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CHECK report for PureCN on tokay1

This page was generated on 2018-04-12 13:28:02 -0400 (Thu, 12 Apr 2018).

Package 1088/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PureCN 1.8.1
Markus Riester
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/PureCN
Branch: RELEASE_3_6
Last Commit: 09a4498
Last Changed Date: 2017-12-09 18:37:29 -0400 (Sat, 09 Dec 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: PureCN
Version: 1.8.1
Command: rm -rf PureCN.buildbin-libdir PureCN.Rcheck && mkdir PureCN.buildbin-libdir PureCN.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PureCN.buildbin-libdir PureCN_1.8.1.tar.gz >PureCN.Rcheck\00install.out 2>&1 && cp PureCN.Rcheck\00install.out PureCN-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=PureCN.buildbin-libdir --install="check:PureCN-install.out" --force-multiarch --no-vignettes --timings PureCN_1.8.1.tar.gz
StartedAt: 2018-04-12 02:19:36 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 02:54:35 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 2099.1 seconds
RetCode: 0
Status:  OK  
CheckDir: PureCN.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf PureCN.buildbin-libdir PureCN.Rcheck && mkdir PureCN.buildbin-libdir PureCN.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PureCN.buildbin-libdir PureCN_1.8.1.tar.gz >PureCN.Rcheck\00install.out 2>&1 && cp PureCN.Rcheck\00install.out PureCN-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=PureCN.buildbin-libdir --install="check:PureCN-install.out" --force-multiarch --no-vignettes --timings PureCN_1.8.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/PureCN.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'PureCN/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PureCN' version '1.8.1'
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 whether package 'PureCN' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    extdata   3.3Mb
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
segmentationPSCBS   128.03   0.55  128.61
runAbsoluteCN        35.51   0.05   35.56
filterTargets        34.00   0.09   34.09
findFocal            22.39   0.03   22.42
correctCoverageBias  17.72   0.04   17.75
segmentationCBS      17.41   0.04   17.45
findBestNormal        9.23   0.01    9.25
annotateTargets       7.78   0.34    8.13
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
segmentationPSCBS   171.37   0.56  172.37
filterTargets        41.56   0.04   41.63
runAbsoluteCN        35.88   0.01   35.89
findFocal            23.53   0.02   23.55
correctCoverageBias  20.88   0.02   20.89
segmentationCBS      20.08   0.04   20.13
findBestNormal       12.98   0.01   13.00
annotateTargets       7.09   0.17    7.29
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/PureCN.Rcheck/00check.log'
for details.

Installation output

PureCN.Rcheck/00install.out


install for i386

* installing *source* package 'PureCN' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'PureCN'
    finding HTML links ... done
    PureCN-defunct                          html  
    PureCN-deprecated                       html  
    annotateTargets                         html  
    autoCurateResults                       html  
    bootstrapResults                        html  
    calculateBamCoverageByInterval          html  
    calculateGCContentByInterval            html  
    calculateLogRatio                       html  
    calculatePowerDetectSomatic             html  
    callAlterations                         html  
    callAlterationsFromSegmentation         html  
    callLOH                                 html  
    callMutationBurden                      html  
    centromeres                             html  
    correctCoverageBias                     html  
    createCurationFile                      html  
    createNormalDatabase                    html  
    createSNPBlacklist                      html  
    createTargetWeights                     html  
    filterTargets                           html  
    filterVcfBasic                          html  
    filterVcfMuTect                         html  
    filterVcfMuTect2                        html  
    findBestNormal                          html  
    findFocal                               html  
    getDiploid                              html  
    getSexFromCoverage                      html  
    getSexFromVcf                           html  
    plotAbs                                 html  
    plotBestNormal                          html  
    poolCoverage                            html  
    predictSomatic                          html  
    purecn.example.output                   html  
    readCoverageFile                        html  
    readCoverageGatk                        html  
    readCurationFile                        html  
    runAbsoluteCN                           html  
    segmentationCBS                         html  
    segmentationPSCBS                       html  
    setMappingBiasVcf                       html  
    setPriorVcf                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'PureCN' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PureCN' as PureCN_1.8.1.zip
* DONE (PureCN)
In R CMD INSTALL
In R CMD INSTALL

Tests output

PureCN.Rcheck/tests_i386/runTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

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.

> BiocGenerics:::testPackage("PureCN")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following object is masked from 'package:base':

    apply


Attaching package: 'Biostrings'

The following object is masked from 'package:DelayedArray':

    type

The following object is masked from 'package:base':

    strsplit


Attaching package: 'VariantAnnotation'

The following object is masked from 'package:base':

    tabulate

Loading required package: GenomicFeatures
Loading required package: AnnotationDbi

'select()' returned many:1 mapping between keys and columns
'select()' returned many:1 mapping between keys and columns
WARN [2018-04-12 02:36:31] Attempted adding gene symbols to intervals. Heuristics have been used to pick symbols for overlapping genes.
WARN [2018-04-12 02:36:31] Chromosome naming style of txdb file (UCSC) was different from interval file (NCBI).
'select()' returned many:1 mapping between keys and columns
'select()' returned many:1 mapping between keys and columns
WARN [2018-04-12 02:36:35] Attempted adding gene symbols to intervals. Heuristics have been used to pick symbols for overlapping genes.
FATAL [2018-04-12 02:36:37] tumor.coverage.file and gc.gene.file do not align. 

FATAL [2018-04-12 02:36:37]  

FATAL [2018-04-12 02:36:37] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:36:37] parameters (PureCN 1.8.1). 

WARN [2018-04-12 02:36:38] No mappability scores provided.
INFO [2018-04-12 02:36:38] Calculating GC-content...
WARN [2018-04-12 02:36:38] No mappability scores provided.
INFO [2018-04-12 02:36:38] Calculating GC-content...
FATAL [2018-04-12 02:36:38] Interval coordinates should start at 1, not at 0 

FATAL [2018-04-12 02:36:38]  

FATAL [2018-04-12 02:36:38] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:36:38] parameters (PureCN 1.8.1). 

INFO [2018-04-12 02:36:38] Tiling off-target regions to an average width of 200000.
WARN [2018-04-12 02:36:39] No mappability scores provided.
INFO [2018-04-12 02:36:39] Calculating GC-content...
WARN [2018-04-12 02:36:39] Intervals contain off-target regions. Will not change intervals.
WARN [2018-04-12 02:36:39] No mappability scores provided.
INFO [2018-04-12 02:36:39] Calculating GC-content...
INFO [2018-04-12 02:36:39] Calculating GC-content...
WARN [2018-04-12 02:36:39] No mappability scores provided.
INFO [2018-04-12 02:36:39] Calculating GC-content...
WARN [2018-04-12 02:36:39] Chromosome naming style of interval file (NCBI) was different from reference (UCSC).
WARN [2018-04-12 02:36:39] No mappability scores provided.
INFO [2018-04-12 02:36:39] Calculating GC-content...
FATAL [2018-04-12 02:36:39] Chromosome naming style of interval file unknown, should be UCSC. 

FATAL [2018-04-12 02:36:39]  

FATAL [2018-04-12 02:36:39] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:36:39] parameters (PureCN 1.8.1). 

WARN [2018-04-12 02:36:39] Chromosome naming style of interval file (NCBI) was different from reference (UCSC).
WARN [2018-04-12 02:36:39] Chromosome naming style of mappability file (NCBI) was different from reference (UCSC).
INFO [2018-04-12 02:36:39] Calculating GC-content...
Minimum 3 supporting reads.
Expected allelic fraction 0.5.
Minimum 3 supporting reads.
Expected allelic fraction 0.5.
Minimum 3 supporting reads.
Expected allelic fraction 0.125.
Minimum 5 supporting reads.
Expected allelic fraction 0.02.
Minimum 3 supporting reads.
FATAL [2018-04-12 02:36:40] Need either f or purity and ploidy. 

FATAL [2018-04-12 02:36:40]  

FATAL [2018-04-12 02:36:40] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:36:40] parameters (PureCN 1.8.1). 

Minimum 3 supporting reads.
FATAL [2018-04-12 02:36:40] f not in expected range. 

FATAL [2018-04-12 02:36:40]  

FATAL [2018-04-12 02:36:40] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:36:40] parameters (PureCN 1.8.1). 

FATAL [2018-04-12 02:36:40] coverage not in expected range (>=2) 

FATAL [2018-04-12 02:36:40]  

FATAL [2018-04-12 02:36:40] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:36:40] parameters (PureCN 1.8.1). 

Minimum 2 supporting reads.
FATAL [2018-04-12 02:36:40] purity not in expected range. 

FATAL [2018-04-12 02:36:40]  

FATAL [2018-04-12 02:36:40] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:36:40] parameters (PureCN 1.8.1). 

Minimum 2 supporting reads.
FATAL [2018-04-12 02:36:40] ploidy not in expected range. 

FATAL [2018-04-12 02:36:40]  

FATAL [2018-04-12 02:36:40] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:36:40] parameters (PureCN 1.8.1). 

FATAL [2018-04-12 02:36:40] cell.fraction not in expected range. 

FATAL [2018-04-12 02:36:40]  

FATAL [2018-04-12 02:36:40] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:36:40] parameters (PureCN 1.8.1). 

INFO [2018-04-12 02:36:41] No on_target column in gc.gene.file. Recreate this file with IntervalFile.R.
INFO [2018-04-12 02:36:41] No mappability column in gc.gene.file.
INFO [2018-04-12 02:36:44] ------------------------------------------------------------
INFO [2018-04-12 02:36:44] PureCN 1.8.1
INFO [2018-04-12 02:36:44] ------------------------------------------------------------
INFO [2018-04-12 02:36:44] Loading coverage files...
INFO [2018-04-12 02:36:44] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2018-04-12 02:36:44] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:36:44] Allosome coverage missing, cannot determine sex.
INFO [2018-04-12 02:36:44] Removing 22 small (< 5bp) targets.
INFO [2018-04-12 02:36:44] Removing 19 targets with low total coverage in normal (< 150.00 reads).
WARN [2018-04-12 02:36:44] No normalDB provided. Provide one for better results.
INFO [2018-04-12 02:36:44] Removing 233 low coverage (< 15.0000X) targets.
INFO [2018-04-12 02:36:44] Using 9547 intervals (9547 on-target, 0 off-target).
INFO [2018-04-12 02:36:44] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2018-04-12 02:36:44] No gc.gene.file provided. Cannot check if data was GC-normalized. Was it?
INFO [2018-04-12 02:36:44] Loading VCF...
INFO [2018-04-12 02:36:44] LIB-02240e4 is tumor in VCF file.
INFO [2018-04-12 02:36:44] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2018-04-12 02:36:44] Found 2331 variants in VCF file.
INFO [2018-04-12 02:36:44] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2018-04-12 02:36:44] Initial testing for significant sample cross-contamination: unlikely
INFO [2018-04-12 02:36:45] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2018-04-12 02:36:45] Removing 16 low quality variants with BQ < 25.
INFO [2018-04-12 02:36:45] Total size of targeted genomic region: 1.63Mb (2.58Mb with 50bp padding).
INFO [2018-04-12 02:36:45] 1.0% of targets contain variants.
INFO [2018-04-12 02:36:45] Removing 2122 variants outside intervals.
INFO [2018-04-12 02:36:45] Found SOMATIC annotation in VCF.
INFO [2018-04-12 02:36:45] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2018-04-12 02:36:45] Found SOMATIC annotation in VCF. Setting mapping bias to 0.973.
INFO [2018-04-12 02:36:45] Sample sex: ?
INFO [2018-04-12 02:36:45] Segmenting data...
INFO [2018-04-12 02:36:45] Setting undo.SD parameter to 1.000000.
INFO [2018-04-12 02:36:51] Setting prune.hclust.h parameter to 0.200000.
INFO [2018-04-12 02:36:51] Using 123 variants.
INFO [2018-04-12 02:36:51] Mean standard deviation of log-ratios: 0.37
INFO [2018-04-12 02:36:51] 2D-grid search of purity and ploidy...
INFO [2018-04-12 02:36:53] Local optima: 0.63/1.9, 0.4/2.2, 0.5/2
INFO [2018-04-12 02:36:53] Testing local optimum 1/3 at purity 0.63 and total ploidy 1.90...
INFO [2018-04-12 02:36:54] Fitting variants for purity 0.65, tumor ploidy 1.73 and contamination 0.01.
INFO [2018-04-12 02:36:55] Optimized purity: 0.65
INFO [2018-04-12 02:36:55] Testing local optimum 2/3 at purity 0.40 and total ploidy 2.20...
INFO [2018-04-12 02:36:56] Fitting variants for purity 0.40, tumor ploidy 2.34 and contamination 0.01.
INFO [2018-04-12 02:36:57] Optimized purity: 0.40
INFO [2018-04-12 02:36:57] Testing local optimum 3/3 at purity 0.50 and total ploidy 2.00...
INFO [2018-04-12 02:36:58] Fitting variants for purity 0.65, tumor ploidy 1.73 and contamination 0.01.
INFO [2018-04-12 02:36:59] Optimized purity: 0.65
INFO [2018-04-12 02:36:59] Done.
INFO [2018-04-12 02:36:59] ------------------------------------------------------------
FATAL [2018-04-12 02:37:01] fun.countMutation not a function. 

FATAL [2018-04-12 02:37:01]  

FATAL [2018-04-12 02:37:01] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:37:01] parameters (PureCN 1.8.1). 

FATAL [2018-04-12 02:37:01] exclude not a GRanges object. 

FATAL [2018-04-12 02:37:01]  

FATAL [2018-04-12 02:37:01] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:37:01] parameters (PureCN 1.8.1). 

FATAL [2018-04-12 02:37:01] callable not a GRanges object. 

FATAL [2018-04-12 02:37:01]  

FATAL [2018-04-12 02:37:01] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:37:01] parameters (PureCN 1.8.1). 

FATAL [2018-04-12 02:37:11] No gc_bias column in gc.gene.file. 

FATAL [2018-04-12 02:37:11]  

FATAL [2018-04-12 02:37:11] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:37:11] parameters (PureCN 1.8.1). 

WARN [2018-04-12 02:37:11] tumor.coverage.file and gc.gene.file do not align.
INFO [2018-04-12 02:37:30] Reading Sample1_PureCN.rds...
INFO [2018-04-12 02:37:30] Reading Sample1_PureCN.rds...
INFO [2018-04-12 02:37:30] Reading Sample1_PureCN.rds...
INFO [2018-04-12 02:37:30] Reading Sample1_PureCN.rds...
INFO [2018-04-12 02:37:31] Reading Sample1_PureCN.rds...
INFO [2018-04-12 02:37:31] Reading Sample1_PureCN.rds...
FATAL [2018-04-12 02:37:31] Purity or Ploidy not numeric or in expected range. 

FATAL [2018-04-12 02:37:31]  

FATAL [2018-04-12 02:37:31] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:37:31] parameters (PureCN 1.8.1). 

INFO [2018-04-12 02:37:31] Reading Sample1_PureCN.rds...
INFO [2018-04-12 02:37:31] Reading Sample1_PureCN.rds...
FATAL [2018-04-12 02:37:31] 'Failed' column in Sample1_PureCN.csv not logical(1). 

FATAL [2018-04-12 02:37:31]  

FATAL [2018-04-12 02:37:31] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:37:31] parameters (PureCN 1.8.1). 

WARN [2018-04-12 02:37:32] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:37:32] Allosome coverage missing, cannot determine sex.
INFO [2018-04-12 02:37:35] Pooling example_normal.txt, example_normal2.txt.
INFO [2018-04-12 02:37:36] Coverage file does not contain read count information, using total coverage for calculating log-ratios.
WARN [2018-04-12 02:37:43] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:37:43] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:37:45] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:37:45] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:37:46] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:37:46] Allosome coverage missing, cannot determine sex.
FATAL [2018-04-12 02:37:46] Length of normal.coverage.files and sex different 

FATAL [2018-04-12 02:37:46]  

FATAL [2018-04-12 02:37:46] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:37:46] parameters (PureCN 1.8.1). 

WARN [2018-04-12 02:37:48] tumor.coverage.file and gc.gene.file do not align.
WARN [2018-04-12 02:37:50] Target intervals were not sorted.
WARN [2018-04-12 02:37:50] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:37:50] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:37:50] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:37:52] Allosome coverage missing, cannot determine sex.
INFO [2018-04-12 02:37:52] Sample sex: NA
FATAL [2018-04-12 02:37:53] tumor.coverage.file and normalDB do not align. 

FATAL [2018-04-12 02:37:53]  

FATAL [2018-04-12 02:37:53] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:37:53] parameters (PureCN 1.8.1). 

INFO [2018-04-12 02:37:54] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2018-04-12 02:37:54] Initial testing for significant sample cross-contamination: unlikely
INFO [2018-04-12 02:37:54] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2018-04-12 02:37:54] Removing 16 low quality variants with BQ < 25.
INFO [2018-04-12 02:37:54] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2018-04-12 02:37:54] Initial testing for significant sample cross-contamination: unlikely
INFO [2018-04-12 02:37:54] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2018-04-12 02:37:54] Removing 6 blacklisted variants.
INFO [2018-04-12 02:37:54] Removing 16 low quality variants with BQ < 25.
WARN [2018-04-12 02:37:54] MuTect stats file lacks contig and position columns.
INFO [2018-04-12 02:37:54] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2018-04-12 02:37:55] Initial testing for significant sample cross-contamination: unlikely
INFO [2018-04-12 02:37:55] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2018-04-12 02:37:55] Removing 16 low quality variants with BQ < 25.
WARN [2018-04-12 02:37:55] MuTect stats file and VCF file do not align perfectly. Will remove 2325 unmatched variants.
WARN [2018-04-12 02:37:55] MuTect stats file lacks failure_reasons column. Keeping all variants listed in stats file.
INFO [2018-04-12 02:37:55] Removing 0 non heterozygous (in matched normal) germline SNPs.
INFO [2018-04-12 02:37:55] Removing 0 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2018-04-12 02:37:55] Removing 0 low quality variants with BQ < 25.
WARN [2018-04-12 02:37:56] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:37:56] Allosome coverage missing, cannot determine sex.
INFO [2018-04-12 02:37:56] Mean coverages: chrX: 108.58, chrY: 108.58, chr1-22: 104.87.
INFO [2018-04-12 02:37:57] Mean coverages: chrX: 108.58, chrY: 2.17, chr1-22: 104.87.
INFO [2018-04-12 02:37:57] Mean coverages: chrX: 108.58, chrY: 5.17, chr1-22: 104.87.
INFO [2018-04-12 02:37:57] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2018-04-12 02:37:57] No germline variants in VCF.
WARN [2018-04-12 02:38:00] Found 4 overlapping intervals, starting at line 2.
INFO [2018-04-12 02:38:00] Loading coverage data...
INFO [2018-04-12 02:38:01] Mean target coverages: 112X (tumor) 99X (normal).
INFO [2018-04-12 02:38:01] Mean target coverages: 112X (tumor) 43X (normal).
INFO [2018-04-12 02:38:02] ------------------------------------------------------------
INFO [2018-04-12 02:38:02] PureCN 1.8.1
INFO [2018-04-12 02:38:02] ------------------------------------------------------------
INFO [2018-04-12 02:38:02] Loading coverage files...
INFO [2018-04-12 02:38:02] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2018-04-12 02:38:02] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:38:02] Allosome coverage missing, cannot determine sex.
INFO [2018-04-12 02:38:02] Removing 22 small (< 5bp) targets.
INFO [2018-04-12 02:38:02] Removing 19 targets with low total coverage in normal (< 150.00 reads).
WARN [2018-04-12 02:38:02] No normalDB provided. Provide one for better results.
INFO [2018-04-12 02:38:02] Removing 233 low coverage (< 15.0000X) targets.
INFO [2018-04-12 02:38:02] Using 9547 intervals (9547 on-target, 0 off-target).
INFO [2018-04-12 02:38:02] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2018-04-12 02:38:03] No gc.gene.file provided. Cannot check if data was GC-normalized. Was it?
INFO [2018-04-12 02:38:03] Sample sex: ?
INFO [2018-04-12 02:38:03] Segmenting data...
INFO [2018-04-12 02:38:03] Target weights found, will use weighted CBS.
INFO [2018-04-12 02:38:03] Setting undo.SD parameter to 1.000000.
Setting multi-figure configuration
INFO [2018-04-12 02:38:09] Mean standard deviation of log-ratios: 0.37
INFO [2018-04-12 02:38:09] 2D-grid search of purity and ploidy...
INFO [2018-04-12 02:38:09] Local optima: 0.65/1.9, 0.33/1.9, 0.38/2.2, 0.27/2.1, 0.29/2, 0.78/2
INFO [2018-04-12 02:38:09] Testing local optimum 1/6 at purity 0.65 and total ploidy 1.90...
INFO [2018-04-12 02:38:10] Testing local optimum 2/6 at purity 0.33 and total ploidy 1.90...
INFO [2018-04-12 02:38:10] Recalibrating log-ratios...
INFO [2018-04-12 02:38:10] Testing local optimum 2/6 at purity 0.33 and total ploidy 1.90...
INFO [2018-04-12 02:38:10] Recalibrating log-ratios...
INFO [2018-04-12 02:38:10] Testing local optimum 2/6 at purity 0.33 and total ploidy 1.90...
INFO [2018-04-12 02:38:11] Recalibrating log-ratios...
INFO [2018-04-12 02:38:11] Testing local optimum 2/6 at purity 0.33 and total ploidy 1.90...
INFO [2018-04-12 02:38:11] Testing local optimum 3/6 at purity 0.38 and total ploidy 2.20...
INFO [2018-04-12 02:38:12] Testing local optimum 4/6 at purity 0.27 and total ploidy 2.10...
INFO [2018-04-12 02:38:12] Recalibrating log-ratios...
INFO [2018-04-12 02:38:12] Testing local optimum 4/6 at purity 0.27 and total ploidy 2.10...
INFO [2018-04-12 02:38:13] Recalibrating log-ratios...
INFO [2018-04-12 02:38:13] Testing local optimum 4/6 at purity 0.27 and total ploidy 2.10...
INFO [2018-04-12 02:38:13] Recalibrating log-ratios...
INFO [2018-04-12 02:38:13] Testing local optimum 4/6 at purity 0.27 and total ploidy 2.10...
INFO [2018-04-12 02:38:13] Testing local optimum 5/6 at purity 0.29 and total ploidy 2.00...
INFO [2018-04-12 02:38:14] Recalibrating log-ratios...
INFO [2018-04-12 02:38:14] Testing local optimum 5/6 at purity 0.29 and total ploidy 2.00...
INFO [2018-04-12 02:38:14] Recalibrating log-ratios...
INFO [2018-04-12 02:38:14] Testing local optimum 5/6 at purity 0.29 and total ploidy 2.00...
INFO [2018-04-12 02:38:14] Recalibrating log-ratios...
INFO [2018-04-12 02:38:14] Testing local optimum 5/6 at purity 0.29 and total ploidy 2.00...
INFO [2018-04-12 02:38:15] Testing local optimum 6/6 at purity 0.78 and total ploidy 2.00...
INFO [2018-04-12 02:38:16] Done.
INFO [2018-04-12 02:38:16] ------------------------------------------------------------
INFO [2018-04-12 02:38:16] Reading C:\Users\biocbuild\bbs-3.6-bioc\tmpdir\RtmpczuZSz\file2f284b26d19.rds...
FATAL [2018-04-12 02:38:16] runAbsoluteCN was run without a VCF file. 

FATAL [2018-04-12 02:38:16]  

FATAL [2018-04-12 02:38:16] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:38:16] parameters (PureCN 1.8.1). 

FATAL [2018-04-12 02:38:16] runAbsoluteCN was run without a VCF file. 

FATAL [2018-04-12 02:38:16]  

FATAL [2018-04-12 02:38:16] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:38:16] parameters (PureCN 1.8.1). 

INFO [2018-04-12 02:38:16] ------------------------------------------------------------
INFO [2018-04-12 02:38:16] PureCN 1.8.1
INFO [2018-04-12 02:38:16] ------------------------------------------------------------
INFO [2018-04-12 02:38:16] Loading coverage files...
FATAL [2018-04-12 02:38:16] Need a normal coverage file if log.ratio and seg.file are not provided. 

FATAL [2018-04-12 02:38:16]  

FATAL [2018-04-12 02:38:16] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:38:16] parameters (PureCN 1.8.1). 

INFO [2018-04-12 02:38:16] ------------------------------------------------------------
INFO [2018-04-12 02:38:16] PureCN 1.8.1
INFO [2018-04-12 02:38:16] ------------------------------------------------------------
FATAL [2018-04-12 02:38:16] min.ploidy or max.ploidy not within expected range. 

FATAL [2018-04-12 02:38:16]  

FATAL [2018-04-12 02:38:16] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:38:16] parameters (PureCN 1.8.1). 

INFO [2018-04-12 02:38:16] ------------------------------------------------------------
INFO [2018-04-12 02:38:16] PureCN 1.8.1
INFO [2018-04-12 02:38:16] ------------------------------------------------------------
FATAL [2018-04-12 02:38:16] min.ploidy or max.ploidy not within expected range. 

FATAL [2018-04-12 02:38:16]  

FATAL [2018-04-12 02:38:16] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:38:16] parameters (PureCN 1.8.1). 

INFO [2018-04-12 02:38:16] ------------------------------------------------------------
INFO [2018-04-12 02:38:16] PureCN 1.8.1
INFO [2018-04-12 02:38:16] ------------------------------------------------------------
INFO [2018-04-12 02:38:16] ------------------------------------------------------------
INFO [2018-04-12 02:38:16] PureCN 1.8.1
INFO [2018-04-12 02:38:16] ------------------------------------------------------------
INFO [2018-04-12 02:38:16] ------------------------------------------------------------
INFO [2018-04-12 02:38:16] PureCN 1.8.1
INFO [2018-04-12 02:38:16] ------------------------------------------------------------
FATAL [2018-04-12 02:38:16] test.purity not within expected range. 

FATAL [2018-04-12 02:38:16]  

FATAL [2018-04-12 02:38:16] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:38:16] parameters (PureCN 1.8.1). 

INFO [2018-04-12 02:38:16] ------------------------------------------------------------
INFO [2018-04-12 02:38:16] PureCN 1.8.1
INFO [2018-04-12 02:38:16] ------------------------------------------------------------
INFO [2018-04-12 02:38:16] Loading coverage files...
FATAL [2018-04-12 02:38:17] Tumor and normal are identical. This won't give any meaningful results 

FATAL [2018-04-12 02:38:17] and I'm stopping here. 

FATAL [2018-04-12 02:38:17]  

FATAL [2018-04-12 02:38:17] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:38:17] parameters (PureCN 1.8.1). 

INFO [2018-04-12 02:38:17] ------------------------------------------------------------
INFO [2018-04-12 02:38:17] PureCN 1.8.1
INFO [2018-04-12 02:38:17] ------------------------------------------------------------
INFO [2018-04-12 02:38:17] Loading coverage files...
FATAL [2018-04-12 02:38:17] Length of log.ratio different from tumor coverage. 

FATAL [2018-04-12 02:38:17]  

FATAL [2018-04-12 02:38:17] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:38:17] parameters (PureCN 1.8.1). 

INFO [2018-04-12 02:38:17] ------------------------------------------------------------
INFO [2018-04-12 02:38:17] PureCN 1.8.1
INFO [2018-04-12 02:38:17] ------------------------------------------------------------
FATAL [2018-04-12 02:38:17] prior.purity must have the same length as test.purity. 

FATAL [2018-04-12 02:38:17]  

FATAL [2018-04-12 02:38:17] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:38:17] parameters (PureCN 1.8.1). 

INFO [2018-04-12 02:38:17] ------------------------------------------------------------
INFO [2018-04-12 02:38:17] PureCN 1.8.1
INFO [2018-04-12 02:38:17] ------------------------------------------------------------
FATAL [2018-04-12 02:38:17] min.gof not within expected range or format. 

FATAL [2018-04-12 02:38:17]  

FATAL [2018-04-12 02:38:17] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:38:17] parameters (PureCN 1.8.1). 

INFO [2018-04-12 02:38:17] ------------------------------------------------------------
INFO [2018-04-12 02:38:17] PureCN 1.8.1
INFO [2018-04-12 02:38:17] ------------------------------------------------------------
FATAL [2018-04-12 02:38:17] prior.purity not within expected range or format. 

FATAL [2018-04-12 02:38:17]  

FATAL [2018-04-12 02:38:17] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:38:17] parameters (PureCN 1.8.1). 

INFO [2018-04-12 02:38:17] ------------------------------------------------------------
INFO [2018-04-12 02:38:17] PureCN 1.8.1
INFO [2018-04-12 02:38:17] ------------------------------------------------------------
FATAL [2018-04-12 02:38:17] prior.purity must add to 1. Sum is 1.5 

FATAL [2018-04-12 02:38:17]  

FATAL [2018-04-12 02:38:17] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:38:17] parameters (PureCN 1.8.1). 

INFO [2018-04-12 02:38:17] ------------------------------------------------------------
INFO [2018-04-12 02:38:17] PureCN 1.8.1
INFO [2018-04-12 02:38:17] ------------------------------------------------------------
FATAL [2018-04-12 02:38:17] max.homozygous.loss not within expected range or format. 

FATAL [2018-04-12 02:38:17]  

FATAL [2018-04-12 02:38:17] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:38:17] parameters (PureCN 1.8.1). 

INFO [2018-04-12 02:38:17] ------------------------------------------------------------
INFO [2018-04-12 02:38:17] PureCN 1.8.1
INFO [2018-04-12 02:38:17] ------------------------------------------------------------
FATAL [2018-04-12 02:38:17] prior.K not within expected range or format. 

FATAL [2018-04-12 02:38:17]  

FATAL [2018-04-12 02:38:17] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:38:17] parameters (PureCN 1.8.1). 

INFO [2018-04-12 02:38:17] ------------------------------------------------------------
INFO [2018-04-12 02:38:17] PureCN 1.8.1
INFO [2018-04-12 02:38:17] ------------------------------------------------------------
FATAL [2018-04-12 02:38:17] prior.contamination not within expected range or format. 

FATAL [2018-04-12 02:38:17]  

FATAL [2018-04-12 02:38:17] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:38:17] parameters (PureCN 1.8.1). 

INFO [2018-04-12 02:38:17] ------------------------------------------------------------
INFO [2018-04-12 02:38:17] PureCN 1.8.1
INFO [2018-04-12 02:38:17] ------------------------------------------------------------
FATAL [2018-04-12 02:38:17] Iterations not in the expected range from 10 to 250. 

FATAL [2018-04-12 02:38:17]  

FATAL [2018-04-12 02:38:17] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:38:17] parameters (PureCN 1.8.1). 

INFO [2018-04-12 02:38:17] ------------------------------------------------------------
INFO [2018-04-12 02:38:17] PureCN 1.8.1
INFO [2018-04-12 02:38:17] ------------------------------------------------------------
FATAL [2018-04-12 02:38:17] Iterations not in the expected range from 10 to 250. 

FATAL [2018-04-12 02:38:17]  

FATAL [2018-04-12 02:38:17] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:38:17] parameters (PureCN 1.8.1). 

INFO [2018-04-12 02:38:17] ------------------------------------------------------------
INFO [2018-04-12 02:38:17] PureCN 1.8.1
INFO [2018-04-12 02:38:17] ------------------------------------------------------------
INFO [2018-04-12 02:38:18] ------------------------------------------------------------
INFO [2018-04-12 02:38:18] PureCN 1.8.1
INFO [2018-04-12 02:38:18] ------------------------------------------------------------
INFO [2018-04-12 02:38:18] Loading coverage files...
FATAL [2018-04-12 02:38:18] Interval files in normal and tumor different. 

FATAL [2018-04-12 02:38:18]  

FATAL [2018-04-12 02:38:18] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:38:18] parameters (PureCN 1.8.1). 

INFO [2018-04-12 02:38:18] ------------------------------------------------------------
INFO [2018-04-12 02:38:18] PureCN 1.8.1
INFO [2018-04-12 02:38:18] ------------------------------------------------------------
INFO [2018-04-12 02:38:18] Loading coverage files...
INFO [2018-04-12 02:38:19] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2018-04-12 02:38:19] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:38:19] Allosome coverage missing, cannot determine sex.
INFO [2018-04-12 02:38:19] Removing 22 small (< 5bp) targets.
INFO [2018-04-12 02:38:19] Removing 19 targets with low total coverage in normal (< 150.00 reads).
WARN [2018-04-12 02:38:19] No normalDB provided. Provide one for better results.
INFO [2018-04-12 02:38:19] Removing 233 low coverage (< 15.0000X) targets.
INFO [2018-04-12 02:38:19] Using 9547 intervals (9547 on-target, 0 off-target).
INFO [2018-04-12 02:38:19] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2018-04-12 02:38:19] No gc.gene.file provided. Cannot check if data was GC-normalized. Was it?
INFO [2018-04-12 02:38:19] Loading VCF...
INFO [2018-04-12 02:38:19] LIB-02240e4 is tumor in VCF file.
INFO [2018-04-12 02:38:19] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2018-04-12 02:38:19] Found 2331 variants in VCF file.
INFO [2018-04-12 02:38:19] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2018-04-12 02:38:19] Initial testing for significant sample cross-contamination: unlikely
INFO [2018-04-12 02:38:19] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2018-04-12 02:38:19] Removing 16 low quality variants with BQ < 25.
INFO [2018-04-12 02:38:19] Total size of targeted genomic region: 1.63Mb (2.58Mb with 50bp padding).
INFO [2018-04-12 02:38:19] 1.0% of targets contain variants.
INFO [2018-04-12 02:38:19] Removing 2122 variants outside intervals.
INFO [2018-04-12 02:38:19] Found SOMATIC annotation in VCF.
INFO [2018-04-12 02:38:19] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2018-04-12 02:38:19] Found SOMATIC annotation in VCF. Setting mapping bias to 0.973.
INFO [2018-04-12 02:38:19] Sample sex: ?
INFO [2018-04-12 02:38:19] Segmenting data...
INFO [2018-04-12 02:38:19] Setting undo.SD parameter to 1.000000.
Setting multi-figure configuration
INFO [2018-04-12 02:38:26] Setting prune.hclust.h parameter to 0.200000.
INFO [2018-04-12 02:38:26] Using 123 variants.
INFO [2018-04-12 02:38:26] Mean standard deviation of log-ratios: 0.37
INFO [2018-04-12 02:38:26] 2D-grid search of purity and ploidy...
INFO [2018-04-12 02:38:34] Local optima: 0.62/1.9, 0.38/2.2, 0.3/1.9, 0.48/2
INFO [2018-04-12 02:38:34] Testing local optimum 1/4 at purity 0.62 and total ploidy 1.90...
INFO [2018-04-12 02:38:35] Fitting variants for purity 0.65, tumor ploidy 1.73 and contamination 0.01.
INFO [2018-04-12 02:38:36] Optimized purity: 0.65
INFO [2018-04-12 02:38:36] Testing local optimum 2/4 at purity 0.38 and total ploidy 2.20...
INFO [2018-04-12 02:38:37] Fitting variants for purity 0.40, tumor ploidy 2.43 and contamination 0.01.
INFO [2018-04-12 02:38:38] Optimized purity: 0.40
INFO [2018-04-12 02:38:38] Testing local optimum 3/4 at purity 0.30 and total ploidy 1.90...
INFO [2018-04-12 02:38:38] Recalibrating log-ratios...
INFO [2018-04-12 02:38:38] Testing local optimum 3/4 at purity 0.30 and total ploidy 1.90...
INFO [2018-04-12 02:38:39] Recalibrating log-ratios...
INFO [2018-04-12 02:38:39] Testing local optimum 3/4 at purity 0.30 and total ploidy 1.90...
INFO [2018-04-12 02:38:39] Recalibrating log-ratios...
INFO [2018-04-12 02:38:39] Testing local optimum 3/4 at purity 0.30 and total ploidy 1.90...
INFO [2018-04-12 02:38:39] Testing local optimum 4/4 at purity 0.48 and total ploidy 2.00...
INFO [2018-04-12 02:38:40] Fitting variants for purity 0.65, tumor ploidy 1.73 and contamination 0.01.
INFO [2018-04-12 02:38:41] Optimized purity: 0.65
INFO [2018-04-12 02:38:41] Done.
INFO [2018-04-12 02:38:41] ------------------------------------------------------------
INFO [2018-04-12 02:38:41] ------------------------------------------------------------
INFO [2018-04-12 02:38:41] PureCN 1.8.1
INFO [2018-04-12 02:38:41] ------------------------------------------------------------
INFO [2018-04-12 02:38:41] Loading coverage files...
INFO [2018-04-12 02:38:42] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2018-04-12 02:38:42] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:38:42] Allosome coverage missing, cannot determine sex.
INFO [2018-04-12 02:38:42] Removing 22 small (< 5bp) targets.
INFO [2018-04-12 02:38:42] Removing 19 targets with low total coverage in normal (< 150.00 reads).
WARN [2018-04-12 02:38:42] No normalDB provided. Provide one for better results.
INFO [2018-04-12 02:38:42] Removing 233 low coverage (< 15.0000X) targets.
INFO [2018-04-12 02:38:42] Using 9547 intervals (9547 on-target, 0 off-target).
INFO [2018-04-12 02:38:42] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2018-04-12 02:38:42] No gc.gene.file provided. Cannot check if data was GC-normalized. Was it?
INFO [2018-04-12 02:38:42] Loading VCF...
INFO [2018-04-12 02:38:42] LIB-02240e4 is tumor in VCF file.
INFO [2018-04-12 02:38:42] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2018-04-12 02:38:42] Found 2331 variants in VCF file.
INFO [2018-04-12 02:38:42] Initial testing for significant sample cross-contamination: unlikely
INFO [2018-04-12 02:38:42] Removing 63 variants with AF < 0.030 or AF >= 0.970 or less than 4 supporting reads or depth < 15.
INFO [2018-04-12 02:38:42] Removing 16 low quality variants with BQ < 25.
INFO [2018-04-12 02:38:43] Total size of targeted genomic region: 1.63Mb (2.58Mb with 50bp padding).
INFO [2018-04-12 02:38:43] 1.0% of targets contain variants.
INFO [2018-04-12 02:38:43] Setting somatic prior probabilities for dbSNP hits to 0.000500 or to 0.500000 otherwise.
INFO [2018-04-12 02:38:43] Sample sex: ?
INFO [2018-04-12 02:38:43] Segmenting data...
INFO [2018-04-12 02:38:43] Setting undo.SD parameter to 1.000000.
Setting multi-figure configuration
INFO [2018-04-12 02:38:50] Setting prune.hclust.h parameter to 0.200000.
INFO [2018-04-12 02:38:50] Removing 282 variants outside segments.
INFO [2018-04-12 02:38:50] Using 1970 variants.
INFO [2018-04-12 02:38:50] Mean standard deviation of log-ratios: 0.37
INFO [2018-04-12 02:38:50] 2D-grid search of purity and ploidy...
INFO [2018-04-12 02:38:52] Local optima: 0.62/1.9, 0.38/2.2, 0.3/1.9, 0.48/2
INFO [2018-04-12 02:38:52] Testing local optimum 1/4 at purity 0.62 and total ploidy 1.90...
INFO [2018-04-12 02:38:53] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01.
INFO [2018-04-12 02:38:57] Optimized purity: 0.65
INFO [2018-04-12 02:38:57] Testing local optimum 2/4 at purity 0.38 and total ploidy 2.20...
INFO [2018-04-12 02:38:59] Fitting variants for purity 0.40, tumor ploidy 2.34 and contamination 0.01.
INFO [2018-04-12 02:39:03] Optimized purity: 0.40
INFO [2018-04-12 02:39:03] Testing local optimum 3/4 at purity 0.30 and total ploidy 1.90...
INFO [2018-04-12 02:39:03] Recalibrating log-ratios...
INFO [2018-04-12 02:39:03] Testing local optimum 3/4 at purity 0.30 and total ploidy 1.90...
INFO [2018-04-12 02:39:04] Recalibrating log-ratios...
INFO [2018-04-12 02:39:04] Testing local optimum 3/4 at purity 0.30 and total ploidy 1.90...
INFO [2018-04-12 02:39:04] Recalibrating log-ratios...
INFO [2018-04-12 02:39:04] Testing local optimum 3/4 at purity 0.30 and total ploidy 1.90...
INFO [2018-04-12 02:39:04] Testing local optimum 4/4 at purity 0.48 and total ploidy 2.00...
INFO [2018-04-12 02:39:06] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01.
INFO [2018-04-12 02:39:10] Optimized purity: 0.65
INFO [2018-04-12 02:39:10] Done.
INFO [2018-04-12 02:39:10] ------------------------------------------------------------
INFO [2018-04-12 02:39:10] ------------------------------------------------------------
INFO [2018-04-12 02:39:10] PureCN 1.8.1
INFO [2018-04-12 02:39:10] ------------------------------------------------------------
INFO [2018-04-12 02:39:10] Loading coverage files...
INFO [2018-04-12 02:39:11] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2018-04-12 02:39:11] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:39:11] Allosome coverage missing, cannot determine sex.
INFO [2018-04-12 02:39:11] No Gene column in gc.gene.file. You won't get gene-level calls.
INFO [2018-04-12 02:39:11] No on_target column in gc.gene.file. Recreate this file with IntervalFile.R.
INFO [2018-04-12 02:39:11] No mappability column in gc.gene.file.
INFO [2018-04-12 02:39:12] Removing 15 low/high GC targets.
INFO [2018-04-12 02:39:12] Removing 21 small (< 5bp) targets.
INFO [2018-04-12 02:39:12] Removing 19 targets with low total coverage in normal (< 150.00 reads).
WARN [2018-04-12 02:39:12] No normalDB provided. Provide one for better results.
INFO [2018-04-12 02:39:12] Removing 232 low coverage (< 15.0000X) targets.
INFO [2018-04-12 02:39:12] Using 9534 intervals (9534 on-target, 0 off-target).
INFO [2018-04-12 02:39:12] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2018-04-12 02:39:12] AT/GC dropout: 1.03 (tumor), 1.03 (normal). 
INFO [2018-04-12 02:39:12] Loading VCF...
INFO [2018-04-12 02:39:12] LIB-02240e4 is tumor in VCF file.
INFO [2018-04-12 02:39:12] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2018-04-12 02:39:12] Found 2331 variants in VCF file.
INFO [2018-04-12 02:39:12] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2018-04-12 02:39:12] Initial testing for significant sample cross-contamination: unlikely
INFO [2018-04-12 02:39:12] Removing 48 variants with AF < 0.030 or AF >= Inf or less than 4 supporting reads or depth < 15.
INFO [2018-04-12 02:39:12] Removing 16 low quality variants with BQ < 25.
INFO [2018-04-12 02:39:12] Total size of targeted genomic region: 1.63Mb (2.58Mb with 50bp padding).
INFO [2018-04-12 02:39:13] 1.0% of targets contain variants.
INFO [2018-04-12 02:39:13] Removing 2122 variants outside intervals.
INFO [2018-04-12 02:39:13] Found SOMATIC annotation in VCF.
INFO [2018-04-12 02:39:13] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2018-04-12 02:39:13] Found SOMATIC annotation in VCF. Setting mapping bias to 0.973.
INFO [2018-04-12 02:39:13] Sample sex: ?
INFO [2018-04-12 02:39:13] Segmenting data...
INFO [2018-04-12 02:39:13] Setting undo.SD parameter to 1.000000.
Setting multi-figure configuration
INFO [2018-04-12 02:39:20] Setting prune.hclust.h parameter to 0.200000.
INFO [2018-04-12 02:39:20] Using 123 variants.
INFO [2018-04-12 02:39:20] Mean standard deviation of log-ratios: 0.37
INFO [2018-04-12 02:39:20] 2D-grid search of purity and ploidy...
INFO [2018-04-12 02:39:20] Local optima: 0.65/1.9, 0.33/1.9, 0.38/2.2, 0.27/2.1, 0.29/2, 0.78/2
INFO [2018-04-12 02:39:20] Testing local optimum 1/6 at purity 0.65 and total ploidy 1.90...
INFO [2018-04-12 02:39:21] Fitting variants for purity 0.65, tumor ploidy 1.73 and contamination 0.01.
INFO [2018-04-12 02:39:22] Optimized purity: 0.65
INFO [2018-04-12 02:39:22] Testing local optimum 2/6 at purity 0.33 and total ploidy 1.90...
INFO [2018-04-12 02:39:22] Recalibrating log-ratios...
INFO [2018-04-12 02:39:22] Testing local optimum 2/6 at purity 0.33 and total ploidy 1.90...
INFO [2018-04-12 02:39:23] Recalibrating log-ratios...
INFO [2018-04-12 02:39:23] Testing local optimum 2/6 at purity 0.33 and total ploidy 1.90...
INFO [2018-04-12 02:39:23] Recalibrating log-ratios...
INFO [2018-04-12 02:39:23] Testing local optimum 2/6 at purity 0.33 and total ploidy 1.90...
INFO [2018-04-12 02:39:23] Testing local optimum 3/6 at purity 0.38 and total ploidy 2.20...
INFO [2018-04-12 02:39:25] Fitting variants for purity 0.40, tumor ploidy 2.34 and contamination 0.01.
INFO [2018-04-12 02:39:25] Optimized purity: 0.40
INFO [2018-04-12 02:39:25] Testing local optimum 4/6 at purity 0.27 and total ploidy 2.10...
INFO [2018-04-12 02:39:26] Recalibrating log-ratios...
INFO [2018-04-12 02:39:26] Testing local optimum 4/6 at purity 0.27 and total ploidy 2.10...
INFO [2018-04-12 02:39:26] Recalibrating log-ratios...
INFO [2018-04-12 02:39:26] Testing local optimum 4/6 at purity 0.27 and total ploidy 2.10...
INFO [2018-04-12 02:39:26] Recalibrating log-ratios...
INFO [2018-04-12 02:39:26] Testing local optimum 4/6 at purity 0.27 and total ploidy 2.10...
INFO [2018-04-12 02:39:27] Testing local optimum 5/6 at purity 0.29 and total ploidy 2.00...
INFO [2018-04-12 02:39:27] Recalibrating log-ratios...
INFO [2018-04-12 02:39:27] Testing local optimum 5/6 at purity 0.29 and total ploidy 2.00...
INFO [2018-04-12 02:39:27] Recalibrating log-ratios...
INFO [2018-04-12 02:39:27] Testing local optimum 5/6 at purity 0.29 and total ploidy 2.00...
INFO [2018-04-12 02:39:28] Recalibrating log-ratios...
INFO [2018-04-12 02:39:28] Testing local optimum 5/6 at purity 0.29 and total ploidy 2.00...
INFO [2018-04-12 02:39:28] Testing local optimum 6/6 at purity 0.78 and total ploidy 2.00...
INFO [2018-04-12 02:39:30] Fitting variants for purity 0.65, tumor ploidy 1.73 and contamination 0.01.
INFO [2018-04-12 02:39:30] Optimized purity: 0.65
INFO [2018-04-12 02:39:30] Done.
INFO [2018-04-12 02:39:30] ------------------------------------------------------------
FATAL [2018-04-12 02:39:30] This function requires gene-level calls. Please add a column 'Gene' 

FATAL [2018-04-12 02:39:30] containing gene symbols to the gc.gene.file. 

FATAL [2018-04-12 02:39:30]  

FATAL [2018-04-12 02:39:30] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:39:30] parameters (PureCN 1.8.1). 

INFO [2018-04-12 02:39:32] ------------------------------------------------------------
INFO [2018-04-12 02:39:32] PureCN 1.8.1
INFO [2018-04-12 02:39:32] ------------------------------------------------------------
INFO [2018-04-12 02:39:32] Loading coverage files...
INFO [2018-04-12 02:39:32] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2018-04-12 02:39:32] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:39:32] Allosome coverage missing, cannot determine sex.
INFO [2018-04-12 02:39:32] Removing 22 small (< 5bp) targets.
INFO [2018-04-12 02:39:32] Removing 19 targets with low total coverage in normal (< 150.00 reads).
WARN [2018-04-12 02:39:32] No normalDB provided. Provide one for better results.
INFO [2018-04-12 02:39:32] Removing 233 low coverage (< 15.0000X) targets.
INFO [2018-04-12 02:39:32] Using 9547 intervals (9547 on-target, 0 off-target).
INFO [2018-04-12 02:39:32] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2018-04-12 02:39:32] No gc.gene.file provided. Cannot check if data was GC-normalized. Was it?
INFO [2018-04-12 02:39:32] Loading VCF...
FATAL [2018-04-12 02:39:32] Different chromosome names in coverage and VCF. 

FATAL [2018-04-12 02:39:32]  

FATAL [2018-04-12 02:39:32] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:39:32] parameters (PureCN 1.8.1). 

INFO [2018-04-12 02:39:32] ------------------------------------------------------------
INFO [2018-04-12 02:39:32] PureCN 1.8.1
INFO [2018-04-12 02:39:32] ------------------------------------------------------------
INFO [2018-04-12 02:39:32] Loading coverage files...
INFO [2018-04-12 02:39:33] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2018-04-12 02:39:33] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:39:33] Allosome coverage missing, cannot determine sex.
INFO [2018-04-12 02:39:33] No on_target column in gc.gene.file. Recreate this file with IntervalFile.R.
INFO [2018-04-12 02:39:33] No mappability column in gc.gene.file.
FATAL [2018-04-12 02:39:33] tumor.coverage.file and gc.gene.file do not align. 

FATAL [2018-04-12 02:39:33]  

FATAL [2018-04-12 02:39:33] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:39:33] parameters (PureCN 1.8.1). 

INFO [2018-04-12 02:39:33] ------------------------------------------------------------
INFO [2018-04-12 02:39:33] PureCN 1.8.1
INFO [2018-04-12 02:39:33] ------------------------------------------------------------
INFO [2018-04-12 02:39:33] Loading coverage files...
INFO [2018-04-12 02:39:33] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2018-04-12 02:39:33] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:39:33] Allosome coverage missing, cannot determine sex.
INFO [2018-04-12 02:39:33] No on_target column in gc.gene.file. Recreate this file with IntervalFile.R.
INFO [2018-04-12 02:39:33] No mappability column in gc.gene.file.
INFO [2018-04-12 02:39:35] Removing 15 low/high GC targets.
INFO [2018-04-12 02:39:35] Removing 21 small (< 5bp) targets.
INFO [2018-04-12 02:39:35] Removing 19 targets with low total coverage in normal (< 150.00 reads).
WARN [2018-04-12 02:39:35] No normalDB provided. Provide one for better results.
INFO [2018-04-12 02:39:35] Removing 232 low coverage (< 15.0000X) targets.
INFO [2018-04-12 02:39:35] Using 9534 intervals (9534 on-target, 0 off-target).
INFO [2018-04-12 02:39:35] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2018-04-12 02:39:35] AT/GC dropout: 1.03 (tumor), 1.03 (normal). 
INFO [2018-04-12 02:39:35] Loading VCF...
INFO [2018-04-12 02:39:35] LIB-02240e4 is tumor in VCF file.
INFO [2018-04-12 02:39:35] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2018-04-12 02:39:35] Found 2331 variants in VCF file.
INFO [2018-04-12 02:39:35] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2018-04-12 02:39:35] Initial testing for significant sample cross-contamination: unlikely
INFO [2018-04-12 02:39:35] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2018-04-12 02:39:35] Removing 16 low quality variants with BQ < 25.
INFO [2018-04-12 02:39:35] Total size of targeted genomic region: 1.63Mb (2.58Mb with 50bp padding).
INFO [2018-04-12 02:39:35] 1.0% of targets contain variants.
INFO [2018-04-12 02:39:35] Removing 2122 variants outside intervals.
INFO [2018-04-12 02:39:35] Found SOMATIC annotation in VCF.
INFO [2018-04-12 02:39:35] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2018-04-12 02:39:35] Found SOMATIC annotation in VCF. Setting mapping bias to 0.973.
INFO [2018-04-12 02:39:35] Sample sex: ?
INFO [2018-04-12 02:39:35] Segmenting data...
INFO [2018-04-12 02:39:35] Setting undo.SD parameter to 1.000000.
INFO [2018-04-12 02:39:42] Setting prune.hclust.h parameter to 0.200000.
INFO [2018-04-12 02:39:42] Using 123 variants.
INFO [2018-04-12 02:39:42] Mean standard deviation of log-ratios: 0.37
INFO [2018-04-12 02:39:42] 2D-grid search of purity and ploidy...
INFO [2018-04-12 02:39:43] Local optima: 0.63/1.9, 0.4/2.2, 0.5/2
INFO [2018-04-12 02:39:43] Testing local optimum 1/3 at purity 0.63 and total ploidy 1.90...
INFO [2018-04-12 02:39:45] Fitting variants for purity 0.65, tumor ploidy 1.73 and contamination 0.01.
INFO [2018-04-12 02:39:45] Optimized purity: 0.65
INFO [2018-04-12 02:39:45] Testing local optimum 2/3 at purity 0.40 and total ploidy 2.20...
INFO [2018-04-12 02:39:47] Fitting variants for purity 0.40, tumor ploidy 2.34 and contamination 0.01.
INFO [2018-04-12 02:39:47] Optimized purity: 0.40
INFO [2018-04-12 02:39:47] Testing local optimum 3/3 at purity 0.50 and total ploidy 2.00...
INFO [2018-04-12 02:39:49] Fitting variants for purity 0.65, tumor ploidy 1.73 and contamination 0.01.
INFO [2018-04-12 02:39:49] Optimized purity: 0.65
INFO [2018-04-12 02:39:49] Done.
INFO [2018-04-12 02:39:49] ------------------------------------------------------------
INFO [2018-04-12 02:39:49] ------------------------------------------------------------
INFO [2018-04-12 02:39:49] PureCN 1.8.1
INFO [2018-04-12 02:39:49] ------------------------------------------------------------
INFO [2018-04-12 02:39:49] Loading coverage files...
INFO [2018-04-12 02:39:50] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2018-04-12 02:39:50] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:39:50] Allosome coverage missing, cannot determine sex.
INFO [2018-04-12 02:39:50] No on_target column in gc.gene.file. Recreate this file with IntervalFile.R.
INFO [2018-04-12 02:39:50] No mappability column in gc.gene.file.
INFO [2018-04-12 02:39:51] Removing 15 low/high GC targets.
INFO [2018-04-12 02:39:51] Removing 21 small (< 5bp) targets.
INFO [2018-04-12 02:39:51] Removing 19 targets with low total coverage in normal (< 150.00 reads).
WARN [2018-04-12 02:39:51] No normalDB provided. Provide one for better results.
INFO [2018-04-12 02:39:51] Removing 232 low coverage (< 15.0000X) targets.
INFO [2018-04-12 02:39:51] Using 9534 intervals (9534 on-target, 0 off-target).
INFO [2018-04-12 02:39:51] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2018-04-12 02:39:51] AT/GC dropout: 1.03 (tumor), 1.03 (normal). 
INFO [2018-04-12 02:39:51] Loading VCF...
INFO [2018-04-12 02:39:51] LIB-02240e4 is tumor in VCF file.
INFO [2018-04-12 02:39:51] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2018-04-12 02:39:51] Found 2331 variants in VCF file.
INFO [2018-04-12 02:39:51] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2018-04-12 02:39:51] Initial testing for significant sample cross-contamination: unlikely
INFO [2018-04-12 02:39:51] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2018-04-12 02:39:51] Removing 16 low quality variants with BQ < 25.
INFO [2018-04-12 02:39:51] Total size of targeted genomic region: 1.63Mb (2.58Mb with 50bp padding).
INFO [2018-04-12 02:39:51] 1.0% of targets contain variants.
INFO [2018-04-12 02:39:51] Removing 2122 variants outside intervals.
INFO [2018-04-12 02:39:51] Found SOMATIC annotation in VCF.
INFO [2018-04-12 02:39:51] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2018-04-12 02:39:52] Found SOMATIC annotation in VCF. Setting mapping bias to 0.973.
INFO [2018-04-12 02:39:52] Sample sex: ?
INFO [2018-04-12 02:39:52] Segmenting data...
INFO [2018-04-12 02:39:52] Setting undo.SD parameter to 1.000000.
INFO [2018-04-12 02:39:58] Setting prune.hclust.h parameter to 0.200000.
INFO [2018-04-12 02:39:58] Using 123 variants.
INFO [2018-04-12 02:39:58] Mean standard deviation of log-ratios: 0.37
INFO [2018-04-12 02:39:58] 2D-grid search of purity and ploidy...
INFO [2018-04-12 02:40:00] Local optima: 0.63/1.9, 0.4/2.2, 0.5/2
INFO [2018-04-12 02:40:00] Testing local optimum 1/3 at purity 0.63 and total ploidy 1.90...
INFO [2018-04-12 02:40:02] Fitting variants for purity 0.65, tumor ploidy 1.73 and contamination 0.01.
INFO [2018-04-12 02:40:02] Optimized purity: 0.65
INFO [2018-04-12 02:40:02] Testing local optimum 2/3 at purity 0.40 and total ploidy 2.20...
INFO [2018-04-12 02:40:04] Fitting variants for purity 0.40, tumor ploidy 2.34 and contamination 0.01.
INFO [2018-04-12 02:40:05] Optimized purity: 0.40
INFO [2018-04-12 02:40:05] Testing local optimum 3/3 at purity 0.50 and total ploidy 2.00...
INFO [2018-04-12 02:40:06] Fitting variants for purity 0.65, tumor ploidy 1.73 and contamination 0.01.
INFO [2018-04-12 02:40:07] Optimized purity: 0.65
INFO [2018-04-12 02:40:07] Done.
INFO [2018-04-12 02:40:07] ------------------------------------------------------------
FATAL [2018-04-12 02:40:07] chr1 not valid chromosome name(s). Valid names are: 

FATAL [2018-04-12 02:40:07] 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22 

FATAL [2018-04-12 02:40:07]  

FATAL [2018-04-12 02:40:07] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:40:07] parameters (PureCN 1.8.1). 

INFO [2018-04-12 02:40:07] ------------------------------------------------------------
INFO [2018-04-12 02:40:07] PureCN 1.8.1
INFO [2018-04-12 02:40:07] ------------------------------------------------------------
INFO [2018-04-12 02:40:07] Loading coverage files...
WARN [2018-04-12 02:40:08] Provided sampleid (Sample2) does not match Sample1 found in segmentation.
WARN [2018-04-12 02:40:08] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:40:08] Allosome coverage missing, cannot determine sex.
INFO [2018-04-12 02:40:08] Using 10039 intervals (10039 on-target, 0 off-target).
INFO [2018-04-12 02:40:08] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2018-04-12 02:40:08] Loading VCF...
INFO [2018-04-12 02:40:08] LIB-02240e4 is tumor in VCF file.
INFO [2018-04-12 02:40:08] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2018-04-12 02:40:08] Found 2331 variants in VCF file.
INFO [2018-04-12 02:40:08] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2018-04-12 02:40:08] Initial testing for significant sample cross-contamination: unlikely
INFO [2018-04-12 02:40:08] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2018-04-12 02:40:08] Removing 16 low quality variants with BQ < 25.
INFO [2018-04-12 02:40:08] Total size of targeted genomic region: 1.71Mb (2.70Mb with 50bp padding).
INFO [2018-04-12 02:40:08] 1.0% of targets contain variants.
INFO [2018-04-12 02:40:08] Removing 2120 variants outside intervals.
INFO [2018-04-12 02:40:08] Found SOMATIC annotation in VCF.
INFO [2018-04-12 02:40:08] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2018-04-12 02:40:08] Found SOMATIC annotation in VCF. Setting mapping bias to 0.976.
INFO [2018-04-12 02:40:08] Sample sex: ?
INFO [2018-04-12 02:40:08] Segmenting data...
WARN [2018-04-12 02:40:08] Provided sampleid (Sample2) does not match Sample1 found in segmentation.
INFO [2018-04-12 02:40:08] Setting undo.SD parameter to 0.000000.
Setting multi-figure configuration
INFO [2018-04-12 02:40:14] Setting prune.hclust.h parameter to 0.200000.
INFO [2018-04-12 02:40:14] Using 125 variants.
INFO [2018-04-12 02:40:14] Mean standard deviation of log-ratios: 0.40
INFO [2018-04-12 02:40:14] 2D-grid search of purity and ploidy...
INFO [2018-04-12 02:40:15] Local optima: 0.67/1.8, 0.4/2.2, 0.5/2
INFO [2018-04-12 02:40:15] Testing local optimum 1/3 at purity 0.67 and total ploidy 1.80...
INFO [2018-04-12 02:40:16] Fitting variants for purity 0.65, tumor ploidy 1.73 and contamination 0.01.
INFO [2018-04-12 02:40:17] Optimized purity: 0.65
INFO [2018-04-12 02:40:17] Testing local optimum 2/3 at purity 0.40 and total ploidy 2.20...
INFO [2018-04-12 02:40:18] Fitting variants for purity 0.40, tumor ploidy 2.33 and contamination 0.01.
INFO [2018-04-12 02:40:19] Optimized purity: 0.40
INFO [2018-04-12 02:40:19] Testing local optimum 3/3 at purity 0.50 and total ploidy 2.00...
INFO [2018-04-12 02:40:19] Fitting variants for purity 0.65, tumor ploidy 1.73 and contamination 0.01.
INFO [2018-04-12 02:40:20] Optimized purity: 0.65
INFO [2018-04-12 02:40:20] Done.
INFO [2018-04-12 02:40:20] ------------------------------------------------------------
WARN [2018-04-12 02:40:20] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:40:20] Allosome coverage missing, cannot determine sex.
Setting multi-figure configuration
FATAL [2018-04-12 02:40:40] Segmentation file expected with colnames ID, chrom, loc.start, loc.end, 

FATAL [2018-04-12 02:40:40] num.mark, seg.mean 

FATAL [2018-04-12 02:40:40]  

FATAL [2018-04-12 02:40:40] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:40:40] parameters (PureCN 1.8.1). 

FATAL [2018-04-12 02:40:40] seg.file contains multiple samples and sampleid missing. 

FATAL [2018-04-12 02:40:40]  

FATAL [2018-04-12 02:40:40] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:40:40] parameters (PureCN 1.8.1). 

FATAL [2018-04-12 02:40:41] seg.file contains multiple samples and sampleid does not match any. 

FATAL [2018-04-12 02:40:41]  

FATAL [2018-04-12 02:40:41] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:40:41] parameters (PureCN 1.8.1). 

WARN [2018-04-12 02:40:41] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:40:41] Allosome coverage missing, cannot determine sex.
Setting multi-figure configuration
WARN [2018-04-12 02:40:57] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:40:57] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:40:59] No normalDB provided. Provide one for better results.
Setting multi-figure configuration
WARN [2018-04-12 02:41:22] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:41:22] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:41:24] Provided sampleid (Sample.1) does not match Sample1 found in segmentation.
Setting multi-figure configuration
WARN [2018-04-12 02:41:54] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:41:54] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:41:54] No normalDB provided. Provide one for better results.
WARN [2018-04-12 02:41:54] Sampleid looks like a normal in VCF, not like a tumor.
Setting multi-figure configuration
WARN [2018-04-12 02:42:21] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:42:21] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:42:21] No normalDB provided. Provide one for better results.
WARN [2018-04-12 02:42:35] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:42:35] Allosome coverage missing, cannot determine sex.
FATAL [2018-04-12 02:42:35] normalDB not a valid normalDB object. Use createNormalDatabase to 

FATAL [2018-04-12 02:42:35] create one. 

FATAL [2018-04-12 02:42:35]  

FATAL [2018-04-12 02:42:35] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:42:35] parameters (PureCN 1.8.1). 

WARN [2018-04-12 02:42:36] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:42:36] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:42:38] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:42:38] Allosome coverage missing, cannot determine sex.
Setting multi-figure configuration
WARN [2018-04-12 02:43:07] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:43:07] Allosome coverage missing, cannot determine sex.
FATAL [2018-04-12 02:43:07] normalDB appears to be empty. 

FATAL [2018-04-12 02:43:07]  

FATAL [2018-04-12 02:43:07] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:43:07] parameters (PureCN 1.8.1). 

WARN [2018-04-12 02:43:07] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:43:07] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:43:33] Provided sampleid (example_tumor.txt) does not match Sample1 found in segmentation.
WARN [2018-04-12 02:43:33] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:43:33] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:43:34] Provided sampleid (example_tumor.txt) does not match Sample1 found in segmentation.
WARN [2018-04-12 02:43:39] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:43:39] Allosome coverage missing, cannot determine sex.
Setting multi-figure configuration
WARN [2018-04-12 02:44:05] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:44:05] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:44:05] Intervals in coverage and gc.gene.file have conflicting on/off-target annotation.
WARN [2018-04-12 02:44:06] No normalDB provided. Provide one for better results.
Setting multi-figure configuration
FATAL [2018-04-12 02:44:20] min.normals must be >=2. 

FATAL [2018-04-12 02:44:20]  

FATAL [2018-04-12 02:44:20] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:44:20] parameters (PureCN 1.8.1). 



RUNIT TEST PROTOCOL -- Thu Apr 12 02:44:20 2018 
*********************************************** 
Number of test functions: 22 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
PureCN RUnit Tests - 22 test functions, 0 errors, 0 failures
Number of test functions: 22 
Number of errors: 0 
Number of failures: 0 
There were 18 warnings (use warnings() to see them)
> 
> proc.time()
   user  system elapsed 
 483.53    2.37  486.04

PureCN.Rcheck/tests_x64/runTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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.

> BiocGenerics:::testPackage("PureCN")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following object is masked from 'package:base':

    apply


Attaching package: 'Biostrings'

The following object is masked from 'package:DelayedArray':

    type

The following object is masked from 'package:base':

    strsplit


Attaching package: 'VariantAnnotation'

The following object is masked from 'package:base':

    tabulate

Loading required package: GenomicFeatures
Loading required package: AnnotationDbi

'select()' returned many:1 mapping between keys and columns
'select()' returned many:1 mapping between keys and columns
WARN [2018-04-12 02:44:41] Attempted adding gene symbols to intervals. Heuristics have been used to pick symbols for overlapping genes.
WARN [2018-04-12 02:44:42] Chromosome naming style of txdb file (UCSC) was different from interval file (NCBI).
'select()' returned many:1 mapping between keys and columns
'select()' returned many:1 mapping between keys and columns
WARN [2018-04-12 02:44:47] Attempted adding gene symbols to intervals. Heuristics have been used to pick symbols for overlapping genes.
FATAL [2018-04-12 02:44:49] tumor.coverage.file and gc.gene.file do not align. 

FATAL [2018-04-12 02:44:49]  

FATAL [2018-04-12 02:44:49] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:44:49] parameters (PureCN 1.8.1). 

WARN [2018-04-12 02:44:50] No mappability scores provided.
INFO [2018-04-12 02:44:50] Calculating GC-content...
WARN [2018-04-12 02:44:50] No mappability scores provided.
INFO [2018-04-12 02:44:50] Calculating GC-content...
FATAL [2018-04-12 02:44:50] Interval coordinates should start at 1, not at 0 

FATAL [2018-04-12 02:44:50]  

FATAL [2018-04-12 02:44:50] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:44:50] parameters (PureCN 1.8.1). 

INFO [2018-04-12 02:44:51] Tiling off-target regions to an average width of 200000.
WARN [2018-04-12 02:44:51] No mappability scores provided.
INFO [2018-04-12 02:44:51] Calculating GC-content...
WARN [2018-04-12 02:44:51] Intervals contain off-target regions. Will not change intervals.
WARN [2018-04-12 02:44:51] No mappability scores provided.
INFO [2018-04-12 02:44:51] Calculating GC-content...
INFO [2018-04-12 02:44:52] Calculating GC-content...
WARN [2018-04-12 02:44:52] No mappability scores provided.
INFO [2018-04-12 02:44:52] Calculating GC-content...
WARN [2018-04-12 02:44:52] Chromosome naming style of interval file (NCBI) was different from reference (UCSC).
WARN [2018-04-12 02:44:52] No mappability scores provided.
INFO [2018-04-12 02:44:52] Calculating GC-content...
FATAL [2018-04-12 02:44:52] Chromosome naming style of interval file unknown, should be UCSC. 

FATAL [2018-04-12 02:44:52]  

FATAL [2018-04-12 02:44:52] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:44:52] parameters (PureCN 1.8.1). 

WARN [2018-04-12 02:44:52] Chromosome naming style of interval file (NCBI) was different from reference (UCSC).
WARN [2018-04-12 02:44:52] Chromosome naming style of mappability file (NCBI) was different from reference (UCSC).
INFO [2018-04-12 02:44:52] Calculating GC-content...
Minimum 3 supporting reads.
Expected allelic fraction 0.5.
Minimum 3 supporting reads.
Expected allelic fraction 0.5.
Minimum 3 supporting reads.
Expected allelic fraction 0.125.
Minimum 5 supporting reads.
Expected allelic fraction 0.02.
Minimum 3 supporting reads.
FATAL [2018-04-12 02:44:53] Need either f or purity and ploidy. 

FATAL [2018-04-12 02:44:53]  

FATAL [2018-04-12 02:44:53] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:44:53] parameters (PureCN 1.8.1). 

Minimum 3 supporting reads.
FATAL [2018-04-12 02:44:53] f not in expected range. 

FATAL [2018-04-12 02:44:53]  

FATAL [2018-04-12 02:44:53] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:44:53] parameters (PureCN 1.8.1). 

FATAL [2018-04-12 02:44:53] coverage not in expected range (>=2) 

FATAL [2018-04-12 02:44:53]  

FATAL [2018-04-12 02:44:53] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:44:53] parameters (PureCN 1.8.1). 

Minimum 2 supporting reads.
FATAL [2018-04-12 02:44:53] purity not in expected range. 

FATAL [2018-04-12 02:44:53]  

FATAL [2018-04-12 02:44:53] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:44:53] parameters (PureCN 1.8.1). 

Minimum 2 supporting reads.
FATAL [2018-04-12 02:44:53] ploidy not in expected range. 

FATAL [2018-04-12 02:44:53]  

FATAL [2018-04-12 02:44:53] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:44:53] parameters (PureCN 1.8.1). 

FATAL [2018-04-12 02:44:53] cell.fraction not in expected range. 

FATAL [2018-04-12 02:44:53]  

FATAL [2018-04-12 02:44:53] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:44:53] parameters (PureCN 1.8.1). 

INFO [2018-04-12 02:44:55] No on_target column in gc.gene.file. Recreate this file with IntervalFile.R.
INFO [2018-04-12 02:44:55] No mappability column in gc.gene.file.
INFO [2018-04-12 02:44:59] ------------------------------------------------------------
INFO [2018-04-12 02:44:59] PureCN 1.8.1
INFO [2018-04-12 02:44:59] ------------------------------------------------------------
INFO [2018-04-12 02:44:59] Loading coverage files...
INFO [2018-04-12 02:44:59] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2018-04-12 02:44:59] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:44:59] Allosome coverage missing, cannot determine sex.
INFO [2018-04-12 02:44:59] Removing 22 small (< 5bp) targets.
INFO [2018-04-12 02:44:59] Removing 19 targets with low total coverage in normal (< 150.00 reads).
WARN [2018-04-12 02:44:59] No normalDB provided. Provide one for better results.
INFO [2018-04-12 02:44:59] Removing 233 low coverage (< 15.0000X) targets.
INFO [2018-04-12 02:44:59] Using 9547 intervals (9547 on-target, 0 off-target).
INFO [2018-04-12 02:44:59] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2018-04-12 02:44:59] No gc.gene.file provided. Cannot check if data was GC-normalized. Was it?
INFO [2018-04-12 02:44:59] Loading VCF...
INFO [2018-04-12 02:44:59] LIB-02240e4 is tumor in VCF file.
INFO [2018-04-12 02:45:00] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2018-04-12 02:45:00] Found 2331 variants in VCF file.
INFO [2018-04-12 02:45:00] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2018-04-12 02:45:00] Initial testing for significant sample cross-contamination: unlikely
INFO [2018-04-12 02:45:00] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2018-04-12 02:45:00] Removing 16 low quality variants with BQ < 25.
INFO [2018-04-12 02:45:00] Total size of targeted genomic region: 1.63Mb (2.58Mb with 50bp padding).
INFO [2018-04-12 02:45:00] 1.0% of targets contain variants.
INFO [2018-04-12 02:45:00] Removing 2122 variants outside intervals.
INFO [2018-04-12 02:45:00] Found SOMATIC annotation in VCF.
INFO [2018-04-12 02:45:00] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2018-04-12 02:45:00] Found SOMATIC annotation in VCF. Setting mapping bias to 0.973.
INFO [2018-04-12 02:45:00] Sample sex: ?
INFO [2018-04-12 02:45:00] Segmenting data...
INFO [2018-04-12 02:45:01] Setting undo.SD parameter to 1.000000.
INFO [2018-04-12 02:45:06] Setting prune.hclust.h parameter to 0.200000.
INFO [2018-04-12 02:45:06] Using 123 variants.
INFO [2018-04-12 02:45:06] Mean standard deviation of log-ratios: 0.37
INFO [2018-04-12 02:45:06] 2D-grid search of purity and ploidy...
INFO [2018-04-12 02:45:08] Local optima: 0.63/1.9, 0.4/2.2, 0.5/2
INFO [2018-04-12 02:45:08] Testing local optimum 1/3 at purity 0.63 and total ploidy 1.90...
INFO [2018-04-12 02:45:10] Fitting variants for purity 0.65, tumor ploidy 1.73 and contamination 0.01.
INFO [2018-04-12 02:45:11] Optimized purity: 0.65
INFO [2018-04-12 02:45:11] Testing local optimum 2/3 at purity 0.40 and total ploidy 2.20...
INFO [2018-04-12 02:45:13] Fitting variants for purity 0.40, tumor ploidy 2.34 and contamination 0.01.
INFO [2018-04-12 02:45:13] Optimized purity: 0.40
INFO [2018-04-12 02:45:13] Testing local optimum 3/3 at purity 0.50 and total ploidy 2.00...
INFO [2018-04-12 02:45:15] Fitting variants for purity 0.65, tumor ploidy 1.73 and contamination 0.01.
INFO [2018-04-12 02:45:16] Optimized purity: 0.65
INFO [2018-04-12 02:45:16] Done.
INFO [2018-04-12 02:45:16] ------------------------------------------------------------
FATAL [2018-04-12 02:45:18] fun.countMutation not a function. 

FATAL [2018-04-12 02:45:18]  

FATAL [2018-04-12 02:45:18] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:45:18] parameters (PureCN 1.8.1). 

FATAL [2018-04-12 02:45:18] exclude not a GRanges object. 

FATAL [2018-04-12 02:45:18]  

FATAL [2018-04-12 02:45:18] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:45:18] parameters (PureCN 1.8.1). 

FATAL [2018-04-12 02:45:18] callable not a GRanges object. 

FATAL [2018-04-12 02:45:18]  

FATAL [2018-04-12 02:45:18] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:45:18] parameters (PureCN 1.8.1). 

FATAL [2018-04-12 02:45:31] No gc_bias column in gc.gene.file. 

FATAL [2018-04-12 02:45:31]  

FATAL [2018-04-12 02:45:31] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:45:31] parameters (PureCN 1.8.1). 

WARN [2018-04-12 02:45:31] tumor.coverage.file and gc.gene.file do not align.
INFO [2018-04-12 02:45:59] Reading Sample1_PureCN.rds...
INFO [2018-04-12 02:45:59] Reading Sample1_PureCN.rds...
INFO [2018-04-12 02:45:59] Reading Sample1_PureCN.rds...
INFO [2018-04-12 02:45:59] Reading Sample1_PureCN.rds...
INFO [2018-04-12 02:46:00] Reading Sample1_PureCN.rds...
INFO [2018-04-12 02:46:00] Reading Sample1_PureCN.rds...
FATAL [2018-04-12 02:46:00] Purity or Ploidy not numeric or in expected range. 

FATAL [2018-04-12 02:46:00]  

FATAL [2018-04-12 02:46:00] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:46:00] parameters (PureCN 1.8.1). 

INFO [2018-04-12 02:46:00] Reading Sample1_PureCN.rds...
INFO [2018-04-12 02:46:00] Reading Sample1_PureCN.rds...
FATAL [2018-04-12 02:46:00] 'Failed' column in Sample1_PureCN.csv not logical(1). 

FATAL [2018-04-12 02:46:00]  

FATAL [2018-04-12 02:46:00] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:46:00] parameters (PureCN 1.8.1). 

WARN [2018-04-12 02:46:02] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:46:02] Allosome coverage missing, cannot determine sex.
INFO [2018-04-12 02:46:05] Pooling example_normal.txt, example_normal2.txt.
INFO [2018-04-12 02:46:06] Coverage file does not contain read count information, using total coverage for calculating log-ratios.
WARN [2018-04-12 02:46:17] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:46:17] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:46:19] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:46:19] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:46:21] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:46:22] Allosome coverage missing, cannot determine sex.
FATAL [2018-04-12 02:46:22] Length of normal.coverage.files and sex different 

FATAL [2018-04-12 02:46:22]  

FATAL [2018-04-12 02:46:22] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:46:22] parameters (PureCN 1.8.1). 

WARN [2018-04-12 02:46:24] tumor.coverage.file and gc.gene.file do not align.
WARN [2018-04-12 02:46:26] Target intervals were not sorted.
WARN [2018-04-12 02:46:27] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:46:27] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:46:27] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:46:29] Allosome coverage missing, cannot determine sex.
INFO [2018-04-12 02:46:29] Sample sex: NA
FATAL [2018-04-12 02:46:31] tumor.coverage.file and normalDB do not align. 

FATAL [2018-04-12 02:46:31]  

FATAL [2018-04-12 02:46:31] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:46:31] parameters (PureCN 1.8.1). 

INFO [2018-04-12 02:46:33] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2018-04-12 02:46:33] Initial testing for significant sample cross-contamination: unlikely
INFO [2018-04-12 02:46:33] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2018-04-12 02:46:33] Removing 16 low quality variants with BQ < 25.
INFO [2018-04-12 02:46:33] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2018-04-12 02:46:33] Initial testing for significant sample cross-contamination: unlikely
INFO [2018-04-12 02:46:34] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2018-04-12 02:46:34] Removing 6 blacklisted variants.
INFO [2018-04-12 02:46:34] Removing 16 low quality variants with BQ < 25.
WARN [2018-04-12 02:46:34] MuTect stats file lacks contig and position columns.
INFO [2018-04-12 02:46:34] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2018-04-12 02:46:34] Initial testing for significant sample cross-contamination: unlikely
INFO [2018-04-12 02:46:34] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2018-04-12 02:46:34] Removing 16 low quality variants with BQ < 25.
WARN [2018-04-12 02:46:35] MuTect stats file and VCF file do not align perfectly. Will remove 2325 unmatched variants.
WARN [2018-04-12 02:46:35] MuTect stats file lacks failure_reasons column. Keeping all variants listed in stats file.
INFO [2018-04-12 02:46:35] Removing 0 non heterozygous (in matched normal) germline SNPs.
INFO [2018-04-12 02:46:35] Removing 0 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2018-04-12 02:46:35] Removing 0 low quality variants with BQ < 25.
WARN [2018-04-12 02:46:38] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:46:38] Allosome coverage missing, cannot determine sex.
INFO [2018-04-12 02:46:38] Mean coverages: chrX: 108.58, chrY: 108.58, chr1-22: 104.87.
INFO [2018-04-12 02:46:38] Mean coverages: chrX: 108.58, chrY: 2.17, chr1-22: 104.87.
INFO [2018-04-12 02:46:38] Mean coverages: chrX: 108.58, chrY: 5.17, chr1-22: 104.87.
INFO [2018-04-12 02:46:40] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2018-04-12 02:46:40] No germline variants in VCF.
WARN [2018-04-12 02:46:45] Found 4 overlapping intervals, starting at line 2.
INFO [2018-04-12 02:46:47] Loading coverage data...
INFO [2018-04-12 02:46:49] Mean target coverages: 112X (tumor) 99X (normal).
INFO [2018-04-12 02:46:49] Mean target coverages: 112X (tumor) 43X (normal).
INFO [2018-04-12 02:46:50] ------------------------------------------------------------
INFO [2018-04-12 02:46:50] PureCN 1.8.1
INFO [2018-04-12 02:46:50] ------------------------------------------------------------
INFO [2018-04-12 02:46:50] Loading coverage files...
INFO [2018-04-12 02:46:51] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2018-04-12 02:46:51] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:46:51] Allosome coverage missing, cannot determine sex.
INFO [2018-04-12 02:46:51] Removing 22 small (< 5bp) targets.
INFO [2018-04-12 02:46:51] Removing 19 targets with low total coverage in normal (< 150.00 reads).
WARN [2018-04-12 02:46:51] No normalDB provided. Provide one for better results.
INFO [2018-04-12 02:46:51] Removing 233 low coverage (< 15.0000X) targets.
INFO [2018-04-12 02:46:51] Using 9547 intervals (9547 on-target, 0 off-target).
INFO [2018-04-12 02:46:51] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2018-04-12 02:46:51] No gc.gene.file provided. Cannot check if data was GC-normalized. Was it?
INFO [2018-04-12 02:46:51] Sample sex: ?
INFO [2018-04-12 02:46:51] Segmenting data...
INFO [2018-04-12 02:46:52] Target weights found, will use weighted CBS.
INFO [2018-04-12 02:46:52] Setting undo.SD parameter to 1.000000.
Setting multi-figure configuration
INFO [2018-04-12 02:46:57] Mean standard deviation of log-ratios: 0.37
INFO [2018-04-12 02:46:57] 2D-grid search of purity and ploidy...
INFO [2018-04-12 02:46:57] Local optima: 0.65/1.9, 0.33/1.9, 0.38/2.2, 0.27/2.1, 0.29/2, 0.78/2
INFO [2018-04-12 02:46:57] Testing local optimum 1/6 at purity 0.65 and total ploidy 1.90...
INFO [2018-04-12 02:46:58] Testing local optimum 2/6 at purity 0.33 and total ploidy 1.90...
INFO [2018-04-12 02:46:58] Recalibrating log-ratios...
INFO [2018-04-12 02:46:58] Testing local optimum 2/6 at purity 0.33 and total ploidy 1.90...
INFO [2018-04-12 02:46:59] Recalibrating log-ratios...
INFO [2018-04-12 02:46:59] Testing local optimum 2/6 at purity 0.33 and total ploidy 1.90...
INFO [2018-04-12 02:47:00] Recalibrating log-ratios...
INFO [2018-04-12 02:47:00] Testing local optimum 2/6 at purity 0.33 and total ploidy 1.90...
INFO [2018-04-12 02:47:00] Testing local optimum 3/6 at purity 0.38 and total ploidy 2.20...
INFO [2018-04-12 02:47:02] Testing local optimum 4/6 at purity 0.27 and total ploidy 2.10...
INFO [2018-04-12 02:47:03] Recalibrating log-ratios...
INFO [2018-04-12 02:47:03] Testing local optimum 4/6 at purity 0.27 and total ploidy 2.10...
INFO [2018-04-12 02:47:03] Recalibrating log-ratios...
INFO [2018-04-12 02:47:03] Testing local optimum 4/6 at purity 0.27 and total ploidy 2.10...
INFO [2018-04-12 02:47:04] Recalibrating log-ratios...
INFO [2018-04-12 02:47:04] Testing local optimum 4/6 at purity 0.27 and total ploidy 2.10...
INFO [2018-04-12 02:47:04] Testing local optimum 5/6 at purity 0.29 and total ploidy 2.00...
INFO [2018-04-12 02:47:05] Recalibrating log-ratios...
INFO [2018-04-12 02:47:05] Testing local optimum 5/6 at purity 0.29 and total ploidy 2.00...
INFO [2018-04-12 02:47:06] Recalibrating log-ratios...
INFO [2018-04-12 02:47:06] Testing local optimum 5/6 at purity 0.29 and total ploidy 2.00...
INFO [2018-04-12 02:47:06] Recalibrating log-ratios...
INFO [2018-04-12 02:47:06] Testing local optimum 5/6 at purity 0.29 and total ploidy 2.00...
INFO [2018-04-12 02:47:07] Testing local optimum 6/6 at purity 0.78 and total ploidy 2.00...
INFO [2018-04-12 02:47:08] Done.
INFO [2018-04-12 02:47:08] ------------------------------------------------------------
INFO [2018-04-12 02:47:08] Reading C:\Users\biocbuild\bbs-3.6-bioc\tmpdir\RtmpgZF7rP\file33743a214754.rds...
FATAL [2018-04-12 02:47:08] runAbsoluteCN was run without a VCF file. 

FATAL [2018-04-12 02:47:08]  

FATAL [2018-04-12 02:47:08] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:47:08] parameters (PureCN 1.8.1). 

FATAL [2018-04-12 02:47:08] runAbsoluteCN was run without a VCF file. 

FATAL [2018-04-12 02:47:08]  

FATAL [2018-04-12 02:47:08] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:47:08] parameters (PureCN 1.8.1). 

INFO [2018-04-12 02:47:08] ------------------------------------------------------------
INFO [2018-04-12 02:47:08] PureCN 1.8.1
INFO [2018-04-12 02:47:08] ------------------------------------------------------------
INFO [2018-04-12 02:47:08] Loading coverage files...
FATAL [2018-04-12 02:47:09] Need a normal coverage file if log.ratio and seg.file are not provided. 

FATAL [2018-04-12 02:47:09]  

FATAL [2018-04-12 02:47:09] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:47:09] parameters (PureCN 1.8.1). 

INFO [2018-04-12 02:47:09] ------------------------------------------------------------
INFO [2018-04-12 02:47:09] PureCN 1.8.1
INFO [2018-04-12 02:47:09] ------------------------------------------------------------
FATAL [2018-04-12 02:47:09] min.ploidy or max.ploidy not within expected range. 

FATAL [2018-04-12 02:47:09]  

FATAL [2018-04-12 02:47:09] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:47:09] parameters (PureCN 1.8.1). 

INFO [2018-04-12 02:47:09] ------------------------------------------------------------
INFO [2018-04-12 02:47:09] PureCN 1.8.1
INFO [2018-04-12 02:47:09] ------------------------------------------------------------
FATAL [2018-04-12 02:47:09] min.ploidy or max.ploidy not within expected range. 

FATAL [2018-04-12 02:47:09]  

FATAL [2018-04-12 02:47:09] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:47:09] parameters (PureCN 1.8.1). 

INFO [2018-04-12 02:47:09] ------------------------------------------------------------
INFO [2018-04-12 02:47:09] PureCN 1.8.1
INFO [2018-04-12 02:47:09] ------------------------------------------------------------
INFO [2018-04-12 02:47:09] ------------------------------------------------------------
INFO [2018-04-12 02:47:09] PureCN 1.8.1
INFO [2018-04-12 02:47:09] ------------------------------------------------------------
INFO [2018-04-12 02:47:09] ------------------------------------------------------------
INFO [2018-04-12 02:47:09] PureCN 1.8.1
INFO [2018-04-12 02:47:09] ------------------------------------------------------------
FATAL [2018-04-12 02:47:09] test.purity not within expected range. 

FATAL [2018-04-12 02:47:09]  

FATAL [2018-04-12 02:47:09] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:47:09] parameters (PureCN 1.8.1). 

INFO [2018-04-12 02:47:09] ------------------------------------------------------------
INFO [2018-04-12 02:47:09] PureCN 1.8.1
INFO [2018-04-12 02:47:09] ------------------------------------------------------------
INFO [2018-04-12 02:47:09] Loading coverage files...
FATAL [2018-04-12 02:47:10] Tumor and normal are identical. This won't give any meaningful results 

FATAL [2018-04-12 02:47:10] and I'm stopping here. 

FATAL [2018-04-12 02:47:10]  

FATAL [2018-04-12 02:47:10] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:47:10] parameters (PureCN 1.8.1). 

INFO [2018-04-12 02:47:10] ------------------------------------------------------------
INFO [2018-04-12 02:47:10] PureCN 1.8.1
INFO [2018-04-12 02:47:10] ------------------------------------------------------------
INFO [2018-04-12 02:47:10] Loading coverage files...
FATAL [2018-04-12 02:47:10] Length of log.ratio different from tumor coverage. 

FATAL [2018-04-12 02:47:10]  

FATAL [2018-04-12 02:47:10] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:47:10] parameters (PureCN 1.8.1). 

INFO [2018-04-12 02:47:10] ------------------------------------------------------------
INFO [2018-04-12 02:47:10] PureCN 1.8.1
INFO [2018-04-12 02:47:10] ------------------------------------------------------------
FATAL [2018-04-12 02:47:10] prior.purity must have the same length as test.purity. 

FATAL [2018-04-12 02:47:10]  

FATAL [2018-04-12 02:47:10] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:47:10] parameters (PureCN 1.8.1). 

INFO [2018-04-12 02:47:10] ------------------------------------------------------------
INFO [2018-04-12 02:47:10] PureCN 1.8.1
INFO [2018-04-12 02:47:10] ------------------------------------------------------------
FATAL [2018-04-12 02:47:10] min.gof not within expected range or format. 

FATAL [2018-04-12 02:47:10]  

FATAL [2018-04-12 02:47:10] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:47:10] parameters (PureCN 1.8.1). 

INFO [2018-04-12 02:47:10] ------------------------------------------------------------
INFO [2018-04-12 02:47:10] PureCN 1.8.1
INFO [2018-04-12 02:47:10] ------------------------------------------------------------
FATAL [2018-04-12 02:47:10] prior.purity not within expected range or format. 

FATAL [2018-04-12 02:47:10]  

FATAL [2018-04-12 02:47:10] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:47:10] parameters (PureCN 1.8.1). 

INFO [2018-04-12 02:47:10] ------------------------------------------------------------
INFO [2018-04-12 02:47:10] PureCN 1.8.1
INFO [2018-04-12 02:47:10] ------------------------------------------------------------
FATAL [2018-04-12 02:47:10] prior.purity must add to 1. Sum is 1.5 

FATAL [2018-04-12 02:47:10]  

FATAL [2018-04-12 02:47:10] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:47:10] parameters (PureCN 1.8.1). 

INFO [2018-04-12 02:47:10] ------------------------------------------------------------
INFO [2018-04-12 02:47:10] PureCN 1.8.1
INFO [2018-04-12 02:47:10] ------------------------------------------------------------
FATAL [2018-04-12 02:47:10] max.homozygous.loss not within expected range or format. 

FATAL [2018-04-12 02:47:10]  

FATAL [2018-04-12 02:47:10] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:47:10] parameters (PureCN 1.8.1). 

INFO [2018-04-12 02:47:10] ------------------------------------------------------------
INFO [2018-04-12 02:47:10] PureCN 1.8.1
INFO [2018-04-12 02:47:10] ------------------------------------------------------------
FATAL [2018-04-12 02:47:10] prior.K not within expected range or format. 

FATAL [2018-04-12 02:47:10]  

FATAL [2018-04-12 02:47:10] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:47:10] parameters (PureCN 1.8.1). 

INFO [2018-04-12 02:47:10] ------------------------------------------------------------
INFO [2018-04-12 02:47:10] PureCN 1.8.1
INFO [2018-04-12 02:47:10] ------------------------------------------------------------
FATAL [2018-04-12 02:47:10] prior.contamination not within expected range or format. 

FATAL [2018-04-12 02:47:10]  

FATAL [2018-04-12 02:47:10] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:47:10] parameters (PureCN 1.8.1). 

INFO [2018-04-12 02:47:10] ------------------------------------------------------------
INFO [2018-04-12 02:47:10] PureCN 1.8.1
INFO [2018-04-12 02:47:10] ------------------------------------------------------------
FATAL [2018-04-12 02:47:10] Iterations not in the expected range from 10 to 250. 

FATAL [2018-04-12 02:47:10]  

FATAL [2018-04-12 02:47:10] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:47:10] parameters (PureCN 1.8.1). 

INFO [2018-04-12 02:47:10] ------------------------------------------------------------
INFO [2018-04-12 02:47:10] PureCN 1.8.1
INFO [2018-04-12 02:47:10] ------------------------------------------------------------
FATAL [2018-04-12 02:47:10] Iterations not in the expected range from 10 to 250. 

FATAL [2018-04-12 02:47:10]  

FATAL [2018-04-12 02:47:10] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:47:10] parameters (PureCN 1.8.1). 

INFO [2018-04-12 02:47:10] ------------------------------------------------------------
INFO [2018-04-12 02:47:10] PureCN 1.8.1
INFO [2018-04-12 02:47:10] ------------------------------------------------------------
INFO [2018-04-12 02:47:11] ------------------------------------------------------------
INFO [2018-04-12 02:47:11] PureCN 1.8.1
INFO [2018-04-12 02:47:11] ------------------------------------------------------------
INFO [2018-04-12 02:47:11] Loading coverage files...
FATAL [2018-04-12 02:47:11] Interval files in normal and tumor different. 

FATAL [2018-04-12 02:47:11]  

FATAL [2018-04-12 02:47:11] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:47:11] parameters (PureCN 1.8.1). 

INFO [2018-04-12 02:47:11] ------------------------------------------------------------
INFO [2018-04-12 02:47:11] PureCN 1.8.1
INFO [2018-04-12 02:47:11] ------------------------------------------------------------
INFO [2018-04-12 02:47:11] Loading coverage files...
INFO [2018-04-12 02:47:13] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2018-04-12 02:47:13] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:47:13] Allosome coverage missing, cannot determine sex.
INFO [2018-04-12 02:47:13] Removing 22 small (< 5bp) targets.
INFO [2018-04-12 02:47:13] Removing 19 targets with low total coverage in normal (< 150.00 reads).
WARN [2018-04-12 02:47:13] No normalDB provided. Provide one for better results.
INFO [2018-04-12 02:47:13] Removing 233 low coverage (< 15.0000X) targets.
INFO [2018-04-12 02:47:13] Using 9547 intervals (9547 on-target, 0 off-target).
INFO [2018-04-12 02:47:13] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2018-04-12 02:47:13] No gc.gene.file provided. Cannot check if data was GC-normalized. Was it?
INFO [2018-04-12 02:47:13] Loading VCF...
INFO [2018-04-12 02:47:13] LIB-02240e4 is tumor in VCF file.
INFO [2018-04-12 02:47:13] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2018-04-12 02:47:13] Found 2331 variants in VCF file.
INFO [2018-04-12 02:47:13] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2018-04-12 02:47:13] Initial testing for significant sample cross-contamination: unlikely
INFO [2018-04-12 02:47:14] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2018-04-12 02:47:14] Removing 16 low quality variants with BQ < 25.
INFO [2018-04-12 02:47:14] Total size of targeted genomic region: 1.63Mb (2.58Mb with 50bp padding).
INFO [2018-04-12 02:47:14] 1.0% of targets contain variants.
INFO [2018-04-12 02:47:14] Removing 2122 variants outside intervals.
INFO [2018-04-12 02:47:14] Found SOMATIC annotation in VCF.
INFO [2018-04-12 02:47:14] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2018-04-12 02:47:14] Found SOMATIC annotation in VCF. Setting mapping bias to 0.973.
INFO [2018-04-12 02:47:14] Sample sex: ?
INFO [2018-04-12 02:47:14] Segmenting data...
INFO [2018-04-12 02:47:14] Setting undo.SD parameter to 1.000000.
Setting multi-figure configuration
INFO [2018-04-12 02:47:20] Setting prune.hclust.h parameter to 0.200000.
INFO [2018-04-12 02:47:20] Using 123 variants.
INFO [2018-04-12 02:47:20] Mean standard deviation of log-ratios: 0.37
INFO [2018-04-12 02:47:20] 2D-grid search of purity and ploidy...
INFO [2018-04-12 02:47:36] Local optima: 0.62/1.9, 0.38/2.2, 0.3/1.9, 0.48/2
INFO [2018-04-12 02:47:36] Testing local optimum 1/4 at purity 0.62 and total ploidy 1.90...
INFO [2018-04-12 02:47:38] Fitting variants for purity 0.65, tumor ploidy 1.73 and contamination 0.01.
INFO [2018-04-12 02:47:39] Optimized purity: 0.65
INFO [2018-04-12 02:47:39] Testing local optimum 2/4 at purity 0.38 and total ploidy 2.20...
INFO [2018-04-12 02:47:41] Fitting variants for purity 0.40, tumor ploidy 2.43 and contamination 0.01.
INFO [2018-04-12 02:47:42] Optimized purity: 0.40
INFO [2018-04-12 02:47:42] Testing local optimum 3/4 at purity 0.30 and total ploidy 1.90...
INFO [2018-04-12 02:47:42] Recalibrating log-ratios...
INFO [2018-04-12 02:47:42] Testing local optimum 3/4 at purity 0.30 and total ploidy 1.90...
INFO [2018-04-12 02:47:43] Recalibrating log-ratios...
INFO [2018-04-12 02:47:43] Testing local optimum 3/4 at purity 0.30 and total ploidy 1.90...
INFO [2018-04-12 02:47:44] Recalibrating log-ratios...
INFO [2018-04-12 02:47:44] Testing local optimum 3/4 at purity 0.30 and total ploidy 1.90...
INFO [2018-04-12 02:47:44] Testing local optimum 4/4 at purity 0.48 and total ploidy 2.00...
INFO [2018-04-12 02:47:46] Fitting variants for purity 0.65, tumor ploidy 1.73 and contamination 0.01.
INFO [2018-04-12 02:47:47] Optimized purity: 0.65
INFO [2018-04-12 02:47:47] Done.
INFO [2018-04-12 02:47:47] ------------------------------------------------------------
INFO [2018-04-12 02:47:47] ------------------------------------------------------------
INFO [2018-04-12 02:47:47] PureCN 1.8.1
INFO [2018-04-12 02:47:47] ------------------------------------------------------------
INFO [2018-04-12 02:47:47] Loading coverage files...
INFO [2018-04-12 02:47:48] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2018-04-12 02:47:48] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:47:48] Allosome coverage missing, cannot determine sex.
INFO [2018-04-12 02:47:48] Removing 22 small (< 5bp) targets.
INFO [2018-04-12 02:47:48] Removing 19 targets with low total coverage in normal (< 150.00 reads).
WARN [2018-04-12 02:47:48] No normalDB provided. Provide one for better results.
INFO [2018-04-12 02:47:48] Removing 233 low coverage (< 15.0000X) targets.
INFO [2018-04-12 02:47:48] Using 9547 intervals (9547 on-target, 0 off-target).
INFO [2018-04-12 02:47:48] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2018-04-12 02:47:48] No gc.gene.file provided. Cannot check if data was GC-normalized. Was it?
INFO [2018-04-12 02:47:48] Loading VCF...
INFO [2018-04-12 02:47:48] LIB-02240e4 is tumor in VCF file.
INFO [2018-04-12 02:47:48] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2018-04-12 02:47:48] Found 2331 variants in VCF file.
INFO [2018-04-12 02:47:49] Initial testing for significant sample cross-contamination: unlikely
INFO [2018-04-12 02:47:49] Removing 63 variants with AF < 0.030 or AF >= 0.970 or less than 4 supporting reads or depth < 15.
INFO [2018-04-12 02:47:49] Removing 16 low quality variants with BQ < 25.
INFO [2018-04-12 02:47:49] Total size of targeted genomic region: 1.63Mb (2.58Mb with 50bp padding).
INFO [2018-04-12 02:47:49] 1.0% of targets contain variants.
INFO [2018-04-12 02:47:49] Setting somatic prior probabilities for dbSNP hits to 0.000500 or to 0.500000 otherwise.
INFO [2018-04-12 02:47:49] Sample sex: ?
INFO [2018-04-12 02:47:49] Segmenting data...
INFO [2018-04-12 02:47:49] Setting undo.SD parameter to 1.000000.
Setting multi-figure configuration
INFO [2018-04-12 02:47:55] Setting prune.hclust.h parameter to 0.200000.
INFO [2018-04-12 02:47:55] Removing 282 variants outside segments.
INFO [2018-04-12 02:47:55] Using 1970 variants.
INFO [2018-04-12 02:47:55] Mean standard deviation of log-ratios: 0.37
INFO [2018-04-12 02:47:55] 2D-grid search of purity and ploidy...
INFO [2018-04-12 02:47:59] Local optima: 0.62/1.9, 0.38/2.2, 0.3/1.9, 0.48/2
INFO [2018-04-12 02:47:59] Testing local optimum 1/4 at purity 0.62 and total ploidy 1.90...
INFO [2018-04-12 02:48:00] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01.
INFO [2018-04-12 02:48:06] Optimized purity: 0.65
INFO [2018-04-12 02:48:06] Testing local optimum 2/4 at purity 0.38 and total ploidy 2.20...
INFO [2018-04-12 02:48:07] Fitting variants for purity 0.40, tumor ploidy 2.34 and contamination 0.01.
INFO [2018-04-12 02:48:12] Optimized purity: 0.40
INFO [2018-04-12 02:48:12] Testing local optimum 3/4 at purity 0.30 and total ploidy 1.90...
INFO [2018-04-12 02:48:13] Recalibrating log-ratios...
INFO [2018-04-12 02:48:13] Testing local optimum 3/4 at purity 0.30 and total ploidy 1.90...
INFO [2018-04-12 02:48:13] Recalibrating log-ratios...
INFO [2018-04-12 02:48:13] Testing local optimum 3/4 at purity 0.30 and total ploidy 1.90...
INFO [2018-04-12 02:48:13] Recalibrating log-ratios...
INFO [2018-04-12 02:48:13] Testing local optimum 3/4 at purity 0.30 and total ploidy 1.90...
INFO [2018-04-12 02:48:14] Testing local optimum 4/4 at purity 0.48 and total ploidy 2.00...
INFO [2018-04-12 02:48:15] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01.
INFO [2018-04-12 02:48:20] Optimized purity: 0.65
INFO [2018-04-12 02:48:20] Done.
INFO [2018-04-12 02:48:20] ------------------------------------------------------------
INFO [2018-04-12 02:48:20] ------------------------------------------------------------
INFO [2018-04-12 02:48:20] PureCN 1.8.1
INFO [2018-04-12 02:48:20] ------------------------------------------------------------
INFO [2018-04-12 02:48:20] Loading coverage files...
INFO [2018-04-12 02:48:21] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2018-04-12 02:48:21] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:48:21] Allosome coverage missing, cannot determine sex.
INFO [2018-04-12 02:48:21] No Gene column in gc.gene.file. You won't get gene-level calls.
INFO [2018-04-12 02:48:21] No on_target column in gc.gene.file. Recreate this file with IntervalFile.R.
INFO [2018-04-12 02:48:21] No mappability column in gc.gene.file.
INFO [2018-04-12 02:48:22] Removing 15 low/high GC targets.
INFO [2018-04-12 02:48:22] Removing 21 small (< 5bp) targets.
INFO [2018-04-12 02:48:22] Removing 19 targets with low total coverage in normal (< 150.00 reads).
WARN [2018-04-12 02:48:22] No normalDB provided. Provide one for better results.
INFO [2018-04-12 02:48:22] Removing 232 low coverage (< 15.0000X) targets.
INFO [2018-04-12 02:48:22] Using 9534 intervals (9534 on-target, 0 off-target).
INFO [2018-04-12 02:48:22] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2018-04-12 02:48:22] AT/GC dropout: 1.03 (tumor), 1.03 (normal). 
INFO [2018-04-12 02:48:22] Loading VCF...
INFO [2018-04-12 02:48:22] LIB-02240e4 is tumor in VCF file.
INFO [2018-04-12 02:48:22] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2018-04-12 02:48:22] Found 2331 variants in VCF file.
INFO [2018-04-12 02:48:22] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2018-04-12 02:48:22] Initial testing for significant sample cross-contamination: unlikely
INFO [2018-04-12 02:48:22] Removing 48 variants with AF < 0.030 or AF >= Inf or less than 4 supporting reads or depth < 15.
INFO [2018-04-12 02:48:22] Removing 16 low quality variants with BQ < 25.
INFO [2018-04-12 02:48:22] Total size of targeted genomic region: 1.63Mb (2.58Mb with 50bp padding).
INFO [2018-04-12 02:48:22] 1.0% of targets contain variants.
INFO [2018-04-12 02:48:22] Removing 2122 variants outside intervals.
INFO [2018-04-12 02:48:22] Found SOMATIC annotation in VCF.
INFO [2018-04-12 02:48:22] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2018-04-12 02:48:22] Found SOMATIC annotation in VCF. Setting mapping bias to 0.973.
INFO [2018-04-12 02:48:22] Sample sex: ?
INFO [2018-04-12 02:48:22] Segmenting data...
INFO [2018-04-12 02:48:22] Setting undo.SD parameter to 1.000000.
Setting multi-figure configuration
INFO [2018-04-12 02:48:28] Setting prune.hclust.h parameter to 0.200000.
INFO [2018-04-12 02:48:28] Using 123 variants.
INFO [2018-04-12 02:48:28] Mean standard deviation of log-ratios: 0.37
INFO [2018-04-12 02:48:28] 2D-grid search of purity and ploidy...
INFO [2018-04-12 02:48:28] Local optima: 0.65/1.9, 0.33/1.9, 0.38/2.2, 0.27/2.1, 0.29/2, 0.78/2
INFO [2018-04-12 02:48:28] Testing local optimum 1/6 at purity 0.65 and total ploidy 1.90...
INFO [2018-04-12 02:48:30] Fitting variants for purity 0.65, tumor ploidy 1.73 and contamination 0.01.
INFO [2018-04-12 02:48:31] Optimized purity: 0.65
INFO [2018-04-12 02:48:31] Testing local optimum 2/6 at purity 0.33 and total ploidy 1.90...
INFO [2018-04-12 02:48:31] Recalibrating log-ratios...
INFO [2018-04-12 02:48:31] Testing local optimum 2/6 at purity 0.33 and total ploidy 1.90...
INFO [2018-04-12 02:48:32] Recalibrating log-ratios...
INFO [2018-04-12 02:48:32] Testing local optimum 2/6 at purity 0.33 and total ploidy 1.90...
INFO [2018-04-12 02:48:32] Recalibrating log-ratios...
INFO [2018-04-12 02:48:32] Testing local optimum 2/6 at purity 0.33 and total ploidy 1.90...
INFO [2018-04-12 02:48:33] Testing local optimum 3/6 at purity 0.38 and total ploidy 2.20...
INFO [2018-04-12 02:48:35] Fitting variants for purity 0.40, tumor ploidy 2.34 and contamination 0.01.
INFO [2018-04-12 02:48:36] Optimized purity: 0.40
INFO [2018-04-12 02:48:36] Testing local optimum 4/6 at purity 0.27 and total ploidy 2.10...
INFO [2018-04-12 02:48:37] Recalibrating log-ratios...
INFO [2018-04-12 02:48:37] Testing local optimum 4/6 at purity 0.27 and total ploidy 2.10...
INFO [2018-04-12 02:48:37] Recalibrating log-ratios...
INFO [2018-04-12 02:48:37] Testing local optimum 4/6 at purity 0.27 and total ploidy 2.10...
INFO [2018-04-12 02:48:38] Recalibrating log-ratios...
INFO [2018-04-12 02:48:38] Testing local optimum 4/6 at purity 0.27 and total ploidy 2.10...
INFO [2018-04-12 02:48:38] Testing local optimum 5/6 at purity 0.29 and total ploidy 2.00...
INFO [2018-04-12 02:48:39] Recalibrating log-ratios...
INFO [2018-04-12 02:48:39] Testing local optimum 5/6 at purity 0.29 and total ploidy 2.00...
INFO [2018-04-12 02:48:39] Recalibrating log-ratios...
INFO [2018-04-12 02:48:39] Testing local optimum 5/6 at purity 0.29 and total ploidy 2.00...
INFO [2018-04-12 02:48:40] Recalibrating log-ratios...
INFO [2018-04-12 02:48:40] Testing local optimum 5/6 at purity 0.29 and total ploidy 2.00...
INFO [2018-04-12 02:48:40] Testing local optimum 6/6 at purity 0.78 and total ploidy 2.00...
INFO [2018-04-12 02:48:42] Fitting variants for purity 0.65, tumor ploidy 1.73 and contamination 0.01.
INFO [2018-04-12 02:48:43] Optimized purity: 0.65
INFO [2018-04-12 02:48:43] Done.
INFO [2018-04-12 02:48:43] ------------------------------------------------------------
FATAL [2018-04-12 02:48:43] This function requires gene-level calls. Please add a column 'Gene' 

FATAL [2018-04-12 02:48:43] containing gene symbols to the gc.gene.file. 

FATAL [2018-04-12 02:48:43]  

FATAL [2018-04-12 02:48:43] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:48:43] parameters (PureCN 1.8.1). 

INFO [2018-04-12 02:48:45] ------------------------------------------------------------
INFO [2018-04-12 02:48:45] PureCN 1.8.1
INFO [2018-04-12 02:48:45] ------------------------------------------------------------
INFO [2018-04-12 02:48:45] Loading coverage files...
INFO [2018-04-12 02:48:46] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2018-04-12 02:48:46] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:48:46] Allosome coverage missing, cannot determine sex.
INFO [2018-04-12 02:48:46] Removing 22 small (< 5bp) targets.
INFO [2018-04-12 02:48:46] Removing 19 targets with low total coverage in normal (< 150.00 reads).
WARN [2018-04-12 02:48:46] No normalDB provided. Provide one for better results.
INFO [2018-04-12 02:48:46] Removing 233 low coverage (< 15.0000X) targets.
INFO [2018-04-12 02:48:46] Using 9547 intervals (9547 on-target, 0 off-target).
INFO [2018-04-12 02:48:46] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2018-04-12 02:48:46] No gc.gene.file provided. Cannot check if data was GC-normalized. Was it?
INFO [2018-04-12 02:48:46] Loading VCF...
FATAL [2018-04-12 02:48:46] Different chromosome names in coverage and VCF. 

FATAL [2018-04-12 02:48:46]  

FATAL [2018-04-12 02:48:46] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:48:46] parameters (PureCN 1.8.1). 

INFO [2018-04-12 02:48:46] ------------------------------------------------------------
INFO [2018-04-12 02:48:46] PureCN 1.8.1
INFO [2018-04-12 02:48:46] ------------------------------------------------------------
INFO [2018-04-12 02:48:46] Loading coverage files...
INFO [2018-04-12 02:48:46] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2018-04-12 02:48:48] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:48:48] Allosome coverage missing, cannot determine sex.
INFO [2018-04-12 02:48:48] No on_target column in gc.gene.file. Recreate this file with IntervalFile.R.
INFO [2018-04-12 02:48:48] No mappability column in gc.gene.file.
FATAL [2018-04-12 02:48:48] tumor.coverage.file and gc.gene.file do not align. 

FATAL [2018-04-12 02:48:48]  

FATAL [2018-04-12 02:48:48] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:48:48] parameters (PureCN 1.8.1). 

INFO [2018-04-12 02:48:48] ------------------------------------------------------------
INFO [2018-04-12 02:48:48] PureCN 1.8.1
INFO [2018-04-12 02:48:48] ------------------------------------------------------------
INFO [2018-04-12 02:48:48] Loading coverage files...
INFO [2018-04-12 02:48:48] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2018-04-12 02:48:48] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:48:48] Allosome coverage missing, cannot determine sex.
INFO [2018-04-12 02:48:48] No on_target column in gc.gene.file. Recreate this file with IntervalFile.R.
INFO [2018-04-12 02:48:48] No mappability column in gc.gene.file.
INFO [2018-04-12 02:48:50] Removing 15 low/high GC targets.
INFO [2018-04-12 02:48:50] Removing 21 small (< 5bp) targets.
INFO [2018-04-12 02:48:50] Removing 19 targets with low total coverage in normal (< 150.00 reads).
WARN [2018-04-12 02:48:50] No normalDB provided. Provide one for better results.
INFO [2018-04-12 02:48:50] Removing 232 low coverage (< 15.0000X) targets.
INFO [2018-04-12 02:48:50] Using 9534 intervals (9534 on-target, 0 off-target).
INFO [2018-04-12 02:48:50] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2018-04-12 02:48:50] AT/GC dropout: 1.03 (tumor), 1.03 (normal). 
INFO [2018-04-12 02:48:50] Loading VCF...
INFO [2018-04-12 02:48:50] LIB-02240e4 is tumor in VCF file.
INFO [2018-04-12 02:48:50] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2018-04-12 02:48:50] Found 2331 variants in VCF file.
INFO [2018-04-12 02:48:51] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2018-04-12 02:48:51] Initial testing for significant sample cross-contamination: unlikely
INFO [2018-04-12 02:48:51] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2018-04-12 02:48:51] Removing 16 low quality variants with BQ < 25.
INFO [2018-04-12 02:48:51] Total size of targeted genomic region: 1.63Mb (2.58Mb with 50bp padding).
INFO [2018-04-12 02:48:51] 1.0% of targets contain variants.
INFO [2018-04-12 02:48:51] Removing 2122 variants outside intervals.
INFO [2018-04-12 02:48:51] Found SOMATIC annotation in VCF.
INFO [2018-04-12 02:48:51] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2018-04-12 02:48:51] Found SOMATIC annotation in VCF. Setting mapping bias to 0.973.
INFO [2018-04-12 02:48:51] Sample sex: ?
INFO [2018-04-12 02:48:51] Segmenting data...
INFO [2018-04-12 02:48:51] Setting undo.SD parameter to 1.000000.
INFO [2018-04-12 02:48:57] Setting prune.hclust.h parameter to 0.200000.
INFO [2018-04-12 02:48:57] Using 123 variants.
INFO [2018-04-12 02:48:57] Mean standard deviation of log-ratios: 0.37
INFO [2018-04-12 02:48:57] 2D-grid search of purity and ploidy...
INFO [2018-04-12 02:49:00] Local optima: 0.63/1.9, 0.4/2.2, 0.5/2
INFO [2018-04-12 02:49:00] Testing local optimum 1/3 at purity 0.63 and total ploidy 1.90...
INFO [2018-04-12 02:49:02] Fitting variants for purity 0.65, tumor ploidy 1.73 and contamination 0.01.
INFO [2018-04-12 02:49:03] Optimized purity: 0.65
INFO [2018-04-12 02:49:03] Testing local optimum 2/3 at purity 0.40 and total ploidy 2.20...
INFO [2018-04-12 02:49:05] Fitting variants for purity 0.40, tumor ploidy 2.34 and contamination 0.01.
INFO [2018-04-12 02:49:06] Optimized purity: 0.40
INFO [2018-04-12 02:49:06] Testing local optimum 3/3 at purity 0.50 and total ploidy 2.00...
INFO [2018-04-12 02:49:08] Fitting variants for purity 0.65, tumor ploidy 1.73 and contamination 0.01.
INFO [2018-04-12 02:49:08] Optimized purity: 0.65
INFO [2018-04-12 02:49:08] Done.
INFO [2018-04-12 02:49:08] ------------------------------------------------------------
INFO [2018-04-12 02:49:09] ------------------------------------------------------------
INFO [2018-04-12 02:49:09] PureCN 1.8.1
INFO [2018-04-12 02:49:09] ------------------------------------------------------------
INFO [2018-04-12 02:49:09] Loading coverage files...
INFO [2018-04-12 02:49:09] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2018-04-12 02:49:09] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:49:09] Allosome coverage missing, cannot determine sex.
INFO [2018-04-12 02:49:09] No on_target column in gc.gene.file. Recreate this file with IntervalFile.R.
INFO [2018-04-12 02:49:09] No mappability column in gc.gene.file.
INFO [2018-04-12 02:49:10] Removing 15 low/high GC targets.
INFO [2018-04-12 02:49:10] Removing 21 small (< 5bp) targets.
INFO [2018-04-12 02:49:10] Removing 19 targets with low total coverage in normal (< 150.00 reads).
WARN [2018-04-12 02:49:10] No normalDB provided. Provide one for better results.
INFO [2018-04-12 02:49:10] Removing 232 low coverage (< 15.0000X) targets.
INFO [2018-04-12 02:49:10] Using 9534 intervals (9534 on-target, 0 off-target).
INFO [2018-04-12 02:49:10] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2018-04-12 02:49:10] AT/GC dropout: 1.03 (tumor), 1.03 (normal). 
INFO [2018-04-12 02:49:10] Loading VCF...
INFO [2018-04-12 02:49:10] LIB-02240e4 is tumor in VCF file.
INFO [2018-04-12 02:49:10] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2018-04-12 02:49:10] Found 2331 variants in VCF file.
INFO [2018-04-12 02:49:10] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2018-04-12 02:49:11] Initial testing for significant sample cross-contamination: unlikely
INFO [2018-04-12 02:49:11] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2018-04-12 02:49:11] Removing 16 low quality variants with BQ < 25.
INFO [2018-04-12 02:49:11] Total size of targeted genomic region: 1.63Mb (2.58Mb with 50bp padding).
INFO [2018-04-12 02:49:11] 1.0% of targets contain variants.
INFO [2018-04-12 02:49:11] Removing 2122 variants outside intervals.
INFO [2018-04-12 02:49:11] Found SOMATIC annotation in VCF.
INFO [2018-04-12 02:49:11] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2018-04-12 02:49:11] Found SOMATIC annotation in VCF. Setting mapping bias to 0.973.
INFO [2018-04-12 02:49:11] Sample sex: ?
INFO [2018-04-12 02:49:11] Segmenting data...
INFO [2018-04-12 02:49:11] Setting undo.SD parameter to 1.000000.
INFO [2018-04-12 02:49:17] Setting prune.hclust.h parameter to 0.200000.
INFO [2018-04-12 02:49:17] Using 123 variants.
INFO [2018-04-12 02:49:17] Mean standard deviation of log-ratios: 0.37
INFO [2018-04-12 02:49:17] 2D-grid search of purity and ploidy...
INFO [2018-04-12 02:49:19] Local optima: 0.63/1.9, 0.4/2.2, 0.5/2
INFO [2018-04-12 02:49:19] Testing local optimum 1/3 at purity 0.63 and total ploidy 1.90...
INFO [2018-04-12 02:49:21] Fitting variants for purity 0.65, tumor ploidy 1.73 and contamination 0.01.
INFO [2018-04-12 02:49:22] Optimized purity: 0.65
INFO [2018-04-12 02:49:22] Testing local optimum 2/3 at purity 0.40 and total ploidy 2.20...
INFO [2018-04-12 02:49:25] Fitting variants for purity 0.40, tumor ploidy 2.34 and contamination 0.01.
INFO [2018-04-12 02:49:26] Optimized purity: 0.40
INFO [2018-04-12 02:49:26] Testing local optimum 3/3 at purity 0.50 and total ploidy 2.00...
INFO [2018-04-12 02:49:28] Fitting variants for purity 0.65, tumor ploidy 1.73 and contamination 0.01.
INFO [2018-04-12 02:49:29] Optimized purity: 0.65
INFO [2018-04-12 02:49:29] Done.
INFO [2018-04-12 02:49:30] ------------------------------------------------------------
FATAL [2018-04-12 02:49:31] chr1 not valid chromosome name(s). Valid names are: 

FATAL [2018-04-12 02:49:31] 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22 

FATAL [2018-04-12 02:49:31]  

FATAL [2018-04-12 02:49:31] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:49:31] parameters (PureCN 1.8.1). 

INFO [2018-04-12 02:49:31] ------------------------------------------------------------
INFO [2018-04-12 02:49:31] PureCN 1.8.1
INFO [2018-04-12 02:49:31] ------------------------------------------------------------
INFO [2018-04-12 02:49:31] Loading coverage files...
WARN [2018-04-12 02:49:31] Provided sampleid (Sample2) does not match Sample1 found in segmentation.
WARN [2018-04-12 02:49:31] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:49:31] Allosome coverage missing, cannot determine sex.
INFO [2018-04-12 02:49:31] Using 10039 intervals (10039 on-target, 0 off-target).
INFO [2018-04-12 02:49:31] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2018-04-12 02:49:31] Loading VCF...
INFO [2018-04-12 02:49:32] LIB-02240e4 is tumor in VCF file.
INFO [2018-04-12 02:49:32] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2018-04-12 02:49:32] Found 2331 variants in VCF file.
INFO [2018-04-12 02:49:32] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2018-04-12 02:49:32] Initial testing for significant sample cross-contamination: unlikely
INFO [2018-04-12 02:49:32] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2018-04-12 02:49:32] Removing 16 low quality variants with BQ < 25.
INFO [2018-04-12 02:49:32] Total size of targeted genomic region: 1.71Mb (2.70Mb with 50bp padding).
INFO [2018-04-12 02:49:32] 1.0% of targets contain variants.
INFO [2018-04-12 02:49:32] Removing 2120 variants outside intervals.
INFO [2018-04-12 02:49:33] Found SOMATIC annotation in VCF.
INFO [2018-04-12 02:49:33] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2018-04-12 02:49:33] Found SOMATIC annotation in VCF. Setting mapping bias to 0.976.
INFO [2018-04-12 02:49:33] Sample sex: ?
INFO [2018-04-12 02:49:33] Segmenting data...
WARN [2018-04-12 02:49:33] Provided sampleid (Sample2) does not match Sample1 found in segmentation.
INFO [2018-04-12 02:49:33] Setting undo.SD parameter to 0.000000.
Setting multi-figure configuration
INFO [2018-04-12 02:49:37] Setting prune.hclust.h parameter to 0.200000.
INFO [2018-04-12 02:49:38] Using 125 variants.
INFO [2018-04-12 02:49:38] Mean standard deviation of log-ratios: 0.40
INFO [2018-04-12 02:49:38] 2D-grid search of purity and ploidy...
INFO [2018-04-12 02:49:41] Local optima: 0.67/1.8, 0.4/2.2, 0.5/2
INFO [2018-04-12 02:49:41] Testing local optimum 1/3 at purity 0.67 and total ploidy 1.80...
INFO [2018-04-12 02:49:42] Fitting variants for purity 0.65, tumor ploidy 1.73 and contamination 0.01.
INFO [2018-04-12 02:49:43] Optimized purity: 0.65
INFO [2018-04-12 02:49:43] Testing local optimum 2/3 at purity 0.40 and total ploidy 2.20...
INFO [2018-04-12 02:49:45] Fitting variants for purity 0.40, tumor ploidy 2.33 and contamination 0.01.
INFO [2018-04-12 02:49:46] Optimized purity: 0.40
INFO [2018-04-12 02:49:46] Testing local optimum 3/3 at purity 0.50 and total ploidy 2.00...
INFO [2018-04-12 02:49:47] Fitting variants for purity 0.65, tumor ploidy 1.73 and contamination 0.01.
INFO [2018-04-12 02:49:48] Optimized purity: 0.65
INFO [2018-04-12 02:49:48] Done.
INFO [2018-04-12 02:49:48] ------------------------------------------------------------
WARN [2018-04-12 02:49:48] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:49:48] Allosome coverage missing, cannot determine sex.
Setting multi-figure configuration
FATAL [2018-04-12 02:50:19] Segmentation file expected with colnames ID, chrom, loc.start, loc.end, 

FATAL [2018-04-12 02:50:19] num.mark, seg.mean 

FATAL [2018-04-12 02:50:19]  

FATAL [2018-04-12 02:50:19] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:50:19] parameters (PureCN 1.8.1). 

FATAL [2018-04-12 02:50:19] seg.file contains multiple samples and sampleid missing. 

FATAL [2018-04-12 02:50:19]  

FATAL [2018-04-12 02:50:19] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:50:19] parameters (PureCN 1.8.1). 

FATAL [2018-04-12 02:50:20] seg.file contains multiple samples and sampleid does not match any. 

FATAL [2018-04-12 02:50:20]  

FATAL [2018-04-12 02:50:20] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:50:20] parameters (PureCN 1.8.1). 

WARN [2018-04-12 02:50:20] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:50:20] Allosome coverage missing, cannot determine sex.
Setting multi-figure configuration
WARN [2018-04-12 02:50:43] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:50:43] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:50:44] No normalDB provided. Provide one for better results.
Setting multi-figure configuration
WARN [2018-04-12 02:51:12] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:51:12] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:51:14] Provided sampleid (Sample.1) does not match Sample1 found in segmentation.
Setting multi-figure configuration
WARN [2018-04-12 02:51:50] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:51:50] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:51:50] No normalDB provided. Provide one for better results.
WARN [2018-04-12 02:51:51] Sampleid looks like a normal in VCF, not like a tumor.
Setting multi-figure configuration
WARN [2018-04-12 02:52:20] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:52:20] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:52:20] No normalDB provided. Provide one for better results.
WARN [2018-04-12 02:52:37] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:52:37] Allosome coverage missing, cannot determine sex.
FATAL [2018-04-12 02:52:37] normalDB not a valid normalDB object. Use createNormalDatabase to 

FATAL [2018-04-12 02:52:37] create one. 

FATAL [2018-04-12 02:52:37]  

FATAL [2018-04-12 02:52:37] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:52:37] parameters (PureCN 1.8.1). 

WARN [2018-04-12 02:52:38] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:52:38] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:52:40] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:52:40] Allosome coverage missing, cannot determine sex.
Setting multi-figure configuration
WARN [2018-04-12 02:53:14] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:53:14] Allosome coverage missing, cannot determine sex.
FATAL [2018-04-12 02:53:14] normalDB appears to be empty. 

FATAL [2018-04-12 02:53:14]  

FATAL [2018-04-12 02:53:14] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:53:14] parameters (PureCN 1.8.1). 

WARN [2018-04-12 02:53:14] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:53:15] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:53:41] Provided sampleid (example_tumor.txt) does not match Sample1 found in segmentation.
WARN [2018-04-12 02:53:41] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:53:41] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:53:41] Provided sampleid (example_tumor.txt) does not match Sample1 found in segmentation.
WARN [2018-04-12 02:53:48] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:53:48] Allosome coverage missing, cannot determine sex.
Setting multi-figure configuration
WARN [2018-04-12 02:54:11] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:54:11] Allosome coverage missing, cannot determine sex.
WARN [2018-04-12 02:54:11] Intervals in coverage and gc.gene.file have conflicting on/off-target annotation.
WARN [2018-04-12 02:54:12] No normalDB provided. Provide one for better results.
Setting multi-figure configuration
FATAL [2018-04-12 02:54:26] min.normals must be >=2. 

FATAL [2018-04-12 02:54:26]  

FATAL [2018-04-12 02:54:26] This is most likely a user error due to invalid input data or 

FATAL [2018-04-12 02:54:26] parameters (PureCN 1.8.1). 



RUNIT TEST PROTOCOL -- Thu Apr 12 02:54:27 2018 
*********************************************** 
Number of test functions: 22 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
PureCN RUnit Tests - 22 test functions, 0 errors, 0 failures
Number of test functions: 22 
Number of errors: 0 
Number of failures: 0 
There were 18 warnings (use warnings() to see them)
> 
> proc.time()
   user  system elapsed 
 604.09    2.06  606.54

Example timings

PureCN.Rcheck/examples_i386/PureCN-Ex.timings

nameusersystemelapsed
annotateTargets7.780.348.13
bootstrapResults0.530.000.53
calculateBamCoverageByInterval0.360.000.36
calculateGCContentByInterval0.380.030.40
calculateLogRatio0.920.010.94
calculatePowerDetectSomatic1.340.001.35
callAlterations0.210.000.20
callAlterationsFromSegmentation1.840.021.86
callLOH0.280.000.28
callMutationBurden1.750.001.75
centromeres0.000.010.02
correctCoverageBias17.72 0.0417.75
createCurationFile0.420.030.45
createNormalDatabase1.610.001.61
createTargetWeights1.640.001.64
filterTargets34.00 0.0934.09
filterVcfBasic0.720.020.74
filterVcfMuTect0.420.000.42
filterVcfMuTect20.570.000.56
findBestNormal9.230.019.25
findFocal22.39 0.0322.42
getSexFromCoverage0.310.000.32
getSexFromVcf0.250.000.25
plotAbs0.940.030.96
plotBestNormal2.950.002.96
poolCoverage2.890.022.90
predictSomatic0.540.020.55
readCoverageFile0.320.000.33
readCurationFile0.320.010.33
runAbsoluteCN35.51 0.0535.56
segmentationCBS17.41 0.0417.45
segmentationPSCBS128.03 0.55128.61
setMappingBiasVcf0.190.000.19
setPriorVcf0.210.000.21

PureCN.Rcheck/examples_x64/PureCN-Ex.timings

nameusersystemelapsed
annotateTargets7.090.177.29
bootstrapResults0.530.020.54
calculateBamCoverageByInterval0.420.010.44
calculateGCContentByInterval0.390.000.39
calculateLogRatio0.970.020.98
calculatePowerDetectSomatic1.400.001.41
callAlterations0.160.000.15
callAlterationsFromSegmentation2.550.012.57
callLOH0.250.000.25
callMutationBurden1.490.021.50
centromeres000
correctCoverageBias20.88 0.0220.89
createCurationFile0.370.030.40
createNormalDatabase2.020.002.02
createTargetWeights1.670.001.67
filterTargets41.56 0.0441.63
filterVcfBasic0.850.040.87
filterVcfMuTect0.50.00.5
filterVcfMuTect20.560.000.56
findBestNormal12.98 0.0113.00
findFocal23.53 0.0223.55
getSexFromCoverage0.350.000.34
getSexFromVcf0.360.010.38
plotAbs1.080.021.09
plotBestNormal3.530.013.55
poolCoverage3.370.003.38
predictSomatic0.470.000.46
readCoverageFile0.310.000.32
readCurationFile0.280.020.29
runAbsoluteCN35.88 0.0135.89
segmentationCBS20.08 0.0420.13
segmentationPSCBS171.37 0.56172.37
setMappingBiasVcf0.210.000.21
setPriorVcf0.180.000.18