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CHECK report for PureCN on merida2

This page was generated on 2018-10-17 08:56:30 -0400 (Wed, 17 Oct 2018).

Package 1149/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PureCN 1.10.0
Markus Riester
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/PureCN
Branch: RELEASE_3_7
Last Commit: 21a4b58
Last Changed Date: 2018-04-30 10:35:41 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: PureCN
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PureCN.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PureCN_1.10.0.tar.gz
StartedAt: 2018-10-16 23:23:53 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 23:42:05 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 1091.5 seconds
RetCode: 0
Status:  OK 
CheckDir: PureCN.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PureCN.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PureCN_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/PureCN.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PureCN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PureCN’ version ‘1.10.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘PureCN’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
segmentationPSCBS 48.990  2.110  48.022
runAbsoluteCN     44.933  3.212  41.689
filterTargets     33.579  2.001  32.528
segmentationCBS   28.538  1.982  27.355
findFocal         26.976  1.936  25.681
annotateTargets   14.166  0.273  14.488
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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: OK

Installation output

PureCN.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL PureCN
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘PureCN’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (PureCN)

Tests output

PureCN.Rcheck/tests/testthat.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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.

> library(testthat)
> library(PureCN)
Loading required package: DNAcopy
Loading required package: VariantAnnotation
Loading required package: BiocGenerics
Loading required package: parallel

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, basename, cbind, colMeans, colSums, colnames,
    dirname, 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

Loading required package: GenomeInfoDb
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

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

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    aperm, apply

Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

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

> 
> test_check("PureCN")
WARN [2018-10-16 23:32:37] Attempted adding gene symbols to intervals. Heuristics have been used to pick symbols for overlapping genes.
WARN [2018-10-16 23:32:37] Chromosome naming style of txdb file (UCSC) was different from interval file (NCBI).
WARN [2018-10-16 23:32:50] Attempted adding gene symbols to intervals. Heuristics have been used to pick symbols for overlapping genes.
FATAL [2018-10-16 23:32:52] tumor.coverage.file and interval.file do not align. 

FATAL [2018-10-16 23:32:52]  

FATAL [2018-10-16 23:32:52] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:32:52] parameters (PureCN 1.10.0). 

FATAL [2018-10-16 23:32:52] Need either f or purity and ploidy. 

FATAL [2018-10-16 23:32:52]  

FATAL [2018-10-16 23:32:52] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:32:52] parameters (PureCN 1.10.0). 

FATAL [2018-10-16 23:32:52] f not in expected range. 

FATAL [2018-10-16 23:32:52]  

FATAL [2018-10-16 23:32:52] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:32:52] parameters (PureCN 1.10.0). 

FATAL [2018-10-16 23:32:52] coverage not in expected range (>=2) 

FATAL [2018-10-16 23:32:52]  

FATAL [2018-10-16 23:32:52] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:32:52] parameters (PureCN 1.10.0). 

FATAL [2018-10-16 23:32:52] purity not in expected range. 

FATAL [2018-10-16 23:32:52]  

FATAL [2018-10-16 23:32:52] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:32:52] parameters (PureCN 1.10.0). 

FATAL [2018-10-16 23:32:52] ploidy not in expected range. 

FATAL [2018-10-16 23:32:52]  

FATAL [2018-10-16 23:32:52] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:32:52] parameters (PureCN 1.10.0). 

FATAL [2018-10-16 23:32:52] cell.fraction not in expected range. 

FATAL [2018-10-16 23:32:52]  

FATAL [2018-10-16 23:32:52] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:32:52] parameters (PureCN 1.10.0). 

INFO [2018-10-16 23:32:58] ------------------------------------------------------------
INFO [2018-10-16 23:32:58] PureCN 1.10.0
INFO [2018-10-16 23:32:58] ------------------------------------------------------------
INFO [2018-10-16 23:32:58] Loading coverage files...
INFO [2018-10-16 23:32:58] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2018-10-16 23:32:58] Allosome coverage missing, cannot determine sex.
WARN [2018-10-16 23:32:58] Allosome coverage missing, cannot determine sex.
INFO [2018-10-16 23:32:58] Removing 228 intervals with missing log.ratio.
INFO [2018-10-16 23:32:58] Removing 22 small (< 5bp) targets.
INFO [2018-10-16 23:32:58] Removing 19 targets with low total coverage in normal (< 150.00 reads).
WARN [2018-10-16 23:32:58] No normalDB provided. Provide one for better results.
INFO [2018-10-16 23:32:58] Removing 233 low coverage (< 15.0000X) targets.
INFO [2018-10-16 23:32:58] Using 9547 intervals (9547 on-target, 0 off-target).
INFO [2018-10-16 23:32:58] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2018-10-16 23:32:58] No interval.file provided. Cannot check if data was GC-normalized. Was it?
INFO [2018-10-16 23:32:58] Loading VCF...
INFO [2018-10-16 23:32:58] Found 2331 variants in VCF file.
INFO [2018-10-16 23:32:58] 2282 (97.9%) variants annotated as likely germline (DB INFO flag).
INFO [2018-10-16 23:32:59] LIB-02240e4 is tumor in VCF file.
INFO [2018-10-16 23:32:59] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2018-10-16 23:32:59] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2018-10-16 23:33:00] Initial testing for significant sample cross-contamination: unlikely
INFO [2018-10-16 23:33:01] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2018-10-16 23:33:01] Removing 16 low quality variants with BQ < 25.
INFO [2018-10-16 23:33:01] Total size of targeted genomic region: 1.63Mb (2.58Mb with 50bp padding).
INFO [2018-10-16 23:33:01] 1.0% of targets contain variants.
INFO [2018-10-16 23:33:01] Removing 2122 variants outside intervals.
INFO [2018-10-16 23:33:01] Found SOMATIC annotation in VCF.
INFO [2018-10-16 23:33:01] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2018-10-16 23:33:02] Found SOMATIC annotation in VCF. Setting mapping bias to 0.973.
INFO [2018-10-16 23:33:02] Sample sex: ?
INFO [2018-10-16 23:33:02] Segmenting data...
INFO [2018-10-16 23:33:02] Loading pre-computed boundaries for DNAcopy...
INFO [2018-10-16 23:33:02] Setting undo.SD parameter to 1.000000.
INFO [2018-10-16 23:33:03] Setting prune.hclust.h parameter to 0.200000.
INFO [2018-10-16 23:33:03] Found 54 segments with median size of 24.88Mb.
INFO [2018-10-16 23:33:03] Using 123 variants.
INFO [2018-10-16 23:33:03] Mean standard deviation of log-ratios: 0.37
INFO [2018-10-16 23:33:03] 2D-grid search of purity and ploidy...
INFO [2018-10-16 23:33:06] Local optima: 0.63/1.9, 0.4/2.2, 0.5/2
INFO [2018-10-16 23:33:06] Testing local optimum 1/3 at purity 0.63 and total ploidy 1.90...
INFO [2018-10-16 23:33:07] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01.
INFO [2018-10-16 23:33:09] Optimized purity: 0.65
INFO [2018-10-16 23:33:09] Testing local optimum 2/3 at purity 0.40 and total ploidy 2.20...
INFO [2018-10-16 23:33:11] Fitting variants for purity 0.40, tumor ploidy 2.34 and contamination 0.01.
INFO [2018-10-16 23:33:12] Optimized purity: 0.40
INFO [2018-10-16 23:33:12] Testing local optimum 3/3 at purity 0.50 and total ploidy 2.00...
INFO [2018-10-16 23:33:13] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01.
INFO [2018-10-16 23:33:15] Optimized purity: 0.65
INFO [2018-10-16 23:33:15] Done.
INFO [2018-10-16 23:33:15] ------------------------------------------------------------
FATAL [2018-10-16 23:33:17] exclude not a GRanges object. 

FATAL [2018-10-16 23:33:17]  

FATAL [2018-10-16 23:33:17] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:33:17] parameters (PureCN 1.10.0). 

FATAL [2018-10-16 23:33:17] callable not a GRanges object. 

FATAL [2018-10-16 23:33:17]  

FATAL [2018-10-16 23:33:17] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:33:17] parameters (PureCN 1.10.0). 

WARN [2018-10-16 23:33:31] tumor.coverage.file and interval.file do not align.
FATAL [2018-10-16 23:33:33] No gc_bias column in interval.file. 

FATAL [2018-10-16 23:33:33]  

FATAL [2018-10-16 23:33:33] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:33:33] parameters (PureCN 1.10.0). 

FATAL [2018-10-16 23:33:34] Provided coverage is zero, most likely due to a corrupt BAM file. 

FATAL [2018-10-16 23:33:34]  

FATAL [2018-10-16 23:33:34] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:33:34] parameters (PureCN 1.10.0). 

INFO [2018-10-16 23:33:43] Reading /tmp/Rtmpw2y1S1/file1ca867e8b6fb.rds...
INFO [2018-10-16 23:33:43] Reading /tmp/Rtmpw2y1S1/file1ca867e8b6fb.rds...
INFO [2018-10-16 23:33:43] Reading /tmp/Rtmpw2y1S1/file1ca867e8b6fb.rds...
INFO [2018-10-16 23:33:43] Reading /tmp/Rtmpw2y1S1/file1ca867e8b6fb.rds...
INFO [2018-10-16 23:33:44] Reading /tmp/Rtmpw2y1S1/file1ca867e8b6fb.rds...
INFO [2018-10-16 23:33:44] Reading /tmp/Rtmpw2y1S1/file1ca867e8b6fb.rds...
FATAL [2018-10-16 23:33:44] Purity or Ploidy not numeric or in expected range. 

FATAL [2018-10-16 23:33:44]  

FATAL [2018-10-16 23:33:44] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:33:44] parameters (PureCN 1.10.0). 

INFO [2018-10-16 23:33:44] Reading /tmp/Rtmpw2y1S1/file1ca867e8b6fb.rds...
INFO [2018-10-16 23:33:44] Reading /tmp/Rtmpw2y1S1/file1ca867e8b6fb.rds...
FATAL [2018-10-16 23:33:44] 'Failed' column in /tmp/Rtmpw2y1S1/file1ca867e8b6fb.csv not logical(1). 

FATAL [2018-10-16 23:33:44]  

FATAL [2018-10-16 23:33:44] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:33:44] parameters (PureCN 1.10.0). 

INFO [2018-10-16 23:33:45] 576 on-target bins with low coverage in all samples.
WARN [2018-10-16 23:33:45] You are likely not using the correct baits file!
WARN [2018-10-16 23:33:45] Allosome coverage missing, cannot determine sex.
WARN [2018-10-16 23:33:45] Allosome coverage missing, cannot determine sex.
INFO [2018-10-16 23:33:45] Processing on-target regions...
INFO [2018-10-16 23:33:46] Removing 930 targets with low coverage in normalDB.
INFO [2018-10-16 23:33:46] Removing 1 targets with zero coverage in more than 3% of normalDB.
INFO [2018-10-16 23:33:51] 576 on-target bins with low coverage in all samples.
WARN [2018-10-16 23:33:51] You are likely not using the correct baits file!
WARN [2018-10-16 23:33:51] Allosome coverage missing, cannot determine sex.
WARN [2018-10-16 23:33:51] Allosome coverage missing, cannot determine sex.
INFO [2018-10-16 23:33:51] Processing on-target regions...
INFO [2018-10-16 23:33:52] Removing 930 targets with low coverage in normalDB.
INFO [2018-10-16 23:33:52] Removing 1 targets with zero coverage in more than 3% of normalDB.
INFO [2018-10-16 23:33:55] 576 on-target bins with low coverage in all samples.
WARN [2018-10-16 23:33:55] You are likely not using the correct baits file!
WARN [2018-10-16 23:33:55] Allosome coverage missing, cannot determine sex.
WARN [2018-10-16 23:33:55] Allosome coverage missing, cannot determine sex.
INFO [2018-10-16 23:33:55] Processing on-target regions...
INFO [2018-10-16 23:33:56] Removing 930 targets with low coverage in normalDB.
INFO [2018-10-16 23:33:56] Removing 1 targets with zero coverage in more than 3% of normalDB.
INFO [2018-10-16 23:33:58] 576 on-target bins with low coverage in all samples.
WARN [2018-10-16 23:33:58] You are likely not using the correct baits file!
WARN [2018-10-16 23:33:58] Allosome coverage missing, cannot determine sex.
WARN [2018-10-16 23:33:58] Allosome coverage missing, cannot determine sex.
FATAL [2018-10-16 23:33:58] Length of normal.coverage.files and sex different 

FATAL [2018-10-16 23:33:58]  

FATAL [2018-10-16 23:33:58] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:33:58] parameters (PureCN 1.10.0). 

WARN [2018-10-16 23:34:04] Target intervals were not sorted.
INFO [2018-10-16 23:34:04] 560 on-target bins with low coverage in all samples.
WARN [2018-10-16 23:34:04] You are likely not using the correct baits file!
WARN [2018-10-16 23:34:04] Allosome coverage missing, cannot determine sex.
WARN [2018-10-16 23:34:04] Allosome coverage missing, cannot determine sex.
WARN [2018-10-16 23:34:04] Allosome coverage missing, cannot determine sex.
INFO [2018-10-16 23:34:04] Processing on-target regions...
INFO [2018-10-16 23:34:05] Removing 978 targets with low coverage in normalDB.
INFO [2018-10-16 23:34:05] Removing 11 targets with zero coverage in more than 3% of normalDB.
FATAL [2018-10-16 23:34:08] tumor.coverage.file and normalDB do not align. 

FATAL [2018-10-16 23:34:08]  

FATAL [2018-10-16 23:34:08] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:34:08] parameters (PureCN 1.10.0). 

INFO [2018-10-16 23:34:08] ------------------------------------------------------------
INFO [2018-10-16 23:34:08] PureCN 1.10.0
INFO [2018-10-16 23:34:08] ------------------------------------------------------------
INFO [2018-10-16 23:34:08] Loading coverage files...
INFO [2018-10-16 23:34:09] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2018-10-16 23:34:09] Allosome coverage missing, cannot determine sex.
WARN [2018-10-16 23:34:09] Allosome coverage missing, cannot determine sex.
INFO [2018-10-16 23:34:09] Removing 228 intervals with missing log.ratio.
FATAL [2018-10-16 23:34:09] normalDB incompatible with this PureCN version. Please re-run 

FATAL [2018-10-16 23:34:09] NormalDB.R. 

FATAL [2018-10-16 23:34:09]  

FATAL [2018-10-16 23:34:09] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:34:09] parameters (PureCN 1.10.0). 

FATAL [2018-10-16 23:34:09] normalDB incompatible with this PureCN version. Please re-run 

FATAL [2018-10-16 23:34:09] NormalDB.R. 

FATAL [2018-10-16 23:34:09]  

FATAL [2018-10-16 23:34:09] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:34:09] parameters (PureCN 1.10.0). 

INFO [2018-10-16 23:34:10] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2018-10-16 23:34:11] Initial testing for significant sample cross-contamination: unlikely
INFO [2018-10-16 23:34:12] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2018-10-16 23:34:12] Removing 16 low quality variants with BQ < 25.
INFO [2018-10-16 23:34:12] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2018-10-16 23:34:13] Initial testing for significant sample cross-contamination: unlikely
INFO [2018-10-16 23:34:14] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2018-10-16 23:34:14] Removing 6 blacklisted variants.
INFO [2018-10-16 23:34:14] Removing 16 low quality variants with BQ < 25.
INFO [2018-10-16 23:34:14] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2018-10-16 23:34:16] Initial testing for significant sample cross-contamination: unlikely
INFO [2018-10-16 23:34:16] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2018-10-16 23:34:16] Removing 16 low quality variants with BQ < 25.
WARN [2018-10-16 23:34:16] MuTect stats file lacks contig and position columns.
INFO [2018-10-16 23:34:17] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2018-10-16 23:34:18] Initial testing for significant sample cross-contamination: unlikely
INFO [2018-10-16 23:34:18] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2018-10-16 23:34:18] Removing 16 low quality variants with BQ < 25.
WARN [2018-10-16 23:34:19] MuTect stats file and VCF file do not align perfectly. Will remove 2325 unmatched variants.
WARN [2018-10-16 23:34:19] MuTect stats file lacks failure_reasons column. Keeping all variants listed in stats file.
INFO [2018-10-16 23:34:19] Removing 0 non heterozygous (in matched normal) germline SNPs.
INFO [2018-10-16 23:34:20] Removing 0 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2018-10-16 23:34:20] Removing 0 low quality variants with BQ < 25.
INFO [2018-10-16 23:34:21] Found 11 variants in VCF file.
WARN [2018-10-16 23:34:21] vcf.file has no DB info field for membership in germline databases. Guessing it based on available dbSNP ID.
INFO [2018-10-16 23:34:21] 1 (9.1%) variants annotated as likely germline (DB INFO flag).
INFO [2018-10-16 23:34:27] Found 11 variants in VCF file.
WARN [2018-10-16 23:34:27] vcf.file has no DB info field for membership in germline databases. Guessing it based on available dbSNP ID.
INFO [2018-10-16 23:34:28] 1 (9.1%) variants annotated as likely germline (DB INFO flag).
WARN [2018-10-16 23:34:29] Allosome coverage missing, cannot determine sex.
WARN [2018-10-16 23:34:30] Allosome coverage missing, cannot determine sex.
INFO [2018-10-16 23:34:30] Mean coverages: chrX: 108.58, chrY: 108.58, chr1-22: 104.87.
INFO [2018-10-16 23:34:30] Mean coverages: chrX: 108.58, chrY: 2.17, chr1-22: 104.87.
INFO [2018-10-16 23:34:30] Mean coverages: chrX: 108.58, chrY: 5.17, chr1-22: 104.87.
INFO [2018-10-16 23:34:31] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2018-10-16 23:34:31] No germline variants in VCF.
FATAL [2018-10-16 23:34:31] No solution with id hello 

FATAL [2018-10-16 23:34:31]  

FATAL [2018-10-16 23:34:31] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:34:31] parameters (PureCN 1.10.0). 

FATAL [2018-10-16 23:34:31] No solution with id 10 

FATAL [2018-10-16 23:34:31]  

FATAL [2018-10-16 23:34:31] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:34:31] parameters (PureCN 1.10.0). 

FATAL [2018-10-16 23:34:33] all.data and w have different lengths. 

FATAL [2018-10-16 23:34:33]  

FATAL [2018-10-16 23:34:33] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:34:33] parameters (PureCN 1.10.0). 

WARN [2018-10-16 23:34:33] No mappability scores provided.
WARN [2018-10-16 23:34:33] No reptiming scores provided.
INFO [2018-10-16 23:34:33] Calculating GC-content...
WARN [2018-10-16 23:34:34] No mappability scores provided.
WARN [2018-10-16 23:34:34] No reptiming scores provided.
INFO [2018-10-16 23:34:34] Calculating GC-content...
INFO [2018-10-16 23:34:34] Removing 1 targets overlapping with exclude.
WARN [2018-10-16 23:34:34] No mappability scores provided.
WARN [2018-10-16 23:34:34] No reptiming scores provided.
INFO [2018-10-16 23:34:34] Calculating GC-content...
FATAL [2018-10-16 23:34:34] off.target.padding must be negative. 

FATAL [2018-10-16 23:34:34]  

FATAL [2018-10-16 23:34:34] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:34:34] parameters (PureCN 1.10.0). 

FATAL [2018-10-16 23:34:34] Interval coordinates should start at 1, not at 0 

FATAL [2018-10-16 23:34:34]  

FATAL [2018-10-16 23:34:34] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:34:34] parameters (PureCN 1.10.0). 

FATAL [2018-10-16 23:34:35] No off-target regions after filtering for mappability and 

FATAL [2018-10-16 23:34:35] off.target.padding 

FATAL [2018-10-16 23:34:35]  

FATAL [2018-10-16 23:34:35] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:34:35] parameters (PureCN 1.10.0). 

WARN [2018-10-16 23:34:35] No mappability scores provided.
INFO [2018-10-16 23:34:35] Calculating GC-content...
INFO [2018-10-16 23:34:35] Splitting 1 large targets to an average width of 200.
WARN [2018-10-16 23:34:35] No mappability scores provided.
WARN [2018-10-16 23:34:35] No reptiming scores provided.
INFO [2018-10-16 23:34:35] Calculating GC-content...
WARN [2018-10-16 23:34:36] No mappability scores provided.
WARN [2018-10-16 23:34:36] No reptiming scores provided.
INFO [2018-10-16 23:34:36] Calculating GC-content...
INFO [2018-10-16 23:34:36] Tiling off-target regions to an average width of 200000.
WARN [2018-10-16 23:34:36] No mappability scores provided.
WARN [2018-10-16 23:34:36] No reptiming scores provided.
INFO [2018-10-16 23:34:36] Calculating GC-content...
WARN [2018-10-16 23:34:37] Intervals contain off-target regions. Will not change intervals.
WARN [2018-10-16 23:34:37] No mappability scores provided.
WARN [2018-10-16 23:34:37] No reptiming scores provided.
INFO [2018-10-16 23:34:37] Calculating GC-content...
WARN [2018-10-16 23:34:37] No reptiming scores provided.
INFO [2018-10-16 23:34:37] Calculating GC-content...
WARN [2018-10-16 23:34:37] No reptiming scores provided.
INFO [2018-10-16 23:34:37] Calculating GC-content...
WARN [2018-10-16 23:34:38] 1 intervals without mapping score.
INFO [2018-10-16 23:34:38] Removing 1 targets with low mappability score (<0.50).
WARN [2018-10-16 23:34:38] No reptiming scores provided.
INFO [2018-10-16 23:34:38] Calculating GC-content...
INFO [2018-10-16 23:34:39] Tiling off-target regions to an average width of 200000.
WARN [2018-10-16 23:34:39] No reptiming scores provided.
INFO [2018-10-16 23:34:39] Calculating GC-content...
WARN [2018-10-16 23:34:40] No mappability scores provided.
WARN [2018-10-16 23:34:40] No reptiming scores provided.
INFO [2018-10-16 23:34:40] Calculating GC-content...
WARN [2018-10-16 23:34:40] Chromosome naming style of interval file (NCBI) was different from reference (UCSC).
WARN [2018-10-16 23:34:40] No mappability scores provided.
WARN [2018-10-16 23:34:40] No reptiming scores provided.
INFO [2018-10-16 23:34:40] Calculating GC-content...
FATAL [2018-10-16 23:34:40] Chromosome naming style of interval file unknown, should be UCSC. 

FATAL [2018-10-16 23:34:40]  

FATAL [2018-10-16 23:34:40] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:34:40] parameters (PureCN 1.10.0). 

WARN [2018-10-16 23:34:40] Chromosome naming style of interval file (NCBI) was different from reference (UCSC).
WARN [2018-10-16 23:34:40] Chromosome naming style of mappability file (NCBI) was different from reference (UCSC).
WARN [2018-10-16 23:34:41] No reptiming scores provided.
INFO [2018-10-16 23:34:41] Calculating GC-content...
INFO [2018-10-16 23:34:42] Loading coverage data...
INFO [2018-10-16 23:34:43] Mean target coverages: 71X (tumor) 99X (normal).
INFO [2018-10-16 23:34:43] Mean target coverages: 71X (tumor) 43X (normal).
INFO [2018-10-16 23:34:45] ------------------------------------------------------------
INFO [2018-10-16 23:34:45] PureCN 1.10.0
INFO [2018-10-16 23:34:45] ------------------------------------------------------------
INFO [2018-10-16 23:34:45] Using BiocParallel for parallel optimization.
INFO [2018-10-16 23:34:45] Loading coverage files...
INFO [2018-10-16 23:34:45] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2018-10-16 23:34:45] Allosome coverage missing, cannot determine sex.
WARN [2018-10-16 23:34:45] Allosome coverage missing, cannot determine sex.
INFO [2018-10-16 23:34:45] Removing 228 intervals with missing log.ratio.
INFO [2018-10-16 23:34:45] Removing 22 small (< 5bp) targets.
INFO [2018-10-16 23:34:45] Removing 19 targets with low total coverage in normal (< 150.00 reads).
WARN [2018-10-16 23:34:45] No normalDB provided. Provide one for better results.
INFO [2018-10-16 23:34:45] Removing 233 low coverage (< 15.0000X) targets.
INFO [2018-10-16 23:34:46] Using 9547 intervals (9547 on-target, 0 off-target).
INFO [2018-10-16 23:34:46] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2018-10-16 23:34:46] No interval.file provided. Cannot check if data was GC-normalized. Was it?
INFO [2018-10-16 23:34:46] Sample sex: ?
INFO [2018-10-16 23:34:46] Segmenting data...
INFO [2018-10-16 23:34:46] Target weights found, will use weighted CBS.
INFO [2018-10-16 23:34:46] Loading pre-computed boundaries for DNAcopy...
INFO [2018-10-16 23:34:46] Setting undo.SD parameter to 1.000000.
Setting multi-figure configuration
INFO [2018-10-16 23:34:47] Found 54 segments with median size of 25.38Mb.
INFO [2018-10-16 23:34:47] Mean standard deviation of log-ratios: 0.37
INFO [2018-10-16 23:34:47] 2D-grid search of purity and ploidy...
INFO [2018-10-16 23:34:47] 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 [2018-10-16 23:34:53] Done.
INFO [2018-10-16 23:34:53] ------------------------------------------------------------
INFO [2018-10-16 23:34:53] Reading /tmp/Rtmpw2y1S1/file1ca852b5aa7d.rds...
FATAL [2018-10-16 23:34:53] runAbsoluteCN was run without a VCF file. 

FATAL [2018-10-16 23:34:53]  

FATAL [2018-10-16 23:34:53] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:34:53] parameters (PureCN 1.10.0). 

FATAL [2018-10-16 23:34:53] runAbsoluteCN was run without a VCF file. 

FATAL [2018-10-16 23:34:53]  

FATAL [2018-10-16 23:34:53] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:34:53] parameters (PureCN 1.10.0). 

INFO [2018-10-16 23:34:53] ------------------------------------------------------------
INFO [2018-10-16 23:34:53] PureCN 1.10.0
INFO [2018-10-16 23:34:53] ------------------------------------------------------------
INFO [2018-10-16 23:34:53] Loading coverage files...
FATAL [2018-10-16 23:34:53] Need a normal coverage file if log.ratio and seg.file are not provided. 

FATAL [2018-10-16 23:34:53]  

FATAL [2018-10-16 23:34:53] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:34:53] parameters (PureCN 1.10.0). 

INFO [2018-10-16 23:34:53] ------------------------------------------------------------
INFO [2018-10-16 23:34:53] PureCN 1.10.0
INFO [2018-10-16 23:34:53] ------------------------------------------------------------
FATAL [2018-10-16 23:34:53] min.ploidy or max.ploidy not within expected range. 

FATAL [2018-10-16 23:34:53]  

FATAL [2018-10-16 23:34:53] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:34:53] parameters (PureCN 1.10.0). 

INFO [2018-10-16 23:34:54] ------------------------------------------------------------
INFO [2018-10-16 23:34:54] PureCN 1.10.0
INFO [2018-10-16 23:34:54] ------------------------------------------------------------
FATAL [2018-10-16 23:34:54] min.ploidy or max.ploidy not within expected range. 

FATAL [2018-10-16 23:34:54]  

FATAL [2018-10-16 23:34:54] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:34:54] parameters (PureCN 1.10.0). 

INFO [2018-10-16 23:34:54] ------------------------------------------------------------
INFO [2018-10-16 23:34:54] PureCN 1.10.0
INFO [2018-10-16 23:34:54] ------------------------------------------------------------
INFO [2018-10-16 23:34:54] ------------------------------------------------------------
INFO [2018-10-16 23:34:54] PureCN 1.10.0
INFO [2018-10-16 23:34:54] ------------------------------------------------------------
INFO [2018-10-16 23:34:54] ------------------------------------------------------------
INFO [2018-10-16 23:34:54] PureCN 1.10.0
INFO [2018-10-16 23:34:54] ------------------------------------------------------------
FATAL [2018-10-16 23:34:54] test.num.copy not within expected range. 

FATAL [2018-10-16 23:34:54]  

FATAL [2018-10-16 23:34:54] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:34:54] parameters (PureCN 1.10.0). 

INFO [2018-10-16 23:34:54] ------------------------------------------------------------
INFO [2018-10-16 23:34:54] PureCN 1.10.0
INFO [2018-10-16 23:34:54] ------------------------------------------------------------
WARN [2018-10-16 23:34:54] test.num.copy outside recommended range.
FATAL [2018-10-16 23:34:54] max.non.clonal not within expected range or format. 

FATAL [2018-10-16 23:34:54]  

FATAL [2018-10-16 23:34:54] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:34:54] parameters (PureCN 1.10.0). 

INFO [2018-10-16 23:34:54] ------------------------------------------------------------
INFO [2018-10-16 23:34:54] PureCN 1.10.0
INFO [2018-10-16 23:34:54] ------------------------------------------------------------
WARN [2018-10-16 23:34:54] test.num.copy outside recommended range.
FATAL [2018-10-16 23:34:54] max.non.clonal not within expected range or format. 

FATAL [2018-10-16 23:34:54]  

FATAL [2018-10-16 23:34:54] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:34:54] parameters (PureCN 1.10.0). 

INFO [2018-10-16 23:34:54] ------------------------------------------------------------
INFO [2018-10-16 23:34:54] PureCN 1.10.0
INFO [2018-10-16 23:34:54] ------------------------------------------------------------
FATAL [2018-10-16 23:34:54] test.purity not within expected range. 

FATAL [2018-10-16 23:34:54]  

FATAL [2018-10-16 23:34:54] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:34:54] parameters (PureCN 1.10.0). 

INFO [2018-10-16 23:34:54] ------------------------------------------------------------
INFO [2018-10-16 23:34:54] PureCN 1.10.0
INFO [2018-10-16 23:34:54] ------------------------------------------------------------
INFO [2018-10-16 23:34:54] Loading coverage files...
FATAL [2018-10-16 23:34:55] Tumor and normal are identical. This won't give any meaningful results 

FATAL [2018-10-16 23:34:55] and I'm stopping here. 

FATAL [2018-10-16 23:34:55]  

FATAL [2018-10-16 23:34:55] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:34:55] parameters (PureCN 1.10.0). 

INFO [2018-10-16 23:34:55] ------------------------------------------------------------
INFO [2018-10-16 23:34:55] PureCN 1.10.0
INFO [2018-10-16 23:34:55] ------------------------------------------------------------
INFO [2018-10-16 23:34:55] Loading coverage files...
FATAL [2018-10-16 23:34:55] Length of log.ratio different from tumor coverage. 

FATAL [2018-10-16 23:34:55]  

FATAL [2018-10-16 23:34:55] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:34:55] parameters (PureCN 1.10.0). 

INFO [2018-10-16 23:34:55] ------------------------------------------------------------
INFO [2018-10-16 23:34:55] PureCN 1.10.0
INFO [2018-10-16 23:34:55] ------------------------------------------------------------
FATAL [2018-10-16 23:34:55] prior.purity must have the same length as test.purity. 

FATAL [2018-10-16 23:34:55]  

FATAL [2018-10-16 23:34:55] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:34:55] parameters (PureCN 1.10.0). 

INFO [2018-10-16 23:34:55] ------------------------------------------------------------
INFO [2018-10-16 23:34:55] PureCN 1.10.0
INFO [2018-10-16 23:34:55] ------------------------------------------------------------
FATAL [2018-10-16 23:34:55] min.gof not within expected range or format. 

FATAL [2018-10-16 23:34:55]  

FATAL [2018-10-16 23:34:55] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:34:55] parameters (PureCN 1.10.0). 

INFO [2018-10-16 23:34:55] ------------------------------------------------------------
INFO [2018-10-16 23:34:55] PureCN 1.10.0
INFO [2018-10-16 23:34:55] ------------------------------------------------------------
FATAL [2018-10-16 23:34:55] prior.purity not within expected range or format. 

FATAL [2018-10-16 23:34:55]  

FATAL [2018-10-16 23:34:55] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:34:55] parameters (PureCN 1.10.0). 

INFO [2018-10-16 23:34:55] ------------------------------------------------------------
INFO [2018-10-16 23:34:55] PureCN 1.10.0
INFO [2018-10-16 23:34:55] ------------------------------------------------------------
FATAL [2018-10-16 23:34:55] prior.purity must add to 1. Sum is 1.5 

FATAL [2018-10-16 23:34:55]  

FATAL [2018-10-16 23:34:55] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:34:55] parameters (PureCN 1.10.0). 

INFO [2018-10-16 23:34:55] ------------------------------------------------------------
INFO [2018-10-16 23:34:55] PureCN 1.10.0
INFO [2018-10-16 23:34:55] ------------------------------------------------------------
FATAL [2018-10-16 23:34:55] max.homozygous.loss not within expected range or format. 

FATAL [2018-10-16 23:34:55]  

FATAL [2018-10-16 23:34:55] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:34:55] parameters (PureCN 1.10.0). 

INFO [2018-10-16 23:34:55] ------------------------------------------------------------
INFO [2018-10-16 23:34:55] PureCN 1.10.0
INFO [2018-10-16 23:34:55] ------------------------------------------------------------
FATAL [2018-10-16 23:34:55] prior.K not within expected range or format. 

FATAL [2018-10-16 23:34:55]  

FATAL [2018-10-16 23:34:55] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:34:55] parameters (PureCN 1.10.0). 

INFO [2018-10-16 23:34:55] ------------------------------------------------------------
INFO [2018-10-16 23:34:55] PureCN 1.10.0
INFO [2018-10-16 23:34:55] ------------------------------------------------------------
FATAL [2018-10-16 23:34:55] prior.contamination not within expected range or format. 

FATAL [2018-10-16 23:34:55]  

FATAL [2018-10-16 23:34:55] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:34:55] parameters (PureCN 1.10.0). 

INFO [2018-10-16 23:34:55] ------------------------------------------------------------
INFO [2018-10-16 23:34:55] PureCN 1.10.0
INFO [2018-10-16 23:34:55] ------------------------------------------------------------
FATAL [2018-10-16 23:34:55] Iterations not in the expected range from 10 to 250. 

FATAL [2018-10-16 23:34:55]  

FATAL [2018-10-16 23:34:55] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:34:55] parameters (PureCN 1.10.0). 

INFO [2018-10-16 23:34:55] ------------------------------------------------------------
INFO [2018-10-16 23:34:55] PureCN 1.10.0
INFO [2018-10-16 23:34:55] ------------------------------------------------------------
FATAL [2018-10-16 23:34:55] Iterations not in the expected range from 10 to 250. 

FATAL [2018-10-16 23:34:55]  

FATAL [2018-10-16 23:34:55] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:34:55] parameters (PureCN 1.10.0). 

INFO [2018-10-16 23:34:55] ------------------------------------------------------------
INFO [2018-10-16 23:34:55] PureCN 1.10.0
INFO [2018-10-16 23:34:55] ------------------------------------------------------------
INFO [2018-10-16 23:34:56] ------------------------------------------------------------
INFO [2018-10-16 23:34:56] PureCN 1.10.0
INFO [2018-10-16 23:34:56] ------------------------------------------------------------
INFO [2018-10-16 23:34:56] Loading coverage files...
FATAL [2018-10-16 23:34:56] Interval files in normal and tumor different. 

FATAL [2018-10-16 23:34:56]  

FATAL [2018-10-16 23:34:56] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:34:56] parameters (PureCN 1.10.0). 

INFO [2018-10-16 23:34:56] ------------------------------------------------------------
INFO [2018-10-16 23:34:56] PureCN 1.10.0
INFO [2018-10-16 23:34:56] ------------------------------------------------------------
INFO [2018-10-16 23:34:56] Loading coverage files...
INFO [2018-10-16 23:34:57] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2018-10-16 23:34:57] Allosome coverage missing, cannot determine sex.
WARN [2018-10-16 23:34:57] Allosome coverage missing, cannot determine sex.
INFO [2018-10-16 23:34:57] Removing 228 intervals with missing log.ratio.
INFO [2018-10-16 23:34:57] Removing 22 small (< 5bp) targets.
INFO [2018-10-16 23:34:57] Removing 19 targets with low total coverage in normal (< 150.00 reads).
WARN [2018-10-16 23:34:57] No normalDB provided. Provide one for better results.
INFO [2018-10-16 23:34:57] Removing 233 low coverage (< 15.0000X) targets.
INFO [2018-10-16 23:34:57] Using 9547 intervals (9547 on-target, 0 off-target).
INFO [2018-10-16 23:34:57] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2018-10-16 23:34:57] No interval.file provided. Cannot check if data was GC-normalized. Was it?
INFO [2018-10-16 23:34:57] Loading VCF...
INFO [2018-10-16 23:34:57] Found 2331 variants in VCF file.
INFO [2018-10-16 23:34:58] 2282 (97.9%) variants annotated as likely germline (DB INFO flag).
INFO [2018-10-16 23:34:58] LIB-02240e4 is tumor in VCF file.
INFO [2018-10-16 23:34:58] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2018-10-16 23:34:59] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2018-10-16 23:35:00] Initial testing for significant sample cross-contamination: unlikely
INFO [2018-10-16 23:35:00] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2018-10-16 23:35:00] Removing 16 low quality variants with BQ < 25.
INFO [2018-10-16 23:35:00] Total size of targeted genomic region: 1.63Mb (2.58Mb with 50bp padding).
INFO [2018-10-16 23:35:01] 1.0% of targets contain variants.
INFO [2018-10-16 23:35:01] Removing 2122 variants outside intervals.
INFO [2018-10-16 23:35:01] Found SOMATIC annotation in VCF.
INFO [2018-10-16 23:35:01] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2018-10-16 23:35:01] Found SOMATIC annotation in VCF. Setting mapping bias to 0.973.
INFO [2018-10-16 23:35:01] Sample sex: ?
INFO [2018-10-16 23:35:01] Segmenting data...
INFO [2018-10-16 23:35:01] Loading pre-computed boundaries for DNAcopy...
INFO [2018-10-16 23:35:01] Setting undo.SD parameter to 1.000000.
INFO [2018-10-16 23:35:02] Setting prune.hclust.h parameter to 0.200000.
INFO [2018-10-16 23:35:03] Found 54 segments with median size of 24.88Mb.
INFO [2018-10-16 23:35:03] Using 123 variants.
INFO [2018-10-16 23:35:03] Mean standard deviation of log-ratios: 0.37
INFO [2018-10-16 23:35:03] 2D-grid search of purity and ploidy...
INFO [2018-10-16 23:35:04] Local optima: 0.62/1.9, 0.3/1.9, 0.32/2
INFO [2018-10-16 23:35:04] Testing local optimum 1/3 at purity 0.62 and total ploidy 1.90...
INFO [2018-10-16 23:35:06] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01.
INFO [2018-10-16 23:35:08] Optimized purity: 0.65
INFO [2018-10-16 23:35:08] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2018-10-16 23:35:08] Recalibrating log-ratios...
INFO [2018-10-16 23:35:09] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2018-10-16 23:35:09] Recalibrating log-ratios...
INFO [2018-10-16 23:35:09] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2018-10-16 23:35:10] Recalibrating log-ratios...
INFO [2018-10-16 23:35:10] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2018-10-16 23:35:10] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2018-10-16 23:35:11] Recalibrating log-ratios...
INFO [2018-10-16 23:35:11] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2018-10-16 23:35:11] Recalibrating log-ratios...
INFO [2018-10-16 23:35:11] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2018-10-16 23:35:12] Recalibrating log-ratios...
INFO [2018-10-16 23:35:12] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2018-10-16 23:35:12] Done.
INFO [2018-10-16 23:35:12] ------------------------------------------------------------
INFO [2018-10-16 23:35:13] ------------------------------------------------------------
INFO [2018-10-16 23:35:13] PureCN 1.10.0
INFO [2018-10-16 23:35:13] ------------------------------------------------------------
INFO [2018-10-16 23:35:13] Loading coverage files...
INFO [2018-10-16 23:35:13] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2018-10-16 23:35:13] Allosome coverage missing, cannot determine sex.
WARN [2018-10-16 23:35:13] Allosome coverage missing, cannot determine sex.
INFO [2018-10-16 23:35:13] Removing 228 intervals with missing log.ratio.
INFO [2018-10-16 23:35:13] Removing 22 small (< 5bp) targets.
INFO [2018-10-16 23:35:13] Removing 19 targets with low total coverage in normal (< 150.00 reads).
WARN [2018-10-16 23:35:13] No normalDB provided. Provide one for better results.
INFO [2018-10-16 23:35:13] Removing 233 low coverage (< 15.0000X) targets.
INFO [2018-10-16 23:35:13] Using 9547 intervals (9547 on-target, 0 off-target).
INFO [2018-10-16 23:35:13] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2018-10-16 23:35:13] No interval.file provided. Cannot check if data was GC-normalized. Was it?
INFO [2018-10-16 23:35:14] Loading VCF...
INFO [2018-10-16 23:35:14] Found 2331 variants in VCF file.
WARN [2018-10-16 23:35:14] DB INFO flag contains NAs
INFO [2018-10-16 23:35:14] 2277 (97.7%) variants annotated as likely germline (DB INFO flag).
WARN [2018-10-16 23:35:14] DP FORMAT field contains NAs. Removing 3 variants.
INFO [2018-10-16 23:35:14] LIB-02240e4 is tumor in VCF file.
INFO [2018-10-16 23:35:15] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2018-10-16 23:35:16] Initial testing for significant sample cross-contamination: unlikely
INFO [2018-10-16 23:35:16] Removing 62 variants with AF < 0.030 or AF >= 0.970 or less than 4 supporting reads or depth < 15.
INFO [2018-10-16 23:35:16] Removing 16 low quality variants with BQ < 25.
INFO [2018-10-16 23:35:16] Total size of targeted genomic region: 1.63Mb (2.58Mb with 50bp padding).
INFO [2018-10-16 23:35:17] 1.0% of targets contain variants.
INFO [2018-10-16 23:35:17] Setting somatic prior probabilities for dbSNP hits to 0.000500 or to 0.500000 otherwise.
INFO [2018-10-16 23:35:17] Sample sex: ?
INFO [2018-10-16 23:35:17] Segmenting data...
INFO [2018-10-16 23:35:17] Loading pre-computed boundaries for DNAcopy...
INFO [2018-10-16 23:35:17] Setting undo.SD parameter to 1.000000.
Setting multi-figure configuration
INFO [2018-10-16 23:35:20] Setting prune.hclust.h parameter to 0.200000.
INFO [2018-10-16 23:35:20] Found 59 segments with median size of 17.67Mb.
INFO [2018-10-16 23:35:20] Removing 280 variants outside segments.
INFO [2018-10-16 23:35:20] Using 1970 variants.
INFO [2018-10-16 23:35:20] Mean standard deviation of log-ratios: 0.37
INFO [2018-10-16 23:35:20] 2D-grid search of purity and ploidy...
INFO [2018-10-16 23:35:22] Local optima: 0.62/1.9, 0.3/1.9, 0.32/2
INFO [2018-10-16 23:35:22] Testing local optimum 1/3 at purity 0.62 and total ploidy 1.90...
INFO [2018-10-16 23:35:23] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01.
INFO [2018-10-16 23:35:39] Optimized purity: 0.65
INFO [2018-10-16 23:35:39] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2018-10-16 23:35:39] Recalibrating log-ratios...
INFO [2018-10-16 23:35:39] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2018-10-16 23:35:40] Recalibrating log-ratios...
INFO [2018-10-16 23:35:40] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2018-10-16 23:35:40] Recalibrating log-ratios...
INFO [2018-10-16 23:35:40] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2018-10-16 23:35:41] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2018-10-16 23:35:42] Recalibrating log-ratios...
INFO [2018-10-16 23:35:42] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2018-10-16 23:35:42] Recalibrating log-ratios...
INFO [2018-10-16 23:35:42] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2018-10-16 23:35:43] Recalibrating log-ratios...
INFO [2018-10-16 23:35:43] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2018-10-16 23:35:43] Done.
INFO [2018-10-16 23:35:43] ------------------------------------------------------------
INFO [2018-10-16 23:35:44] ------------------------------------------------------------
INFO [2018-10-16 23:35:44] PureCN 1.10.0
INFO [2018-10-16 23:35:44] ------------------------------------------------------------
INFO [2018-10-16 23:35:44] Loading coverage files...
INFO [2018-10-16 23:35:44] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2018-10-16 23:35:44] Allosome coverage missing, cannot determine sex.
WARN [2018-10-16 23:35:44] Allosome coverage missing, cannot determine sex.
INFO [2018-10-16 23:35:45] No Gene column in interval.file. You won't get gene-level calls.
INFO [2018-10-16 23:35:45] Removing 228 intervals with missing log.ratio.
INFO [2018-10-16 23:35:45] Removing 15 low/high GC targets.
INFO [2018-10-16 23:35:45] Removing 21 small (< 5bp) targets.
INFO [2018-10-16 23:35:45] Removing 19 targets with low total coverage in normal (< 150.00 reads).
WARN [2018-10-16 23:35:45] No normalDB provided. Provide one for better results.
INFO [2018-10-16 23:35:45] Removing 232 low coverage (< 15.0000X) targets.
INFO [2018-10-16 23:35:45] Using 9534 intervals (9534 on-target, 0 off-target).
INFO [2018-10-16 23:35:45] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2018-10-16 23:35:45] AT/GC dropout: 1.03 (tumor), 1.03 (normal). 
INFO [2018-10-16 23:35:45] Loading VCF...
INFO [2018-10-16 23:35:45] Found 2331 variants in VCF file.
INFO [2018-10-16 23:35:46] 2282 (97.9%) variants annotated as likely germline (DB INFO flag).
INFO [2018-10-16 23:35:46] LIB-02240e4 is tumor in VCF file.
INFO [2018-10-16 23:35:48] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2018-10-16 23:35:48] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2018-10-16 23:35:49] Initial testing for significant sample cross-contamination: unlikely
INFO [2018-10-16 23:35:49] Removing 48 variants with AF < 0.030 or AF >= Inf or less than 4 supporting reads or depth < 15.
INFO [2018-10-16 23:35:50] Removing 16 low quality variants with BQ < 25.
INFO [2018-10-16 23:35:50] Total size of targeted genomic region: 1.63Mb (2.58Mb with 50bp padding).
INFO [2018-10-16 23:35:50] 1.0% of targets contain variants.
INFO [2018-10-16 23:35:50] Removing 2122 variants outside intervals.
INFO [2018-10-16 23:35:50] Found SOMATIC annotation in VCF.
INFO [2018-10-16 23:35:50] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2018-10-16 23:35:50] Found SOMATIC annotation in VCF. Setting mapping bias to 0.973.
INFO [2018-10-16 23:35:50] Sample sex: ?
INFO [2018-10-16 23:35:50] Segmenting data...
INFO [2018-10-16 23:35:50] Loading pre-computed boundaries for DNAcopy...
INFO [2018-10-16 23:35:50] Setting undo.SD parameter to 1.000000.
Setting multi-figure configuration
INFO [2018-10-16 23:35:52] Setting prune.hclust.h parameter to 0.200000.
INFO [2018-10-16 23:35:52] Found 54 segments with median size of 24.88Mb.
INFO [2018-10-16 23:35:52] Using 123 variants.
INFO [2018-10-16 23:35:52] Mean standard deviation of log-ratios: 0.37
INFO [2018-10-16 23:35:52] 2D-grid search of purity and ploidy...
INFO [2018-10-16 23:35:52] 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 [2018-10-16 23:35:52] Testing local optimum 1/6 at purity 0.65 and total ploidy 1.90...
INFO [2018-10-16 23:35:54] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01.
INFO [2018-10-16 23:35:56] Optimized purity: 0.65
INFO [2018-10-16 23:35:56] Testing local optimum 2/6 at purity 0.33 and total ploidy 1.90...
INFO [2018-10-16 23:35:56] Recalibrating log-ratios...
INFO [2018-10-16 23:35:56] Testing local optimum 2/6 at purity 0.33 and total ploidy 1.90...
INFO [2018-10-16 23:35:57] Recalibrating log-ratios...
INFO [2018-10-16 23:35:57] Testing local optimum 2/6 at purity 0.33 and total ploidy 1.90...
INFO [2018-10-16 23:35:57] Recalibrating log-ratios...
INFO [2018-10-16 23:35:57] Testing local optimum 2/6 at purity 0.33 and total ploidy 1.90...
INFO [2018-10-16 23:35:58] Testing local optimum 3/6 at purity 0.38 and total ploidy 2.20...
INFO [2018-10-16 23:36:00] Fitting variants for purity 0.40, tumor ploidy 2.34 and contamination 0.01.
INFO [2018-10-16 23:36:01] Optimized purity: 0.40
INFO [2018-10-16 23:36:01] Testing local optimum 4/6 at purity 0.27 and total ploidy 2.10...
INFO [2018-10-16 23:36:02] Recalibrating log-ratios...
INFO [2018-10-16 23:36:02] Testing local optimum 4/6 at purity 0.27 and total ploidy 2.10...
INFO [2018-10-16 23:36:02] Recalibrating log-ratios...
INFO [2018-10-16 23:36:02] Testing local optimum 4/6 at purity 0.27 and total ploidy 2.10...
INFO [2018-10-16 23:36:03] Recalibrating log-ratios...
INFO [2018-10-16 23:36:03] Testing local optimum 4/6 at purity 0.27 and total ploidy 2.10...
INFO [2018-10-16 23:36:03] Testing local optimum 5/6 at purity 0.29 and total ploidy 2.00...
INFO [2018-10-16 23:36:04] Recalibrating log-ratios...
INFO [2018-10-16 23:36:04] Testing local optimum 5/6 at purity 0.29 and total ploidy 2.00...
INFO [2018-10-16 23:36:04] Recalibrating log-ratios...
INFO [2018-10-16 23:36:04] Testing local optimum 5/6 at purity 0.29 and total ploidy 2.00...
INFO [2018-10-16 23:36:05] Recalibrating log-ratios...
INFO [2018-10-16 23:36:05] Testing local optimum 5/6 at purity 0.29 and total ploidy 2.00...
INFO [2018-10-16 23:36:05] Testing local optimum 6/6 at purity 0.78 and total ploidy 2.00...
INFO [2018-10-16 23:36:06] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01.
INFO [2018-10-16 23:36:08] Optimized purity: 0.65
INFO [2018-10-16 23:36:08] Done.
INFO [2018-10-16 23:36:08] ------------------------------------------------------------
FATAL [2018-10-16 23:36:08] This function requires gene-level calls. Please add a column 'Gene' 

FATAL [2018-10-16 23:36:08] containing gene symbols to the interval.file. 

FATAL [2018-10-16 23:36:08]  

FATAL [2018-10-16 23:36:08] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:36:08] parameters (PureCN 1.10.0). 

INFO [2018-10-16 23:36:10] ------------------------------------------------------------
INFO [2018-10-16 23:36:10] PureCN 1.10.0
INFO [2018-10-16 23:36:10] ------------------------------------------------------------
INFO [2018-10-16 23:36:10] Loading coverage files...
INFO [2018-10-16 23:36:11] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2018-10-16 23:36:11] Allosome coverage missing, cannot determine sex.
WARN [2018-10-16 23:36:11] Allosome coverage missing, cannot determine sex.
INFO [2018-10-16 23:36:11] Removing 228 intervals with missing log.ratio.
INFO [2018-10-16 23:36:11] Removing 22 small (< 5bp) targets.
INFO [2018-10-16 23:36:11] Removing 19 targets with low total coverage in normal (< 150.00 reads).
WARN [2018-10-16 23:36:11] No normalDB provided. Provide one for better results.
INFO [2018-10-16 23:36:11] Removing 233 low coverage (< 15.0000X) targets.
INFO [2018-10-16 23:36:11] Using 9547 intervals (9547 on-target, 0 off-target).
INFO [2018-10-16 23:36:11] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2018-10-16 23:36:11] No interval.file provided. Cannot check if data was GC-normalized. Was it?
INFO [2018-10-16 23:36:11] Loading VCF...
INFO [2018-10-16 23:36:11] Found 2331 variants in VCF file.
INFO [2018-10-16 23:36:11] 2282 (97.9%) variants annotated as likely germline (DB INFO flag).
FATAL [2018-10-16 23:36:12] Different chromosome names in coverage and VCF. 

FATAL [2018-10-16 23:36:12]  

FATAL [2018-10-16 23:36:12] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:36:12] parameters (PureCN 1.10.0). 

INFO [2018-10-16 23:36:12] ------------------------------------------------------------
INFO [2018-10-16 23:36:12] PureCN 1.10.0
INFO [2018-10-16 23:36:12] ------------------------------------------------------------
INFO [2018-10-16 23:36:12] Loading coverage files...
INFO [2018-10-16 23:36:12] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2018-10-16 23:36:12] Allosome coverage missing, cannot determine sex.
WARN [2018-10-16 23:36:12] Allosome coverage missing, cannot determine sex.
FATAL [2018-10-16 23:36:12] tumor.coverage.file and interval.file do not align. 

FATAL [2018-10-16 23:36:12]  

FATAL [2018-10-16 23:36:12] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:36:12] parameters (PureCN 1.10.0). 

INFO [2018-10-16 23:36:12] ------------------------------------------------------------
INFO [2018-10-16 23:36:12] PureCN 1.10.0
INFO [2018-10-16 23:36:12] ------------------------------------------------------------
INFO [2018-10-16 23:36:12] Loading coverage files...
INFO [2018-10-16 23:36:13] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2018-10-16 23:36:13] Allosome coverage missing, cannot determine sex.
WARN [2018-10-16 23:36:13] Allosome coverage missing, cannot determine sex.
INFO [2018-10-16 23:36:14] Removing 228 intervals with missing log.ratio.
INFO [2018-10-16 23:36:14] Removing 15 low/high GC targets.
INFO [2018-10-16 23:36:14] Removing 21 small (< 5bp) targets.
INFO [2018-10-16 23:36:14] Removing 19 targets with low total coverage in normal (< 150.00 reads).
WARN [2018-10-16 23:36:14] No normalDB provided. Provide one for better results.
INFO [2018-10-16 23:36:14] Removing 232 low coverage (< 15.0000X) targets.
INFO [2018-10-16 23:36:14] Using 9534 intervals (9534 on-target, 0 off-target).
INFO [2018-10-16 23:36:14] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2018-10-16 23:36:14] AT/GC dropout: 1.03 (tumor), 1.03 (normal). 
INFO [2018-10-16 23:36:14] Loading VCF...
INFO [2018-10-16 23:36:14] Found 2331 variants in VCF file.
INFO [2018-10-16 23:36:14] 2282 (97.9%) variants annotated as likely germline (DB INFO flag).
INFO [2018-10-16 23:36:15] LIB-02240e4 is tumor in VCF file.
INFO [2018-10-16 23:36:15] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2018-10-16 23:36:15] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2018-10-16 23:36:17] Initial testing for significant sample cross-contamination: unlikely
INFO [2018-10-16 23:36:17] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2018-10-16 23:36:17] Removing 16 low quality variants with BQ < 25.
INFO [2018-10-16 23:36:17] Total size of targeted genomic region: 1.63Mb (2.58Mb with 50bp padding).
INFO [2018-10-16 23:36:17] 1.0% of targets contain variants.
INFO [2018-10-16 23:36:18] Removing 2122 variants outside intervals.
INFO [2018-10-16 23:36:18] Found SOMATIC annotation in VCF.
INFO [2018-10-16 23:36:18] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2018-10-16 23:36:18] Found SOMATIC annotation in VCF. Setting mapping bias to 0.973.
INFO [2018-10-16 23:36:18] Sample sex: ?
INFO [2018-10-16 23:36:18] Segmenting data...
INFO [2018-10-16 23:36:18] Loading pre-computed boundaries for DNAcopy...
INFO [2018-10-16 23:36:18] Setting undo.SD parameter to 1.000000.
INFO [2018-10-16 23:36:19] Setting prune.hclust.h parameter to 0.200000.
INFO [2018-10-16 23:36:20] Found 54 segments with median size of 24.88Mb.
INFO [2018-10-16 23:36:20] Using 123 variants.
INFO [2018-10-16 23:36:20] Mean standard deviation of log-ratios: 0.37
INFO [2018-10-16 23:36:20] 2D-grid search of purity and ploidy...
INFO [2018-10-16 23:36:21] Local optima: 0.63/1.9, 0.4/2.1
INFO [2018-10-16 23:36:21] Testing local optimum 1/2 at purity 0.63 and total ploidy 1.90...
INFO [2018-10-16 23:36:23] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01.
INFO [2018-10-16 23:36:25] Optimized purity: 0.65
INFO [2018-10-16 23:36:25] Testing local optimum 2/2 at purity 0.40 and total ploidy 2.10...
INFO [2018-10-16 23:36:25] Recalibrating log-ratios...
INFO [2018-10-16 23:36:25] Testing local optimum 2/2 at purity 0.40 and total ploidy 2.10...
INFO [2018-10-16 23:36:26] Recalibrating log-ratios...
INFO [2018-10-16 23:36:26] Testing local optimum 2/2 at purity 0.40 and total ploidy 2.10...
INFO [2018-10-16 23:36:26] Recalibrating log-ratios...
INFO [2018-10-16 23:36:26] Testing local optimum 2/2 at purity 0.40 and total ploidy 2.10...
INFO [2018-10-16 23:36:26] Done.
INFO [2018-10-16 23:36:26] ------------------------------------------------------------
INFO [2018-10-16 23:36:26] ------------------------------------------------------------
INFO [2018-10-16 23:36:26] PureCN 1.10.0
INFO [2018-10-16 23:36:26] ------------------------------------------------------------
INFO [2018-10-16 23:36:26] Loading coverage files...
INFO [2018-10-16 23:36:27] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2018-10-16 23:36:27] Allosome coverage missing, cannot determine sex.
WARN [2018-10-16 23:36:27] Allosome coverage missing, cannot determine sex.
INFO [2018-10-16 23:36:28] Removing 228 intervals with missing log.ratio.
INFO [2018-10-16 23:36:28] Removing 15 low/high GC targets.
INFO [2018-10-16 23:36:28] Removing 21 small (< 5bp) targets.
INFO [2018-10-16 23:36:28] Removing 19 targets with low total coverage in normal (< 150.00 reads).
WARN [2018-10-16 23:36:28] No normalDB provided. Provide one for better results.
INFO [2018-10-16 23:36:28] Removing 232 low coverage (< 15.0000X) targets.
INFO [2018-10-16 23:36:28] Using 9534 intervals (9534 on-target, 0 off-target).
INFO [2018-10-16 23:36:28] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2018-10-16 23:36:28] AT/GC dropout: 1.03 (tumor), 1.03 (normal). 
INFO [2018-10-16 23:36:28] Loading VCF...
INFO [2018-10-16 23:36:28] Found 2331 variants in VCF file.
INFO [2018-10-16 23:36:28] 2282 (97.9%) variants annotated as likely germline (DB INFO flag).
INFO [2018-10-16 23:36:29] LIB-02240e4 is tumor in VCF file.
INFO [2018-10-16 23:36:29] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2018-10-16 23:36:30] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2018-10-16 23:36:31] Initial testing for significant sample cross-contamination: unlikely
INFO [2018-10-16 23:36:31] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2018-10-16 23:36:31] Removing 16 low quality variants with BQ < 25.
INFO [2018-10-16 23:36:31] Total size of targeted genomic region: 1.63Mb (2.58Mb with 50bp padding).
INFO [2018-10-16 23:36:31] 1.0% of targets contain variants.
INFO [2018-10-16 23:36:31] Removing 2122 variants outside intervals.
INFO [2018-10-16 23:36:32] Found SOMATIC annotation in VCF.
INFO [2018-10-16 23:36:32] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2018-10-16 23:36:32] Found SOMATIC annotation in VCF. Setting mapping bias to 0.973.
INFO [2018-10-16 23:36:32] Sample sex: ?
INFO [2018-10-16 23:36:32] Segmenting data...
INFO [2018-10-16 23:36:32] Loading pre-computed boundaries for DNAcopy...
INFO [2018-10-16 23:36:32] Setting undo.SD parameter to 1.000000.
INFO [2018-10-16 23:36:33] Setting prune.hclust.h parameter to 0.200000.
INFO [2018-10-16 23:36:33] Found 54 segments with median size of 24.88Mb.
INFO [2018-10-16 23:36:33] Using 123 variants.
INFO [2018-10-16 23:36:34] Mean standard deviation of log-ratios: 0.37
INFO [2018-10-16 23:36:34] 2D-grid search of purity and ploidy...
INFO [2018-10-16 23:36:35] Local optima: 0.63/1.9, 0.4/2.1
INFO [2018-10-16 23:36:35] Testing local optimum 1/2 at purity 0.63 and total ploidy 1.90...
INFO [2018-10-16 23:36:37] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01.
INFO [2018-10-16 23:36:39] Optimized purity: 0.65
INFO [2018-10-16 23:36:39] Testing local optimum 2/2 at purity 0.40 and total ploidy 2.10...
INFO [2018-10-16 23:36:39] Recalibrating log-ratios...
INFO [2018-10-16 23:36:39] Testing local optimum 2/2 at purity 0.40 and total ploidy 2.10...
INFO [2018-10-16 23:36:40] Recalibrating log-ratios...
INFO [2018-10-16 23:36:40] Testing local optimum 2/2 at purity 0.40 and total ploidy 2.10...
INFO [2018-10-16 23:36:40] Recalibrating log-ratios...
INFO [2018-10-16 23:36:40] Testing local optimum 2/2 at purity 0.40 and total ploidy 2.10...
INFO [2018-10-16 23:36:40] Done.
INFO [2018-10-16 23:36:40] ------------------------------------------------------------
FATAL [2018-10-16 23:36:41] chr1 not valid chromosome name(s). Valid names are: 

FATAL [2018-10-16 23:36:41] 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22 

FATAL [2018-10-16 23:36:41]  

FATAL [2018-10-16 23:36:41] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:36:41] parameters (PureCN 1.10.0). 

INFO [2018-10-16 23:36:41] ------------------------------------------------------------
INFO [2018-10-16 23:36:41] PureCN 1.10.0
INFO [2018-10-16 23:36:41] ------------------------------------------------------------
INFO [2018-10-16 23:36:41] Loading coverage files...
WARN [2018-10-16 23:36:41] Provided sampleid (Sample2) does not match Sample1 found in segmentation.
WARN [2018-10-16 23:36:41] Allosome coverage missing, cannot determine sex.
WARN [2018-10-16 23:36:41] Allosome coverage missing, cannot determine sex.
INFO [2018-10-16 23:36:41] Removing 10 intervals with missing log.ratio.
INFO [2018-10-16 23:36:41] Using 10039 intervals (10039 on-target, 0 off-target).
INFO [2018-10-16 23:36:41] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2018-10-16 23:36:41] Loading VCF...
INFO [2018-10-16 23:36:42] Found 2331 variants in VCF file.
INFO [2018-10-16 23:36:42] 2282 (97.9%) variants annotated as likely germline (DB INFO flag).
INFO [2018-10-16 23:36:42] LIB-02240e4 is tumor in VCF file.
INFO [2018-10-16 23:36:42] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2018-10-16 23:36:43] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2018-10-16 23:36:44] Initial testing for significant sample cross-contamination: unlikely
INFO [2018-10-16 23:36:44] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2018-10-16 23:36:44] Removing 16 low quality variants with BQ < 25.
INFO [2018-10-16 23:36:44] Total size of targeted genomic region: 1.71Mb (2.70Mb with 50bp padding).
INFO [2018-10-16 23:36:45] 1.0% of targets contain variants.
INFO [2018-10-16 23:36:45] Removing 2120 variants outside intervals.
INFO [2018-10-16 23:36:45] Found SOMATIC annotation in VCF.
INFO [2018-10-16 23:36:45] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2018-10-16 23:36:45] Found SOMATIC annotation in VCF. Setting mapping bias to 0.976.
INFO [2018-10-16 23:36:45] Sample sex: ?
INFO [2018-10-16 23:36:45] Segmenting data...
WARN [2018-10-16 23:36:45] Provided sampleid (Sample2) does not match Sample1 found in segmentation.
INFO [2018-10-16 23:36:45] Loading pre-computed boundaries for DNAcopy...
INFO [2018-10-16 23:36:45] Setting undo.SD parameter to 0.000000.
Setting multi-figure configuration
INFO [2018-10-16 23:36:46] Setting prune.hclust.h parameter to 0.200000.
INFO [2018-10-16 23:36:46] Found 54 segments with median size of 24.88Mb.
INFO [2018-10-16 23:36:46] Using 125 variants.
INFO [2018-10-16 23:36:46] Mean standard deviation of log-ratios: 0.40
INFO [2018-10-16 23:36:46] 2D-grid search of purity and ploidy...
INFO [2018-10-16 23:36:47] Local optima: 0.6/1.9, 0.4/2.1
INFO [2018-10-16 23:36:47] Testing local optimum 1/2 at purity 0.60 and total ploidy 1.90...
INFO [2018-10-16 23:36:48] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01.
INFO [2018-10-16 23:36:50] Optimized purity: 0.65
INFO [2018-10-16 23:36:50] Testing local optimum 2/2 at purity 0.40 and total ploidy 2.10...
INFO [2018-10-16 23:36:51] Recalibrating log-ratios...
INFO [2018-10-16 23:36:51] Testing local optimum 2/2 at purity 0.40 and total ploidy 2.10...
INFO [2018-10-16 23:36:51] Recalibrating log-ratios...
INFO [2018-10-16 23:36:51] Testing local optimum 2/2 at purity 0.40 and total ploidy 2.10...
INFO [2018-10-16 23:36:52] Recalibrating log-ratios...
INFO [2018-10-16 23:36:52] Testing local optimum 2/2 at purity 0.40 and total ploidy 2.10...
INFO [2018-10-16 23:36:52] Done.
INFO [2018-10-16 23:36:52] ------------------------------------------------------------
WARN [2018-10-16 23:36:53] Allosome coverage missing, cannot determine sex.
WARN [2018-10-16 23:36:53] Allosome coverage missing, cannot determine sex.
Setting multi-figure configuration
FATAL [2018-10-16 23:37:05] Segmentation file expected with colnames ID, chrom, loc.start, loc.end, 

FATAL [2018-10-16 23:37:05] num.mark, seg.mean 

FATAL [2018-10-16 23:37:05]  

FATAL [2018-10-16 23:37:05] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:37:05] parameters (PureCN 1.10.0). 

FATAL [2018-10-16 23:37:05] seg.file contains multiple samples and sampleid missing. 

FATAL [2018-10-16 23:37:05]  

FATAL [2018-10-16 23:37:05] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:37:05] parameters (PureCN 1.10.0). 

FATAL [2018-10-16 23:37:05] seg.file contains multiple samples and sampleid does not match any. 

FATAL [2018-10-16 23:37:05]  

FATAL [2018-10-16 23:37:05] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:37:05] parameters (PureCN 1.10.0). 

WARN [2018-10-16 23:37:06] Allosome coverage missing, cannot determine sex.
WARN [2018-10-16 23:37:06] Allosome coverage missing, cannot determine sex.
Setting multi-figure configuration
WARN [2018-10-16 23:37:20] Provided sampleid (example_tumor.txt) does not match Sample1 found in segmentation.
WARN [2018-10-16 23:37:20] Allosome coverage missing, cannot determine sex.
WARN [2018-10-16 23:37:20] Allosome coverage missing, cannot determine sex.
WARN [2018-10-16 23:37:20] Provided sampleid (example_tumor.txt) does not match Sample1 found in segmentation.
WARN [2018-10-16 23:37:25] Allosome coverage missing, cannot determine sex.
WARN [2018-10-16 23:37:25] Allosome coverage missing, cannot determine sex.
WARN [2018-10-16 23:37:27] No normalDB provided. Provide one for better results.
WARN [2018-10-16 23:37:40] Allosome coverage missing, cannot determine sex.
WARN [2018-10-16 23:37:40] Allosome coverage missing, cannot determine sex.
WARN [2018-10-16 23:37:45] Provided sampleid (Sample.1) does not match Sample1 found in segmentation.
Setting multi-figure configuration
WARN [2018-10-16 23:40:26] Allosome coverage missing, cannot determine sex.
WARN [2018-10-16 23:40:26] Allosome coverage missing, cannot determine sex.
WARN [2018-10-16 23:40:26] No normalDB provided. Provide one for better results.
WARN [2018-10-16 23:40:28] Sampleid looks like a normal in VCF, not like a tumor.
WARN [2018-10-16 23:40:42] Allosome coverage missing, cannot determine sex.
WARN [2018-10-16 23:40:42] Allosome coverage missing, cannot determine sex.
WARN [2018-10-16 23:40:42] No normalDB provided. Provide one for better results.
WARN [2018-10-16 23:40:52] Allosome coverage missing, cannot determine sex.
WARN [2018-10-16 23:40:52] Allosome coverage missing, cannot determine sex.
FATAL [2018-10-16 23:40:52] normalDB not a valid normalDB object. Use createNormalDatabase to 

FATAL [2018-10-16 23:40:52] create one. 

FATAL [2018-10-16 23:40:52]  

FATAL [2018-10-16 23:40:52] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:40:52] parameters (PureCN 1.10.0). 

WARN [2018-10-16 23:40:53] You are likely not using the correct baits file!
WARN [2018-10-16 23:40:53] Allosome coverage missing, cannot determine sex.
WARN [2018-10-16 23:40:53] Allosome coverage missing, cannot determine sex.
WARN [2018-10-16 23:40:57] Allosome coverage missing, cannot determine sex.
WARN [2018-10-16 23:40:57] Allosome coverage missing, cannot determine sex.
FATAL [2018-10-16 23:40:57] normalDB appears to be empty. 

FATAL [2018-10-16 23:40:57]  

FATAL [2018-10-16 23:40:57] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:40:57] parameters (PureCN 1.10.0). 

WARN [2018-10-16 23:40:57] Allosome coverage missing, cannot determine sex.
WARN [2018-10-16 23:40:57] Allosome coverage missing, cannot determine sex.
WARN [2018-10-16 23:40:58] Intervals in coverage and interval.file have conflicting on/off-target annotation.
FATAL [2018-10-16 23:41:38] min.normals must be >=2. 

FATAL [2018-10-16 23:41:38]  

FATAL [2018-10-16 23:41:38] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:41:38] parameters (PureCN 1.10.0). 

FATAL [2018-10-16 23:41:57] The normal.panel.vcf.file contains only a single sample. 

FATAL [2018-10-16 23:41:57]  

FATAL [2018-10-16 23:41:57] This is most likely a user error due to invalid input data or 

FATAL [2018-10-16 23:41:57] parameters (PureCN 1.10.0). 

══ testthat results  ═══════════════════════════════════════════════════════════
OK: 293 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
586.981   9.388 589.984

Example timings

PureCN.Rcheck/PureCN-Ex.timings

nameusersystemelapsed
annotateTargets14.166 0.27314.488
bootstrapResults1.4660.0601.528
calculateBamCoverageByInterval0.2670.0100.281
calculateLogRatio0.8600.0720.936
calculateMappingBiasVcf0.7240.0050.733
calculatePowerDetectSomatic1.8650.0261.902
calculateTangentNormal4.0830.0424.135
callAlterations0.1920.0110.202
callAlterationsFromSegmentation2.9550.6092.437
callLOH0.2190.0090.228
callMutationBurden1.6260.0291.662
centromeres0.0030.0030.006
correctCoverageBias2.0940.0202.119
createCurationFile0.4910.0160.514
createNormalDatabase3.3780.0213.405
createTargetWeights2.1630.0172.188
filterTargets33.579 2.00132.528
filterVcfBasic2.2750.0092.291
filterVcfMuTect2.2550.0062.270
filterVcfMuTect22.1650.0062.178
findFocal26.976 1.93625.681
getSexFromCoverage0.2750.0030.279
getSexFromVcf0.6030.0050.609
plotAbs0.4060.0110.423
poolCoverage0.7100.0030.716
predictSomatic0.7750.0090.788
preprocessIntervals0.6380.0040.646
readCoverageFile0.2940.0010.298
readCurationFile0.3220.0120.335
runAbsoluteCN44.933 3.21241.689
segmentationCBS28.538 1.98227.355
segmentationPSCBS48.990 2.11048.022
setMappingBiasVcf0.4980.0030.506
setPriorVcf0.4490.0030.455