Markus Riester
| Snapshot Date: 2024-11-08 13:40 -0500 (Fri, 08 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/PureCN |
| git_branch: RELEASE_3_20 |
| git_last_commit: 7a189a9 |
| git_last_commit_date: 2024-10-29 10:10:26 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-11-09 21:31 -0500 (Sat, 09 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4505 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4506 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4538 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4486 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
| 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 1618/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| PureCN 2.12.0 (landing page) Markus Riester
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the PureCN package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PureCN.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: PureCN |
| Version: 2.12.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PureCN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PureCN_2.12.0.tar.gz |
| StartedAt: 2024-11-09 10:18:38 -0500 (Sat, 09 Nov 2024) |
| EndedAt: 2024-11-09 10:26:59 -0500 (Sat, 09 Nov 2024) |
| EllapsedTime: 500.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: PureCN.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PureCN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PureCN_2.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/PureCN.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PureCN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PureCN’ version ‘2.12.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
NOTE
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 11.848 0.118 11.966
segmentationPSCBS 7.824 0.119 7.947
filterIntervals 6.814 0.119 6.935
runAbsoluteCN 5.458 0.107 5.565
* 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: 1 NOTE
See
‘/Users/biocbuild/bbs-3.20-bioc/meat/PureCN.Rcheck/00check.log’
for details.
PureCN.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PureCN ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘PureCN’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (PureCN)
PureCN.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(PureCN)
Loading required package: DNAcopy
Loading required package: VariantAnnotation
Loading required package: BiocGenerics
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, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
tapply, union, 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 [2024-11-09 10:25:09] Attempted adding gene symbols to intervals. Heuristics have been used to pick symbols for overlapping genes.
WARN [2024-11-09 10:25:09] Chromosome naming style of txdb file (UCSC) was different from interval file (Ensembl).
WARN [2024-11-09 10:25:11] Attempted adding gene symbols to intervals. Heuristics have been used to pick symbols for overlapping genes.
FATAL [2024-11-09 10:25:11] tumor.coverage.file and interval.file do not align.
FATAL [2024-11-09 10:25:11]
FATAL [2024-11-09 10:25:11] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:25:11] parameters (PureCN 2.12.0).
WARN [2024-11-09 10:25:11] Cannot find all contig lengths while exporting interval file.
INFO [2024-11-09 10:25:12] Processing seq1:1-21 (1/3)...
INFO [2024-11-09 10:25:12] Processing seq1:1227-1247 (2/3)...
INFO [2024-11-09 10:25:12] Processing seq2:594-614 (3/3)...
WARN [2024-11-09 10:25:13] Large potential mis-calibration of on- and off-target log2 ratios: 0.26
FATAL [2024-11-09 10:25:13] Need either f or purity and ploidy.
FATAL [2024-11-09 10:25:13]
FATAL [2024-11-09 10:25:13] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:25:13] parameters (PureCN 2.12.0).
FATAL [2024-11-09 10:25:13] f not in expected range.
FATAL [2024-11-09 10:25:13]
FATAL [2024-11-09 10:25:13] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:25:13] parameters (PureCN 2.12.0).
FATAL [2024-11-09 10:25:13] coverage not in expected range (>=2)
FATAL [2024-11-09 10:25:13]
FATAL [2024-11-09 10:25:13] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:25:13] parameters (PureCN 2.12.0).
FATAL [2024-11-09 10:25:13] purity not in expected range.
FATAL [2024-11-09 10:25:13]
FATAL [2024-11-09 10:25:13] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:25:13] parameters (PureCN 2.12.0).
FATAL [2024-11-09 10:25:13] ploidy not in expected range.
FATAL [2024-11-09 10:25:13]
FATAL [2024-11-09 10:25:13] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:25:13] parameters (PureCN 2.12.0).
FATAL [2024-11-09 10:25:13] cell.fraction not in expected range.
FATAL [2024-11-09 10:25:13]
FATAL [2024-11-09 10:25:13] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:25:13] parameters (PureCN 2.12.0).
INFO [2024-11-09 10:25:13] 576 on-target bins with low coverage in all samples.
WARN [2024-11-09 10:25:13] You are likely not using the correct baits file!
WARN [2024-11-09 10:25:13] Allosome coverage missing, cannot determine sex.
WARN [2024-11-09 10:25:13] Allosome coverage missing, cannot determine sex.
INFO [2024-11-09 10:25:13] Processing on-target regions...
INFO [2024-11-09 10:25:14] Removing 930 intervals with low coverage in normalDB.
INFO [2024-11-09 10:25:14] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2024-11-09 10:25:14] Tumor/normal noise ratio: 19.041
WARN [2024-11-09 10:25:14] Extensive noise in tumor compared to normals.
INFO [2024-11-09 10:25:27] Tumor/normal noise ratio: 19.041
WARN [2024-11-09 10:25:27] Extensive noise in tumor compared to normals.
INFO [2024-11-09 10:25:28] Using BiocParallel for parallel optimization.
FATAL [2024-11-09 10:25:32] pvalue.cutoff not within expected range or format.
FATAL [2024-11-09 10:25:32]
FATAL [2024-11-09 10:25:32] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:25:32] parameters (PureCN 2.12.0).
FATAL [2024-11-09 10:25:32] pvalue.cutoff not within expected range or format.
FATAL [2024-11-09 10:25:32]
FATAL [2024-11-09 10:25:32] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:25:32] parameters (PureCN 2.12.0).
FATAL [2024-11-09 10:25:32] percentile.cutoff not in expected range (0 to 100).
FATAL [2024-11-09 10:25:32]
FATAL [2024-11-09 10:25:32] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:25:32] parameters (PureCN 2.12.0).
FATAL [2024-11-09 10:25:32] percentile.cutoff not in expected range (0 to 100).
FATAL [2024-11-09 10:25:32]
FATAL [2024-11-09 10:25:32] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:25:32] parameters (PureCN 2.12.0).
FATAL [2024-11-09 10:25:32] purity not within expected range or format.
FATAL [2024-11-09 10:25:32]
FATAL [2024-11-09 10:25:32] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:25:32] parameters (PureCN 2.12.0).
FATAL [2024-11-09 10:25:32] purity not within expected range or format.
FATAL [2024-11-09 10:25:32]
FATAL [2024-11-09 10:25:32] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:25:32] parameters (PureCN 2.12.0).
INFO [2024-11-09 10:25:33] ------------------------------------------------------------
INFO [2024-11-09 10:25:33] PureCN 2.12.0
INFO [2024-11-09 10:25:33] ------------------------------------------------------------
INFO [2024-11-09 10:25:33] Loading coverage files...
INFO [2024-11-09 10:25:33] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2024-11-09 10:25:33] Allosome coverage missing, cannot determine sex.
WARN [2024-11-09 10:25:33] Allosome coverage missing, cannot determine sex.
INFO [2024-11-09 10:25:33] Removing 228 intervals with missing log.ratio.
INFO [2024-11-09 10:25:33] Removing 22 small (< 5bp) intervals.
INFO [2024-11-09 10:25:33] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2024-11-09 10:25:33] No normalDB provided. Provide one for better results.
INFO [2024-11-09 10:25:33] Removing 1724 low count (< 100 total reads) intervals.
INFO [2024-11-09 10:25:33] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2024-11-09 10:25:33] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2024-11-09 10:25:33] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2024-11-09 10:25:33] No interval.file provided. Cannot check for any GC-biases.
INFO [2024-11-09 10:25:33] Loading VCF...
INFO [2024-11-09 10:25:33] Found 127 variants in VCF file.
INFO [2024-11-09 10:25:33] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2024-11-09 10:25:33] LIB-02240e4 is tumor in VCF file.
INFO [2024-11-09 10:25:33] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2024-11-09 10:25:33] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2024-11-09 10:25:33] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2024-11-09 10:25:33] Base quality scores range from 29 to 35 (offset by 1)
INFO [2024-11-09 10:25:33] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2024-11-09 10:25:33] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2024-11-09 10:25:33] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding).
INFO [2024-11-09 10:25:33] 1.2% of targets contain variants.
INFO [2024-11-09 10:25:33] Removing 4 variants outside intervals.
INFO [2024-11-09 10:25:33] Found SOMATIC annotation in VCF.
INFO [2024-11-09 10:25:33] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2024-11-09 10:25:33] Found SOMATIC annotation in VCF. Setting mapping bias to 0.972.
INFO [2024-11-09 10:25:33] Excluding 0 novel or poor quality variants from segmentation.
INFO [2024-11-09 10:25:33] Sample sex: ?
INFO [2024-11-09 10:25:33] Segmenting data...
INFO [2024-11-09 10:25:33] Loading pre-computed boundaries for DNAcopy...
INFO [2024-11-09 10:25:33] Setting undo.SD parameter to 1.000000.
INFO [2024-11-09 10:25:34] Setting prune.hclust.h parameter to 0.200000.
INFO [2024-11-09 10:25:34] Found 59 segments with median size of 17.67Mb.
INFO [2024-11-09 10:25:34] Using 121 variants.
INFO [2024-11-09 10:25:34] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2024-11-09 10:25:34] 2D-grid search of purity and ploidy...
INFO [2024-11-09 10:25:34] Local optima: 0.63/1.9, 0.5/2
INFO [2024-11-09 10:25:34] Testing local optimum 1/2 at purity 0.63 and total ploidy 1.90...
INFO [2024-11-09 10:25:34] Testing local optimum 2/2 at purity 0.50 and total ploidy 2.00...
INFO [2024-11-09 10:25:35] Skipping 1 solutions that converged to the same optima.
INFO [2024-11-09 10:25:35] Fitting variants with beta model for local optimum 1/2...
INFO [2024-11-09 10:25:35] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2024-11-09 10:25:36] Optimized purity: 0.65
INFO [2024-11-09 10:25:36] Done.
INFO [2024-11-09 10:25:36] ------------------------------------------------------------
INFO [2024-11-09 10:25:36] Estimating callable regions.
FATAL [2024-11-09 10:25:36] exclude not a GRanges object.
FATAL [2024-11-09 10:25:36]
FATAL [2024-11-09 10:25:36] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:25:36] parameters (PureCN 2.12.0).
FATAL [2024-11-09 10:25:36] callable not a GRanges object.
FATAL [2024-11-09 10:25:36]
FATAL [2024-11-09 10:25:36] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:25:36] parameters (PureCN 2.12.0).
WARN [2024-11-09 10:25:39] tumor.coverage.file and interval.file do not align.
INFO [2024-11-09 10:25:39] No Gene column in interval.file. You won't get gene-level calls.
FATAL [2024-11-09 10:25:39] No gc_bias column in interval.file.
FATAL [2024-11-09 10:25:39]
FATAL [2024-11-09 10:25:39] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:25:39] parameters (PureCN 2.12.0).
FATAL [2024-11-09 10:25:39] Provided coverage is zero, most likely due to a corrupt BAM file.
FATAL [2024-11-09 10:25:39]
FATAL [2024-11-09 10:25:39] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:25:39] parameters (PureCN 2.12.0).
INFO [2024-11-09 10:25:40] No reptiming column in interval.file.
INFO [2024-11-09 10:25:41] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpBUOXhJ/file107ad6f1c898e.rds...
INFO [2024-11-09 10:25:41] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpBUOXhJ/file107ad6f1c898e.rds...
INFO [2024-11-09 10:25:41] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpBUOXhJ/file107ad6f1c898e.rds...
INFO [2024-11-09 10:25:41] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpBUOXhJ/file107ad6f1c898e.rds...
INFO [2024-11-09 10:25:41] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpBUOXhJ/file107ad6f1c898e.rds...
INFO [2024-11-09 10:25:41] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpBUOXhJ/file107ad6f1c898e.rds...
FATAL [2024-11-09 10:25:41] Purity or Ploidy not numeric or in expected range.
FATAL [2024-11-09 10:25:41]
FATAL [2024-11-09 10:25:41] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:25:41] parameters (PureCN 2.12.0).
INFO [2024-11-09 10:25:41] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpBUOXhJ/file107ad6f1c898e.rds...
INFO [2024-11-09 10:25:41] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpBUOXhJ/file107ad6f1c898e.rds...
FATAL [2024-11-09 10:25:41] 'Failed' column in
FATAL [2024-11-09 10:25:41] /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpBUOXhJ/file107ad6f1c898e.csv
FATAL [2024-11-09 10:25:41] not logical(1).
FATAL [2024-11-09 10:25:41]
FATAL [2024-11-09 10:25:41] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:25:41] parameters (PureCN 2.12.0).
INFO [2024-11-09 10:25:42] 576 on-target bins with low coverage in all samples.
WARN [2024-11-09 10:25:42] You are likely not using the correct baits file!
WARN [2024-11-09 10:25:42] Allosome coverage missing, cannot determine sex.
WARN [2024-11-09 10:25:42] Allosome coverage missing, cannot determine sex.
INFO [2024-11-09 10:25:42] Processing on-target regions...
INFO [2024-11-09 10:25:42] Removing 930 intervals with low coverage in normalDB.
INFO [2024-11-09 10:25:42] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2024-11-09 10:25:43] 576 on-target bins with low coverage in all samples.
WARN [2024-11-09 10:25:43] You are likely not using the correct baits file!
WARN [2024-11-09 10:25:43] Allosome coverage missing, cannot determine sex.
WARN [2024-11-09 10:25:43] Allosome coverage missing, cannot determine sex.
INFO [2024-11-09 10:25:43] Processing on-target regions...
INFO [2024-11-09 10:25:43] Removing 930 intervals with low coverage in normalDB.
INFO [2024-11-09 10:25:43] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2024-11-09 10:25:44] 576 on-target bins with low coverage in all samples.
WARN [2024-11-09 10:25:44] You are likely not using the correct baits file!
WARN [2024-11-09 10:25:44] Allosome coverage missing, cannot determine sex.
WARN [2024-11-09 10:25:44] Allosome coverage missing, cannot determine sex.
INFO [2024-11-09 10:25:44] Processing on-target regions...
INFO [2024-11-09 10:25:44] Removing 930 intervals with low coverage in normalDB.
INFO [2024-11-09 10:25:44] Removing 1 intervals with zero coverage in more than 3% of normalDB.
WARN [2024-11-09 10:25:44] Allosome coverage missing, cannot determine sex.
INFO [2024-11-09 10:25:44] Sample sex: NA
WARN [2024-11-09 10:25:44] Allosome coverage missing, cannot determine sex.
INFO [2024-11-09 10:25:44] Sample sex: NA
INFO [2024-11-09 10:25:44] 576 on-target bins with low coverage in all samples.
WARN [2024-11-09 10:25:44] You are likely not using the correct baits file!
WARN [2024-11-09 10:25:44] Allosome coverage missing, cannot determine sex.
WARN [2024-11-09 10:25:44] Allosome coverage missing, cannot determine sex.
FATAL [2024-11-09 10:25:44] Length of normal.coverage.files and sex different
FATAL [2024-11-09 10:25:44]
FATAL [2024-11-09 10:25:44] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:25:44] parameters (PureCN 2.12.0).
WARN [2024-11-09 10:25:46] Target intervals were not sorted.
INFO [2024-11-09 10:25:46] 560 on-target bins with low coverage in all samples.
WARN [2024-11-09 10:25:46] You are likely not using the correct baits file!
WARN [2024-11-09 10:25:46] Allosome coverage missing, cannot determine sex.
WARN [2024-11-09 10:25:46] Allosome coverage missing, cannot determine sex.
WARN [2024-11-09 10:25:46] Allosome coverage missing, cannot determine sex.
INFO [2024-11-09 10:25:46] Processing on-target regions...
INFO [2024-11-09 10:25:46] Removing 978 intervals with low coverage in normalDB.
INFO [2024-11-09 10:25:46] Removing 11 intervals with zero coverage in more than 3% of normalDB.
FATAL [2024-11-09 10:25:47] tumor.coverage.file and normalDB do not align.
FATAL [2024-11-09 10:25:47]
FATAL [2024-11-09 10:25:47] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:25:47] parameters (PureCN 2.12.0).
FATAL [2024-11-09 10:25:47] At least 2 normal.coverage.files required.
FATAL [2024-11-09 10:25:47]
FATAL [2024-11-09 10:25:47] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:25:47] parameters (PureCN 2.12.0).
INFO [2024-11-09 10:25:47] ------------------------------------------------------------
INFO [2024-11-09 10:25:47] PureCN 2.12.0
INFO [2024-11-09 10:25:47] ------------------------------------------------------------
INFO [2024-11-09 10:25:47] Loading coverage files...
INFO [2024-11-09 10:25:48] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2024-11-09 10:25:48] Allosome coverage missing, cannot determine sex.
WARN [2024-11-09 10:25:48] Allosome coverage missing, cannot determine sex.
INFO [2024-11-09 10:25:48] Removing 228 intervals with missing log.ratio.
FATAL [2024-11-09 10:25:48] normalDB incompatible with this PureCN version. Please re-run
FATAL [2024-11-09 10:25:48] NormalDB.R.
FATAL [2024-11-09 10:25:48]
FATAL [2024-11-09 10:25:48] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:25:48] parameters (PureCN 2.12.0).
FATAL [2024-11-09 10:25:48] normalDB incompatible with this PureCN version. Please re-run
FATAL [2024-11-09 10:25:48] NormalDB.R.
FATAL [2024-11-09 10:25:48]
FATAL [2024-11-09 10:25:48] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:25:48] parameters (PureCN 2.12.0).
FATAL [2024-11-09 10:25:48] normal.coverage.files with _coverage.txt and _loess.txt suffix
FATAL [2024-11-09 10:25:48] provided. Provide either only GC-normalized or raw coverage files!
FATAL [2024-11-09 10:25:48]
FATAL [2024-11-09 10:25:48] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:25:48] parameters (PureCN 2.12.0).
INFO [2024-11-09 10:25:48] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2024-11-09 10:25:48] Removing 19 low quality variants with non-offset BQ < 25.
INFO [2024-11-09 10:25:48] Base quality scores range from 24 to 35 (offset by 1)
INFO [2024-11-09 10:25:48] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS.
INFO [2024-11-09 10:25:48] Initial testing for significant sample cross-contamination: unlikely
INFO [2024-11-09 10:25:48] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2024-11-09 10:25:48] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2024-11-09 10:25:48] Removing 19 low quality variants with non-offset BQ < 25.
INFO [2024-11-09 10:25:48] Base quality scores range from 24 to 35 (offset by 1)
INFO [2024-11-09 10:25:48] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS.
INFO [2024-11-09 10:25:48] Initial testing for significant sample cross-contamination: unlikely
INFO [2024-11-09 10:25:48] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2024-11-09 10:25:48] Removing 6 blacklisted variants.
INFO [2024-11-09 10:25:48] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2024-11-09 10:25:48] Removing 19 low quality variants with non-offset BQ < 25.
INFO [2024-11-09 10:25:48] Base quality scores range from 24 to 35 (offset by 1)
INFO [2024-11-09 10:25:48] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS.
INFO [2024-11-09 10:25:48] Initial testing for significant sample cross-contamination: unlikely
INFO [2024-11-09 10:25:48] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
WARN [2024-11-09 10:25:48] MuTect stats file lacks contig and position columns.
INFO [2024-11-09 10:25:48] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2024-11-09 10:25:48] Removing 19 low quality variants with non-offset BQ < 25.
INFO [2024-11-09 10:25:48] Base quality scores range from 24 to 35 (offset by 1)
INFO [2024-11-09 10:25:49] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS.
INFO [2024-11-09 10:25:49] Initial testing for significant sample cross-contamination: unlikely
INFO [2024-11-09 10:25:49] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
WARN [2024-11-09 10:25:49] MuTect stats file and VCF file do not align perfectly. Will remove 2325 unmatched variants.
WARN [2024-11-09 10:25:49] MuTect stats file lacks failure_reasons column. Keeping all variants listed in stats file.
INFO [2024-11-09 10:25:49] Removing 0 non heterozygous (in matched normal) germline SNPs.
INFO [2024-11-09 10:25:49] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2024-11-09 10:25:49] Base quality scores range from 31 to 33 (offset by 1)
INFO [2024-11-09 10:25:49] Minimum number of supporting reads ranges from 3 to 4, depending on coverage and BQS.
INFO [2024-11-09 10:25:49] Removing 0 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2024-11-09 10:25:49] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2024-11-09 10:25:49] Base quality scores range from 7 to 35 (offset by 1)
INFO [2024-11-09 10:25:49] Minimum number of supporting reads ranges from 1 to 41, depending on coverage and BQS.
INFO [2024-11-09 10:25:49] Initial testing for significant sample cross-contamination: unlikely
INFO [2024-11-09 10:25:49] Removing 49 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2024-11-09 10:25:49] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2024-11-09 10:25:49] Base quality scores range from 7 to 35 (offset by 1)
INFO [2024-11-09 10:25:49] Minimum number of supporting reads ranges from 1 to 41, depending on coverage and BQS.
INFO [2024-11-09 10:25:49] Initial testing for significant sample cross-contamination: unlikely
INFO [2024-11-09 10:25:49] Removing 49 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2024-11-09 10:25:49] Removing 22 non heterozygous (in matched normal) germline SNPs.
WARN [2024-11-09 10:25:49] Many variants removed by min.base.quality (50) filter. You might want to lower the cutoff.
FATAL [2024-11-09 10:25:49] No variants passed filter BQ.
FATAL [2024-11-09 10:25:49]
FATAL [2024-11-09 10:25:49] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:25:49] parameters (PureCN 2.12.0).
INFO [2024-11-09 10:25:49] Found 11 variants in VCF file.
WARN [2024-11-09 10:25:49] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead.
INFO [2024-11-09 10:25:49] 1 (9.1%) variants annotated as likely germline (DB INFO flag).
INFO [2024-11-09 10:25:50] Found 11 variants in VCF file.
WARN [2024-11-09 10:25:50] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead.
INFO [2024-11-09 10:25:50] 1 (9.1%) variants annotated as likely germline (DB INFO flag).
INFO [2024-11-09 10:25:50] Found 11 variants in VCF file.
WARN [2024-11-09 10:25:50] vcf.file has no DB or POP_AF info field for membership in germline databases. Guessing it based on available dbSNP ID.
INFO [2024-11-09 10:25:50] 1 (9.1%) variants annotated as likely germline (DB INFO flag).
INFO [2024-11-09 10:25:50] Found 1000 variants in VCF file.
INFO [2024-11-09 10:25:50] Removing 2 triallelic sites.
WARN [2024-11-09 10:25:50] Having trouble guessing SOMATIC status...
WARN [2024-11-09 10:25:50] DP FORMAT field contains NAs. Removing 44 variants.
INFO [2024-11-09 10:25:50] 954 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2024-11-09 10:25:51] Found 12 variants in VCF file.
INFO [2024-11-09 10:25:51] Removing 1 triallelic sites.
WARN [2024-11-09 10:25:51] DP FORMAT field contains NAs. Removing 1 variants.
WARN [2024-11-09 10:25:51] vcf.file has no DB info field for membership in germline databases. Found and used somatic status instead.
INFO [2024-11-09 10:25:51] 8 (80.0%) variants annotated as likely germline (DB INFO flag).
WARN [2024-11-09 10:25:51] BQ FORMAT field contains NAs.
INFO [2024-11-09 10:25:51] Found 2331 variants in VCF file.
INFO [2024-11-09 10:25:51] 2282 (97.9%) variants annotated as likely germline (DB INFO flag).
INFO [2024-11-09 10:25:51] Found 2331 variants in VCF file.
INFO [2024-11-09 10:25:51] 2282 (97.9%) variants annotated as likely germline (DB INFO flag).
WARN [2024-11-09 10:25:51] Did not find base quality scores, will use global error rate of 0.0010 instead.
INFO [2024-11-09 10:25:51] Removing 21 low quality variants with non-offset BQ < 25.
INFO [2024-11-09 10:25:51] Base quality scores range from 24 to 35 (offset by 1)
INFO [2024-11-09 10:25:51] Initial testing for significant sample cross-contamination: unlikely
INFO [2024-11-09 10:25:51] Removing 89 variants with AF < 0.030 or AF >= 0.970 or insufficient supporting reads or depth < 15.
INFO [2024-11-09 10:25:51] Found 2331 variants in VCF file.
INFO [2024-11-09 10:25:52] 2282 (97.9%) variants annotated as likely germline (DB INFO flag).
WARN [2024-11-09 10:25:52] BQ FORMAT field contains NAs.
WARN [2024-11-09 10:25:52] Allosome coverage missing, cannot determine sex.
WARN [2024-11-09 10:25:52] Allosome coverage missing, cannot determine sex.
INFO [2024-11-09 10:25:52] Mean coverages: chrX: 108.58, chrY: 108.58, chr1-22: 104.87.
INFO [2024-11-09 10:25:52] Mean coverages: chrX: 108.58, chrY: 2.17, chr1-22: 104.87.
INFO [2024-11-09 10:25:52] Mean coverages: chrX: 108.58, chrY: 5.17, chr1-22: 104.87.
INFO [2024-11-09 10:25:52] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2024-11-09 10:25:52] No germline variants in VCF.
FATAL [2024-11-09 10:25:52] No solution with id hello
FATAL [2024-11-09 10:25:52]
FATAL [2024-11-09 10:25:52] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:25:52] parameters (PureCN 2.12.0).
FATAL [2024-11-09 10:25:52] No solution with id 100
FATAL [2024-11-09 10:25:52]
FATAL [2024-11-09 10:25:52] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:25:52] parameters (PureCN 2.12.0).
FATAL [2024-11-09 10:25:53] all.data and w have different lengths.
FATAL [2024-11-09 10:25:53]
FATAL [2024-11-09 10:25:53] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:25:53] parameters (PureCN 2.12.0).
INFO [2024-11-09 10:25:53] Splitting 5 large targets to an average width of 400.
WARN [2024-11-09 10:25:53] No mappability scores provided.
WARN [2024-11-09 10:25:53] No reptiming scores provided.
INFO [2024-11-09 10:25:53] Calculating GC-content...
INFO [2024-11-09 10:25:53] Splitting 5 large targets to an average width of 400.
WARN [2024-11-09 10:25:53] No mappability scores provided.
WARN [2024-11-09 10:25:53] No reptiming scores provided.
INFO [2024-11-09 10:25:53] Calculating GC-content...
INFO [2024-11-09 10:25:54] Splitting 5 large targets to an average width of 400.
INFO [2024-11-09 10:25:54] Removing 1 targets overlapping with exclude.
WARN [2024-11-09 10:25:54] No mappability scores provided.
WARN [2024-11-09 10:25:54] No reptiming scores provided.
INFO [2024-11-09 10:25:54] Calculating GC-content...
WARN [2024-11-09 10:25:54] Found small target regions (< 100bp). Will resize them.
INFO [2024-11-09 10:25:54] Splitting 5 large targets to an average width of 400.
FATAL [2024-11-09 10:25:54] off.target.padding must be negative.
FATAL [2024-11-09 10:25:54]
FATAL [2024-11-09 10:25:54] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:25:54] parameters (PureCN 2.12.0).
FATAL [2024-11-09 10:25:54] Interval coordinates should start at 1, not at 0
FATAL [2024-11-09 10:25:54]
FATAL [2024-11-09 10:25:54] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:25:54] parameters (PureCN 2.12.0).
WARN [2024-11-09 10:25:54] Found small target regions (< 100bp). Will resize them.
INFO [2024-11-09 10:25:54] Splitting 5 large targets to an average width of 400.
FATAL [2024-11-09 10:25:54] No off-target regions after filtering for mappability and
FATAL [2024-11-09 10:25:54] off.target.padding
FATAL [2024-11-09 10:25:54]
FATAL [2024-11-09 10:25:54] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:25:54] parameters (PureCN 2.12.0).
WARN [2024-11-09 10:25:54] Found small target regions (< 100bp). Will resize them.
INFO [2024-11-09 10:25:54] Splitting 5 large targets to an average width of 400.
WARN [2024-11-09 10:25:54] No mappability scores provided.
INFO [2024-11-09 10:25:54] Calculating GC-content...
WARN [2024-11-09 10:25:54] Found small target regions (< 100bp). Will resize them.
INFO [2024-11-09 10:25:54] Averaging reptiming into bins of size 200...
INFO [2024-11-09 10:25:54] Splitting 5 large targets to an average width of 400.
WARN [2024-11-09 10:25:54] No mappability scores provided.
INFO [2024-11-09 10:25:54] Calculating GC-content...
WARN [2024-11-09 10:25:54] Found small target regions (< 100bp). Will resize them.
INFO [2024-11-09 10:25:54] Splitting 6 large targets to an average width of 200.
WARN [2024-11-09 10:25:54] No mappability scores provided.
WARN [2024-11-09 10:25:54] No reptiming scores provided.
INFO [2024-11-09 10:25:54] Calculating GC-content...
WARN [2024-11-09 10:25:54] Found small target regions (< 100bp). Will resize them.
INFO [2024-11-09 10:25:54] Splitting 5 large targets to an average width of 400.
WARN [2024-11-09 10:25:54] No mappability scores provided.
WARN [2024-11-09 10:25:54] No reptiming scores provided.
INFO [2024-11-09 10:25:54] Calculating GC-content...
INFO [2024-11-09 10:25:54] Splitting 5 large targets to an average width of 400.
INFO [2024-11-09 10:25:54] Tiling off-target regions to an average width of 200000.
WARN [2024-11-09 10:25:54] No mappability scores provided.
WARN [2024-11-09 10:25:54] No reptiming scores provided.
INFO [2024-11-09 10:25:54] Calculating GC-content...
WARN [2024-11-09 10:25:54] Intervals contain off-target regions. Will not change intervals.
WARN [2024-11-09 10:25:54] No mappability scores provided.
WARN [2024-11-09 10:25:54] No reptiming scores provided.
INFO [2024-11-09 10:25:54] Calculating GC-content...
INFO [2024-11-09 10:25:54] Splitting 5 large targets to an average width of 400.
WARN [2024-11-09 10:25:54] No reptiming scores provided.
INFO [2024-11-09 10:25:54] Calculating GC-content...
WARN [2024-11-09 10:25:54] Found small target regions (< 100bp). Will resize them.
INFO [2024-11-09 10:25:54] Splitting 5 large targets to an average width of 400.
WARN [2024-11-09 10:25:54] No reptiming scores provided.
INFO [2024-11-09 10:25:54] Calculating GC-content...
WARN [2024-11-09 10:25:55] Found small target regions (< 100bp). Will resize them.
INFO [2024-11-09 10:25:55] Splitting 5 large targets to an average width of 400.
WARN [2024-11-09 10:25:55] 1 intervals without mappability score (1 on-target).
INFO [2024-11-09 10:25:55] Removing 1 intervals with low mappability score (<0.60).
WARN [2024-11-09 10:25:55] No reptiming scores provided.
INFO [2024-11-09 10:25:55] Calculating GC-content...
WARN [2024-11-09 10:25:55] Found small target regions (< 100bp). Will resize them.
INFO [2024-11-09 10:25:55] Splitting 5 large targets to an average width of 400.
INFO [2024-11-09 10:25:55] Tiling off-target regions to an average width of 200000.
WARN [2024-11-09 10:25:55] No reptiming scores provided.
INFO [2024-11-09 10:25:55] Calculating GC-content...
INFO [2024-11-09 10:25:55] Splitting 5 large targets to an average width of 400.
WARN [2024-11-09 10:25:55] No mappability scores provided.
WARN [2024-11-09 10:25:55] No reptiming scores provided.
INFO [2024-11-09 10:25:55] Calculating GC-content...
WARN [2024-11-09 10:25:55] Chromosome naming style of interval file (Ensembl) was different from reference (UCSC).
INFO [2024-11-09 10:25:55] Splitting 5 large targets to an average width of 400.
WARN [2024-11-09 10:25:55] No mappability scores provided.
WARN [2024-11-09 10:25:55] No reptiming scores provided.
INFO [2024-11-09 10:25:55] Calculating GC-content...
FATAL [2024-11-09 10:25:55] Chromosome naming style of interval file unknown, should be UCSC.
FATAL [2024-11-09 10:25:55]
FATAL [2024-11-09 10:25:55] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:25:55] parameters (PureCN 2.12.0).
WARN [2024-11-09 10:25:55] Chromosome naming style of interval file (Ensembl) was different from reference (UCSC).
WARN [2024-11-09 10:25:55] Chromosome naming style of mappability file (Ensembl) was different from reference (UCSC).
INFO [2024-11-09 10:25:55] Splitting 5 large targets to an average width of 400.
WARN [2024-11-09 10:25:55] No reptiming scores provided.
INFO [2024-11-09 10:25:55] Calculating GC-content...
WARN [2024-11-09 10:25:55] Found small target regions (< 60bp). Will resize them.
INFO [2024-11-09 10:25:55] Splitting 5 large targets to an average width of 400.
WARN [2024-11-09 10:25:55] No mappability scores provided.
WARN [2024-11-09 10:25:55] No reptiming scores provided.
INFO [2024-11-09 10:25:55] Calculating GC-content...
WARN [2024-11-09 10:25:55] Found small target regions (< 60bp). Will drop them.
INFO [2024-11-09 10:25:55] Splitting 4 large targets to an average width of 400.
WARN [2024-11-09 10:25:55] No mappability scores provided.
WARN [2024-11-09 10:25:55] No reptiming scores provided.
INFO [2024-11-09 10:25:55] Calculating GC-content...
WARN [2024-11-09 10:25:56] Found small target regions (< 200bp). Will resize them.
INFO [2024-11-09 10:25:56] Splitting 5 large targets to an average width of 400.
WARN [2024-11-09 10:25:56] No mappability scores provided.
WARN [2024-11-09 10:25:56] No reptiming scores provided.
INFO [2024-11-09 10:25:56] Calculating GC-content...
INFO [2024-11-09 10:25:56] Found 20 variants in VCF file.
INFO [2024-11-09 10:25:56] 20 (100.0%) variants annotated as likely germline (DB INFO flag).
WARN [2024-11-09 10:25:56] Did not find base quality scores, will use global error rate of 0.0010 instead.
INFO [2024-11-09 10:25:56] Found 127 variants in VCF file.
INFO [2024-11-09 10:25:56] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
WARN [2024-11-09 10:25:56] Did not find base quality scores, will use global error rate of 0.0010 instead.
INFO [2024-11-09 10:25:56] ------------------------------------------------------------
INFO [2024-11-09 10:25:56] PureCN 2.12.0
INFO [2024-11-09 10:25:56] ------------------------------------------------------------
INFO [2024-11-09 10:25:56] Loading coverage files...
INFO [2024-11-09 10:25:56] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2024-11-09 10:25:56] Allosome coverage missing, cannot determine sex.
WARN [2024-11-09 10:25:56] Allosome coverage missing, cannot determine sex.
INFO [2024-11-09 10:25:56] Removing 228 intervals with missing log.ratio.
INFO [2024-11-09 10:25:56] Removing 22 small (< 5bp) intervals.
INFO [2024-11-09 10:25:56] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2024-11-09 10:25:56] No normalDB provided. Provide one for better results.
INFO [2024-11-09 10:25:56] Removing 1724 low count (< 100 total reads) intervals.
INFO [2024-11-09 10:25:56] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2024-11-09 10:25:56] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2024-11-09 10:25:56] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2024-11-09 10:25:56] No interval.file provided. Cannot check for any GC-biases.
INFO [2024-11-09 10:25:56] Loading VCF...
INFO [2024-11-09 10:25:56] Found 127 variants in VCF file.
INFO [2024-11-09 10:25:56] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2024-11-09 10:25:57] LIB-02240e4 is tumor in VCF file.
INFO [2024-11-09 10:25:57] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2024-11-09 10:25:57] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2024-11-09 10:25:57] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2024-11-09 10:25:57] Base quality scores range from 29 to 35 (offset by 1)
INFO [2024-11-09 10:25:57] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2024-11-09 10:25:57] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2024-11-09 10:25:57] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding).
INFO [2024-11-09 10:25:57] 1.2% of targets contain variants.
INFO [2024-11-09 10:25:57] Removing 4 variants outside intervals.
INFO [2024-11-09 10:25:57] Found SOMATIC annotation in VCF.
INFO [2024-11-09 10:25:57] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2024-11-09 10:25:57] Found SOMATIC annotation in VCF. Setting mapping bias to 0.972.
INFO [2024-11-09 10:25:57] Excluding 0 novel or poor quality variants from segmentation.
INFO [2024-11-09 10:25:57] Sample sex: ?
INFO [2024-11-09 10:25:57] Segmenting data...
INFO [2024-11-09 10:25:57] Loading pre-computed boundaries for DNAcopy...
INFO [2024-11-09 10:25:57] Setting undo.SD parameter to 1.000000.
INFO [2024-11-09 10:25:57] Setting prune.hclust.h parameter to 0.200000.
INFO [2024-11-09 10:25:57] Found 59 segments with median size of 17.67Mb.
INFO [2024-11-09 10:25:57] Using 121 variants.
INFO [2024-11-09 10:25:57] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2024-11-09 10:25:57] 2D-grid search of purity and ploidy...
INFO [2024-11-09 10:25:57] Local optima: 0.65/1.8, 0.52/2
INFO [2024-11-09 10:25:57] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2024-11-09 10:25:58] Testing local optimum 2/2 at purity 0.52 and total ploidy 2.00...
INFO [2024-11-09 10:25:58] Skipping 1 solutions that converged to the same optima.
INFO [2024-11-09 10:25:58] Fitting variants with beta model for local optimum 1/2...
INFO [2024-11-09 10:25:58] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2024-11-09 10:25:59] Optimized purity: 0.65
INFO [2024-11-09 10:25:59] Done.
INFO [2024-11-09 10:25:59] ------------------------------------------------------------
FATAL [2024-11-09 10:25:59] log.ratio NULL in .writeLogRatioFileGATK4
FATAL [2024-11-09 10:25:59]
FATAL [2024-11-09 10:25:59] This runtime error might be caused by invalid input data or parameters.
FATAL [2024-11-09 10:25:59] Please report bug (PureCN 2.12.0).
INFO [2024-11-09 10:25:59] Loaded provided segmentation file example_seg.txt (format DNAcopy).
INFO [2024-11-09 10:25:59] Re-centering provided segment means (offset -0.0033).
INFO [2024-11-09 10:25:59] Loaded provided segmentation file example_gatk4_modelfinal.seg.gz (format GATK4).
WARN [2024-11-09 10:25:59] Expecting numeric chromosome names in seg.file, assuming file is properly sorted.
INFO [2024-11-09 10:25:59] Re-centering provided segment means (offset -0.0037).
INFO [2024-11-09 10:25:59] 576 on-target bins with low coverage in all samples.
WARN [2024-11-09 10:25:59] You are likely not using the correct baits file!
WARN [2024-11-09 10:25:59] Allosome coverage missing, cannot determine sex.
WARN [2024-11-09 10:25:59] Allosome coverage missing, cannot determine sex.
INFO [2024-11-09 10:25:59] Processing on-target regions...
INFO [2024-11-09 10:26:00] Removing 930 intervals with low coverage in normalDB.
INFO [2024-11-09 10:26:00] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2024-11-09 10:26:00] ------------------------------------------------------------
INFO [2024-11-09 10:26:00] PureCN 2.12.0
INFO [2024-11-09 10:26:00] ------------------------------------------------------------
INFO [2024-11-09 10:26:00] Using BiocParallel for parallel optimization.
INFO [2024-11-09 10:26:00] Loading coverage files...
INFO [2024-11-09 10:26:00] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2024-11-09 10:26:00] Allosome coverage missing, cannot determine sex.
WARN [2024-11-09 10:26:00] Allosome coverage missing, cannot determine sex.
INFO [2024-11-09 10:26:00] Removing 228 intervals with missing log.ratio.
INFO [2024-11-09 10:26:00] Removing 705 intervals excluded in normalDB.
INFO [2024-11-09 10:26:00] normalDB provided. Setting minimum coverage for segmentation to 0.0015X.
INFO [2024-11-09 10:26:00] Removing 1066 low count (< 100 total reads) intervals.
INFO [2024-11-09 10:26:00] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2024-11-09 10:26:00] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2024-11-09 10:26:00] No interval.file provided. Cannot check for any GC-biases.
INFO [2024-11-09 10:26:00] Sample sex: ?
INFO [2024-11-09 10:26:00] Segmenting data...
INFO [2024-11-09 10:26:00] Interval weights found, will use weighted CBS.
INFO [2024-11-09 10:26:00] Loading pre-computed boundaries for DNAcopy...
INFO [2024-11-09 10:26:00] Setting undo.SD parameter to 1.000000.
Setting multi-figure configuration
INFO [2024-11-09 10:26:01] Found 52 segments with median size of 29.35Mb.
INFO [2024-11-09 10:26:01] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2024-11-09 10:26:01] 2D-grid search of purity and ploidy...
INFO [2024-11-09 10:26:01] Local optima: 0.65/1.8, 0.52/2
INFO [2024-11-09 10:26:01] Skipping 1 solutions that converged to the same optima.
INFO [2024-11-09 10:26:01] Done.
INFO [2024-11-09 10:26:01] ------------------------------------------------------------
INFO [2024-11-09 10:26:01] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpBUOXhJ/file107adaf4a3e.rds...
FATAL [2024-11-09 10:26:01] runAbsoluteCN was run without a VCF file.
FATAL [2024-11-09 10:26:01]
FATAL [2024-11-09 10:26:01] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:26:01] parameters (PureCN 2.12.0).
FATAL [2024-11-09 10:26:01] runAbsoluteCN was run without a VCF file.
FATAL [2024-11-09 10:26:01]
FATAL [2024-11-09 10:26:01] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:26:01] parameters (PureCN 2.12.0).
INFO [2024-11-09 10:26:01] ------------------------------------------------------------
INFO [2024-11-09 10:26:01] PureCN 2.12.0
INFO [2024-11-09 10:26:02] ------------------------------------------------------------
INFO [2024-11-09 10:26:02] Loading coverage files...
INFO [2024-11-09 10:26:02] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2024-11-09 10:26:02] Allosome coverage missing, cannot determine sex.
WARN [2024-11-09 10:26:02] Allosome coverage missing, cannot determine sex.
INFO [2024-11-09 10:26:02] Removing 228 intervals with missing log.ratio.
INFO [2024-11-09 10:26:02] Removing 705 intervals excluded in normalDB.
INFO [2024-11-09 10:26:02] normalDB provided. Setting minimum coverage for segmentation to 0.0015X.
INFO [2024-11-09 10:26:02] Removing 1066 low count (< 100 total reads) intervals.
INFO [2024-11-09 10:26:02] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2024-11-09 10:26:02] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2024-11-09 10:26:02] No interval.file provided. Cannot check for any GC-biases.
INFO [2024-11-09 10:26:02] Sample sex: ?
INFO [2024-11-09 10:26:02] Segmenting data...
INFO [2024-11-09 10:26:02] Interval weights found, will use weighted PSCBS.
FATAL [2024-11-09 10:26:02] segmentationPSCBS requires VCF file.
FATAL [2024-11-09 10:26:02]
FATAL [2024-11-09 10:26:02] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:26:02] parameters (PureCN 2.12.0).
INFO [2024-11-09 10:26:04] ------------------------------------------------------------
INFO [2024-11-09 10:26:04] PureCN 2.12.0
INFO [2024-11-09 10:26:04] ------------------------------------------------------------
INFO [2024-11-09 10:26:04] Loading coverage files...
FATAL [2024-11-09 10:26:04] Need a normal coverage file if log.ratio and seg.file are not provided.
FATAL [2024-11-09 10:26:04]
FATAL [2024-11-09 10:26:04] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:26:04] parameters (PureCN 2.12.0).
INFO [2024-11-09 10:26:04] ------------------------------------------------------------
INFO [2024-11-09 10:26:04] PureCN 2.12.0
INFO [2024-11-09 10:26:04] ------------------------------------------------------------
FATAL [2024-11-09 10:26:04] min.ploidy or max.ploidy not within expected range.
FATAL [2024-11-09 10:26:04]
FATAL [2024-11-09 10:26:04] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:26:04] parameters (PureCN 2.12.0).
INFO [2024-11-09 10:26:04] ------------------------------------------------------------
INFO [2024-11-09 10:26:04] PureCN 2.12.0
INFO [2024-11-09 10:26:04] ------------------------------------------------------------
FATAL [2024-11-09 10:26:04] min.ploidy or max.ploidy not within expected range.
FATAL [2024-11-09 10:26:04]
FATAL [2024-11-09 10:26:04] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:26:04] parameters (PureCN 2.12.0).
INFO [2024-11-09 10:26:04] ------------------------------------------------------------
INFO [2024-11-09 10:26:04] PureCN 2.12.0
INFO [2024-11-09 10:26:04] ------------------------------------------------------------
INFO [2024-11-09 10:26:04] ------------------------------------------------------------
INFO [2024-11-09 10:26:04] PureCN 2.12.0
INFO [2024-11-09 10:26:04] ------------------------------------------------------------
INFO [2024-11-09 10:26:04] ------------------------------------------------------------
INFO [2024-11-09 10:26:04] PureCN 2.12.0
INFO [2024-11-09 10:26:04] ------------------------------------------------------------
FATAL [2024-11-09 10:26:04] test.num.copy not within expected range.
FATAL [2024-11-09 10:26:04]
FATAL [2024-11-09 10:26:04] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:26:04] parameters (PureCN 2.12.0).
INFO [2024-11-09 10:26:04] ------------------------------------------------------------
INFO [2024-11-09 10:26:04] PureCN 2.12.0
INFO [2024-11-09 10:26:04] ------------------------------------------------------------
WARN [2024-11-09 10:26:04] test.num.copy outside recommended range.
FATAL [2024-11-09 10:26:04] max.non.clonal not within expected range or format.
FATAL [2024-11-09 10:26:04]
FATAL [2024-11-09 10:26:04] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:26:04] parameters (PureCN 2.12.0).
INFO [2024-11-09 10:26:04] ------------------------------------------------------------
INFO [2024-11-09 10:26:04] PureCN 2.12.0
INFO [2024-11-09 10:26:04] ------------------------------------------------------------
WARN [2024-11-09 10:26:04] test.num.copy outside recommended range.
FATAL [2024-11-09 10:26:04] max.non.clonal not within expected range or format.
FATAL [2024-11-09 10:26:04]
FATAL [2024-11-09 10:26:04] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:26:04] parameters (PureCN 2.12.0).
INFO [2024-11-09 10:26:04] ------------------------------------------------------------
INFO [2024-11-09 10:26:04] PureCN 2.12.0
INFO [2024-11-09 10:26:04] ------------------------------------------------------------
FATAL [2024-11-09 10:26:04] test.purity not within expected range.
FATAL [2024-11-09 10:26:04]
FATAL [2024-11-09 10:26:04] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:26:04] parameters (PureCN 2.12.0).
INFO [2024-11-09 10:26:04] ------------------------------------------------------------
INFO [2024-11-09 10:26:04] PureCN 2.12.0
INFO [2024-11-09 10:26:04] ------------------------------------------------------------
INFO [2024-11-09 10:26:04] Loading coverage files...
FATAL [2024-11-09 10:26:04] Tumor and normal are identical. This won't give any meaningful results
FATAL [2024-11-09 10:26:04] and I'm stopping here.
FATAL [2024-11-09 10:26:04]
FATAL [2024-11-09 10:26:04] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:26:04] parameters (PureCN 2.12.0).
INFO [2024-11-09 10:26:04] ------------------------------------------------------------
INFO [2024-11-09 10:26:04] PureCN 2.12.0
INFO [2024-11-09 10:26:04] ------------------------------------------------------------
INFO [2024-11-09 10:26:04] Loading coverage files...
FATAL [2024-11-09 10:26:04] Length of log.ratio different from tumor coverage.
FATAL [2024-11-09 10:26:04]
FATAL [2024-11-09 10:26:04] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:26:04] parameters (PureCN 2.12.0).
INFO [2024-11-09 10:26:04] ------------------------------------------------------------
INFO [2024-11-09 10:26:04] PureCN 2.12.0
INFO [2024-11-09 10:26:04] ------------------------------------------------------------
FATAL [2024-11-09 10:26:04] prior.purity must have the same length as test.purity.
FATAL [2024-11-09 10:26:04]
FATAL [2024-11-09 10:26:04] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:26:04] parameters (PureCN 2.12.0).
INFO [2024-11-09 10:26:04] ------------------------------------------------------------
INFO [2024-11-09 10:26:04] PureCN 2.12.0
INFO [2024-11-09 10:26:04] ------------------------------------------------------------
FATAL [2024-11-09 10:26:04] min.gof not within expected range or format.
FATAL [2024-11-09 10:26:04]
FATAL [2024-11-09 10:26:04] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:26:04] parameters (PureCN 2.12.0).
INFO [2024-11-09 10:26:04] ------------------------------------------------------------
INFO [2024-11-09 10:26:04] PureCN 2.12.0
INFO [2024-11-09 10:26:04] ------------------------------------------------------------
FATAL [2024-11-09 10:26:04] prior.purity not within expected range or format.
FATAL [2024-11-09 10:26:04]
FATAL [2024-11-09 10:26:04] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:26:04] parameters (PureCN 2.12.0).
INFO [2024-11-09 10:26:04] ------------------------------------------------------------
INFO [2024-11-09 10:26:04] PureCN 2.12.0
INFO [2024-11-09 10:26:04] ------------------------------------------------------------
FATAL [2024-11-09 10:26:04] prior.purity must add to 1. Sum is 1.5
FATAL [2024-11-09 10:26:04]
FATAL [2024-11-09 10:26:04] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:26:04] parameters (PureCN 2.12.0).
INFO [2024-11-09 10:26:04] ------------------------------------------------------------
INFO [2024-11-09 10:26:04] PureCN 2.12.0
INFO [2024-11-09 10:26:04] ------------------------------------------------------------
FATAL [2024-11-09 10:26:04] max.homozygous.loss not within expected range or format.
FATAL [2024-11-09 10:26:04]
FATAL [2024-11-09 10:26:04] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:26:04] parameters (PureCN 2.12.0).
INFO [2024-11-09 10:26:04] ------------------------------------------------------------
INFO [2024-11-09 10:26:04] PureCN 2.12.0
INFO [2024-11-09 10:26:04] ------------------------------------------------------------
FATAL [2024-11-09 10:26:04] prior.K not within expected range or format.
FATAL [2024-11-09 10:26:04]
FATAL [2024-11-09 10:26:04] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:26:04] parameters (PureCN 2.12.0).
INFO [2024-11-09 10:26:04] ------------------------------------------------------------
INFO [2024-11-09 10:26:04] PureCN 2.12.0
INFO [2024-11-09 10:26:04] ------------------------------------------------------------
FATAL [2024-11-09 10:26:04] prior.contamination not within expected range or format.
FATAL [2024-11-09 10:26:04]
FATAL [2024-11-09 10:26:04] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:26:04] parameters (PureCN 2.12.0).
INFO [2024-11-09 10:26:04] ------------------------------------------------------------
INFO [2024-11-09 10:26:04] PureCN 2.12.0
INFO [2024-11-09 10:26:04] ------------------------------------------------------------
FATAL [2024-11-09 10:26:04] Iterations not in the expected range from 10 to 250.
FATAL [2024-11-09 10:26:04]
FATAL [2024-11-09 10:26:04] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:26:04] parameters (PureCN 2.12.0).
INFO [2024-11-09 10:26:04] ------------------------------------------------------------
INFO [2024-11-09 10:26:04] PureCN 2.12.0
INFO [2024-11-09 10:26:04] ------------------------------------------------------------
FATAL [2024-11-09 10:26:04] Iterations not in the expected range from 10 to 250.
FATAL [2024-11-09 10:26:04]
FATAL [2024-11-09 10:26:04] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:26:04] parameters (PureCN 2.12.0).
INFO [2024-11-09 10:26:04] ------------------------------------------------------------
INFO [2024-11-09 10:26:04] PureCN 2.12.0
INFO [2024-11-09 10:26:04] ------------------------------------------------------------
INFO [2024-11-09 10:26:04] Loading coverage files...
FATAL [2024-11-09 10:26:04] Missing tumor.coverage.file requires seg.file or log.ratio and
FATAL [2024-11-09 10:26:04] interval.file.
FATAL [2024-11-09 10:26:04]
FATAL [2024-11-09 10:26:04] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:26:04] parameters (PureCN 2.12.0).
INFO [2024-11-09 10:26:04] ------------------------------------------------------------
INFO [2024-11-09 10:26:04] PureCN 2.12.0
INFO [2024-11-09 10:26:04] ------------------------------------------------------------
INFO [2024-11-09 10:26:04] ------------------------------------------------------------
INFO [2024-11-09 10:26:04] PureCN 2.12.0
INFO [2024-11-09 10:26:04] ------------------------------------------------------------
INFO [2024-11-09 10:26:04] Loading coverage files...
FATAL [2024-11-09 10:26:04] Interval files in normal and tumor different.
FATAL [2024-11-09 10:26:04]
FATAL [2024-11-09 10:26:04] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:26:04] parameters (PureCN 2.12.0).
INFO [2024-11-09 10:26:05] ------------------------------------------------------------
INFO [2024-11-09 10:26:05] PureCN 2.12.0
INFO [2024-11-09 10:26:05] ------------------------------------------------------------
INFO [2024-11-09 10:26:05] Loading coverage files...
INFO [2024-11-09 10:26:05] Mean target coverages: 0X (tumor) 99X (normal).
WARN [2024-11-09 10:26:05] Large difference in coverage of tumor and normal.
FATAL [2024-11-09 10:26:05] No finite intervals.
FATAL [2024-11-09 10:26:05]
FATAL [2024-11-09 10:26:05] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:26:05] parameters (PureCN 2.12.0).
INFO [2024-11-09 10:26:05] ------------------------------------------------------------
INFO [2024-11-09 10:26:05] PureCN 2.12.0
INFO [2024-11-09 10:26:05] ------------------------------------------------------------
INFO [2024-11-09 10:26:05] Loading coverage files...
INFO [2024-11-09 10:26:05] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2024-11-09 10:26:05] Allosome coverage missing, cannot determine sex.
WARN [2024-11-09 10:26:05] Allosome coverage missing, cannot determine sex.
INFO [2024-11-09 10:26:05] Removing 228 intervals with missing log.ratio.
INFO [2024-11-09 10:26:05] Removing 22 small (< 5bp) intervals.
INFO [2024-11-09 10:26:05] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2024-11-09 10:26:05] No normalDB provided. Provide one for better results.
INFO [2024-11-09 10:26:05] Removing 1724 low count (< 100 total reads) intervals.
INFO [2024-11-09 10:26:05] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2024-11-09 10:26:05] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2024-11-09 10:26:05] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2024-11-09 10:26:05] No interval.file provided. Cannot check for any GC-biases.
INFO [2024-11-09 10:26:05] Loading VCF...
INFO [2024-11-09 10:26:05] Found 127 variants in VCF file.
INFO [2024-11-09 10:26:05] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2024-11-09 10:26:05] LIB-02240e4 is tumor in VCF file.
INFO [2024-11-09 10:26:05] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2024-11-09 10:26:05] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2024-11-09 10:26:05] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2024-11-09 10:26:05] Base quality scores range from 29 to 35 (offset by 1)
INFO [2024-11-09 10:26:05] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2024-11-09 10:26:05] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
Error in FileForFormat(resource(con), fileFormat(con)) :
Format 'txt' unsupported
In addition: Warning messages:
1: In for (i in seq_len(n)) { :
closing unused connection 5 (/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpBUOXhJ/file107ad17e3b548.tsv)
2: In for (i in seq_len(n)) { :
closing unused connection 4 (/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/PureCN/extdata/example_gatk4_denoised_cr.tsv.gz)
FATAL [2024-11-09 10:26:05] Could not import snp.blacklist
FATAL [2024-11-09 10:26:05] /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/PureCN/extdata/example_normal.txt.gz:Error
FATAL [2024-11-09 10:26:05] in FileForFormat(resource(con), fileFormat(con)) : Format 'txt'
FATAL [2024-11-09 10:26:05] unsupported
FATAL [2024-11-09 10:26:05]
FATAL [2024-11-09 10:26:05] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:26:05] parameters (PureCN 2.12.0).
INFO [2024-11-09 10:26:05] ------------------------------------------------------------
INFO [2024-11-09 10:26:05] PureCN 2.12.0
INFO [2024-11-09 10:26:05] ------------------------------------------------------------
INFO [2024-11-09 10:26:05] Loading coverage files...
INFO [2024-11-09 10:26:05] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2024-11-09 10:26:05] Allosome coverage missing, cannot determine sex.
WARN [2024-11-09 10:26:05] Allosome coverage missing, cannot determine sex.
INFO [2024-11-09 10:26:05] Removing 228 intervals with missing log.ratio.
INFO [2024-11-09 10:26:05] Removing 22 small (< 5bp) intervals.
INFO [2024-11-09 10:26:05] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2024-11-09 10:26:05] No normalDB provided. Provide one for better results.
INFO [2024-11-09 10:26:05] Removing 233 low coverage (< 15.0000X) intervals.
INFO [2024-11-09 10:26:05] Using 9547 intervals (9547 on-target, 0 off-target).
INFO [2024-11-09 10:26:05] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2024-11-09 10:26:05] No interval.file provided. Cannot check for any GC-biases.
INFO [2024-11-09 10:26:05] Loading VCF...
INFO [2024-11-09 10:26:06] Found 127 variants in VCF file.
INFO [2024-11-09 10:26:06] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2024-11-09 10:26:06] LIB-02240e4 is tumor in VCF file.
INFO [2024-11-09 10:26:06] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2024-11-09 10:26:06] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2024-11-09 10:26:06] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2024-11-09 10:26:06] Base quality scores range from 29 to 35 (offset by 1)
INFO [2024-11-09 10:26:06] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2024-11-09 10:26:06] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2024-11-09 10:26:06] Total size of targeted genomic region: 1.63Mb (2.58Mb with 50bp padding).
INFO [2024-11-09 10:26:06] 1.0% of targets contain variants.
INFO [2024-11-09 10:26:06] Removing 2 variants outside intervals.
INFO [2024-11-09 10:26:06] Found SOMATIC annotation in VCF.
INFO [2024-11-09 10:26:06] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2024-11-09 10:26:06] Found SOMATIC annotation in VCF. Setting mapping bias to 0.973.
INFO [2024-11-09 10:26:06] Excluding 0 novel or poor quality variants from segmentation.
INFO [2024-11-09 10:26:06] Sample sex: ?
INFO [2024-11-09 10:26:06] Segmenting data...
INFO [2024-11-09 10:26:06] Loading pre-computed boundaries for DNAcopy...
INFO [2024-11-09 10:26:06] Setting undo.SD parameter to 1.000000.
INFO [2024-11-09 10:26:06] Setting prune.hclust.h parameter to 0.200000.
INFO [2024-11-09 10:26:06] Found 54 segments with median size of 24.88Mb.
INFO [2024-11-09 10:26:06] Using 123 variants.
INFO [2024-11-09 10:26:06] Mean standard deviation of log-ratios: 0.37 (MAPD: 0.32)
INFO [2024-11-09 10:26:06] 2D-grid search of purity and ploidy...
INFO [2024-11-09 10:26:07] Local optima: 0.62/1.9, 0.3/1.9, 0.32/2
INFO [2024-11-09 10:26:07] Testing local optimum 1/3 at purity 0.62 and total ploidy 1.90...
INFO [2024-11-09 10:26:07] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2024-11-09 10:26:07] Recalibrating log-ratios...
INFO [2024-11-09 10:26:07] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2024-11-09 10:26:07] Recalibrating log-ratios...
INFO [2024-11-09 10:26:07] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2024-11-09 10:26:07] Recalibrating log-ratios...
INFO [2024-11-09 10:26:07] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2024-11-09 10:26:07] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2024-11-09 10:26:07] Recalibrating log-ratios...
INFO [2024-11-09 10:26:07] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2024-11-09 10:26:08] Recalibrating log-ratios...
INFO [2024-11-09 10:26:08] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2024-11-09 10:26:08] Recalibrating log-ratios...
INFO [2024-11-09 10:26:08] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2024-11-09 10:26:08] Skipping 1 solutions that converged to the same optima.
INFO [2024-11-09 10:26:08] Skipping 1 solutions exceeding max.non.clonal (0.20): 0.3/1.9 (purity/tumor ploidy)
INFO [2024-11-09 10:26:08] Fitting variants with beta model for local optimum 1/3...
INFO [2024-11-09 10:26:08] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01.
INFO [2024-11-09 10:26:09] Optimized purity: 0.65
INFO [2024-11-09 10:26:09] Done.
INFO [2024-11-09 10:26:09] ------------------------------------------------------------
INFO [2024-11-09 10:26:09] ------------------------------------------------------------
INFO [2024-11-09 10:26:09] PureCN 2.12.0
INFO [2024-11-09 10:26:09] ------------------------------------------------------------
INFO [2024-11-09 10:26:09] Loading coverage files...
INFO [2024-11-09 10:26:09] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2024-11-09 10:26:09] Allosome coverage missing, cannot determine sex.
WARN [2024-11-09 10:26:09] Allosome coverage missing, cannot determine sex.
INFO [2024-11-09 10:26:09] Removing 228 intervals with missing log.ratio.
INFO [2024-11-09 10:26:09] Removing 22 small (< 5bp) intervals.
INFO [2024-11-09 10:26:09] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2024-11-09 10:26:09] No normalDB provided. Provide one for better results.
INFO [2024-11-09 10:26:09] Removing 1724 low count (< 100 total reads) intervals.
INFO [2024-11-09 10:26:09] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2024-11-09 10:26:09] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2024-11-09 10:26:09] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2024-11-09 10:26:09] No interval.file provided. Cannot check for any GC-biases.
INFO [2024-11-09 10:26:09] Loading VCF...
INFO [2024-11-09 10:26:09] Found 127 variants in VCF file.
WARN [2024-11-09 10:26:09] DP FORMAT field contains NAs. Removing 3 variants.
WARN [2024-11-09 10:26:09] DB INFO flag contains NAs
INFO [2024-11-09 10:26:09] 119 (96.0%) variants annotated as likely germline (DB INFO flag).
INFO [2024-11-09 10:26:09] LIB-02240e4 is tumor in VCF file.
INFO [2024-11-09 10:26:09] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2024-11-09 10:26:09] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2024-11-09 10:26:09] Base quality scores range from 29 to 35 (offset by 1)
INFO [2024-11-09 10:26:09] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2024-11-09 10:26:09] Removing 1 variants with AF < 0.030 or AF >= 0.970 or insufficient supporting reads or depth < 15.
INFO [2024-11-09 10:26:09] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding).
INFO [2024-11-09 10:26:09] 1.2% of targets contain variants.
INFO [2024-11-09 10:26:09] Setting somatic prior probabilities for likely germline hits to 0.000500 or to 0.500000 otherwise.
INFO [2024-11-09 10:26:09] Excluding 5 novel or poor quality variants from segmentation.
INFO [2024-11-09 10:26:09] Sample sex: ?
INFO [2024-11-09 10:26:09] Segmenting data...
INFO [2024-11-09 10:26:09] Loading pre-computed boundaries for DNAcopy...
INFO [2024-11-09 10:26:09] Setting undo.SD parameter to 1.000000.
Setting multi-figure configuration
INFO [2024-11-09 10:26:10] Setting prune.hclust.h parameter to 0.200000.
INFO [2024-11-09 10:26:10] Found 59 segments with median size of 17.67Mb.
INFO [2024-11-09 10:26:10] Using 123 variants.
INFO [2024-11-09 10:26:10] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2024-11-09 10:26:10] 2D-grid search of purity and ploidy...
INFO [2024-11-09 10:26:10] Local optima: 0.62/1.9, 0.3/1.9, 0.32/2
INFO [2024-11-09 10:26:10] Testing local optimum 1/3 at purity 0.62 and total ploidy 1.90...
INFO [2024-11-09 10:26:10] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2024-11-09 10:26:10] Recalibrating log-ratios...
INFO [2024-11-09 10:26:10] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2024-11-09 10:26:11] Recalibrating log-ratios...
INFO [2024-11-09 10:26:11] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2024-11-09 10:26:11] Recalibrating log-ratios...
INFO [2024-11-09 10:26:11] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2024-11-09 10:26:11] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2024-11-09 10:26:11] Recalibrating log-ratios...
INFO [2024-11-09 10:26:11] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2024-11-09 10:26:11] Recalibrating log-ratios...
INFO [2024-11-09 10:26:11] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2024-11-09 10:26:11] Recalibrating log-ratios...
INFO [2024-11-09 10:26:11] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2024-11-09 10:26:11] Skipping 2 solutions exceeding max.non.clonal (0.20): 0.3/1.9, 0.35/1.61 (purity/tumor ploidy)
INFO [2024-11-09 10:26:11] Fitting variants with beta model for local optimum 1/3...
INFO [2024-11-09 10:26:11] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2024-11-09 10:26:12] Optimized purity: 0.65
INFO [2024-11-09 10:26:12] Done.
INFO [2024-11-09 10:26:12] ------------------------------------------------------------
INFO [2024-11-09 10:26:12] ------------------------------------------------------------
INFO [2024-11-09 10:26:12] PureCN 2.12.0
INFO [2024-11-09 10:26:12] ------------------------------------------------------------
INFO [2024-11-09 10:26:12] Loading coverage files...
INFO [2024-11-09 10:26:12] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2024-11-09 10:26:12] Allosome coverage missing, cannot determine sex.
WARN [2024-11-09 10:26:12] Allosome coverage missing, cannot determine sex.
INFO [2024-11-09 10:26:12] No Gene column in interval.file. You won't get gene-level calls.
INFO [2024-11-09 10:26:12] Removing 228 intervals with missing log.ratio.
INFO [2024-11-09 10:26:12] Removing 15 low/high GC targets.
INFO [2024-11-09 10:26:12] Removing 21 small (< 5bp) intervals.
INFO [2024-11-09 10:26:12] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2024-11-09 10:26:12] No normalDB provided. Provide one for better results.
INFO [2024-11-09 10:26:12] Removing 1718 low count (< 100 total reads) intervals.
INFO [2024-11-09 10:26:12] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2024-11-09 10:26:12] Removing 36 low mappability intervals.
INFO [2024-11-09 10:26:12] Using 8006 intervals (8006 on-target, 0 off-target).
INFO [2024-11-09 10:26:12] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2024-11-09 10:26:12] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio).
INFO [2024-11-09 10:26:12] Loading VCF...
INFO [2024-11-09 10:26:13] Found 127 variants in VCF file.
INFO [2024-11-09 10:26:13] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2024-11-09 10:26:13] LIB-02240e4 is tumor in VCF file.
INFO [2024-11-09 10:26:13] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2024-11-09 10:26:13] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2024-11-09 10:26:13] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2024-11-09 10:26:13] Base quality scores range from 29 to 35 (offset by 1)
INFO [2024-11-09 10:26:13] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2024-11-09 10:26:13] Removing 1 variants with AF < 0.030 or AF >= Inf or insufficient supporting reads or depth < 15.
INFO [2024-11-09 10:26:13] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding).
INFO [2024-11-09 10:26:13] 1.2% of targets contain variants.
INFO [2024-11-09 10:26:13] Removing 11 variants outside intervals.
INFO [2024-11-09 10:26:13] Found SOMATIC annotation in VCF.
INFO [2024-11-09 10:26:13] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2024-11-09 10:26:13] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970.
INFO [2024-11-09 10:26:13] Excluding 0 novel or poor quality variants from segmentation.
INFO [2024-11-09 10:26:13] Sample sex: ?
INFO [2024-11-09 10:26:13] Segmenting data...
INFO [2024-11-09 10:26:13] MAPD of 114 allelic fractions: 0.14 (0.15 adjusted).
INFO [2024-11-09 10:26:13] Using unweighted PSCBS.
INFO [2024-11-09 10:26:13] Setting undo.SD parameter to 1.000000.
INFO [2024-11-09 10:26:18] Setting prune.hclust.h parameter to 0.200000.
INFO [2024-11-09 10:26:18] Found 71 segments with median size of 27.72Mb.
INFO [2024-11-09 10:26:18] Using 114 variants.
INFO [2024-11-09 10:26:18] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2024-11-09 10:26:18] 2D-grid search of purity and ploidy...
INFO [2024-11-09 10:26:18] Local optima: 0.65/1.8, 0.38/2.2
INFO [2024-11-09 10:26:18] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2024-11-09 10:26:18] Recalibrating log-ratios...
INFO [2024-11-09 10:26:18] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2024-11-09 10:26:18] Recalibrating log-ratios...
INFO [2024-11-09 10:26:18] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2024-11-09 10:26:18] Recalibrating log-ratios...
INFO [2024-11-09 10:26:18] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2024-11-09 10:26:18] Testing local optimum 2/2 at purity 0.38 and total ploidy 2.20...
INFO [2024-11-09 10:26:18] Skipping 1 solutions exceeding max.non.clonal (0.20): 0.65/2.04 (purity/tumor ploidy)
INFO [2024-11-09 10:26:18] Fitting variants with beta model for local optimum 2/2...
INFO [2024-11-09 10:26:19] Fitting variants for purity 0.40, tumor ploidy 2.53 and contamination 0.01.
INFO [2024-11-09 10:26:19] Optimized purity: 0.40
INFO [2024-11-09 10:26:19] Done.
INFO [2024-11-09 10:26:19] ------------------------------------------------------------
FATAL [2024-11-09 10:26:19] This function requires gene-level calls. Please add a column 'Gene'
FATAL [2024-11-09 10:26:19] containing gene symbols to the interval.file.
FATAL [2024-11-09 10:26:19]
FATAL [2024-11-09 10:26:19] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:26:19] parameters (PureCN 2.12.0).
INFO [2024-11-09 10:26:20] ------------------------------------------------------------
INFO [2024-11-09 10:26:20] PureCN 2.12.0
INFO [2024-11-09 10:26:20] ------------------------------------------------------------
INFO [2024-11-09 10:26:20] Loading coverage files...
INFO [2024-11-09 10:26:20] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2024-11-09 10:26:20] Allosome coverage missing, cannot determine sex.
WARN [2024-11-09 10:26:20] Allosome coverage missing, cannot determine sex.
INFO [2024-11-09 10:26:20] Removing 228 intervals with missing log.ratio.
INFO [2024-11-09 10:26:20] Removing 22 small (< 5bp) intervals.
INFO [2024-11-09 10:26:20] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2024-11-09 10:26:20] No normalDB provided. Provide one for better results.
INFO [2024-11-09 10:26:20] Removing 1724 low count (< 100 total reads) intervals.
INFO [2024-11-09 10:26:20] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2024-11-09 10:26:20] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2024-11-09 10:26:20] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2024-11-09 10:26:20] No interval.file provided. Cannot check for any GC-biases.
INFO [2024-11-09 10:26:20] Loading VCF...
INFO [2024-11-09 10:26:20] Found 127 variants in VCF file.
INFO [2024-11-09 10:26:20] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
FATAL [2024-11-09 10:26:20] Different chromosome names in coverage and VCF.
FATAL [2024-11-09 10:26:20]
FATAL [2024-11-09 10:26:20] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:26:20] parameters (PureCN 2.12.0).
INFO [2024-11-09 10:26:20] ------------------------------------------------------------
INFO [2024-11-09 10:26:20] PureCN 2.12.0
INFO [2024-11-09 10:26:20] ------------------------------------------------------------
INFO [2024-11-09 10:26:20] Loading coverage files...
INFO [2024-11-09 10:26:20] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2024-11-09 10:26:20] Allosome coverage missing, cannot determine sex.
WARN [2024-11-09 10:26:20] Allosome coverage missing, cannot determine sex.
FATAL [2024-11-09 10:26:20] tumor.coverage.file and interval.file do not align.
FATAL [2024-11-09 10:26:20]
FATAL [2024-11-09 10:26:20] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:26:20] parameters (PureCN 2.12.0).
INFO [2024-11-09 10:26:20] ------------------------------------------------------------
INFO [2024-11-09 10:26:20] PureCN 2.12.0
INFO [2024-11-09 10:26:20] ------------------------------------------------------------
INFO [2024-11-09 10:26:20] Loading coverage files...
INFO [2024-11-09 10:26:20] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2024-11-09 10:26:21] Allosome coverage missing, cannot determine sex.
WARN [2024-11-09 10:26:21] Allosome coverage missing, cannot determine sex.
INFO [2024-11-09 10:26:21] Removing 228 intervals with missing log.ratio.
INFO [2024-11-09 10:26:21] Removing 15 low/high GC targets.
INFO [2024-11-09 10:26:21] Removing 21 small (< 5bp) intervals.
INFO [2024-11-09 10:26:21] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2024-11-09 10:26:21] No normalDB provided. Provide one for better results.
INFO [2024-11-09 10:26:21] Removing 1718 low count (< 100 total reads) intervals.
INFO [2024-11-09 10:26:21] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2024-11-09 10:26:21] Removing 36 low mappability intervals.
INFO [2024-11-09 10:26:21] Using 8006 intervals (8006 on-target, 0 off-target).
INFO [2024-11-09 10:26:21] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2024-11-09 10:26:21] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio).
INFO [2024-11-09 10:26:21] Loading VCF...
INFO [2024-11-09 10:26:21] Found 127 variants in VCF file.
INFO [2024-11-09 10:26:21] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2024-11-09 10:26:21] LIB-02240e4 is tumor in VCF file.
INFO [2024-11-09 10:26:21] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2024-11-09 10:26:21] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2024-11-09 10:26:21] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2024-11-09 10:26:21] Base quality scores range from 29 to 35 (offset by 1)
INFO [2024-11-09 10:26:21] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2024-11-09 10:26:21] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2024-11-09 10:26:21] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding).
INFO [2024-11-09 10:26:21] 1.2% of targets contain variants.
INFO [2024-11-09 10:26:21] Removing 11 variants outside intervals.
INFO [2024-11-09 10:26:21] Found SOMATIC annotation in VCF.
INFO [2024-11-09 10:26:21] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2024-11-09 10:26:21] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970.
INFO [2024-11-09 10:26:21] Excluding 0 novel or poor quality variants from segmentation.
INFO [2024-11-09 10:26:21] Sample sex: ?
INFO [2024-11-09 10:26:21] Segmenting data...
INFO [2024-11-09 10:26:21] Loading pre-computed boundaries for DNAcopy...
INFO [2024-11-09 10:26:21] Setting undo.SD parameter to 1.000000.
INFO [2024-11-09 10:26:22] Setting prune.hclust.h parameter to 0.200000.
INFO [2024-11-09 10:26:22] Found 59 segments with median size of 17.67Mb.
INFO [2024-11-09 10:26:22] Using 114 variants.
INFO [2024-11-09 10:26:22] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2024-11-09 10:26:22] 2D-grid search of purity and ploidy...
INFO [2024-11-09 10:26:22] Local optima: 0.63/1.9
INFO [2024-11-09 10:26:22] Testing local optimum 1/1 at purity 0.63 and total ploidy 1.90...
INFO [2024-11-09 10:26:22] Fitting variants with beta model for local optimum 1/1...
INFO [2024-11-09 10:26:22] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2024-11-09 10:26:23] Optimized purity: 0.65
INFO [2024-11-09 10:26:23] Done.
INFO [2024-11-09 10:26:23] ------------------------------------------------------------
INFO [2024-11-09 10:26:23] ------------------------------------------------------------
INFO [2024-11-09 10:26:23] PureCN 2.12.0
INFO [2024-11-09 10:26:23] ------------------------------------------------------------
INFO [2024-11-09 10:26:23] Loading coverage files...
INFO [2024-11-09 10:26:23] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2024-11-09 10:26:23] Allosome coverage missing, cannot determine sex.
WARN [2024-11-09 10:26:23] Allosome coverage missing, cannot determine sex.
INFO [2024-11-09 10:26:23] Removing 228 intervals with missing log.ratio.
INFO [2024-11-09 10:26:23] Removing 15 low/high GC targets.
INFO [2024-11-09 10:26:23] Removing 21 small (< 5bp) intervals.
INFO [2024-11-09 10:26:23] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2024-11-09 10:26:23] No normalDB provided. Provide one for better results.
INFO [2024-11-09 10:26:23] Removing 1718 low count (< 100 total reads) intervals.
INFO [2024-11-09 10:26:23] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2024-11-09 10:26:24] Removing 36 low mappability intervals.
INFO [2024-11-09 10:26:24] Using 8006 intervals (8006 on-target, 0 off-target).
INFO [2024-11-09 10:26:24] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2024-11-09 10:26:24] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio).
INFO [2024-11-09 10:26:24] Loading VCF...
INFO [2024-11-09 10:26:24] Found 127 variants in VCF file.
INFO [2024-11-09 10:26:24] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2024-11-09 10:26:24] LIB-02240e4 is tumor in VCF file.
INFO [2024-11-09 10:26:24] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2024-11-09 10:26:24] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2024-11-09 10:26:24] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2024-11-09 10:26:24] Base quality scores range from 29 to 35 (offset by 1)
INFO [2024-11-09 10:26:24] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2024-11-09 10:26:24] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2024-11-09 10:26:24] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding).
INFO [2024-11-09 10:26:24] 1.2% of targets contain variants.
INFO [2024-11-09 10:26:24] Removing 11 variants outside intervals.
INFO [2024-11-09 10:26:24] Found SOMATIC annotation in VCF.
INFO [2024-11-09 10:26:24] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2024-11-09 10:26:24] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970.
INFO [2024-11-09 10:26:24] Excluding 0 novel or poor quality variants from segmentation.
INFO [2024-11-09 10:26:24] Sample sex: ?
INFO [2024-11-09 10:26:24] Segmenting data...
INFO [2024-11-09 10:26:24] Loading pre-computed boundaries for DNAcopy...
INFO [2024-11-09 10:26:24] Setting undo.SD parameter to 1.000000.
INFO [2024-11-09 10:26:24] Setting prune.hclust.h parameter to 0.200000.
INFO [2024-11-09 10:26:24] Found 59 segments with median size of 17.67Mb.
INFO [2024-11-09 10:26:24] Using 114 variants.
INFO [2024-11-09 10:26:24] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2024-11-09 10:26:24] 2D-grid search of purity and ploidy...
INFO [2024-11-09 10:26:25] Local optima: 0.63/1.9
INFO [2024-11-09 10:26:25] Testing local optimum 1/1 at purity 0.63 and total ploidy 1.90...
INFO [2024-11-09 10:26:25] Fitting variants with beta model for local optimum 1/1...
WARN [2024-11-09 10:26:25] Some gene symbols found on multiple chromosomes. Use of approved symbols suggested.
INFO [2024-11-09 10:26:25] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2024-11-09 10:26:26] Optimized purity: 0.65
INFO [2024-11-09 10:26:26] Done.
INFO [2024-11-09 10:26:26] ------------------------------------------------------------
FATAL [2024-11-09 10:26:26] chr1 not valid chromosome name(s). Valid names are:
FATAL [2024-11-09 10:26:26] 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22
FATAL [2024-11-09 10:26:26]
FATAL [2024-11-09 10:26:26] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:26:26] parameters (PureCN 2.12.0).
INFO [2024-11-09 10:26:26] ------------------------------------------------------------
INFO [2024-11-09 10:26:26] PureCN 2.12.0
INFO [2024-11-09 10:26:26] ------------------------------------------------------------
INFO [2024-11-09 10:26:26] Loading coverage files...
WARN [2024-11-09 10:26:26] Provided sampleid (Sample2) does not match Sample1 found in segmentation.
WARN [2024-11-09 10:26:26] Allosome coverage missing, cannot determine sex.
WARN [2024-11-09 10:26:26] Allosome coverage missing, cannot determine sex.
INFO [2024-11-09 10:26:26] Removing 10 intervals with missing log.ratio.
INFO [2024-11-09 10:26:26] Using 10039 intervals (10039 on-target, 0 off-target).
INFO [2024-11-09 10:26:26] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2024-11-09 10:26:26] Loading VCF...
INFO [2024-11-09 10:26:26] Found 127 variants in VCF file.
INFO [2024-11-09 10:26:26] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2024-11-09 10:26:26] LIB-02240e4 is tumor in VCF file.
INFO [2024-11-09 10:26:26] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2024-11-09 10:26:26] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2024-11-09 10:26:26] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2024-11-09 10:26:26] Base quality scores range from 29 to 35 (offset by 1)
INFO [2024-11-09 10:26:26] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2024-11-09 10:26:26] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2024-11-09 10:26:26] Total size of targeted genomic region: 1.71Mb (2.70Mb with 50bp padding).
INFO [2024-11-09 10:26:26] 1.0% of targets contain variants.
INFO [2024-11-09 10:26:26] Removing 0 variants outside intervals.
INFO [2024-11-09 10:26:26] Found SOMATIC annotation in VCF.
INFO [2024-11-09 10:26:26] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2024-11-09 10:26:26] Found SOMATIC annotation in VCF. Setting mapping bias to 0.976.
INFO [2024-11-09 10:26:26] Excluding 0 novel or poor quality variants from segmentation.
INFO [2024-11-09 10:26:26] Sample sex: ?
INFO [2024-11-09 10:26:26] Segmenting data...
INFO [2024-11-09 10:26:26] Loaded provided segmentation file example_seg.txt (format DNAcopy).
WARN [2024-11-09 10:26:26] Provided sampleid (Sample2) does not match Sample1 found in segmentation.
INFO [2024-11-09 10:26:26] Re-centering provided segment means (offset -0.0033).
INFO [2024-11-09 10:26:26] Loading pre-computed boundaries for DNAcopy...
INFO [2024-11-09 10:26:26] Setting undo.SD parameter to 0.000000.
Setting multi-figure configuration
INFO [2024-11-09 10:26:26] Setting prune.hclust.h parameter to 0.200000.
INFO [2024-11-09 10:26:27] Found 54 segments with median size of 24.88Mb.
INFO [2024-11-09 10:26:27] Using 125 variants.
INFO [2024-11-09 10:26:27] Mean standard deviation of log-ratios: 0.40 (MAPD: 0.00)
INFO [2024-11-09 10:26:27] 2D-grid search of purity and ploidy...
INFO [2024-11-09 10:26:27] Local optima: 0.6/1.9
INFO [2024-11-09 10:26:27] Testing local optimum 1/1 at purity 0.60 and total ploidy 1.90...
INFO [2024-11-09 10:26:27] Fitting variants with beta model for local optimum 1/1...
INFO [2024-11-09 10:26:27] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01.
INFO [2024-11-09 10:26:28] Optimized purity: 0.65
INFO [2024-11-09 10:26:28] Done.
INFO [2024-11-09 10:26:28] ------------------------------------------------------------
WARN [2024-11-09 10:26:28] Allosome coverage missing, cannot determine sex.
WARN [2024-11-09 10:26:28] Allosome coverage missing, cannot determine sex.
Setting multi-figure configuration
FATAL [2024-11-09 10:26:30] Segmentation file expected with colnames ID, chrom, loc.start, loc.end,
FATAL [2024-11-09 10:26:30] num.mark, seg.mean
FATAL [2024-11-09 10:26:30]
FATAL [2024-11-09 10:26:30] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:26:30] parameters (PureCN 2.12.0).
FATAL [2024-11-09 10:26:30] seg.file contains multiple samples and sampleid missing.
FATAL [2024-11-09 10:26:30]
FATAL [2024-11-09 10:26:30] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:26:30] parameters (PureCN 2.12.0).
FATAL [2024-11-09 10:26:30] seg.file contains multiple samples and sampleid does not match any.
FATAL [2024-11-09 10:26:30]
FATAL [2024-11-09 10:26:30] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:26:30] parameters (PureCN 2.12.0).
WARN [2024-11-09 10:26:30] Allosome coverage missing, cannot determine sex.
WARN [2024-11-09 10:26:30] Allosome coverage missing, cannot determine sex.
WARN [2024-11-09 10:26:33] Allosome coverage missing, cannot determine sex.
WARN [2024-11-09 10:26:33] Allosome coverage missing, cannot determine sex.
WARN [2024-11-09 10:26:33] Provided sampleid (example_tumor.txt.gz) does not match Sample1 found in segmentation.
WARN [2024-11-09 10:26:34] Allosome coverage missing, cannot determine sex.
WARN [2024-11-09 10:26:34] Allosome coverage missing, cannot determine sex.
WARN [2024-11-09 10:26:34] No normalDB provided. Provide one for better results.
WARN [2024-11-09 10:26:36] Allosome coverage missing, cannot determine sex.
WARN [2024-11-09 10:26:36] Allosome coverage missing, cannot determine sex.
WARN [2024-11-09 10:26:37] Provided sampleid (Sample.1) does not match Sample1 found in segmentation.
Setting multi-figure configuration
WARN [2024-11-09 10:26:39] Allosome coverage missing, cannot determine sex.
WARN [2024-11-09 10:26:39] Allosome coverage missing, cannot determine sex.
WARN [2024-11-09 10:26:39] No normalDB provided. Provide one for better results.
WARN [2024-11-09 10:26:40] Sampleid looks like a normal in VCF, not like a tumor.
WARN [2024-11-09 10:26:42] Allosome coverage missing, cannot determine sex.
WARN [2024-11-09 10:26:42] Allosome coverage missing, cannot determine sex.
FATAL [2024-11-09 10:26:42] normalDB not a valid normalDB object. Use createNormalDatabase to
FATAL [2024-11-09 10:26:42] create one.
FATAL [2024-11-09 10:26:42]
FATAL [2024-11-09 10:26:42] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:26:42] parameters (PureCN 2.12.0).
WARN [2024-11-09 10:26:42] You are likely not using the correct baits file!
WARN [2024-11-09 10:26:42] Allosome coverage missing, cannot determine sex.
WARN [2024-11-09 10:26:42] Allosome coverage missing, cannot determine sex.
WARN [2024-11-09 10:26:43] Allosome coverage missing, cannot determine sex.
WARN [2024-11-09 10:26:43] Allosome coverage missing, cannot determine sex.
FATAL [2024-11-09 10:26:43] normalDB appears to be empty.
FATAL [2024-11-09 10:26:43]
FATAL [2024-11-09 10:26:43] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:26:43] parameters (PureCN 2.12.0).
WARN [2024-11-09 10:26:43] Allosome coverage missing, cannot determine sex.
WARN [2024-11-09 10:26:43] Allosome coverage missing, cannot determine sex.
WARN [2024-11-09 10:26:43] Intervals in coverage and interval.file have conflicting on/off-target annotation.
WARN [2024-11-09 10:26:46] Allosome coverage missing, cannot determine sex.
WARN [2024-11-09 10:26:46] Allosome coverage missing, cannot determine sex.
FATAL [2024-11-09 10:26:46] Seqlevels missing in provided segmentation: 6
FATAL [2024-11-09 10:26:46]
FATAL [2024-11-09 10:26:46] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:26:46] parameters (PureCN 2.12.0).
sh: gatk: command not found
WARN [2024-11-09 10:26:47] Cannot find gatk binary in path.
WARN [2024-11-09 10:26:47] Allosome coverage missing, cannot determine sex.
WARN [2024-11-09 10:26:47] Allosome coverage missing, cannot determine sex.
WARN [2024-11-09 10:26:47] No normalDB provided. Provide one for better results.
FATAL [2024-11-09 10:26:47] segmentationHclust requires an input segmentation.
FATAL [2024-11-09 10:26:47]
FATAL [2024-11-09 10:26:47] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:26:47] parameters (PureCN 2.12.0).
WARN [2024-11-09 10:26:47] Allosome coverage missing, cannot determine sex.
WARN [2024-11-09 10:26:47] Allosome coverage missing, cannot determine sex.
WARN [2024-11-09 10:26:47] No normalDB provided. Provide one for better results.
FATAL [2024-11-09 10:26:55] The normal.panel.vcf.file contains only a single sample.
FATAL [2024-11-09 10:26:55]
FATAL [2024-11-09 10:26:55] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:26:55] parameters (PureCN 2.12.0).
FATAL [2024-11-09 10:26:55] mapping.bias.file must be a file with *.rds suffix.
FATAL [2024-11-09 10:26:55]
FATAL [2024-11-09 10:26:55] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:26:55] parameters (PureCN 2.12.0).
Failed with error: 'there is no package called 'genomicsdb''
FATAL [2024-11-09 10:26:55] min.normals (0) must be >= 1.
FATAL [2024-11-09 10:26:55]
FATAL [2024-11-09 10:26:55] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:26:55] parameters (PureCN 2.12.0).
FATAL [2024-11-09 10:26:55] min.normals (10) cannot be larger than min.normals.assign.betafit (3).
FATAL [2024-11-09 10:26:55]
FATAL [2024-11-09 10:26:55] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:26:55] parameters (PureCN 2.12.0).
FATAL [2024-11-09 10:26:55] min.normals.assign.betafit (10) cannot be larger than
FATAL [2024-11-09 10:26:55] min.normals.betafit (7).
FATAL [2024-11-09 10:26:55]
FATAL [2024-11-09 10:26:55] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:26:55] parameters (PureCN 2.12.0).
FATAL [2024-11-09 10:26:55] min.normals.betafit (20) cannot be larger than
FATAL [2024-11-09 10:26:55] min.normals.position.specific.fit (10).
FATAL [2024-11-09 10:26:55]
FATAL [2024-11-09 10:26:55] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:26:55] parameters (PureCN 2.12.0).
FATAL [2024-11-09 10:26:55] min.betafit.rho not within expected range or format.
FATAL [2024-11-09 10:26:55]
FATAL [2024-11-09 10:26:55] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:26:55] parameters (PureCN 2.12.0).
FATAL [2024-11-09 10:26:55] max.betafit.rho not within expected range or format.
FATAL [2024-11-09 10:26:55]
FATAL [2024-11-09 10:26:55] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:26:55] parameters (PureCN 2.12.0).
FATAL [2024-11-09 10:26:55] min.betafit.rho (0.9) cannot be larger than max.betafit.rho (0.2).
FATAL [2024-11-09 10:26:55]
FATAL [2024-11-09 10:26:55] This is most likely a user error due to invalid input data or
FATAL [2024-11-09 10:26:55] parameters (PureCN 2.12.0).
[ FAIL 0 | WARN 13 | SKIP 2 | PASS 404 ]
══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• gatk binary > 4.1.7.0 required (1): 'test_segmentation.R:25:4'
• genomicsdb required (1): 'test_setMappingBiasVcf.R:45:5'
[ FAIL 0 | WARN 13 | SKIP 2 | PASS 404 ]
>
> proc.time()
user system elapsed
121.359 4.036 114.691
PureCN.Rcheck/PureCN-Ex.timings
| name | user | system | elapsed | |
| adjustLogRatio | 0.718 | 0.013 | 0.733 | |
| annotateTargets | 2.346 | 0.066 | 2.415 | |
| bootstrapResults | 0.582 | 0.014 | 0.597 | |
| calculateBamCoverageByInterval | 0.061 | 0.002 | 0.064 | |
| calculateLogRatio | 0.193 | 0.010 | 0.203 | |
| calculateMappingBiasGatk4 | 0.000 | 0.001 | 0.000 | |
| calculateMappingBiasVcf | 0.590 | 0.017 | 0.607 | |
| calculatePowerDetectSomatic | 0.431 | 0.005 | 0.436 | |
| calculateTangentNormal | 0.899 | 0.040 | 0.939 | |
| callAlterations | 0.053 | 0.002 | 0.055 | |
| callAlterationsFromSegmentation | 0.474 | 0.011 | 0.489 | |
| callAmplificationsInLowPurity | 11.848 | 0.118 | 11.966 | |
| callCIN | 0.080 | 0.002 | 0.082 | |
| callLOH | 0.070 | 0.002 | 0.072 | |
| callMutationBurden | 0.535 | 0.010 | 0.546 | |
| centromeres | 0.000 | 0.001 | 0.001 | |
| correctCoverageBias | 0.524 | 0.008 | 0.532 | |
| createCurationFile | 0.143 | 0.003 | 0.146 | |
| createNormalDatabase | 0.770 | 0.006 | 0.776 | |
| filterIntervals | 6.814 | 0.119 | 6.935 | |
| filterVcfBasic | 0.202 | 0.002 | 0.204 | |
| filterVcfMuTect | 0.215 | 0.001 | 0.217 | |
| filterVcfMuTect2 | 0.207 | 0.001 | 0.216 | |
| findFocal | 3.920 | 0.022 | 3.943 | |
| getSexFromCoverage | 0.087 | 0.004 | 0.091 | |
| getSexFromVcf | 0.080 | 0.004 | 0.083 | |
| plotAbs | 0.082 | 0.003 | 0.086 | |
| poolCoverage | 0.183 | 0.009 | 0.192 | |
| predictSomatic | 0.156 | 0.002 | 0.157 | |
| preprocessIntervals | 0.215 | 0.003 | 0.219 | |
| processMultipleSamples | 0.808 | 0.013 | 0.821 | |
| readAllelicCountsFile | 0.193 | 0.000 | 0.194 | |
| readCoverageFile | 0.074 | 0.002 | 0.076 | |
| readCurationFile | 0.083 | 0.002 | 0.085 | |
| readIntervalFile | 0.060 | 0.000 | 0.061 | |
| readLogRatioFile | 0.008 | 0.000 | 0.009 | |
| readSegmentationFile | 0.002 | 0.000 | 0.002 | |
| runAbsoluteCN | 5.458 | 0.107 | 5.565 | |
| segmentationCBS | 2.512 | 0.021 | 2.533 | |
| segmentationGATK4 | 0.001 | 0.000 | 0.001 | |
| segmentationHclust | 4.701 | 0.060 | 4.762 | |
| segmentationPSCBS | 7.824 | 0.119 | 7.947 | |
| setMappingBiasVcf | 0.113 | 0.004 | 0.117 | |
| setPriorVcf | 0.087 | 0.003 | 0.090 | |