 5bp) intervals.
INFO [2025-03-24 20:56:27] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-03-24 20:56:27] No normalDB provided. Provide one for better results.
INFO [2025-03-24 20:56:27] Removing 1718 low count (< 100 total reads) intervals.
INFO [2025-03-24 20:56:27] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2025-03-24 20:56:27] Removing 36 low mappability intervals.
INFO [2025-03-24 20:56:27] Using 8006 intervals (8006 on-target, 0 off-target).
INFO [2025-03-24 20:56:27] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-03-24 20:56:27] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio).
INFO [2025-03-24 20:56:27] Loading VCF...
INFO [2025-03-24 20:56:27] Found 127 variants in VCF file.
INFO [2025-03-24 20:56:27] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-03-24 20:56:27] LIB-02240e4 is tumor in VCF file.
INFO [2025-03-24 20:56:27] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-03-24 20:56:27] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-03-24 20:56:27] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-03-24 20:56:27] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-03-24 20:56:27] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-03-24 20:56:27] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-03-24 20:56:27] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding).
INFO [2025-03-24 20:56:27] 1.2% of targets contain variants.
INFO [2025-03-24 20:56:27] Removing 11 variants outside intervals.
INFO [2025-03-24 20:56:27] Found SOMATIC annotation in VCF.
INFO [2025-03-24 20:56:27] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-03-24 20:56:27] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970.
INFO [2025-03-24 20:56:27] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-03-24 20:56:27] Sample sex: ?
INFO [2025-03-24 20:56:27] Segmenting data...
INFO [2025-03-24 20:56:27] Loading pre-computed boundaries for DNAcopy...
INFO [2025-03-24 20:56:27] Setting undo.SD parameter to 1.000000.
INFO [2025-03-24 20:56:28] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-03-24 20:56:28] Found 59 segments with median size of 17.67Mb.
INFO [2025-03-24 20:56:28] Using 114 variants.
INFO [2025-03-24 20:56:28] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2025-03-24 20:56:28] 2D-grid search of purity and ploidy...
INFO [2025-03-24 20:56:28] Local optima: 0.63/1.9
INFO [2025-03-24 20:56:28] Testing local optimum 1/1 at purity 0.63 and total ploidy 1.90...
INFO [2025-03-24 20:56:28] Fitting variants with beta model for local optimum 1/1...
WARN [2025-03-24 20:56:28] Some gene symbols found on multiple chromosomes. Use of approved symbols suggested.
INFO [2025-03-24 20:56:28] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2025-03-24 20:56:29] Optimized purity: 0.65
INFO [2025-03-24 20:56:29] Done.
INFO [2025-03-24 20:56:29] ------------------------------------------------------------
FATAL [2025-03-24 20:56:29] chr1 not valid chromosome name(s). Valid names are:
FATAL [2025-03-24 20:56:29] 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22
FATAL [2025-03-24 20:56:29]
FATAL [2025-03-24 20:56:29] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:56:29] parameters (PureCN 2.13.2).
INFO [2025-03-24 20:56:29] ------------------------------------------------------------
INFO [2025-03-24 20:56:29] PureCN 2.13.2
INFO [2025-03-24 20:56:29] ------------------------------------------------------------
INFO [2025-03-24 20:56:29] Loading coverage files...
WARN [2025-03-24 20:56:30] Provided sampleid (Sample2) does not match Sample1 found in segmentation.
WARN [2025-03-24 20:56:30] Allosome coverage missing, cannot determine sex.
WARN [2025-03-24 20:56:30] Allosome coverage missing, cannot determine sex.
INFO [2025-03-24 20:56:30] Removing 10 intervals with missing log.ratio.
INFO [2025-03-24 20:56:30] Using 10039 intervals (10039 on-target, 0 off-target).
INFO [2025-03-24 20:56:30] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-03-24 20:56:30] Loading VCF...
INFO [2025-03-24 20:56:30] Found 127 variants in VCF file.
INFO [2025-03-24 20:56:30] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-03-24 20:56:30] LIB-02240e4 is tumor in VCF file.
INFO [2025-03-24 20:56:30] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-03-24 20:56:30] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-03-24 20:56:30] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-03-24 20:56:30] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-03-24 20:56:30] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-03-24 20:56:30] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-03-24 20:56:30] Total size of targeted genomic region: 1.71Mb (2.70Mb with 50bp padding).
INFO [2025-03-24 20:56:30] 1.0% of targets contain variants.
INFO [2025-03-24 20:56:30] Removing 0 variants outside intervals.
INFO [2025-03-24 20:56:30] Found SOMATIC annotation in VCF.
INFO [2025-03-24 20:56:30] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-03-24 20:56:30] Found SOMATIC annotation in VCF. Setting mapping bias to 0.976.
INFO [2025-03-24 20:56:30] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-03-24 20:56:30] Sample sex: ?
INFO [2025-03-24 20:56:30] Segmenting data...
INFO [2025-03-24 20:56:30] Loaded provided segmentation file example_seg.txt (format DNAcopy).
WARN [2025-03-24 20:56:30] Provided sampleid (Sample2) does not match Sample1 found in segmentation.
INFO [2025-03-24 20:56:30] Re-centering provided segment means (offset -0.0033).
INFO [2025-03-24 20:56:30] Loading pre-computed boundaries for DNAcopy...
INFO [2025-03-24 20:56:30] Setting undo.SD parameter to 0.000000.
Setting multi-figure configuration
INFO [2025-03-24 20:56:30] Setting prune.hclust.h parameter to 0.200000.
INFO [2025-03-24 20:56:30] Found 54 segments with median size of 24.88Mb.
INFO [2025-03-24 20:56:30] Using 125 variants.
INFO [2025-03-24 20:56:30] Mean standard deviation of log-ratios: 0.40 (MAPD: 0.00)
INFO [2025-03-24 20:56:30] 2D-grid search of purity and ploidy...
INFO [2025-03-24 20:56:31] Local optima: 0.6/1.9
INFO [2025-03-24 20:56:31] Testing local optimum 1/1 at purity 0.60 and total ploidy 1.90...
INFO [2025-03-24 20:56:31] Fitting variants with beta model for local optimum 1/1...
INFO [2025-03-24 20:56:31] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01.
INFO [2025-03-24 20:56:32] Optimized purity: 0.65
INFO [2025-03-24 20:56:32] Done.
INFO [2025-03-24 20:56:32] ------------------------------------------------------------
WARN [2025-03-24 20:56:33] Allosome coverage missing, cannot determine sex.
WARN [2025-03-24 20:56:33] Allosome coverage missing, cannot determine sex.
Setting multi-figure configuration
FATAL [2025-03-24 20:56:35] Segmentation file expected with colnames ID, chrom, loc.start, loc.end,
FATAL [2025-03-24 20:56:35] num.mark, seg.mean
FATAL [2025-03-24 20:56:35]
FATAL [2025-03-24 20:56:35] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:56:35] parameters (PureCN 2.13.2).
FATAL [2025-03-24 20:56:35] seg.file contains multiple samples and sampleid missing.
FATAL [2025-03-24 20:56:35]
FATAL [2025-03-24 20:56:35] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:56:35] parameters (PureCN 2.13.2).
FATAL [2025-03-24 20:56:35] seg.file contains multiple samples and sampleid does not match any.
FATAL [2025-03-24 20:56:35]
FATAL [2025-03-24 20:56:35] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:56:35] parameters (PureCN 2.13.2).
WARN [2025-03-24 20:56:35] Allosome coverage missing, cannot determine sex.
WARN [2025-03-24 20:56:35] Allosome coverage missing, cannot determine sex.
WARN [2025-03-24 20:56:38] Allosome coverage missing, cannot determine sex.
WARN [2025-03-24 20:56:38] Allosome coverage missing, cannot determine sex.
WARN [2025-03-24 20:56:38] Provided sampleid (example_tumor.txt.gz) does not match Sample1 found in segmentation.
WARN [2025-03-24 20:56:39] Allosome coverage missing, cannot determine sex.
WARN [2025-03-24 20:56:39] Allosome coverage missing, cannot determine sex.
WARN [2025-03-24 20:56:39] No normalDB provided. Provide one for better results.
WARN [2025-03-24 20:56:42] Allosome coverage missing, cannot determine sex.
WARN [2025-03-24 20:56:42] Allosome coverage missing, cannot determine sex.
WARN [2025-03-24 20:56:43] Provided sampleid (Sample.1) does not match Sample1 found in segmentation.
Setting multi-figure configuration
WARN [2025-03-24 20:56:45] Allosome coverage missing, cannot determine sex.
WARN [2025-03-24 20:56:45] Allosome coverage missing, cannot determine sex.
WARN [2025-03-24 20:56:45] No normalDB provided. Provide one for better results.
WARN [2025-03-24 20:56:45] Sampleid looks like a normal in VCF, not like a tumor.
WARN [2025-03-24 20:56:47] Allosome coverage missing, cannot determine sex.
WARN [2025-03-24 20:56:47] Allosome coverage missing, cannot determine sex.
FATAL [2025-03-24 20:56:47] normalDB not a valid normalDB object. Use createNormalDatabase to
FATAL [2025-03-24 20:56:47] create one.
FATAL [2025-03-24 20:56:47]
FATAL [2025-03-24 20:56:47] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:56:47] parameters (PureCN 2.13.2).
WARN [2025-03-24 20:56:48] You are likely not using the correct baits file!
WARN [2025-03-24 20:56:48] Allosome coverage missing, cannot determine sex.
WARN [2025-03-24 20:56:48] Allosome coverage missing, cannot determine sex.
WARN [2025-03-24 20:56:48] Allosome coverage missing, cannot determine sex.
WARN [2025-03-24 20:56:48] Allosome coverage missing, cannot determine sex.
FATAL [2025-03-24 20:56:48] normalDB appears to be empty.
FATAL [2025-03-24 20:56:48]
FATAL [2025-03-24 20:56:48] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:56:48] parameters (PureCN 2.13.2).
WARN [2025-03-24 20:56:49] Allosome coverage missing, cannot determine sex.
WARN [2025-03-24 20:56:49] Allosome coverage missing, cannot determine sex.
WARN [2025-03-24 20:56:49] Intervals in coverage and interval.file have conflicting on/off-target annotation.
WARN [2025-03-24 20:56:52] Allosome coverage missing, cannot determine sex.
WARN [2025-03-24 20:56:52] Allosome coverage missing, cannot determine sex.
FATAL [2025-03-24 20:56:53] Seqlevels missing in provided segmentation: 6
FATAL [2025-03-24 20:56:53]
FATAL [2025-03-24 20:56:53] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:56:53] parameters (PureCN 2.13.2).
sh: gatk: command not found
WARN [2025-03-24 20:56:53] Cannot find gatk binary in path.
WARN [2025-03-24 20:56:53] Allosome coverage missing, cannot determine sex.
WARN [2025-03-24 20:56:53] Allosome coverage missing, cannot determine sex.
WARN [2025-03-24 20:56:53] No normalDB provided. Provide one for better results.
FATAL [2025-03-24 20:56:53] segmentationHclust requires an input segmentation.
FATAL [2025-03-24 20:56:53]
FATAL [2025-03-24 20:56:53] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:56:53] parameters (PureCN 2.13.2).
WARN [2025-03-24 20:56:54] Allosome coverage missing, cannot determine sex.
WARN [2025-03-24 20:56:54] Allosome coverage missing, cannot determine sex.
WARN [2025-03-24 20:56:54] No normalDB provided. Provide one for better results.
FATAL [2025-03-24 20:57:02] The normal.panel.vcf.file contains only a single sample.
FATAL [2025-03-24 20:57:02]
FATAL [2025-03-24 20:57:02] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:57:02] parameters (PureCN 2.13.2).
FATAL [2025-03-24 20:57:03] mapping.bias.file must be a file with *.rds suffix.
FATAL [2025-03-24 20:57:03]
FATAL [2025-03-24 20:57:03] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:57:03] parameters (PureCN 2.13.2).
Failed with error: 'there is no package called 'genomicsdb''
FATAL [2025-03-24 20:57:03] min.normals (0) must be >= 1.
FATAL [2025-03-24 20:57:03]
FATAL [2025-03-24 20:57:03] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:57:03] parameters (PureCN 2.13.2).
FATAL [2025-03-24 20:57:03] min.normals (10) cannot be larger than min.normals.assign.betafit (3).
FATAL [2025-03-24 20:57:03]
FATAL [2025-03-24 20:57:03] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:57:03] parameters (PureCN 2.13.2).
FATAL [2025-03-24 20:57:03] min.normals.assign.betafit (10) cannot be larger than
FATAL [2025-03-24 20:57:03] min.normals.betafit (7).
FATAL [2025-03-24 20:57:03]
FATAL [2025-03-24 20:57:03] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:57:03] parameters (PureCN 2.13.2).
FATAL [2025-03-24 20:57:03] min.normals.betafit (20) cannot be larger than
FATAL [2025-03-24 20:57:03] min.normals.position.specific.fit (10).
FATAL [2025-03-24 20:57:03]
FATAL [2025-03-24 20:57:03] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:57:03] parameters (PureCN 2.13.2).
FATAL [2025-03-24 20:57:03] min.betafit.rho not within expected range or format.
FATAL [2025-03-24 20:57:03]
FATAL [2025-03-24 20:57:03] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:57:03] parameters (PureCN 2.13.2).
FATAL [2025-03-24 20:57:03] max.betafit.rho not within expected range or format.
FATAL [2025-03-24 20:57:03]
FATAL [2025-03-24 20:57:03] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:57:03] parameters (PureCN 2.13.2).
FATAL [2025-03-24 20:57:03] min.betafit.rho (0.9) cannot be larger than max.betafit.rho (0.2).
FATAL [2025-03-24 20:57:03]
FATAL [2025-03-24 20:57:03] This is most likely a user error due to invalid input data or
FATAL [2025-03-24 20:57:03] parameters (PureCN 2.13.2).
[ FAIL 0 | WARN 13 | SKIP 2 | PASS 405 ]
══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• gatk binary > 4.1.7.0 required (1): 'test_segmentation.R:25:4'
• genomicsdb required (1): 'test_setMappingBiasVcf.R:45:5'
[ FAIL 0 | WARN 13 | SKIP 2 | PASS 405 ]
>
> proc.time()
user system elapsed
137.910 5.422 130.661
PureCN.Rcheck/PureCN-Ex.timings
| name | user | system | elapsed | |
| adjustLogRatio | 0.788 | 0.012 | 0.803 | |
| annotateTargets | 2.522 | 0.094 | 2.619 | |
| bootstrapResults | 0.211 | 0.019 | 0.230 | |
| calculateBamCoverageByInterval | 0.067 | 0.001 | 0.070 | |
| calculateLogRatio | 0.235 | 0.011 | 0.247 | |
| calculateMappingBiasGatk4 | 0 | 0 | 0 | |
| calculateMappingBiasVcf | 0.645 | 0.019 | 0.666 | |
| calculatePowerDetectSomatic | 0.476 | 0.005 | 0.481 | |
| calculateTangentNormal | 1.459 | 0.023 | 1.485 | |
| callAlterations | 0.055 | 0.003 | 0.057 | |
| callAlterationsFromSegmentation | 0.534 | 0.013 | 0.535 | |
| callAmplificationsInLowPurity | 12.911 | 0.212 | 12.948 | |
| callCIN | 0.084 | 0.002 | 0.087 | |
| callLOH | 0.073 | 0.001 | 0.075 | |
| callMutationBurden | 0.544 | 0.013 | 0.559 | |
| centromeres | 0.001 | 0.001 | 0.001 | |
| correctCoverageBias | 0.583 | 0.014 | 0.600 | |
| createCurationFile | 0.152 | 0.003 | 0.154 | |
| createNormalDatabase | 0.838 | 0.013 | 0.851 | |
| filterIntervals | 7.486 | 0.177 | 7.293 | |
| filterVcfBasic | 0.223 | 0.003 | 0.226 | |
| filterVcfMuTect | 0.236 | 0.004 | 0.253 | |
| filterVcfMuTect2 | 0.235 | 0.003 | 0.244 | |
| findFocal | 3.666 | 0.028 | 3.736 | |
| findHighQualitySNPs | 0.578 | 0.008 | 0.588 | |
| getSexFromCoverage | 0.097 | 0.005 | 0.102 | |
| getSexFromVcf | 0.096 | 0.003 | 0.100 | |
| plotAbs | 0.090 | 0.004 | 0.094 | |
| poolCoverage | 0.227 | 0.010 | 0.242 | |
| predictSomatic | 0.178 | 0.003 | 0.183 | |
| preprocessIntervals | 0.209 | 0.004 | 0.214 | |
| processMultipleSamples | 0.868 | 0.020 | 0.892 | |
| readAllelicCountsFile | 0.201 | 0.004 | 0.212 | |
| readCoverageFile | 0.091 | 0.005 | 0.098 | |
| readCurationFile | 0.090 | 0.004 | 0.093 | |
| readIntervalFile | 0.064 | 0.002 | 0.067 | |
| readLogRatioFile | 0.010 | 0.000 | 0.011 | |
| readSegmentationFile | 0.003 | 0.000 | 0.003 | |
| runAbsoluteCN | 6.100 | 0.128 | 6.259 | |
| segmentationCBS | 2.725 | 0.030 | 2.763 | |
| segmentationGATK4 | 0.001 | 0.000 | 0.001 | |
| segmentationHclust | 4.990 | 0.094 | 5.111 | |
| segmentationPSCBS | 8.767 | 0.161 | 8.950 | |
| setMappingBiasVcf | 0.107 | 0.004 | 0.111 | |
| setPriorVcf | 0.092 | 0.004 | 0.095 | |