Back to Multiple platform build/check report for BioC 3.20:   simplified   long
ABCDEFGHIJKLMNO[P]QRSTUVWXYZ

This page was generated on 2024-06-21 13:21 -0400 (Fri, 21 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4690
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4404
kjohnson3macOS 13.6.5 Venturaarm644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4353
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 1585/2242HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PureCN 2.11.0  (landing page)
Markus Riester
Snapshot Date: 2024-06-20 14:00 -0400 (Thu, 20 Jun 2024)
git_url: https://git.bioconductor.org/packages/PureCN
git_branch: devel
git_last_commit: 8829f97
git_last_commit_date: 2024-04-30 10:50:39 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for PureCN on nebbiolo2

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.

raw results


Summary

Package: PureCN
Version: 2.11.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:PureCN.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings PureCN_2.11.0.tar.gz
StartedAt: 2024-06-21 02:28:53 -0400 (Fri, 21 Jun 2024)
EndedAt: 2024-06-21 02:46:56 -0400 (Fri, 21 Jun 2024)
EllapsedTime: 1083.2 seconds
RetCode: 0
Status:   OK  
CheckDir: PureCN.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:PureCN.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings PureCN_2.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/PureCN.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘PureCN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PureCN’ version ‘2.11.0’
* checking package namespace information ... OK
* checking package dependencies ... 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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
callAmplificationsInLowPurity 40.809  0.363  41.173
segmentationPSCBS             25.988  0.124  26.112
filterIntervals               21.114  0.124  21.228
runAbsoluteCN                 18.057  0.084  18.141
segmentationHclust            16.890  0.176  17.067
findFocal                     11.567  0.092  11.669
segmentationCBS                8.880  0.040   8.920
annotateTargets                6.147  0.232   6.380
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/PureCN.Rcheck/00check.log’
for details.


Installation output

PureCN.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL PureCN
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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)

Tests output

PureCN.Rcheck/tests/testthat.Rout


R version 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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, 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 [2024-06-21 02:37:13] Attempted adding gene symbols to intervals. Heuristics have been used to pick symbols for overlapping genes.
WARN [2024-06-21 02:37:13] Chromosome naming style of txdb file (UCSC) was different from interval file (Ensembl).
WARN [2024-06-21 02:37:18] Attempted adding gene symbols to intervals. Heuristics have been used to pick symbols for overlapping genes.
FATAL [2024-06-21 02:37:21] tumor.coverage.file and interval.file do not align. 

FATAL [2024-06-21 02:37:21]  

FATAL [2024-06-21 02:37:21] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:37:21] parameters (PureCN 2.11.0). 

WARN [2024-06-21 02:37:21] Cannot find all contig lengths while exporting interval file.
INFO [2024-06-21 02:37:22] Processing seq1:1-21 (1/3)...
INFO [2024-06-21 02:37:22] Processing seq1:1227-1247 (2/3)...
INFO [2024-06-21 02:37:23] Processing seq2:594-614 (3/3)...
WARN [2024-06-21 02:37:24] Large potential mis-calibration of on- and off-target log2 ratios: 0.26
FATAL [2024-06-21 02:37:24] Need either f or purity and ploidy. 

FATAL [2024-06-21 02:37:24]  

FATAL [2024-06-21 02:37:24] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:37:24] parameters (PureCN 2.11.0). 

FATAL [2024-06-21 02:37:24] f not in expected range. 

FATAL [2024-06-21 02:37:24]  

FATAL [2024-06-21 02:37:24] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:37:24] parameters (PureCN 2.11.0). 

FATAL [2024-06-21 02:37:24] coverage not in expected range (>=2) 

FATAL [2024-06-21 02:37:24]  

FATAL [2024-06-21 02:37:24] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:37:24] parameters (PureCN 2.11.0). 

FATAL [2024-06-21 02:37:24] purity not in expected range. 

FATAL [2024-06-21 02:37:24]  

FATAL [2024-06-21 02:37:24] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:37:24] parameters (PureCN 2.11.0). 

FATAL [2024-06-21 02:37:24] ploidy not in expected range. 

FATAL [2024-06-21 02:37:24]  

FATAL [2024-06-21 02:37:24] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:37:24] parameters (PureCN 2.11.0). 

FATAL [2024-06-21 02:37:24] cell.fraction not in expected range. 

FATAL [2024-06-21 02:37:24]  

FATAL [2024-06-21 02:37:24] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:37:24] parameters (PureCN 2.11.0). 

INFO [2024-06-21 02:37:26] 576 on-target bins with low coverage in all samples.
WARN [2024-06-21 02:37:26] You are likely not using the correct baits file!
WARN [2024-06-21 02:37:26] Allosome coverage missing, cannot determine sex.
WARN [2024-06-21 02:37:26] Allosome coverage missing, cannot determine sex.
INFO [2024-06-21 02:37:26] Processing on-target regions...
INFO [2024-06-21 02:37:27] Removing 930 intervals with low coverage in normalDB.
INFO [2024-06-21 02:37:27] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2024-06-21 02:37:28] Tumor/normal noise ratio: 19.041
WARN [2024-06-21 02:37:28] Extensive noise in tumor compared to normals.
INFO [2024-06-21 02:38:15] Tumor/normal noise ratio: 19.041
WARN [2024-06-21 02:38:15] Extensive noise in tumor compared to normals.
INFO [2024-06-21 02:38:19] Using BiocParallel for parallel optimization.
FATAL [2024-06-21 02:38:33] pvalue.cutoff not within expected range or format. 

FATAL [2024-06-21 02:38:33]  

FATAL [2024-06-21 02:38:33] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:38:33] parameters (PureCN 2.11.0). 

FATAL [2024-06-21 02:38:33] pvalue.cutoff not within expected range or format. 

FATAL [2024-06-21 02:38:33]  

FATAL [2024-06-21 02:38:33] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:38:33] parameters (PureCN 2.11.0). 

FATAL [2024-06-21 02:38:33] percentile.cutoff not in expected range (0 to 100). 

FATAL [2024-06-21 02:38:33]  

FATAL [2024-06-21 02:38:33] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:38:33] parameters (PureCN 2.11.0). 

FATAL [2024-06-21 02:38:33] percentile.cutoff not in expected range (0 to 100). 

FATAL [2024-06-21 02:38:33]  

FATAL [2024-06-21 02:38:33] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:38:33] parameters (PureCN 2.11.0). 

FATAL [2024-06-21 02:38:33] purity not within expected range or format. 

FATAL [2024-06-21 02:38:33]  

FATAL [2024-06-21 02:38:33] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:38:33] parameters (PureCN 2.11.0). 

FATAL [2024-06-21 02:38:33] purity not within expected range or format. 

FATAL [2024-06-21 02:38:33]  

FATAL [2024-06-21 02:38:33] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:38:33] parameters (PureCN 2.11.0). 

INFO [2024-06-21 02:38:35] ------------------------------------------------------------
INFO [2024-06-21 02:38:35] PureCN 2.11.0
INFO [2024-06-21 02:38:35] ------------------------------------------------------------
INFO [2024-06-21 02:38:35] Loading coverage files...
INFO [2024-06-21 02:38:35] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2024-06-21 02:38:35] Allosome coverage missing, cannot determine sex.
WARN [2024-06-21 02:38:35] Allosome coverage missing, cannot determine sex.
INFO [2024-06-21 02:38:35] Removing 228 intervals with missing log.ratio.
INFO [2024-06-21 02:38:35] Removing 22 small (< 5bp) intervals.
INFO [2024-06-21 02:38:35] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2024-06-21 02:38:35] No normalDB provided. Provide one for better results.
INFO [2024-06-21 02:38:35] Removing 1724 low count (< 100 total reads) intervals.
INFO [2024-06-21 02:38:35] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2024-06-21 02:38:35] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2024-06-21 02:38:35] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2024-06-21 02:38:35] No interval.file provided. Cannot check for any GC-biases.
INFO [2024-06-21 02:38:35] Loading VCF...
INFO [2024-06-21 02:38:35] Found 127 variants in VCF file.
INFO [2024-06-21 02:38:35] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2024-06-21 02:38:35] LIB-02240e4 is tumor in VCF file.
INFO [2024-06-21 02:38:35] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2024-06-21 02:38:35] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2024-06-21 02:38:35] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2024-06-21 02:38:36] Base quality scores range from 29 to 35 (offset by 1)
INFO [2024-06-21 02:38:36] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2024-06-21 02:38:36] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2024-06-21 02:38:36] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding).
INFO [2024-06-21 02:38:36] 1.2% of targets contain variants.
INFO [2024-06-21 02:38:36] Removing 4 variants outside intervals.
INFO [2024-06-21 02:38:36] Found SOMATIC annotation in VCF.
INFO [2024-06-21 02:38:36] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2024-06-21 02:38:36] Found SOMATIC annotation in VCF. Setting mapping bias to 0.972.
INFO [2024-06-21 02:38:36] Excluding 0 novel or poor quality variants from segmentation.
INFO [2024-06-21 02:38:37] Sample sex: ?
INFO [2024-06-21 02:38:37] Segmenting data...
INFO [2024-06-21 02:38:37] Loading pre-computed boundaries for DNAcopy...
INFO [2024-06-21 02:38:37] Setting undo.SD parameter to 1.000000.
INFO [2024-06-21 02:38:37] Setting prune.hclust.h parameter to 0.200000.
INFO [2024-06-21 02:38:38] Found 59 segments with median size of 17.67Mb.
INFO [2024-06-21 02:38:38] Using 121 variants.
INFO [2024-06-21 02:38:38] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2024-06-21 02:38:38] 2D-grid search of purity and ploidy...
INFO [2024-06-21 02:38:39] Local optima: 0.63/1.9, 0.5/2
INFO [2024-06-21 02:38:39] Testing local optimum 1/2 at purity 0.63 and total ploidy 1.90...
INFO [2024-06-21 02:38:40] Testing local optimum 2/2 at purity 0.50 and total ploidy 2.00...
INFO [2024-06-21 02:38:41] Skipping 1 solutions that converged to the same optima.
INFO [2024-06-21 02:38:41] Fitting variants with beta model for local optimum 1/2...
INFO [2024-06-21 02:38:41] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2024-06-21 02:38:44] Optimized purity: 0.65
INFO [2024-06-21 02:38:44] Done.
INFO [2024-06-21 02:38:44] ------------------------------------------------------------
INFO [2024-06-21 02:38:45] Estimating callable regions.
FATAL [2024-06-21 02:38:46] exclude not a GRanges object. 

FATAL [2024-06-21 02:38:46]  

FATAL [2024-06-21 02:38:46] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:38:46] parameters (PureCN 2.11.0). 

FATAL [2024-06-21 02:38:46] callable not a GRanges object. 

FATAL [2024-06-21 02:38:46]  

FATAL [2024-06-21 02:38:46] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:38:46] parameters (PureCN 2.11.0). 

WARN [2024-06-21 02:38:56] tumor.coverage.file and interval.file do not align.
INFO [2024-06-21 02:38:57] No Gene column in interval.file. You won't get gene-level calls.
FATAL [2024-06-21 02:38:58] No gc_bias column in interval.file. 

FATAL [2024-06-21 02:38:58]  

FATAL [2024-06-21 02:38:58] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:38:58] parameters (PureCN 2.11.0). 

FATAL [2024-06-21 02:38:59] Provided coverage is zero, most likely due to a corrupt BAM file. 

FATAL [2024-06-21 02:38:59]  

FATAL [2024-06-21 02:38:59] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:38:59] parameters (PureCN 2.11.0). 

INFO [2024-06-21 02:39:01] No reptiming column in interval.file.
INFO [2024-06-21 02:39:04] Reading /tmp/Rtmp6peUvj/file15dcd365083b41.rds...
INFO [2024-06-21 02:39:04] Reading /tmp/Rtmp6peUvj/file15dcd365083b41.rds...
INFO [2024-06-21 02:39:04] Reading /tmp/Rtmp6peUvj/file15dcd365083b41.rds...
INFO [2024-06-21 02:39:04] Reading /tmp/Rtmp6peUvj/file15dcd365083b41.rds...
INFO [2024-06-21 02:39:05] Reading /tmp/Rtmp6peUvj/file15dcd365083b41.rds...
INFO [2024-06-21 02:39:05] Reading /tmp/Rtmp6peUvj/file15dcd365083b41.rds...
FATAL [2024-06-21 02:39:05] Purity or Ploidy not numeric or in expected range. 

FATAL [2024-06-21 02:39:05]  

FATAL [2024-06-21 02:39:05] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:39:05] parameters (PureCN 2.11.0). 

INFO [2024-06-21 02:39:05] Reading /tmp/Rtmp6peUvj/file15dcd365083b41.rds...
INFO [2024-06-21 02:39:05] Reading /tmp/Rtmp6peUvj/file15dcd365083b41.rds...
FATAL [2024-06-21 02:39:05] 'Failed' column in /tmp/Rtmp6peUvj/file15dcd365083b41.csv not 

FATAL [2024-06-21 02:39:05] logical(1). 

FATAL [2024-06-21 02:39:05]  

FATAL [2024-06-21 02:39:05] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:39:05] parameters (PureCN 2.11.0). 

INFO [2024-06-21 02:39:06] 576 on-target bins with low coverage in all samples.
WARN [2024-06-21 02:39:06] You are likely not using the correct baits file!
WARN [2024-06-21 02:39:06] Allosome coverage missing, cannot determine sex.
WARN [2024-06-21 02:39:06] Allosome coverage missing, cannot determine sex.
INFO [2024-06-21 02:39:06] Processing on-target regions...
INFO [2024-06-21 02:39:06] Removing 930 intervals with low coverage in normalDB.
INFO [2024-06-21 02:39:06] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2024-06-21 02:39:10] 576 on-target bins with low coverage in all samples.
WARN [2024-06-21 02:39:10] You are likely not using the correct baits file!
WARN [2024-06-21 02:39:10] Allosome coverage missing, cannot determine sex.
WARN [2024-06-21 02:39:10] Allosome coverage missing, cannot determine sex.
INFO [2024-06-21 02:39:10] Processing on-target regions...
INFO [2024-06-21 02:39:10] Removing 930 intervals with low coverage in normalDB.
INFO [2024-06-21 02:39:10] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2024-06-21 02:39:12] 576 on-target bins with low coverage in all samples.
WARN [2024-06-21 02:39:12] You are likely not using the correct baits file!
WARN [2024-06-21 02:39:12] Allosome coverage missing, cannot determine sex.
WARN [2024-06-21 02:39:12] Allosome coverage missing, cannot determine sex.
INFO [2024-06-21 02:39:12] Processing on-target regions...
INFO [2024-06-21 02:39:13] Removing 930 intervals with low coverage in normalDB.
INFO [2024-06-21 02:39:13] Removing 1 intervals with zero coverage in more than 3% of normalDB.
WARN [2024-06-21 02:39:13] Allosome coverage missing, cannot determine sex.
INFO [2024-06-21 02:39:13] Sample sex: NA
WARN [2024-06-21 02:39:14] Allosome coverage missing, cannot determine sex.
INFO [2024-06-21 02:39:14] Sample sex: NA
INFO [2024-06-21 02:39:15] 576 on-target bins with low coverage in all samples.
WARN [2024-06-21 02:39:15] You are likely not using the correct baits file!
WARN [2024-06-21 02:39:15] Allosome coverage missing, cannot determine sex.
WARN [2024-06-21 02:39:15] Allosome coverage missing, cannot determine sex.
FATAL [2024-06-21 02:39:15] Length of normal.coverage.files and sex different 

FATAL [2024-06-21 02:39:15]  

FATAL [2024-06-21 02:39:15] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:39:15] parameters (PureCN 2.11.0). 

WARN [2024-06-21 02:39:19] Target intervals were not sorted.
INFO [2024-06-21 02:39:19] 560 on-target bins with low coverage in all samples.
WARN [2024-06-21 02:39:19] You are likely not using the correct baits file!
WARN [2024-06-21 02:39:19] Allosome coverage missing, cannot determine sex.
WARN [2024-06-21 02:39:19] Allosome coverage missing, cannot determine sex.
WARN [2024-06-21 02:39:19] Allosome coverage missing, cannot determine sex.
INFO [2024-06-21 02:39:19] Processing on-target regions...
INFO [2024-06-21 02:39:21] Removing 978 intervals with low coverage in normalDB.
INFO [2024-06-21 02:39:21] Removing 11 intervals with zero coverage in more than 3% of normalDB.
FATAL [2024-06-21 02:39:23] tumor.coverage.file and normalDB do not align. 

FATAL [2024-06-21 02:39:23]  

FATAL [2024-06-21 02:39:23] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:39:23] parameters (PureCN 2.11.0). 

FATAL [2024-06-21 02:39:23] At least 2 normal.coverage.files required. 

FATAL [2024-06-21 02:39:23]  

FATAL [2024-06-21 02:39:23] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:39:23] parameters (PureCN 2.11.0). 

INFO [2024-06-21 02:39:26] ------------------------------------------------------------
INFO [2024-06-21 02:39:26] PureCN 2.11.0
INFO [2024-06-21 02:39:26] ------------------------------------------------------------
INFO [2024-06-21 02:39:26] Loading coverage files...
INFO [2024-06-21 02:39:26] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2024-06-21 02:39:26] Allosome coverage missing, cannot determine sex.
WARN [2024-06-21 02:39:26] Allosome coverage missing, cannot determine sex.
INFO [2024-06-21 02:39:26] Removing 228 intervals with missing log.ratio.
FATAL [2024-06-21 02:39:26] normalDB incompatible with this PureCN version. Please re-run 

FATAL [2024-06-21 02:39:26] NormalDB.R. 

FATAL [2024-06-21 02:39:26]  

FATAL [2024-06-21 02:39:26] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:39:26] parameters (PureCN 2.11.0). 

FATAL [2024-06-21 02:39:27] normalDB incompatible with this PureCN version. Please re-run 

FATAL [2024-06-21 02:39:27] NormalDB.R. 

FATAL [2024-06-21 02:39:27]  

FATAL [2024-06-21 02:39:27] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:39:27] parameters (PureCN 2.11.0). 

FATAL [2024-06-21 02:39:27] normal.coverage.files with _coverage.txt and _loess.txt suffix 

FATAL [2024-06-21 02:39:27] provided. Provide either only GC-normalized or raw coverage files! 

FATAL [2024-06-21 02:39:27]  

FATAL [2024-06-21 02:39:27] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:39:27] parameters (PureCN 2.11.0). 

INFO [2024-06-21 02:39:27] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2024-06-21 02:39:27] Removing 19 low quality variants with non-offset BQ < 25.
INFO [2024-06-21 02:39:27] Base quality scores range from 24 to 35 (offset by 1)
INFO [2024-06-21 02:39:27] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS.
INFO [2024-06-21 02:39:28] Initial testing for significant sample cross-contamination: unlikely
INFO [2024-06-21 02:39:28] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2024-06-21 02:39:28] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2024-06-21 02:39:28] Removing 19 low quality variants with non-offset BQ < 25.
INFO [2024-06-21 02:39:28] Base quality scores range from 24 to 35 (offset by 1)
INFO [2024-06-21 02:39:28] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS.
INFO [2024-06-21 02:39:28] Initial testing for significant sample cross-contamination: unlikely
INFO [2024-06-21 02:39:28] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2024-06-21 02:39:29] Removing 6 blacklisted variants.
INFO [2024-06-21 02:39:29] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2024-06-21 02:39:29] Removing 19 low quality variants with non-offset BQ < 25.
INFO [2024-06-21 02:39:29] Base quality scores range from 24 to 35 (offset by 1)
INFO [2024-06-21 02:39:29] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS.
INFO [2024-06-21 02:39:29] Initial testing for significant sample cross-contamination: unlikely
INFO [2024-06-21 02:39:29] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
WARN [2024-06-21 02:39:29] MuTect stats file lacks contig and position columns.
INFO [2024-06-21 02:39:29] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2024-06-21 02:39:29] Removing 19 low quality variants with non-offset BQ < 25.
INFO [2024-06-21 02:39:30] Base quality scores range from 24 to 35 (offset by 1)
INFO [2024-06-21 02:39:30] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS.
INFO [2024-06-21 02:39:30] Initial testing for significant sample cross-contamination: unlikely
INFO [2024-06-21 02:39:30] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
WARN [2024-06-21 02:39:30] MuTect stats file and VCF file do not align perfectly. Will remove 2325 unmatched variants.
WARN [2024-06-21 02:39:30] MuTect stats file lacks failure_reasons column. Keeping all variants listed in stats file.
INFO [2024-06-21 02:39:30] Removing 0 non heterozygous (in matched normal) germline SNPs.
INFO [2024-06-21 02:39:30] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2024-06-21 02:39:30] Base quality scores range from 31 to 33 (offset by 1)
INFO [2024-06-21 02:39:30] Minimum number of supporting reads ranges from 3 to 4, depending on coverage and BQS.
INFO [2024-06-21 02:39:31] Removing 0 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2024-06-21 02:39:31] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2024-06-21 02:39:31] Base quality scores range from 7 to 35 (offset by 1)
INFO [2024-06-21 02:39:31] Minimum number of supporting reads ranges from 1 to 41, depending on coverage and BQS.
INFO [2024-06-21 02:39:31] Initial testing for significant sample cross-contamination: unlikely
INFO [2024-06-21 02:39:31] Removing 49 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2024-06-21 02:39:31] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2024-06-21 02:39:31] Base quality scores range from 7 to 35 (offset by 1)
INFO [2024-06-21 02:39:31] Minimum number of supporting reads ranges from 1 to 41, depending on coverage and BQS.
INFO [2024-06-21 02:39:32] Initial testing for significant sample cross-contamination: unlikely
INFO [2024-06-21 02:39:32] Removing 49 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2024-06-21 02:39:32] Removing 22 non heterozygous (in matched normal) germline SNPs.
WARN [2024-06-21 02:39:32] Many variants removed by min.base.quality (50) filter. You might want to lower the cutoff.
FATAL [2024-06-21 02:39:32] No variants passed filter BQ. 

FATAL [2024-06-21 02:39:32]  

FATAL [2024-06-21 02:39:32] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:39:32] parameters (PureCN 2.11.0). 

INFO [2024-06-21 02:39:32] Found 11 variants in VCF file.
WARN [2024-06-21 02:39:33] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead.
INFO [2024-06-21 02:39:33] 1 (9.1%) variants annotated as likely germline (DB INFO flag).
INFO [2024-06-21 02:39:35] Found 11 variants in VCF file.
WARN [2024-06-21 02:39:35] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead.
INFO [2024-06-21 02:39:35] 1 (9.1%) variants annotated as likely germline (DB INFO flag).
INFO [2024-06-21 02:39:35] Found 11 variants in VCF file.
WARN [2024-06-21 02:39:36] vcf.file has no DB or POP_AF info field for membership in germline databases. Guessing it based on available dbSNP ID.
INFO [2024-06-21 02:39:36] 1 (9.1%) variants annotated as likely germline (DB INFO flag).
INFO [2024-06-21 02:39:36] Found 1000 variants in VCF file.
INFO [2024-06-21 02:39:36] Removing 2 triallelic sites.
WARN [2024-06-21 02:39:36] Having trouble guessing SOMATIC status...
WARN [2024-06-21 02:39:36] DP FORMAT field contains NAs. Removing 44 variants.
INFO [2024-06-21 02:39:36] 954 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2024-06-21 02:39:38] Found 12 variants in VCF file.
INFO [2024-06-21 02:39:38] Removing 1 triallelic sites.
WARN [2024-06-21 02:39:38] DP FORMAT field contains NAs. Removing 1 variants.
WARN [2024-06-21 02:39:38] vcf.file has no DB info field for membership in germline databases. Found and used somatic status instead.
INFO [2024-06-21 02:39:38] 8 (80.0%) variants annotated as likely germline (DB INFO flag).
WARN [2024-06-21 02:39:39] BQ FORMAT field contains NAs.
INFO [2024-06-21 02:39:39] Found 2331 variants in VCF file.
INFO [2024-06-21 02:39:39] 2282 (97.9%) variants annotated as likely germline (DB INFO flag).
INFO [2024-06-21 02:39:40] Found 2331 variants in VCF file.
INFO [2024-06-21 02:39:40] 2282 (97.9%) variants annotated as likely germline (DB INFO flag).
WARN [2024-06-21 02:39:40] Did not find base quality scores, will use global error rate of 0.0010 instead.
INFO [2024-06-21 02:39:40] Removing 21 low quality variants with non-offset BQ < 25.
INFO [2024-06-21 02:39:40] Base quality scores range from 24 to 35 (offset by 1)
INFO [2024-06-21 02:39:40] Initial testing for significant sample cross-contamination: unlikely
INFO [2024-06-21 02:39:40] Removing 89 variants with AF < 0.030 or AF >= 0.970 or insufficient supporting reads or depth < 15.
INFO [2024-06-21 02:39:41] Found 2331 variants in VCF file.
INFO [2024-06-21 02:39:41] 2282 (97.9%) variants annotated as likely germline (DB INFO flag).
WARN [2024-06-21 02:39:41] BQ FORMAT field contains NAs.
WARN [2024-06-21 02:39:42] Allosome coverage missing, cannot determine sex.
WARN [2024-06-21 02:39:42] Allosome coverage missing, cannot determine sex.
INFO [2024-06-21 02:39:42] Mean coverages: chrX: 108.58, chrY: 108.58, chr1-22: 104.87.
INFO [2024-06-21 02:39:42] Mean coverages: chrX: 108.58, chrY: 2.17, chr1-22: 104.87.
INFO [2024-06-21 02:39:42] Mean coverages: chrX: 108.58, chrY: 5.17, chr1-22: 104.87.
INFO [2024-06-21 02:39:43] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2024-06-21 02:39:43] No germline variants in VCF.
FATAL [2024-06-21 02:39:43] No solution with id hello 

FATAL [2024-06-21 02:39:43]  

FATAL [2024-06-21 02:39:43] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:39:43] parameters (PureCN 2.11.0). 

FATAL [2024-06-21 02:39:43] No solution with id 100 

FATAL [2024-06-21 02:39:43]  

FATAL [2024-06-21 02:39:43] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:39:43] parameters (PureCN 2.11.0). 

FATAL [2024-06-21 02:39:44] all.data and w have different lengths. 

FATAL [2024-06-21 02:39:44]  

FATAL [2024-06-21 02:39:44] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:39:44] parameters (PureCN 2.11.0). 

INFO [2024-06-21 02:39:45] Splitting 5 large targets to an average width of 400.
WARN [2024-06-21 02:39:45] No mappability scores provided.
WARN [2024-06-21 02:39:45] No reptiming scores provided.
INFO [2024-06-21 02:39:45] Calculating GC-content...
INFO [2024-06-21 02:39:45] Splitting 5 large targets to an average width of 400.
WARN [2024-06-21 02:39:45] No mappability scores provided.
WARN [2024-06-21 02:39:45] No reptiming scores provided.
INFO [2024-06-21 02:39:45] Calculating GC-content...
INFO [2024-06-21 02:39:46] Splitting 5 large targets to an average width of 400.
INFO [2024-06-21 02:39:46] Removing 1 targets overlapping with exclude.
WARN [2024-06-21 02:39:46] No mappability scores provided.
WARN [2024-06-21 02:39:46] No reptiming scores provided.
INFO [2024-06-21 02:39:46] Calculating GC-content...
WARN [2024-06-21 02:39:46] Found small target regions (< 100bp). Will resize them.
INFO [2024-06-21 02:39:46] Splitting 5 large targets to an average width of 400.
FATAL [2024-06-21 02:39:46] off.target.padding must be negative. 

FATAL [2024-06-21 02:39:46]  

FATAL [2024-06-21 02:39:46] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:39:46] parameters (PureCN 2.11.0). 

FATAL [2024-06-21 02:39:46] Interval coordinates should start at 1, not at 0 

FATAL [2024-06-21 02:39:46]  

FATAL [2024-06-21 02:39:46] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:39:46] parameters (PureCN 2.11.0). 

WARN [2024-06-21 02:39:47] Found small target regions (< 100bp). Will resize them.
INFO [2024-06-21 02:39:47] Splitting 5 large targets to an average width of 400.
FATAL [2024-06-21 02:39:47] No off-target regions after filtering for mappability and 

FATAL [2024-06-21 02:39:47] off.target.padding 

FATAL [2024-06-21 02:39:47]  

FATAL [2024-06-21 02:39:47] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:39:47] parameters (PureCN 2.11.0). 

WARN [2024-06-21 02:39:47] Found small target regions (< 100bp). Will resize them.
INFO [2024-06-21 02:39:47] Splitting 5 large targets to an average width of 400.
WARN [2024-06-21 02:39:47] No mappability scores provided.
INFO [2024-06-21 02:39:47] Calculating GC-content...
WARN [2024-06-21 02:39:47] Found small target regions (< 100bp). Will resize them.
INFO [2024-06-21 02:39:47] Averaging reptiming into bins of size 200...
INFO [2024-06-21 02:39:47] Splitting 5 large targets to an average width of 400.
WARN [2024-06-21 02:39:47] No mappability scores provided.
INFO [2024-06-21 02:39:47] Calculating GC-content...
WARN [2024-06-21 02:39:48] Found small target regions (< 100bp). Will resize them.
INFO [2024-06-21 02:39:48] Splitting 6 large targets to an average width of 200.
WARN [2024-06-21 02:39:48] No mappability scores provided.
WARN [2024-06-21 02:39:48] No reptiming scores provided.
INFO [2024-06-21 02:39:48] Calculating GC-content...
WARN [2024-06-21 02:39:48] Found small target regions (< 100bp). Will resize them.
INFO [2024-06-21 02:39:48] Splitting 5 large targets to an average width of 400.
WARN [2024-06-21 02:39:48] No mappability scores provided.
WARN [2024-06-21 02:39:48] No reptiming scores provided.
INFO [2024-06-21 02:39:48] Calculating GC-content...
INFO [2024-06-21 02:39:48] Splitting 5 large targets to an average width of 400.
INFO [2024-06-21 02:39:48] Tiling off-target regions to an average width of 200000.
WARN [2024-06-21 02:39:49] No mappability scores provided.
WARN [2024-06-21 02:39:49] No reptiming scores provided.
INFO [2024-06-21 02:39:49] Calculating GC-content...
WARN [2024-06-21 02:39:49] Intervals contain off-target regions. Will not change intervals.
WARN [2024-06-21 02:39:49] No mappability scores provided.
WARN [2024-06-21 02:39:49] No reptiming scores provided.
INFO [2024-06-21 02:39:49] Calculating GC-content...
INFO [2024-06-21 02:39:49] Splitting 5 large targets to an average width of 400.
WARN [2024-06-21 02:39:49] No reptiming scores provided.
INFO [2024-06-21 02:39:49] Calculating GC-content...
WARN [2024-06-21 02:39:49] Found small target regions (< 100bp). Will resize them.
INFO [2024-06-21 02:39:49] Splitting 5 large targets to an average width of 400.
WARN [2024-06-21 02:39:49] No reptiming scores provided.
INFO [2024-06-21 02:39:49] Calculating GC-content...
WARN [2024-06-21 02:39:50] Found small target regions (< 100bp). Will resize them.
INFO [2024-06-21 02:39:50] Splitting 5 large targets to an average width of 400.
WARN [2024-06-21 02:39:51] 1 intervals without mappability score (1 on-target).
INFO [2024-06-21 02:39:51] Removing 1 intervals with low mappability score (<0.60).
WARN [2024-06-21 02:39:51] No reptiming scores provided.
INFO [2024-06-21 02:39:51] Calculating GC-content...
WARN [2024-06-21 02:39:51] Found small target regions (< 100bp). Will resize them.
INFO [2024-06-21 02:39:51] Splitting 5 large targets to an average width of 400.
INFO [2024-06-21 02:39:51] Tiling off-target regions to an average width of 200000.
WARN [2024-06-21 02:39:51] No reptiming scores provided.
INFO [2024-06-21 02:39:51] Calculating GC-content...
INFO [2024-06-21 02:39:52] Splitting 5 large targets to an average width of 400.
WARN [2024-06-21 02:39:52] No mappability scores provided.
WARN [2024-06-21 02:39:52] No reptiming scores provided.
INFO [2024-06-21 02:39:52] Calculating GC-content...
WARN [2024-06-21 02:39:52] Chromosome naming style of interval file (Ensembl) was different from reference (UCSC).
INFO [2024-06-21 02:39:52] Splitting 5 large targets to an average width of 400.
WARN [2024-06-21 02:39:52] No mappability scores provided.
WARN [2024-06-21 02:39:52] No reptiming scores provided.
INFO [2024-06-21 02:39:52] Calculating GC-content...
FATAL [2024-06-21 02:39:52] Chromosome naming style of interval file unknown, should be UCSC. 

FATAL [2024-06-21 02:39:52]  

FATAL [2024-06-21 02:39:52] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:39:52] parameters (PureCN 2.11.0). 

WARN [2024-06-21 02:39:53] Chromosome naming style of interval file (Ensembl) was different from reference (UCSC).
WARN [2024-06-21 02:39:53] Chromosome naming style of mappability file (Ensembl) was different from reference (UCSC).
INFO [2024-06-21 02:39:53] Splitting 5 large targets to an average width of 400.
WARN [2024-06-21 02:39:53] No reptiming scores provided.
INFO [2024-06-21 02:39:53] Calculating GC-content...
WARN [2024-06-21 02:39:53] Found small target regions (< 60bp). Will resize them.
INFO [2024-06-21 02:39:53] Splitting 5 large targets to an average width of 400.
WARN [2024-06-21 02:39:53] No mappability scores provided.
WARN [2024-06-21 02:39:53] No reptiming scores provided.
INFO [2024-06-21 02:39:53] Calculating GC-content...
WARN [2024-06-21 02:39:53] Found small target regions (< 60bp). Will drop them.
INFO [2024-06-21 02:39:53] Splitting 4 large targets to an average width of 400.
WARN [2024-06-21 02:39:53] No mappability scores provided.
WARN [2024-06-21 02:39:53] No reptiming scores provided.
INFO [2024-06-21 02:39:53] Calculating GC-content...
WARN [2024-06-21 02:39:54] Found small target regions (< 200bp). Will resize them.
INFO [2024-06-21 02:39:54] Splitting 5 large targets to an average width of 400.
WARN [2024-06-21 02:39:54] No mappability scores provided.
WARN [2024-06-21 02:39:54] No reptiming scores provided.
INFO [2024-06-21 02:39:54] Calculating GC-content...
INFO [2024-06-21 02:39:54] Found 20 variants in VCF file.
INFO [2024-06-21 02:39:55] 20 (100.0%) variants annotated as likely germline (DB INFO flag).
WARN [2024-06-21 02:39:55] Did not find base quality scores, will use global error rate of 0.0010 instead.
INFO [2024-06-21 02:39:56] Found 127 variants in VCF file.
INFO [2024-06-21 02:39:56] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
WARN [2024-06-21 02:39:56] Did not find base quality scores, will use global error rate of 0.0010 instead.
INFO [2024-06-21 02:39:56] ------------------------------------------------------------
INFO [2024-06-21 02:39:56] PureCN 2.11.0
INFO [2024-06-21 02:39:56] ------------------------------------------------------------
INFO [2024-06-21 02:39:56] Loading coverage files...
INFO [2024-06-21 02:39:57] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2024-06-21 02:39:57] Allosome coverage missing, cannot determine sex.
WARN [2024-06-21 02:39:57] Allosome coverage missing, cannot determine sex.
INFO [2024-06-21 02:39:57] Removing 228 intervals with missing log.ratio.
INFO [2024-06-21 02:39:57] Removing 22 small (< 5bp) intervals.
INFO [2024-06-21 02:39:57] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2024-06-21 02:39:57] No normalDB provided. Provide one for better results.
INFO [2024-06-21 02:39:57] Removing 1724 low count (< 100 total reads) intervals.
INFO [2024-06-21 02:39:57] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2024-06-21 02:39:57] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2024-06-21 02:39:57] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2024-06-21 02:39:57] No interval.file provided. Cannot check for any GC-biases.
INFO [2024-06-21 02:39:57] Loading VCF...
INFO [2024-06-21 02:39:57] Found 127 variants in VCF file.
INFO [2024-06-21 02:39:57] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2024-06-21 02:39:57] LIB-02240e4 is tumor in VCF file.
INFO [2024-06-21 02:39:57] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2024-06-21 02:39:57] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2024-06-21 02:39:57] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2024-06-21 02:39:57] Base quality scores range from 29 to 35 (offset by 1)
INFO [2024-06-21 02:39:57] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2024-06-21 02:39:58] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2024-06-21 02:39:58] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding).
INFO [2024-06-21 02:39:58] 1.2% of targets contain variants.
INFO [2024-06-21 02:39:58] Removing 4 variants outside intervals.
INFO [2024-06-21 02:39:58] Found SOMATIC annotation in VCF.
INFO [2024-06-21 02:39:58] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2024-06-21 02:39:58] Found SOMATIC annotation in VCF. Setting mapping bias to 0.972.
INFO [2024-06-21 02:39:58] Excluding 0 novel or poor quality variants from segmentation.
INFO [2024-06-21 02:39:58] Sample sex: ?
INFO [2024-06-21 02:39:58] Segmenting data...
INFO [2024-06-21 02:39:58] Loading pre-computed boundaries for DNAcopy...
INFO [2024-06-21 02:39:58] Setting undo.SD parameter to 1.000000.
INFO [2024-06-21 02:39:59] Setting prune.hclust.h parameter to 0.200000.
INFO [2024-06-21 02:39:59] Found 59 segments with median size of 17.67Mb.
INFO [2024-06-21 02:39:59] Using 121 variants.
INFO [2024-06-21 02:39:59] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2024-06-21 02:39:59] 2D-grid search of purity and ploidy...
INFO [2024-06-21 02:39:59] Local optima: 0.65/1.8, 0.52/2
INFO [2024-06-21 02:39:59] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2024-06-21 02:40:00] Testing local optimum 2/2 at purity 0.52 and total ploidy 2.00...
INFO [2024-06-21 02:40:01] Skipping 1 solutions that converged to the same optima.
INFO [2024-06-21 02:40:01] Fitting variants with beta model for local optimum 1/2...
INFO [2024-06-21 02:40:01] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2024-06-21 02:40:04] Optimized purity: 0.65
INFO [2024-06-21 02:40:04] Done.
INFO [2024-06-21 02:40:04] ------------------------------------------------------------
FATAL [2024-06-21 02:40:05] log.ratio NULL in .writeLogRatioFileGATK4 

FATAL [2024-06-21 02:40:05]  

FATAL [2024-06-21 02:40:05] This runtime error might be caused by invalid input data or parameters. 

FATAL [2024-06-21 02:40:05] Please report bug (PureCN 2.11.0). 

INFO [2024-06-21 02:40:05] Loaded provided segmentation file example_seg.txt (format DNAcopy).
INFO [2024-06-21 02:40:05] Re-centering provided segment means (offset -0.0033).
INFO [2024-06-21 02:40:05] Loaded provided segmentation file example_gatk4_modelfinal.seg.gz (format GATK4).
WARN [2024-06-21 02:40:05] Expecting numeric chromosome names in seg.file, assuming file is properly sorted.
INFO [2024-06-21 02:40:05] Re-centering provided segment means (offset -0.0037).
INFO [2024-06-21 02:40:06] 576 on-target bins with low coverage in all samples.
WARN [2024-06-21 02:40:06] You are likely not using the correct baits file!
WARN [2024-06-21 02:40:06] Allosome coverage missing, cannot determine sex.
WARN [2024-06-21 02:40:06] Allosome coverage missing, cannot determine sex.
INFO [2024-06-21 02:40:06] Processing on-target regions...
INFO [2024-06-21 02:40:07] Removing 930 intervals with low coverage in normalDB.
INFO [2024-06-21 02:40:07] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2024-06-21 02:40:08] ------------------------------------------------------------
INFO [2024-06-21 02:40:08] PureCN 2.11.0
INFO [2024-06-21 02:40:08] ------------------------------------------------------------
INFO [2024-06-21 02:40:08] Using BiocParallel for parallel optimization.
INFO [2024-06-21 02:40:08] Loading coverage files...
INFO [2024-06-21 02:40:09] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2024-06-21 02:40:09] Allosome coverage missing, cannot determine sex.
WARN [2024-06-21 02:40:09] Allosome coverage missing, cannot determine sex.
INFO [2024-06-21 02:40:09] Removing 228 intervals with missing log.ratio.
INFO [2024-06-21 02:40:09] Removing 705 intervals excluded in normalDB.
INFO [2024-06-21 02:40:09] normalDB provided. Setting minimum coverage for segmentation to 0.0015X.
INFO [2024-06-21 02:40:09] Removing 1066 low count (< 100 total reads) intervals.
INFO [2024-06-21 02:40:09] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2024-06-21 02:40:09] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2024-06-21 02:40:09] No interval.file provided. Cannot check for any GC-biases.
INFO [2024-06-21 02:40:09] Sample sex: ?
INFO [2024-06-21 02:40:09] Segmenting data...
INFO [2024-06-21 02:40:09] Interval weights found, will use weighted CBS.
INFO [2024-06-21 02:40:09] Loading pre-computed boundaries for DNAcopy...
INFO [2024-06-21 02:40:09] Setting undo.SD parameter to 1.000000.
Setting multi-figure configuration
INFO [2024-06-21 02:40:10] Found 52 segments with median size of 29.35Mb.
INFO [2024-06-21 02:40:10] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2024-06-21 02:40:10] 2D-grid search of purity and ploidy...
INFO [2024-06-21 02:40:10] Local optima: 0.65/1.8, 0.52/2
INFO [2024-06-21 02:40:12] Skipping 1 solutions that converged to the same optima.
INFO [2024-06-21 02:40:12] Done.
INFO [2024-06-21 02:40:12] ------------------------------------------------------------
INFO [2024-06-21 02:40:12] Reading /tmp/Rtmp6peUvj/file15dcd3194203d2.rds...
FATAL [2024-06-21 02:40:12] runAbsoluteCN was run without a VCF file. 

FATAL [2024-06-21 02:40:12]  

FATAL [2024-06-21 02:40:12] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:40:12] parameters (PureCN 2.11.0). 

FATAL [2024-06-21 02:40:12] runAbsoluteCN was run without a VCF file. 

FATAL [2024-06-21 02:40:12]  

FATAL [2024-06-21 02:40:12] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:40:12] parameters (PureCN 2.11.0). 

INFO [2024-06-21 02:40:12] ------------------------------------------------------------
INFO [2024-06-21 02:40:12] PureCN 2.11.0
INFO [2024-06-21 02:40:12] ------------------------------------------------------------
INFO [2024-06-21 02:40:12] Loading coverage files...
INFO [2024-06-21 02:40:13] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2024-06-21 02:40:13] Allosome coverage missing, cannot determine sex.
WARN [2024-06-21 02:40:13] Allosome coverage missing, cannot determine sex.
INFO [2024-06-21 02:40:13] Removing 228 intervals with missing log.ratio.
INFO [2024-06-21 02:40:13] Removing 705 intervals excluded in normalDB.
INFO [2024-06-21 02:40:13] normalDB provided. Setting minimum coverage for segmentation to 0.0015X.
INFO [2024-06-21 02:40:13] Removing 1066 low count (< 100 total reads) intervals.
INFO [2024-06-21 02:40:13] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2024-06-21 02:40:13] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2024-06-21 02:40:13] No interval.file provided. Cannot check for any GC-biases.
INFO [2024-06-21 02:40:13] Sample sex: ?
INFO [2024-06-21 02:40:13] Segmenting data...
INFO [2024-06-21 02:40:14] Interval weights found, will use weighted PSCBS.
FATAL [2024-06-21 02:40:14] segmentationPSCBS requires VCF file. 

FATAL [2024-06-21 02:40:14]  

FATAL [2024-06-21 02:40:14] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:40:14] parameters (PureCN 2.11.0). 

INFO [2024-06-21 02:40:20] ------------------------------------------------------------
INFO [2024-06-21 02:40:20] PureCN 2.11.0
INFO [2024-06-21 02:40:20] ------------------------------------------------------------
INFO [2024-06-21 02:40:20] Loading coverage files...
FATAL [2024-06-21 02:40:20] Need a normal coverage file if log.ratio and seg.file are not provided. 

FATAL [2024-06-21 02:40:20]  

FATAL [2024-06-21 02:40:20] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:40:20] parameters (PureCN 2.11.0). 

INFO [2024-06-21 02:40:20] ------------------------------------------------------------
INFO [2024-06-21 02:40:20] PureCN 2.11.0
INFO [2024-06-21 02:40:20] ------------------------------------------------------------
FATAL [2024-06-21 02:40:20] min.ploidy or max.ploidy not within expected range. 

FATAL [2024-06-21 02:40:20]  

FATAL [2024-06-21 02:40:20] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:40:20] parameters (PureCN 2.11.0). 

INFO [2024-06-21 02:40:20] ------------------------------------------------------------
INFO [2024-06-21 02:40:20] PureCN 2.11.0
INFO [2024-06-21 02:40:20] ------------------------------------------------------------
FATAL [2024-06-21 02:40:20] min.ploidy or max.ploidy not within expected range. 

FATAL [2024-06-21 02:40:20]  

FATAL [2024-06-21 02:40:20] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:40:20] parameters (PureCN 2.11.0). 

INFO [2024-06-21 02:40:20] ------------------------------------------------------------
INFO [2024-06-21 02:40:20] PureCN 2.11.0
INFO [2024-06-21 02:40:20] ------------------------------------------------------------
INFO [2024-06-21 02:40:20] ------------------------------------------------------------
INFO [2024-06-21 02:40:20] PureCN 2.11.0
INFO [2024-06-21 02:40:20] ------------------------------------------------------------
INFO [2024-06-21 02:40:20] ------------------------------------------------------------
INFO [2024-06-21 02:40:20] PureCN 2.11.0
INFO [2024-06-21 02:40:20] ------------------------------------------------------------
FATAL [2024-06-21 02:40:20] test.num.copy not within expected range. 

FATAL [2024-06-21 02:40:20]  

FATAL [2024-06-21 02:40:20] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:40:20] parameters (PureCN 2.11.0). 

INFO [2024-06-21 02:40:20] ------------------------------------------------------------
INFO [2024-06-21 02:40:20] PureCN 2.11.0
INFO [2024-06-21 02:40:20] ------------------------------------------------------------
WARN [2024-06-21 02:40:20] test.num.copy outside recommended range.
FATAL [2024-06-21 02:40:20] max.non.clonal not within expected range or format. 

FATAL [2024-06-21 02:40:20]  

FATAL [2024-06-21 02:40:20] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:40:20] parameters (PureCN 2.11.0). 

INFO [2024-06-21 02:40:20] ------------------------------------------------------------
INFO [2024-06-21 02:40:20] PureCN 2.11.0
INFO [2024-06-21 02:40:20] ------------------------------------------------------------
WARN [2024-06-21 02:40:20] test.num.copy outside recommended range.
FATAL [2024-06-21 02:40:20] max.non.clonal not within expected range or format. 

FATAL [2024-06-21 02:40:20]  

FATAL [2024-06-21 02:40:20] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:40:20] parameters (PureCN 2.11.0). 

INFO [2024-06-21 02:40:20] ------------------------------------------------------------
INFO [2024-06-21 02:40:20] PureCN 2.11.0
INFO [2024-06-21 02:40:20] ------------------------------------------------------------
FATAL [2024-06-21 02:40:20] test.purity not within expected range. 

FATAL [2024-06-21 02:40:20]  

FATAL [2024-06-21 02:40:20] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:40:20] parameters (PureCN 2.11.0). 

INFO [2024-06-21 02:40:20] ------------------------------------------------------------
INFO [2024-06-21 02:40:20] PureCN 2.11.0
INFO [2024-06-21 02:40:20] ------------------------------------------------------------
INFO [2024-06-21 02:40:20] Loading coverage files...
FATAL [2024-06-21 02:40:21] Tumor and normal are identical. This won't give any meaningful results 

FATAL [2024-06-21 02:40:21] and I'm stopping here. 

FATAL [2024-06-21 02:40:21]  

FATAL [2024-06-21 02:40:21] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:40:21] parameters (PureCN 2.11.0). 

INFO [2024-06-21 02:40:21] ------------------------------------------------------------
INFO [2024-06-21 02:40:21] PureCN 2.11.0
INFO [2024-06-21 02:40:21] ------------------------------------------------------------
INFO [2024-06-21 02:40:21] Loading coverage files...
FATAL [2024-06-21 02:40:21] Length of log.ratio different from tumor coverage. 

FATAL [2024-06-21 02:40:21]  

FATAL [2024-06-21 02:40:21] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:40:21] parameters (PureCN 2.11.0). 

INFO [2024-06-21 02:40:21] ------------------------------------------------------------
INFO [2024-06-21 02:40:21] PureCN 2.11.0
INFO [2024-06-21 02:40:21] ------------------------------------------------------------
FATAL [2024-06-21 02:40:21] prior.purity must have the same length as test.purity. 

FATAL [2024-06-21 02:40:21]  

FATAL [2024-06-21 02:40:21] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:40:21] parameters (PureCN 2.11.0). 

INFO [2024-06-21 02:40:21] ------------------------------------------------------------
INFO [2024-06-21 02:40:21] PureCN 2.11.0
INFO [2024-06-21 02:40:21] ------------------------------------------------------------
FATAL [2024-06-21 02:40:21] min.gof not within expected range or format. 

FATAL [2024-06-21 02:40:21]  

FATAL [2024-06-21 02:40:21] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:40:21] parameters (PureCN 2.11.0). 

INFO [2024-06-21 02:40:21] ------------------------------------------------------------
INFO [2024-06-21 02:40:21] PureCN 2.11.0
INFO [2024-06-21 02:40:21] ------------------------------------------------------------
FATAL [2024-06-21 02:40:21] prior.purity not within expected range or format. 

FATAL [2024-06-21 02:40:21]  

FATAL [2024-06-21 02:40:21] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:40:21] parameters (PureCN 2.11.0). 

INFO [2024-06-21 02:40:21] ------------------------------------------------------------
INFO [2024-06-21 02:40:21] PureCN 2.11.0
INFO [2024-06-21 02:40:21] ------------------------------------------------------------
FATAL [2024-06-21 02:40:21] prior.purity must add to 1. Sum is 1.5 

FATAL [2024-06-21 02:40:21]  

FATAL [2024-06-21 02:40:21] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:40:21] parameters (PureCN 2.11.0). 

INFO [2024-06-21 02:40:21] ------------------------------------------------------------
INFO [2024-06-21 02:40:21] PureCN 2.11.0
INFO [2024-06-21 02:40:21] ------------------------------------------------------------
FATAL [2024-06-21 02:40:21] max.homozygous.loss not within expected range or format. 

FATAL [2024-06-21 02:40:21]  

FATAL [2024-06-21 02:40:21] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:40:21] parameters (PureCN 2.11.0). 

INFO [2024-06-21 02:40:21] ------------------------------------------------------------
INFO [2024-06-21 02:40:21] PureCN 2.11.0
INFO [2024-06-21 02:40:21] ------------------------------------------------------------
FATAL [2024-06-21 02:40:21] prior.K not within expected range or format. 

FATAL [2024-06-21 02:40:21]  

FATAL [2024-06-21 02:40:21] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:40:21] parameters (PureCN 2.11.0). 

INFO [2024-06-21 02:40:21] ------------------------------------------------------------
INFO [2024-06-21 02:40:21] PureCN 2.11.0
INFO [2024-06-21 02:40:21] ------------------------------------------------------------
FATAL [2024-06-21 02:40:21] prior.contamination not within expected range or format. 

FATAL [2024-06-21 02:40:21]  

FATAL [2024-06-21 02:40:21] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:40:21] parameters (PureCN 2.11.0). 

INFO [2024-06-21 02:40:21] ------------------------------------------------------------
INFO [2024-06-21 02:40:21] PureCN 2.11.0
INFO [2024-06-21 02:40:21] ------------------------------------------------------------
FATAL [2024-06-21 02:40:21] Iterations not in the expected range from 10 to 250. 

FATAL [2024-06-21 02:40:21]  

FATAL [2024-06-21 02:40:21] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:40:21] parameters (PureCN 2.11.0). 

INFO [2024-06-21 02:40:21] ------------------------------------------------------------
INFO [2024-06-21 02:40:21] PureCN 2.11.0
INFO [2024-06-21 02:40:21] ------------------------------------------------------------
FATAL [2024-06-21 02:40:21] Iterations not in the expected range from 10 to 250. 

FATAL [2024-06-21 02:40:21]  

FATAL [2024-06-21 02:40:21] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:40:21] parameters (PureCN 2.11.0). 

INFO [2024-06-21 02:40:21] ------------------------------------------------------------
INFO [2024-06-21 02:40:21] PureCN 2.11.0
INFO [2024-06-21 02:40:21] ------------------------------------------------------------
INFO [2024-06-21 02:40:21] Loading coverage files...
FATAL [2024-06-21 02:40:22] Missing tumor.coverage.file requires seg.file or log.ratio and 

FATAL [2024-06-21 02:40:22] interval.file. 

FATAL [2024-06-21 02:40:22]  

FATAL [2024-06-21 02:40:22] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:40:22] parameters (PureCN 2.11.0). 

INFO [2024-06-21 02:40:22] ------------------------------------------------------------
INFO [2024-06-21 02:40:22] PureCN 2.11.0
INFO [2024-06-21 02:40:22] ------------------------------------------------------------
INFO [2024-06-21 02:40:22] ------------------------------------------------------------
INFO [2024-06-21 02:40:22] PureCN 2.11.0
INFO [2024-06-21 02:40:22] ------------------------------------------------------------
INFO [2024-06-21 02:40:22] Loading coverage files...
FATAL [2024-06-21 02:40:22] Interval files in normal and tumor different. 

FATAL [2024-06-21 02:40:22]  

FATAL [2024-06-21 02:40:22] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:40:22] parameters (PureCN 2.11.0). 

INFO [2024-06-21 02:40:23] ------------------------------------------------------------
INFO [2024-06-21 02:40:23] PureCN 2.11.0
INFO [2024-06-21 02:40:23] ------------------------------------------------------------
INFO [2024-06-21 02:40:23] Loading coverage files...
INFO [2024-06-21 02:40:23] Mean target coverages: 0X (tumor) 99X (normal).
WARN [2024-06-21 02:40:23] Large difference in coverage of tumor and normal.
FATAL [2024-06-21 02:40:23] No finite intervals. 

FATAL [2024-06-21 02:40:23]  

FATAL [2024-06-21 02:40:23] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:40:23] parameters (PureCN 2.11.0). 

INFO [2024-06-21 02:40:23] ------------------------------------------------------------
INFO [2024-06-21 02:40:23] PureCN 2.11.0
INFO [2024-06-21 02:40:23] ------------------------------------------------------------
INFO [2024-06-21 02:40:23] Loading coverage files...
INFO [2024-06-21 02:40:24] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2024-06-21 02:40:24] Allosome coverage missing, cannot determine sex.
WARN [2024-06-21 02:40:24] Allosome coverage missing, cannot determine sex.
INFO [2024-06-21 02:40:24] Removing 228 intervals with missing log.ratio.
INFO [2024-06-21 02:40:24] Removing 22 small (< 5bp) intervals.
INFO [2024-06-21 02:40:24] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2024-06-21 02:40:24] No normalDB provided. Provide one for better results.
INFO [2024-06-21 02:40:24] Removing 1724 low count (< 100 total reads) intervals.
INFO [2024-06-21 02:40:24] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2024-06-21 02:40:24] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2024-06-21 02:40:24] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2024-06-21 02:40:24] No interval.file provided. Cannot check for any GC-biases.
INFO [2024-06-21 02:40:24] Loading VCF...
INFO [2024-06-21 02:40:24] Found 127 variants in VCF file.
INFO [2024-06-21 02:40:24] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2024-06-21 02:40:25] LIB-02240e4 is tumor in VCF file.
INFO [2024-06-21 02:40:25] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2024-06-21 02:40:25] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2024-06-21 02:40:25] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2024-06-21 02:40:25] Base quality scores range from 29 to 35 (offset by 1)
INFO [2024-06-21 02:40:25] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2024-06-21 02:40:25] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
Error in FileForFormat(resource(con), fileFormat(con)) : 
  Format 'txt' unsupported
In addition: Warning messages:
1: In for (getMethodName in getMethodNames) { :
  closing unused connection 5 (/tmp/Rtmp6peUvj/file15dcd317e5961f.tsv)
2: In for (getMethodName in getMethodNames) { :
  closing unused connection 4 (/home/biocbuild/bbs-3.20-bioc/R/site-library/PureCN/extdata/example_gatk4_denoised_cr.tsv.gz)
FATAL [2024-06-21 02:40:25] Could not import snp.blacklist 

FATAL [2024-06-21 02:40:25] /home/biocbuild/bbs-3.20-bioc/R/site-library/PureCN/extdata/example_normal.txt.gz:Error 

FATAL [2024-06-21 02:40:25] in FileForFormat(resource(con), fileFormat(con)) : Format 'txt' 

FATAL [2024-06-21 02:40:25] unsupported 

FATAL [2024-06-21 02:40:25]  

FATAL [2024-06-21 02:40:25] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:40:25] parameters (PureCN 2.11.0). 

INFO [2024-06-21 02:40:25] ------------------------------------------------------------
INFO [2024-06-21 02:40:25] PureCN 2.11.0
INFO [2024-06-21 02:40:25] ------------------------------------------------------------
INFO [2024-06-21 02:40:25] Loading coverage files...
INFO [2024-06-21 02:40:26] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2024-06-21 02:40:26] Allosome coverage missing, cannot determine sex.
WARN [2024-06-21 02:40:26] Allosome coverage missing, cannot determine sex.
INFO [2024-06-21 02:40:26] Removing 228 intervals with missing log.ratio.
INFO [2024-06-21 02:40:26] Removing 22 small (< 5bp) intervals.
INFO [2024-06-21 02:40:26] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2024-06-21 02:40:26] No normalDB provided. Provide one for better results.
INFO [2024-06-21 02:40:26] Removing 233 low coverage (< 15.0000X) intervals.
INFO [2024-06-21 02:40:26] Using 9547 intervals (9547 on-target, 0 off-target).
INFO [2024-06-21 02:40:26] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2024-06-21 02:40:26] No interval.file provided. Cannot check for any GC-biases.
INFO [2024-06-21 02:40:26] Loading VCF...
INFO [2024-06-21 02:40:26] Found 127 variants in VCF file.
INFO [2024-06-21 02:40:26] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2024-06-21 02:40:27] LIB-02240e4 is tumor in VCF file.
INFO [2024-06-21 02:40:27] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2024-06-21 02:40:27] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2024-06-21 02:40:27] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2024-06-21 02:40:27] Base quality scores range from 29 to 35 (offset by 1)
INFO [2024-06-21 02:40:27] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2024-06-21 02:40:27] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2024-06-21 02:40:27] Total size of targeted genomic region: 1.63Mb (2.58Mb with 50bp padding).
INFO [2024-06-21 02:40:27] 1.0% of targets contain variants.
INFO [2024-06-21 02:40:27] Removing 2 variants outside intervals.
INFO [2024-06-21 02:40:28] Found SOMATIC annotation in VCF.
INFO [2024-06-21 02:40:28] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2024-06-21 02:40:28] Found SOMATIC annotation in VCF. Setting mapping bias to 0.973.
INFO [2024-06-21 02:40:28] Excluding 0 novel or poor quality variants from segmentation.
INFO [2024-06-21 02:40:28] Sample sex: ?
INFO [2024-06-21 02:40:28] Segmenting data...
INFO [2024-06-21 02:40:28] Loading pre-computed boundaries for DNAcopy...
INFO [2024-06-21 02:40:28] Setting undo.SD parameter to 1.000000.
INFO [2024-06-21 02:40:29] Setting prune.hclust.h parameter to 0.200000.
INFO [2024-06-21 02:40:29] Found 54 segments with median size of 24.88Mb.
INFO [2024-06-21 02:40:29] Using 123 variants.
INFO [2024-06-21 02:40:29] Mean standard deviation of log-ratios: 0.37 (MAPD: 0.32)
INFO [2024-06-21 02:40:29] 2D-grid search of purity and ploidy...
INFO [2024-06-21 02:40:30] Local optima: 0.62/1.9, 0.3/1.9, 0.32/2
INFO [2024-06-21 02:40:30] Testing local optimum 1/3 at purity 0.62 and total ploidy 1.90...
INFO [2024-06-21 02:40:31] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2024-06-21 02:40:31] Recalibrating log-ratios...
INFO [2024-06-21 02:40:31] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2024-06-21 02:40:31] Recalibrating log-ratios...
INFO [2024-06-21 02:40:31] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2024-06-21 02:40:32] Recalibrating log-ratios...
INFO [2024-06-21 02:40:32] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2024-06-21 02:40:32] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2024-06-21 02:40:32] Recalibrating log-ratios...
INFO [2024-06-21 02:40:32] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2024-06-21 02:40:33] Recalibrating log-ratios...
INFO [2024-06-21 02:40:33] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2024-06-21 02:40:33] Recalibrating log-ratios...
INFO [2024-06-21 02:40:33] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2024-06-21 02:40:33] Skipping 1 solutions that converged to the same optima.
INFO [2024-06-21 02:40:33] Skipping 1 solutions exceeding max.non.clonal (0.20): 0.3/1.9 (purity/tumor ploidy)
INFO [2024-06-21 02:40:33] Fitting variants with beta model for local optimum 1/3...
INFO [2024-06-21 02:40:33] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01.
INFO [2024-06-21 02:40:36] Optimized purity: 0.65
INFO [2024-06-21 02:40:36] Done.
INFO [2024-06-21 02:40:36] ------------------------------------------------------------
INFO [2024-06-21 02:40:37] ------------------------------------------------------------
INFO [2024-06-21 02:40:37] PureCN 2.11.0
INFO [2024-06-21 02:40:37] ------------------------------------------------------------
INFO [2024-06-21 02:40:37] Loading coverage files...
INFO [2024-06-21 02:40:37] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2024-06-21 02:40:37] Allosome coverage missing, cannot determine sex.
WARN [2024-06-21 02:40:37] Allosome coverage missing, cannot determine sex.
INFO [2024-06-21 02:40:38] Removing 228 intervals with missing log.ratio.
INFO [2024-06-21 02:40:38] Removing 22 small (< 5bp) intervals.
INFO [2024-06-21 02:40:38] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2024-06-21 02:40:38] No normalDB provided. Provide one for better results.
INFO [2024-06-21 02:40:38] Removing 1724 low count (< 100 total reads) intervals.
INFO [2024-06-21 02:40:38] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2024-06-21 02:40:38] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2024-06-21 02:40:38] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2024-06-21 02:40:38] No interval.file provided. Cannot check for any GC-biases.
INFO [2024-06-21 02:40:38] Loading VCF...
INFO [2024-06-21 02:40:38] Found 127 variants in VCF file.
WARN [2024-06-21 02:40:38] DP FORMAT field contains NAs. Removing 3 variants.
WARN [2024-06-21 02:40:38] DB INFO flag contains NAs
INFO [2024-06-21 02:40:38] 119 (96.0%) variants annotated as likely germline (DB INFO flag).
INFO [2024-06-21 02:40:38] LIB-02240e4 is tumor in VCF file.
INFO [2024-06-21 02:40:38] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2024-06-21 02:40:38] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2024-06-21 02:40:38] Base quality scores range from 29 to 35 (offset by 1)
INFO [2024-06-21 02:40:38] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2024-06-21 02:40:39] Removing 1 variants with AF < 0.030 or AF >= 0.970 or insufficient supporting reads or depth < 15.
INFO [2024-06-21 02:40:39] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding).
INFO [2024-06-21 02:40:39] 1.2% of targets contain variants.
INFO [2024-06-21 02:40:39] Setting somatic prior probabilities for likely germline hits to 0.000500 or to 0.500000 otherwise.
INFO [2024-06-21 02:40:39] Excluding 5 novel or poor quality variants from segmentation.
INFO [2024-06-21 02:40:39] Sample sex: ?
INFO [2024-06-21 02:40:39] Segmenting data...
INFO [2024-06-21 02:40:39] Loading pre-computed boundaries for DNAcopy...
INFO [2024-06-21 02:40:39] Setting undo.SD parameter to 1.000000.
Setting multi-figure configuration
INFO [2024-06-21 02:40:40] Setting prune.hclust.h parameter to 0.200000.
INFO [2024-06-21 02:40:40] Found 59 segments with median size of 17.67Mb.
INFO [2024-06-21 02:40:40] Using 123 variants.
INFO [2024-06-21 02:40:40] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2024-06-21 02:40:40] 2D-grid search of purity and ploidy...
INFO [2024-06-21 02:40:41] Local optima: 0.62/1.9, 0.3/1.9, 0.32/2
INFO [2024-06-21 02:40:41] Testing local optimum 1/3 at purity 0.62 and total ploidy 1.90...
INFO [2024-06-21 02:40:42] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2024-06-21 02:40:42] Recalibrating log-ratios...
INFO [2024-06-21 02:40:42] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2024-06-21 02:40:42] Recalibrating log-ratios...
INFO [2024-06-21 02:40:42] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2024-06-21 02:40:43] Recalibrating log-ratios...
INFO [2024-06-21 02:40:43] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2024-06-21 02:40:43] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2024-06-21 02:40:43] Recalibrating log-ratios...
INFO [2024-06-21 02:40:43] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2024-06-21 02:40:43] Recalibrating log-ratios...
INFO [2024-06-21 02:40:43] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2024-06-21 02:40:44] Recalibrating log-ratios...
INFO [2024-06-21 02:40:44] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2024-06-21 02:40:44] Skipping 2 solutions exceeding max.non.clonal (0.20): 0.3/1.9, 0.35/1.61 (purity/tumor ploidy)
INFO [2024-06-21 02:40:44] Fitting variants with beta model for local optimum 1/3...
INFO [2024-06-21 02:40:44] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2024-06-21 02:40:47] Optimized purity: 0.65
INFO [2024-06-21 02:40:47] Done.
INFO [2024-06-21 02:40:47] ------------------------------------------------------------
INFO [2024-06-21 02:40:47] ------------------------------------------------------------
INFO [2024-06-21 02:40:47] PureCN 2.11.0
INFO [2024-06-21 02:40:47] ------------------------------------------------------------
INFO [2024-06-21 02:40:47] Loading coverage files...
INFO [2024-06-21 02:40:48] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2024-06-21 02:40:48] Allosome coverage missing, cannot determine sex.
WARN [2024-06-21 02:40:48] Allosome coverage missing, cannot determine sex.
INFO [2024-06-21 02:40:48] No Gene column in interval.file. You won't get gene-level calls.
INFO [2024-06-21 02:40:49] Removing 228 intervals with missing log.ratio.
INFO [2024-06-21 02:40:49] Removing 15 low/high GC targets.
INFO [2024-06-21 02:40:49] Removing 21 small (< 5bp) intervals.
INFO [2024-06-21 02:40:49] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2024-06-21 02:40:49] No normalDB provided. Provide one for better results.
INFO [2024-06-21 02:40:49] Removing 1718 low count (< 100 total reads) intervals.
INFO [2024-06-21 02:40:49] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2024-06-21 02:40:49] Removing 36 low mappability intervals.
INFO [2024-06-21 02:40:49] Using 8006 intervals (8006 on-target, 0 off-target).
INFO [2024-06-21 02:40:49] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2024-06-21 02:40:49] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio). 
INFO [2024-06-21 02:40:49] Loading VCF...
INFO [2024-06-21 02:40:49] Found 127 variants in VCF file.
INFO [2024-06-21 02:40:49] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2024-06-21 02:40:49] LIB-02240e4 is tumor in VCF file.
INFO [2024-06-21 02:40:49] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2024-06-21 02:40:49] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2024-06-21 02:40:49] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2024-06-21 02:40:49] Base quality scores range from 29 to 35 (offset by 1)
INFO [2024-06-21 02:40:49] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2024-06-21 02:40:50] Removing 1 variants with AF < 0.030 or AF >= Inf or insufficient supporting reads or depth < 15.
INFO [2024-06-21 02:40:50] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding).
INFO [2024-06-21 02:40:50] 1.2% of targets contain variants.
INFO [2024-06-21 02:40:50] Removing 11 variants outside intervals.
INFO [2024-06-21 02:40:50] Found SOMATIC annotation in VCF.
INFO [2024-06-21 02:40:50] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2024-06-21 02:40:50] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970.
INFO [2024-06-21 02:40:50] Excluding 0 novel or poor quality variants from segmentation.
INFO [2024-06-21 02:40:50] Sample sex: ?
INFO [2024-06-21 02:40:50] Segmenting data...
INFO [2024-06-21 02:40:50] MAPD of 114 allelic fractions: 0.14 (0.15 adjusted).
INFO [2024-06-21 02:40:50] Using unweighted PSCBS.
INFO [2024-06-21 02:40:51] Setting undo.SD parameter to 1.000000.
INFO [2024-06-21 02:41:06] Setting prune.hclust.h parameter to 0.200000.
INFO [2024-06-21 02:41:06] Found 71 segments with median size of 27.72Mb.
INFO [2024-06-21 02:41:06] Using 114 variants.
INFO [2024-06-21 02:41:06] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2024-06-21 02:41:06] 2D-grid search of purity and ploidy...
INFO [2024-06-21 02:41:06] Local optima: 0.65/1.8, 0.38/2.2
INFO [2024-06-21 02:41:06] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2024-06-21 02:41:06] Recalibrating log-ratios...
INFO [2024-06-21 02:41:06] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2024-06-21 02:41:07] Recalibrating log-ratios...
INFO [2024-06-21 02:41:07] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2024-06-21 02:41:07] Recalibrating log-ratios...
INFO [2024-06-21 02:41:07] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80...
INFO [2024-06-21 02:41:07] Testing local optimum 2/2 at purity 0.38 and total ploidy 2.20...
INFO [2024-06-21 02:41:09] Skipping 1 solutions exceeding max.non.clonal (0.20): 0.65/2.04 (purity/tumor ploidy)
INFO [2024-06-21 02:41:09] Fitting variants with beta model for local optimum 2/2...
INFO [2024-06-21 02:41:09] Fitting variants for purity 0.40, tumor ploidy 2.53 and contamination 0.01.
INFO [2024-06-21 02:41:12] Optimized purity: 0.40
INFO [2024-06-21 02:41:12] Done.
INFO [2024-06-21 02:41:12] ------------------------------------------------------------
FATAL [2024-06-21 02:41:12] This function requires gene-level calls. Please add a column 'Gene' 

FATAL [2024-06-21 02:41:12] containing gene symbols to the interval.file. 

FATAL [2024-06-21 02:41:12]  

FATAL [2024-06-21 02:41:12] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:41:12] parameters (PureCN 2.11.0). 

INFO [2024-06-21 02:41:14] ------------------------------------------------------------
INFO [2024-06-21 02:41:14] PureCN 2.11.0
INFO [2024-06-21 02:41:14] ------------------------------------------------------------
INFO [2024-06-21 02:41:14] Loading coverage files...
INFO [2024-06-21 02:41:14] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2024-06-21 02:41:14] Allosome coverage missing, cannot determine sex.
WARN [2024-06-21 02:41:14] Allosome coverage missing, cannot determine sex.
INFO [2024-06-21 02:41:15] Removing 228 intervals with missing log.ratio.
INFO [2024-06-21 02:41:15] Removing 22 small (< 5bp) intervals.
INFO [2024-06-21 02:41:15] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2024-06-21 02:41:15] No normalDB provided. Provide one for better results.
INFO [2024-06-21 02:41:15] Removing 1724 low count (< 100 total reads) intervals.
INFO [2024-06-21 02:41:15] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2024-06-21 02:41:15] Using 8050 intervals (8050 on-target, 0 off-target).
INFO [2024-06-21 02:41:15] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2024-06-21 02:41:15] No interval.file provided. Cannot check for any GC-biases.
INFO [2024-06-21 02:41:15] Loading VCF...
INFO [2024-06-21 02:41:15] Found 127 variants in VCF file.
INFO [2024-06-21 02:41:15] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
FATAL [2024-06-21 02:41:15] Different chromosome names in coverage and VCF. 

FATAL [2024-06-21 02:41:15]  

FATAL [2024-06-21 02:41:15] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:41:15] parameters (PureCN 2.11.0). 

INFO [2024-06-21 02:41:15] ------------------------------------------------------------
INFO [2024-06-21 02:41:15] PureCN 2.11.0
INFO [2024-06-21 02:41:15] ------------------------------------------------------------
INFO [2024-06-21 02:41:15] Loading coverage files...
INFO [2024-06-21 02:41:15] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2024-06-21 02:41:15] Allosome coverage missing, cannot determine sex.
WARN [2024-06-21 02:41:15] Allosome coverage missing, cannot determine sex.
FATAL [2024-06-21 02:41:15] tumor.coverage.file and interval.file do not align. 

FATAL [2024-06-21 02:41:15]  

FATAL [2024-06-21 02:41:15] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:41:15] parameters (PureCN 2.11.0). 

INFO [2024-06-21 02:41:16] ------------------------------------------------------------
INFO [2024-06-21 02:41:16] PureCN 2.11.0
INFO [2024-06-21 02:41:16] ------------------------------------------------------------
INFO [2024-06-21 02:41:16] Loading coverage files...
INFO [2024-06-21 02:41:16] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2024-06-21 02:41:16] Allosome coverage missing, cannot determine sex.
WARN [2024-06-21 02:41:16] Allosome coverage missing, cannot determine sex.
INFO [2024-06-21 02:41:17] Removing 228 intervals with missing log.ratio.
INFO [2024-06-21 02:41:17] Removing 15 low/high GC targets.
INFO [2024-06-21 02:41:17] Removing 21 small (< 5bp) intervals.
INFO [2024-06-21 02:41:17] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2024-06-21 02:41:17] No normalDB provided. Provide one for better results.
INFO [2024-06-21 02:41:17] Removing 1718 low count (< 100 total reads) intervals.
INFO [2024-06-21 02:41:17] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2024-06-21 02:41:17] Removing 36 low mappability intervals.
INFO [2024-06-21 02:41:17] Using 8006 intervals (8006 on-target, 0 off-target).
INFO [2024-06-21 02:41:17] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2024-06-21 02:41:17] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio). 
INFO [2024-06-21 02:41:17] Loading VCF...
INFO [2024-06-21 02:41:17] Found 127 variants in VCF file.
INFO [2024-06-21 02:41:17] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2024-06-21 02:41:17] LIB-02240e4 is tumor in VCF file.
INFO [2024-06-21 02:41:17] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2024-06-21 02:41:18] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2024-06-21 02:41:18] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2024-06-21 02:41:18] Base quality scores range from 29 to 35 (offset by 1)
INFO [2024-06-21 02:41:18] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2024-06-21 02:41:18] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2024-06-21 02:41:18] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding).
INFO [2024-06-21 02:41:18] 1.2% of targets contain variants.
INFO [2024-06-21 02:41:18] Removing 11 variants outside intervals.
INFO [2024-06-21 02:41:18] Found SOMATIC annotation in VCF.
INFO [2024-06-21 02:41:18] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2024-06-21 02:41:18] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970.
INFO [2024-06-21 02:41:19] Excluding 0 novel or poor quality variants from segmentation.
INFO [2024-06-21 02:41:19] Sample sex: ?
INFO [2024-06-21 02:41:19] Segmenting data...
INFO [2024-06-21 02:41:19] Loading pre-computed boundaries for DNAcopy...
INFO [2024-06-21 02:41:19] Setting undo.SD parameter to 1.000000.
INFO [2024-06-21 02:41:19] Setting prune.hclust.h parameter to 0.200000.
INFO [2024-06-21 02:41:19] Found 59 segments with median size of 17.67Mb.
INFO [2024-06-21 02:41:20] Using 114 variants.
INFO [2024-06-21 02:41:20] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2024-06-21 02:41:20] 2D-grid search of purity and ploidy...
INFO [2024-06-21 02:41:20] Local optima: 0.63/1.9
INFO [2024-06-21 02:41:20] Testing local optimum 1/1 at purity 0.63 and total ploidy 1.90...
INFO [2024-06-21 02:41:21] Fitting variants with beta model for local optimum 1/1...
INFO [2024-06-21 02:41:21] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2024-06-21 02:41:24] Optimized purity: 0.65
INFO [2024-06-21 02:41:24] Done.
INFO [2024-06-21 02:41:24] ------------------------------------------------------------
INFO [2024-06-21 02:41:24] ------------------------------------------------------------
INFO [2024-06-21 02:41:24] PureCN 2.11.0
INFO [2024-06-21 02:41:24] ------------------------------------------------------------
INFO [2024-06-21 02:41:24] Loading coverage files...
INFO [2024-06-21 02:41:24] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2024-06-21 02:41:24] Allosome coverage missing, cannot determine sex.
WARN [2024-06-21 02:41:24] Allosome coverage missing, cannot determine sex.
INFO [2024-06-21 02:41:26] Removing 228 intervals with missing log.ratio.
INFO [2024-06-21 02:41:26] Removing 15 low/high GC targets.
INFO [2024-06-21 02:41:26] Removing 21 small (< 5bp) intervals.
INFO [2024-06-21 02:41:26] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2024-06-21 02:41:26] No normalDB provided. Provide one for better results.
INFO [2024-06-21 02:41:26] Removing 1718 low count (< 100 total reads) intervals.
INFO [2024-06-21 02:41:26] Removing 6 low coverage (< 15.0000X) intervals.
INFO [2024-06-21 02:41:26] Removing 36 low mappability intervals.
INFO [2024-06-21 02:41:26] Using 8006 intervals (8006 on-target, 0 off-target).
INFO [2024-06-21 02:41:26] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2024-06-21 02:41:26] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio). 
INFO [2024-06-21 02:41:26] Loading VCF...
INFO [2024-06-21 02:41:26] Found 127 variants in VCF file.
INFO [2024-06-21 02:41:26] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2024-06-21 02:41:26] LIB-02240e4 is tumor in VCF file.
INFO [2024-06-21 02:41:26] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2024-06-21 02:41:26] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2024-06-21 02:41:26] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2024-06-21 02:41:26] Base quality scores range from 29 to 35 (offset by 1)
INFO [2024-06-21 02:41:26] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2024-06-21 02:41:26] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2024-06-21 02:41:26] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding).
INFO [2024-06-21 02:41:27] 1.2% of targets contain variants.
INFO [2024-06-21 02:41:27] Removing 11 variants outside intervals.
INFO [2024-06-21 02:41:27] Found SOMATIC annotation in VCF.
INFO [2024-06-21 02:41:27] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2024-06-21 02:41:27] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970.
INFO [2024-06-21 02:41:27] Excluding 0 novel or poor quality variants from segmentation.
INFO [2024-06-21 02:41:27] Sample sex: ?
INFO [2024-06-21 02:41:27] Segmenting data...
INFO [2024-06-21 02:41:27] Loading pre-computed boundaries for DNAcopy...
INFO [2024-06-21 02:41:27] Setting undo.SD parameter to 1.000000.
INFO [2024-06-21 02:41:28] Setting prune.hclust.h parameter to 0.200000.
INFO [2024-06-21 02:41:28] Found 59 segments with median size of 17.67Mb.
INFO [2024-06-21 02:41:28] Using 114 variants.
INFO [2024-06-21 02:41:28] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30)
INFO [2024-06-21 02:41:28] 2D-grid search of purity and ploidy...
INFO [2024-06-21 02:41:29] Local optima: 0.63/1.9
INFO [2024-06-21 02:41:29] Testing local optimum 1/1 at purity 0.63 and total ploidy 1.90...
INFO [2024-06-21 02:41:29] Fitting variants with beta model for local optimum 1/1...
WARN [2024-06-21 02:41:30] Some gene symbols found on multiple chromosomes. Use of approved symbols suggested.
INFO [2024-06-21 02:41:30] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01.
INFO [2024-06-21 02:41:33] Optimized purity: 0.65
INFO [2024-06-21 02:41:33] Done.
INFO [2024-06-21 02:41:33] ------------------------------------------------------------
FATAL [2024-06-21 02:41:33] chr1 not valid chromosome name(s). Valid names are: 

FATAL [2024-06-21 02:41:33] 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22 

FATAL [2024-06-21 02:41:33]  

FATAL [2024-06-21 02:41:33] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:41:33] parameters (PureCN 2.11.0). 

INFO [2024-06-21 02:41:33] ------------------------------------------------------------
INFO [2024-06-21 02:41:33] PureCN 2.11.0
INFO [2024-06-21 02:41:33] ------------------------------------------------------------
INFO [2024-06-21 02:41:33] Loading coverage files...
WARN [2024-06-21 02:41:33] Provided sampleid (Sample2) does not match Sample1 found in segmentation.
WARN [2024-06-21 02:41:33] Allosome coverage missing, cannot determine sex.
WARN [2024-06-21 02:41:33] Allosome coverage missing, cannot determine sex.
INFO [2024-06-21 02:41:33] Removing 10 intervals with missing log.ratio.
INFO [2024-06-21 02:41:33] Using 10039 intervals (10039 on-target, 0 off-target).
INFO [2024-06-21 02:41:33] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2024-06-21 02:41:33] Loading VCF...
INFO [2024-06-21 02:41:34] Found 127 variants in VCF file.
INFO [2024-06-21 02:41:34] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2024-06-21 02:41:34] LIB-02240e4 is tumor in VCF file.
INFO [2024-06-21 02:41:34] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2024-06-21 02:41:34] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2024-06-21 02:41:34] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2024-06-21 02:41:34] Base quality scores range from 29 to 35 (offset by 1)
INFO [2024-06-21 02:41:34] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2024-06-21 02:41:34] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2024-06-21 02:41:34] Total size of targeted genomic region: 1.71Mb (2.70Mb with 50bp padding).
INFO [2024-06-21 02:41:35] 1.0% of targets contain variants.
INFO [2024-06-21 02:41:35] Removing 0 variants outside intervals.
INFO [2024-06-21 02:41:35] Found SOMATIC annotation in VCF.
INFO [2024-06-21 02:41:35] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2024-06-21 02:41:35] Found SOMATIC annotation in VCF. Setting mapping bias to 0.976.
INFO [2024-06-21 02:41:35] Excluding 0 novel or poor quality variants from segmentation.
INFO [2024-06-21 02:41:35] Sample sex: ?
INFO [2024-06-21 02:41:35] Segmenting data...
INFO [2024-06-21 02:41:35] Loaded provided segmentation file example_seg.txt (format DNAcopy).
WARN [2024-06-21 02:41:35] Provided sampleid (Sample2) does not match Sample1 found in segmentation.
INFO [2024-06-21 02:41:35] Re-centering provided segment means (offset -0.0033).
INFO [2024-06-21 02:41:35] Loading pre-computed boundaries for DNAcopy...
INFO [2024-06-21 02:41:35] Setting undo.SD parameter to 0.000000.
Setting multi-figure configuration
INFO [2024-06-21 02:41:35] Setting prune.hclust.h parameter to 0.200000.
INFO [2024-06-21 02:41:35] Found 54 segments with median size of 24.88Mb.
INFO [2024-06-21 02:41:35] Using 125 variants.
INFO [2024-06-21 02:41:35] Mean standard deviation of log-ratios: 0.40 (MAPD: 0.00)
INFO [2024-06-21 02:41:35] 2D-grid search of purity and ploidy...
INFO [2024-06-21 02:41:36] Local optima: 0.6/1.9
INFO [2024-06-21 02:41:36] Testing local optimum 1/1 at purity 0.60 and total ploidy 1.90...
INFO [2024-06-21 02:41:37] Fitting variants with beta model for local optimum 1/1...
INFO [2024-06-21 02:41:37] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01.
INFO [2024-06-21 02:41:40] Optimized purity: 0.65
INFO [2024-06-21 02:41:40] Done.
INFO [2024-06-21 02:41:40] ------------------------------------------------------------
WARN [2024-06-21 02:41:40] Allosome coverage missing, cannot determine sex.
WARN [2024-06-21 02:41:40] Allosome coverage missing, cannot determine sex.
Setting multi-figure configuration
FATAL [2024-06-21 02:41:48] Segmentation file expected with colnames ID, chrom, loc.start, loc.end, 

FATAL [2024-06-21 02:41:48] num.mark, seg.mean 

FATAL [2024-06-21 02:41:48]  

FATAL [2024-06-21 02:41:48] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:41:48] parameters (PureCN 2.11.0). 

FATAL [2024-06-21 02:41:49] seg.file contains multiple samples and sampleid missing. 

FATAL [2024-06-21 02:41:49]  

FATAL [2024-06-21 02:41:49] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:41:49] parameters (PureCN 2.11.0). 

FATAL [2024-06-21 02:41:49] seg.file contains multiple samples and sampleid does not match any. 

FATAL [2024-06-21 02:41:49]  

FATAL [2024-06-21 02:41:49] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:41:49] parameters (PureCN 2.11.0). 

WARN [2024-06-21 02:41:49] Allosome coverage missing, cannot determine sex.
WARN [2024-06-21 02:41:49] Allosome coverage missing, cannot determine sex.
WARN [2024-06-21 02:41:59] Allosome coverage missing, cannot determine sex.
WARN [2024-06-21 02:41:59] Allosome coverage missing, cannot determine sex.
WARN [2024-06-21 02:41:59] Provided sampleid (example_tumor.txt.gz) does not match Sample1 found in segmentation.
WARN [2024-06-21 02:42:02] Allosome coverage missing, cannot determine sex.
WARN [2024-06-21 02:42:02] Allosome coverage missing, cannot determine sex.
WARN [2024-06-21 02:42:03] No normalDB provided. Provide one for better results.
WARN [2024-06-21 02:42:10] Allosome coverage missing, cannot determine sex.
WARN [2024-06-21 02:42:10] Allosome coverage missing, cannot determine sex.
WARN [2024-06-21 02:42:13] Provided sampleid (Sample.1) does not match Sample1 found in segmentation.
Setting multi-figure configuration
WARN [2024-06-21 02:42:19] Allosome coverage missing, cannot determine sex.
WARN [2024-06-21 02:42:19] Allosome coverage missing, cannot determine sex.
WARN [2024-06-21 02:42:19] No normalDB provided. Provide one for better results.
WARN [2024-06-21 02:42:20] Sampleid looks like a normal in VCF, not like a tumor.
WARN [2024-06-21 02:42:26] Allosome coverage missing, cannot determine sex.
WARN [2024-06-21 02:42:26] Allosome coverage missing, cannot determine sex.
FATAL [2024-06-21 02:42:26] normalDB not a valid normalDB object. Use createNormalDatabase to 

FATAL [2024-06-21 02:42:26] create one. 

FATAL [2024-06-21 02:42:26]  

FATAL [2024-06-21 02:42:26] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:42:26] parameters (PureCN 2.11.0). 

WARN [2024-06-21 02:42:26] You are likely not using the correct baits file!
WARN [2024-06-21 02:42:26] Allosome coverage missing, cannot determine sex.
WARN [2024-06-21 02:42:26] Allosome coverage missing, cannot determine sex.
WARN [2024-06-21 02:42:29] Allosome coverage missing, cannot determine sex.
WARN [2024-06-21 02:42:29] Allosome coverage missing, cannot determine sex.
FATAL [2024-06-21 02:42:29] normalDB appears to be empty. 

FATAL [2024-06-21 02:42:29]  

FATAL [2024-06-21 02:42:29] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:42:29] parameters (PureCN 2.11.0). 

WARN [2024-06-21 02:42:30] Allosome coverage missing, cannot determine sex.
WARN [2024-06-21 02:42:30] Allosome coverage missing, cannot determine sex.
WARN [2024-06-21 02:42:30] Intervals in coverage and interval.file have conflicting on/off-target annotation.
WARN [2024-06-21 02:42:40] Allosome coverage missing, cannot determine sex.
WARN [2024-06-21 02:42:40] Allosome coverage missing, cannot determine sex.
FATAL [2024-06-21 02:42:40] Seqlevels missing in provided segmentation: 6 

FATAL [2024-06-21 02:42:40]  

FATAL [2024-06-21 02:42:40] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:42:40] parameters (PureCN 2.11.0). 

sh: 1: gatk: not found
WARN [2024-06-21 02:42:42] Cannot find gatk binary in path.
WARN [2024-06-21 02:42:42] Allosome coverage missing, cannot determine sex.
WARN [2024-06-21 02:42:42] Allosome coverage missing, cannot determine sex.
WARN [2024-06-21 02:42:42] No normalDB provided. Provide one for better results.
FATAL [2024-06-21 02:42:42] segmentationHclust requires an input segmentation. 

FATAL [2024-06-21 02:42:42]  

FATAL [2024-06-21 02:42:42] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:42:42] parameters (PureCN 2.11.0). 

WARN [2024-06-21 02:42:43] Allosome coverage missing, cannot determine sex.
WARN [2024-06-21 02:42:43] Allosome coverage missing, cannot determine sex.
WARN [2024-06-21 02:42:43] No normalDB provided. Provide one for better results.
FATAL [2024-06-21 02:43:12] The normal.panel.vcf.file contains only a single sample. 

FATAL [2024-06-21 02:43:12]  

FATAL [2024-06-21 02:43:12] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:43:12] parameters (PureCN 2.11.0). 

FATAL [2024-06-21 02:43:12] mapping.bias.file must be a file with *.rds suffix. 

FATAL [2024-06-21 02:43:12]  

FATAL [2024-06-21 02:43:12] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:43:12] parameters (PureCN 2.11.0). 

Failed with error:  'there is no package called 'genomicsdb''
FATAL [2024-06-21 02:43:13] min.normals (0) must be >= 1. 

FATAL [2024-06-21 02:43:13]  

FATAL [2024-06-21 02:43:13] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:43:13] parameters (PureCN 2.11.0). 

FATAL [2024-06-21 02:43:14] min.normals (10) cannot be larger than min.normals.assign.betafit (3). 

FATAL [2024-06-21 02:43:14]  

FATAL [2024-06-21 02:43:14] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:43:14] parameters (PureCN 2.11.0). 

FATAL [2024-06-21 02:43:14] min.normals.assign.betafit (10) cannot be larger than 

FATAL [2024-06-21 02:43:14] min.normals.betafit (7). 

FATAL [2024-06-21 02:43:14]  

FATAL [2024-06-21 02:43:14] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:43:14] parameters (PureCN 2.11.0). 

FATAL [2024-06-21 02:43:14] min.normals.betafit (20) cannot be larger than 

FATAL [2024-06-21 02:43:14] min.normals.position.specific.fit (10). 

FATAL [2024-06-21 02:43:14]  

FATAL [2024-06-21 02:43:14] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:43:14] parameters (PureCN 2.11.0). 

FATAL [2024-06-21 02:43:14] min.betafit.rho not within expected range or format. 

FATAL [2024-06-21 02:43:14]  

FATAL [2024-06-21 02:43:14] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:43:14] parameters (PureCN 2.11.0). 

FATAL [2024-06-21 02:43:14] max.betafit.rho not within expected range or format. 

FATAL [2024-06-21 02:43:14]  

FATAL [2024-06-21 02:43:14] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:43:14] parameters (PureCN 2.11.0). 

FATAL [2024-06-21 02:43:15] min.betafit.rho (0.9) cannot be larger than max.betafit.rho (0.2). 

FATAL [2024-06-21 02:43:15]  

FATAL [2024-06-21 02:43:15] This is most likely a user error due to invalid input data or 

FATAL [2024-06-21 02:43:15] parameters (PureCN 2.11.0). 

[ 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 
408.166  12.324 383.194 

Example timings

PureCN.Rcheck/PureCN-Ex.timings

nameusersystemelapsed
adjustLogRatio2.0670.0482.115
annotateTargets6.1470.2326.380
bootstrapResults0.5880.0040.593
calculateBamCoverageByInterval0.2130.0120.226
calculateLogRatio0.6580.0040.662
calculateMappingBiasGatk4000
calculateMappingBiasVcf2.0100.1242.134
calculatePowerDetectSomatic1.3250.0161.341
calculateTangentNormal3.9710.2324.204
callAlterations0.1280.0000.128
callAlterationsFromSegmentation1.6190.0241.636
callAmplificationsInLowPurity40.809 0.36341.173
callCIN0.2180.0000.218
callLOH0.1800.0040.184
callMutationBurden1.6310.0281.658
centromeres0.0010.0000.002
correctCoverageBias1.8090.0601.870
createCurationFile0.3030.0120.316
createNormalDatabase2.4690.0232.494
filterIntervals21.114 0.12421.228
filterVcfBasic0.7440.0120.757
filterVcfMuTect0.7750.0040.779
filterVcfMuTect20.7440.0280.772
findFocal11.567 0.09211.669
getSexFromCoverage0.2680.0080.276
getSexFromVcf0.3640.0040.368
plotAbs0.2390.0080.247
poolCoverage0.6210.0000.621
predictSomatic0.5470.0000.547
preprocessIntervals0.7240.0120.736
processMultipleSamples2.5540.0122.566
readAllelicCountsFile0.7780.0000.779
readCoverageFile0.2560.0040.260
readCurationFile0.1960.0040.201
readIntervalFile0.160.000.16
readLogRatioFile0.0290.0000.029
readSegmentationFile0.0070.0000.007
runAbsoluteCN18.057 0.08418.141
segmentationCBS8.880.048.92
segmentationGATK40.0030.0000.002
segmentationHclust16.890 0.17617.067
segmentationPSCBS25.988 0.12426.112
setMappingBiasVcf0.3550.0240.379
setPriorVcf0.2930.0120.306