Multiple platform build/check report for BioC 3.9 - CHECK report for PureCN on tokay2


R Under development (unstable) (2019-01-10 r75962) -- "Unsuffered Consequences"
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Platform: i386-w64-mingw32/i386 (32-bit)

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> 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, 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

Attaching package: 'IRanges'

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

    windows

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, rowsum

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 [2019-02-09 05:23:07] Attempted adding gene symbols to intervals. Heuristics have been used to pick symbols for overlapping genes.
WARN [2019-02-09 05:23:08] Chromosome naming style of txdb file (UCSC) was different from interval file (NCBI).
WARN [2019-02-09 05:23:12] Attempted adding gene symbols to intervals. Heuristics have been used to pick symbols for overlapping genes.
FATAL [2019-02-09 05:23:15] tumor.coverage.file and interval.file do not align. 

FATAL [2019-02-09 05:23:15]  

FATAL [2019-02-09 05:23:15] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:23:15] parameters (PureCN 1.13.18). 

FATAL [2019-02-09 05:23:15] Need either f or purity and ploidy. 

FATAL [2019-02-09 05:23:15]  

FATAL [2019-02-09 05:23:15] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:23:15] parameters (PureCN 1.13.18). 

FATAL [2019-02-09 05:23:15] f not in expected range. 

FATAL [2019-02-09 05:23:15]  

FATAL [2019-02-09 05:23:15] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:23:15] parameters (PureCN 1.13.18). 

FATAL [2019-02-09 05:23:15] coverage not in expected range (>=2) 

FATAL [2019-02-09 05:23:15]  

FATAL [2019-02-09 05:23:15] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:23:15] parameters (PureCN 1.13.18). 

FATAL [2019-02-09 05:23:15] purity not in expected range. 

FATAL [2019-02-09 05:23:15]  

FATAL [2019-02-09 05:23:15] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:23:15] parameters (PureCN 1.13.18). 

FATAL [2019-02-09 05:23:15] ploidy not in expected range. 

FATAL [2019-02-09 05:23:15]  

FATAL [2019-02-09 05:23:15] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:23:15] parameters (PureCN 1.13.18). 

FATAL [2019-02-09 05:23:15] cell.fraction not in expected range. 

FATAL [2019-02-09 05:23:15]  

FATAL [2019-02-09 05:23:15] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:23:15] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:23:18] ------------------------------------------------------------
INFO [2019-02-09 05:23:18] PureCN 1.13.18
INFO [2019-02-09 05:23:18] ------------------------------------------------------------
INFO [2019-02-09 05:23:18] Loading coverage files...
INFO [2019-02-09 05:23:18] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2019-02-09 05:23:18] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:23:18] Allosome coverage missing, cannot determine sex.
INFO [2019-02-09 05:23:18] Removing 228 intervals with missing log.ratio.
INFO [2019-02-09 05:23:18] Removing 22 small (< 5bp) intervals.
INFO [2019-02-09 05:23:18] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2019-02-09 05:23:18] No normalDB provided. Provide one for better results.
INFO [2019-02-09 05:23:18] Removing 233 low coverage (< 15.0000X) intervals.
INFO [2019-02-09 05:23:18] Using 9547 intervals (9547 on-target, 0 off-target).
INFO [2019-02-09 05:23:18] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2019-02-09 05:23:19] No interval.file provided. Cannot check if data was GC-normalized. Was it?
INFO [2019-02-09 05:23:19] Loading VCF...
INFO [2019-02-09 05:23:19] Found 127 variants in VCF file.
INFO [2019-02-09 05:23:19] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2019-02-09 05:23:19] LIB-02240e4 is tumor in VCF file.
INFO [2019-02-09 05:23:19] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2019-02-09 05:23:19] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2019-02-09 05:23:19] Removing 1 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2019-02-09 05:23:20] Removing 0 low quality variants with BQ < 25.
INFO [2019-02-09 05:23:20] Total size of targeted genomic region: 1.63Mb (2.58Mb with 50bp padding).
INFO [2019-02-09 05:23:20] 1.0% of targets contain variants.
INFO [2019-02-09 05:23:20] Removing 2 variants outside intervals.
INFO [2019-02-09 05:23:20] Found SOMATIC annotation in VCF.
INFO [2019-02-09 05:23:20] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2019-02-09 05:23:20] Found SOMATIC annotation in VCF. Setting mapping bias to 0.973.
INFO [2019-02-09 05:23:20] Excluding 0 novel or poor quality variants from segmentation.
INFO [2019-02-09 05:23:20] Sample sex: ?
INFO [2019-02-09 05:23:20] Segmenting data...
INFO [2019-02-09 05:23:20] Loading pre-computed boundaries for DNAcopy...
INFO [2019-02-09 05:23:20] Setting undo.SD parameter to 1.000000.
INFO [2019-02-09 05:23:22] Setting prune.hclust.h parameter to 0.200000.
INFO [2019-02-09 05:23:22] Found 54 segments with median size of 24.88Mb.
INFO [2019-02-09 05:23:22] Using 123 variants.
INFO [2019-02-09 05:23:22] Mean standard deviation of log-ratios: 0.37
INFO [2019-02-09 05:23:22] 2D-grid search of purity and ploidy...
INFO [2019-02-09 05:23:25] Local optima: 0.63/1.9, 0.4/2.2, 0.5/2
INFO [2019-02-09 05:23:25] Testing local optimum 1/3 at purity 0.63 and total ploidy 1.90...
INFO [2019-02-09 05:23:26] Testing local optimum 2/3 at purity 0.40 and total ploidy 2.20...
INFO [2019-02-09 05:23:28] Testing local optimum 3/3 at purity 0.50 and total ploidy 2.00...
INFO [2019-02-09 05:23:30] Skipping 1 solutions that converged to the same optima.
INFO [2019-02-09 05:23:30] Fitting variants for local optimum 1/3...
INFO [2019-02-09 05:23:30] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01.
INFO [2019-02-09 05:23:31] Optimized purity: 0.65
INFO [2019-02-09 05:23:31] Fitting variants for local optimum 2/3...
INFO [2019-02-09 05:23:31] Fitting variants for purity 0.40, tumor ploidy 2.34 and contamination 0.01.
INFO [2019-02-09 05:23:32] Optimized purity: 0.40
INFO [2019-02-09 05:23:32] Done.
INFO [2019-02-09 05:23:32] ------------------------------------------------------------
FATAL [2019-02-09 05:23:35] exclude not a GRanges object. 

FATAL [2019-02-09 05:23:35]  

FATAL [2019-02-09 05:23:35] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:23:35] parameters (PureCN 1.13.18). 

FATAL [2019-02-09 05:23:35] callable not a GRanges object. 

FATAL [2019-02-09 05:23:35]  

FATAL [2019-02-09 05:23:35] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:23:35] parameters (PureCN 1.13.18). 

WARN [2019-02-09 05:23:48] tumor.coverage.file and interval.file do not align.
FATAL [2019-02-09 05:23:50] No gc_bias column in interval.file. 

FATAL [2019-02-09 05:23:50]  

FATAL [2019-02-09 05:23:50] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:23:50] parameters (PureCN 1.13.18). 

FATAL [2019-02-09 05:23:51] Provided coverage is zero, most likely due to a corrupt BAM file. 

FATAL [2019-02-09 05:23:51]  

FATAL [2019-02-09 05:23:51] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:23:51] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:23:58] Reading C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\RtmpglNOT1\file24bc7b3a733c.rds...
INFO [2019-02-09 05:23:58] Reading C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\RtmpglNOT1\file24bc7b3a733c.rds...
INFO [2019-02-09 05:23:58] Reading C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\RtmpglNOT1\file24bc7b3a733c.rds...
INFO [2019-02-09 05:23:58] Reading C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\RtmpglNOT1\file24bc7b3a733c.rds...
INFO [2019-02-09 05:23:59] Reading C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\RtmpglNOT1\file24bc7b3a733c.rds...
INFO [2019-02-09 05:23:59] Reading C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\RtmpglNOT1\file24bc7b3a733c.rds...
FATAL [2019-02-09 05:23:59] Purity or Ploidy not numeric or in expected range. 

FATAL [2019-02-09 05:23:59]  

FATAL [2019-02-09 05:23:59] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:23:59] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:23:59] Reading C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\RtmpglNOT1\file24bc7b3a733c.rds...
INFO [2019-02-09 05:23:59] Reading C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\RtmpglNOT1\file24bc7b3a733c.rds...
FATAL [2019-02-09 05:23:59] 'Failed' column in 

FATAL [2019-02-09 05:23:59] C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\RtmpglNOT1\file24bc7b3a733c.csv 

FATAL [2019-02-09 05:23:59] not logical(1). 

FATAL [2019-02-09 05:23:59]  

FATAL [2019-02-09 05:23:59] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:23:59] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:24:00] 576 on-target bins with low coverage in all samples.
WARN [2019-02-09 05:24:00] You are likely not using the correct baits file!
WARN [2019-02-09 05:24:00] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:24:00] Allosome coverage missing, cannot determine sex.
INFO [2019-02-09 05:24:00] Processing on-target regions...
INFO [2019-02-09 05:24:01] Removing 930 intervals with low coverage in normalDB.
INFO [2019-02-09 05:24:01] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2019-02-09 05:24:03] 576 on-target bins with low coverage in all samples.
WARN [2019-02-09 05:24:03] You are likely not using the correct baits file!
WARN [2019-02-09 05:24:03] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:24:03] Allosome coverage missing, cannot determine sex.
INFO [2019-02-09 05:24:03] Processing on-target regions...
INFO [2019-02-09 05:24:04] Removing 930 intervals with low coverage in normalDB.
INFO [2019-02-09 05:24:04] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2019-02-09 05:24:05] 576 on-target bins with low coverage in all samples.
WARN [2019-02-09 05:24:05] You are likely not using the correct baits file!
WARN [2019-02-09 05:24:05] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:24:05] Allosome coverage missing, cannot determine sex.
INFO [2019-02-09 05:24:05] Processing on-target regions...
INFO [2019-02-09 05:24:06] Removing 930 intervals with low coverage in normalDB.
INFO [2019-02-09 05:24:06] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2019-02-09 05:24:07] 576 on-target bins with low coverage in all samples.
WARN [2019-02-09 05:24:07] You are likely not using the correct baits file!
WARN [2019-02-09 05:24:08] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:24:08] Allosome coverage missing, cannot determine sex.
FATAL [2019-02-09 05:24:08] Length of normal.coverage.files and sex different 

FATAL [2019-02-09 05:24:08]  

FATAL [2019-02-09 05:24:08] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:24:08] parameters (PureCN 1.13.18). 

WARN [2019-02-09 05:24:11] Target intervals were not sorted.
INFO [2019-02-09 05:24:11] 560 on-target bins with low coverage in all samples.
WARN [2019-02-09 05:24:11] You are likely not using the correct baits file!
WARN [2019-02-09 05:24:11] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:24:11] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:24:11] Allosome coverage missing, cannot determine sex.
INFO [2019-02-09 05:24:11] Processing on-target regions...
INFO [2019-02-09 05:24:12] Removing 978 intervals with low coverage in normalDB.
INFO [2019-02-09 05:24:12] Removing 11 intervals with zero coverage in more than 3% of normalDB.
FATAL [2019-02-09 05:24:13] tumor.coverage.file and normalDB do not align. 

FATAL [2019-02-09 05:24:13]  

FATAL [2019-02-09 05:24:13] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:24:13] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:24:13] ------------------------------------------------------------
INFO [2019-02-09 05:24:13] PureCN 1.13.18
INFO [2019-02-09 05:24:13] ------------------------------------------------------------
INFO [2019-02-09 05:24:13] Loading coverage files...
INFO [2019-02-09 05:24:13] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2019-02-09 05:24:13] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:24:13] Allosome coverage missing, cannot determine sex.
INFO [2019-02-09 05:24:13] Removing 228 intervals with missing log.ratio.
FATAL [2019-02-09 05:24:13] normalDB incompatible with this PureCN version. Please re-run 

FATAL [2019-02-09 05:24:13] NormalDB.R. 

FATAL [2019-02-09 05:24:13]  

FATAL [2019-02-09 05:24:13] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:24:13] parameters (PureCN 1.13.18). 

FATAL [2019-02-09 05:24:14] normalDB incompatible with this PureCN version. Please re-run 

FATAL [2019-02-09 05:24:14] NormalDB.R. 

FATAL [2019-02-09 05:24:14]  

FATAL [2019-02-09 05:24:14] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:24:14] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:24:15] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2019-02-09 05:24:15] Initial testing for significant sample cross-contamination: unlikely
INFO [2019-02-09 05:24:16] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2019-02-09 05:24:16] Removing 16 low quality variants with BQ < 25.
INFO [2019-02-09 05:24:16] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2019-02-09 05:24:16] Initial testing for significant sample cross-contamination: unlikely
INFO [2019-02-09 05:24:16] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2019-02-09 05:24:17] Removing 6 blacklisted variants.
INFO [2019-02-09 05:24:17] Removing 16 low quality variants with BQ < 25.
INFO [2019-02-09 05:24:17] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2019-02-09 05:24:17] Initial testing for significant sample cross-contamination: unlikely
INFO [2019-02-09 05:24:17] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2019-02-09 05:24:17] Removing 16 low quality variants with BQ < 25.
WARN [2019-02-09 05:24:18] MuTect stats file lacks contig and position columns.
INFO [2019-02-09 05:24:18] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2019-02-09 05:24:18] Initial testing for significant sample cross-contamination: unlikely
INFO [2019-02-09 05:24:18] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2019-02-09 05:24:18] Removing 16 low quality variants with BQ < 25.
WARN [2019-02-09 05:24:18] MuTect stats file and VCF file do not align perfectly. Will remove 2325 unmatched variants.
WARN [2019-02-09 05:24:18] MuTect stats file lacks failure_reasons column. Keeping all variants listed in stats file.
INFO [2019-02-09 05:24:19] Removing 0 non heterozygous (in matched normal) germline SNPs.
INFO [2019-02-09 05:24:19] Removing 0 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2019-02-09 05:24:19] Removing 0 low quality variants with BQ < 25.
INFO [2019-02-09 05:24:19] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2019-02-09 05:24:19] Initial testing for significant sample cross-contamination: unlikely
INFO [2019-02-09 05:24:20] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2019-02-09 05:24:20] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2019-02-09 05:24:20] Initial testing for significant sample cross-contamination: unlikely
INFO [2019-02-09 05:24:20] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2019-02-09 05:24:21] Found 11 variants in VCF file.
WARN [2019-02-09 05:24:21] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead.
INFO [2019-02-09 05:24:21] 1 (9.1%) variants annotated as likely germline (DB INFO flag).
INFO [2019-02-09 05:24:24] Found 11 variants in VCF file.
WARN [2019-02-09 05:24:24] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead.
INFO [2019-02-09 05:24:25] 1 (9.1%) variants annotated as likely germline (DB INFO flag).
INFO [2019-02-09 05:24:25] Found 11 variants in VCF file.
WARN [2019-02-09 05:24:25] vcf.file has no DB or POP_AF info field for membership in germline databases. Guessing it based on available dbSNP ID.
INFO [2019-02-09 05:24:26] 1 (9.1%) variants annotated as likely germline (DB INFO flag).
INFO [2019-02-09 05:24:27] Found 1000 variants in VCF file.
INFO [2019-02-09 05:24:27] Removing 2 triallelic sites.
WARN [2019-02-09 05:24:27] DP FORMAT field contains NAs. Removing 44 variants.
INFO [2019-02-09 05:24:27] 954 (100.0%) variants annotated as likely germline (DB INFO flag).
WARN [2019-02-09 05:24:28] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:24:28] Allosome coverage missing, cannot determine sex.
INFO [2019-02-09 05:24:29] Mean coverages: chrX: 108.58, chrY: 108.58, chr1-22: 104.87.
INFO [2019-02-09 05:24:29] Mean coverages: chrX: 108.58, chrY: 2.17, chr1-22: 104.87.
INFO [2019-02-09 05:24:29] Mean coverages: chrX: 108.58, chrY: 5.17, chr1-22: 104.87.
INFO [2019-02-09 05:24:29] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2019-02-09 05:24:29] No germline variants in VCF.
FATAL [2019-02-09 05:24:29] No solution with id hello 

FATAL [2019-02-09 05:24:29]  

FATAL [2019-02-09 05:24:29] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:24:29] parameters (PureCN 1.13.18). 

FATAL [2019-02-09 05:24:29] No solution with id 10 

FATAL [2019-02-09 05:24:29]  

FATAL [2019-02-09 05:24:29] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:24:29] parameters (PureCN 1.13.18). 

FATAL [2019-02-09 05:24:30] all.data and w have different lengths. 

FATAL [2019-02-09 05:24:30]  

FATAL [2019-02-09 05:24:30] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:24:30] parameters (PureCN 1.13.18). 

WARN [2019-02-09 05:24:31] No mappability scores provided.
WARN [2019-02-09 05:24:31] No reptiming scores provided.
INFO [2019-02-09 05:24:31] Calculating GC-content...
WARN [2019-02-09 05:24:31] No mappability scores provided.
WARN [2019-02-09 05:24:31] No reptiming scores provided.
INFO [2019-02-09 05:24:31] Calculating GC-content...
INFO [2019-02-09 05:24:31] Removing 1 targets overlapping with exclude.
WARN [2019-02-09 05:24:31] No mappability scores provided.
WARN [2019-02-09 05:24:31] No reptiming scores provided.
INFO [2019-02-09 05:24:31] Calculating GC-content...
FATAL [2019-02-09 05:24:31] off.target.padding must be negative. 

FATAL [2019-02-09 05:24:31]  

FATAL [2019-02-09 05:24:31] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:24:31] parameters (PureCN 1.13.18). 

FATAL [2019-02-09 05:24:31] Interval coordinates should start at 1, not at 0 

FATAL [2019-02-09 05:24:31]  

FATAL [2019-02-09 05:24:31] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:24:31] parameters (PureCN 1.13.18). 

FATAL [2019-02-09 05:24:32] No off-target regions after filtering for mappability and 

FATAL [2019-02-09 05:24:32] off.target.padding 

FATAL [2019-02-09 05:24:32]  

FATAL [2019-02-09 05:24:32] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:24:32] parameters (PureCN 1.13.18). 

WARN [2019-02-09 05:24:32] No mappability scores provided.
INFO [2019-02-09 05:24:32] Calculating GC-content...
INFO [2019-02-09 05:24:32] Averaging reptiming into bins of size 200...
WARN [2019-02-09 05:24:32] No mappability scores provided.
INFO [2019-02-09 05:24:32] Calculating GC-content...
INFO [2019-02-09 05:24:32] Splitting 1 large targets to an average width of 200.
WARN [2019-02-09 05:24:32] No mappability scores provided.
WARN [2019-02-09 05:24:32] No reptiming scores provided.
INFO [2019-02-09 05:24:32] Calculating GC-content...
WARN [2019-02-09 05:24:32] No mappability scores provided.
WARN [2019-02-09 05:24:32] No reptiming scores provided.
INFO [2019-02-09 05:24:32] Calculating GC-content...
INFO [2019-02-09 05:24:33] Tiling off-target regions to an average width of 200000.
WARN [2019-02-09 05:24:33] No mappability scores provided.
WARN [2019-02-09 05:24:33] No reptiming scores provided.
INFO [2019-02-09 05:24:33] Calculating GC-content...
WARN [2019-02-09 05:24:33] Intervals contain off-target regions. Will not change intervals.
WARN [2019-02-09 05:24:33] No mappability scores provided.
WARN [2019-02-09 05:24:33] No reptiming scores provided.
INFO [2019-02-09 05:24:33] Calculating GC-content...
WARN [2019-02-09 05:24:33] No reptiming scores provided.
INFO [2019-02-09 05:24:33] Calculating GC-content...
WARN [2019-02-09 05:24:34] 1 intervals without mappability score (1 on-target).
INFO [2019-02-09 05:24:34] Removing 1 intervals with low mappability score (<0.50).
WARN [2019-02-09 05:24:34] No reptiming scores provided.
INFO [2019-02-09 05:24:34] Calculating GC-content...
INFO [2019-02-09 05:24:34] Tiling off-target regions to an average width of 200000.
WARN [2019-02-09 05:24:34] No reptiming scores provided.
INFO [2019-02-09 05:24:34] Calculating GC-content...
WARN [2019-02-09 05:24:35] No mappability scores provided.
WARN [2019-02-09 05:24:35] No reptiming scores provided.
INFO [2019-02-09 05:24:35] Calculating GC-content...
WARN [2019-02-09 05:24:35] Chromosome naming style of interval file (NCBI) was different from reference (UCSC).
WARN [2019-02-09 05:24:35] No mappability scores provided.
WARN [2019-02-09 05:24:35] No reptiming scores provided.
INFO [2019-02-09 05:24:35] Calculating GC-content...
FATAL [2019-02-09 05:24:35] Chromosome naming style of interval file unknown, should be UCSC. 

FATAL [2019-02-09 05:24:35]  

FATAL [2019-02-09 05:24:35] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:24:35] parameters (PureCN 1.13.18). 

WARN [2019-02-09 05:24:35] Chromosome naming style of interval file (NCBI) was different from reference (UCSC).
WARN [2019-02-09 05:24:35] Chromosome naming style of mappability file (NCBI) was different from reference (UCSC).
WARN [2019-02-09 05:24:35] No reptiming scores provided.
INFO [2019-02-09 05:24:35] Calculating GC-content...
WARN [2019-02-09 05:24:35] Found small target regions (< 60bp). Will resize them.
WARN [2019-02-09 05:24:35] No mappability scores provided.
WARN [2019-02-09 05:24:35] No reptiming scores provided.
INFO [2019-02-09 05:24:35] Calculating GC-content...
WARN [2019-02-09 05:24:36] Found small target regions (< 60bp). Will drop them.
WARN [2019-02-09 05:24:36] No mappability scores provided.
WARN [2019-02-09 05:24:36] No reptiming scores provided.
INFO [2019-02-09 05:24:36] Calculating GC-content...
WARN [2019-02-09 05:24:36] Found small target regions (< 200bp). Will resize them.
WARN [2019-02-09 05:24:36] No mappability scores provided.
WARN [2019-02-09 05:24:36] No reptiming scores provided.
INFO [2019-02-09 05:24:36] Calculating GC-content...
INFO [2019-02-09 05:24:36] 576 on-target bins with low coverage in all samples.
WARN [2019-02-09 05:24:36] You are likely not using the correct baits file!
WARN [2019-02-09 05:24:36] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:24:36] Allosome coverage missing, cannot determine sex.
INFO [2019-02-09 05:24:36] Processing on-target regions...
INFO [2019-02-09 05:24:37] Removing 930 intervals with low coverage in normalDB.
INFO [2019-02-09 05:24:37] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2019-02-09 05:24:38] Loading coverage data...
INFO [2019-02-09 05:24:38] Mean target coverages: 71X (tumor) 99X (normal).
INFO [2019-02-09 05:24:38] Mean target coverages: 71X (tumor) 43X (normal).
INFO [2019-02-09 05:24:40] Interval weights found, but currently not supported by copynumber. Will simply exclude intervals with low weight.
multipcf finished for chromosome arm 1p 
multipcf finished for chromosome arm 1q 
multipcf finished for chromosome arm 2p 
multipcf finished for chromosome arm 2q 
multipcf finished for chromosome arm 3p 
multipcf finished for chromosome arm 3q 
multipcf finished for chromosome arm 4p 
multipcf finished for chromosome arm 4q 
multipcf finished for chromosome arm 5p 
multipcf finished for chromosome arm 5q 
multipcf finished for chromosome arm 6p 
multipcf finished for chromosome arm 6q 
multipcf finished for chromosome arm 7p 
multipcf finished for chromosome arm 7q 
multipcf finished for chromosome arm 8p 
multipcf finished for chromosome arm 8q 
multipcf finished for chromosome arm 9p 
multipcf finished for chromosome arm 9q 
multipcf finished for chromosome arm 10p 
multipcf finished for chromosome arm 10q 
multipcf finished for chromosome arm 11p 
multipcf finished for chromosome arm 11q 
multipcf finished for chromosome arm 12p 
multipcf finished for chromosome arm 12q 
multipcf finished for chromosome arm 13q 
multipcf finished for chromosome arm 14q 
multipcf finished for chromosome arm 15q 
multipcf finished for chromosome arm 16p 
multipcf finished for chromosome arm 16q 
multipcf finished for chromosome arm 17p 
multipcf finished for chromosome arm 17q 
multipcf finished for chromosome arm 18p 
multipcf finished for chromosome arm 18q 
multipcf finished for chromosome arm 19p 
multipcf finished for chromosome arm 19q 
multipcf finished for chromosome arm 20p 
multipcf finished for chromosome arm 20q 
multipcf finished for chromosome arm 21q 
multipcf finished for chromosome arm 22q 
INFO [2019-02-09 05:24:42] ------------------------------------------------------------
INFO [2019-02-09 05:24:42] PureCN 1.13.18
INFO [2019-02-09 05:24:42] ------------------------------------------------------------
INFO [2019-02-09 05:24:42] Loading coverage files...
INFO [2019-02-09 05:24:43] seg.file and normal.coverage.file provided. Using both.
INFO [2019-02-09 05:24:43] Mean target coverages: 112X (tumor) 105X (normal).
WARN [2019-02-09 05:24:43] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:24:43] Allosome coverage missing, cannot determine sex.
INFO [2019-02-09 05:24:43] Removing 199 intervals with missing log.ratio.
INFO [2019-02-09 05:24:43] Using 9850 intervals (9850 on-target, 0 off-target).
INFO [2019-02-09 05:24:43] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2019-02-09 05:24:43] Loading VCF...
INFO [2019-02-09 05:24:43] Found 127 variants in VCF file.
INFO [2019-02-09 05:24:43] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2019-02-09 05:24:43] LIB-02240e4 is tumor in VCF file.
INFO [2019-02-09 05:24:43] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2019-02-09 05:24:43] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2019-02-09 05:24:44] Removing 1 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2019-02-09 05:24:44] Removing 0 low quality variants with BQ < 25.
INFO [2019-02-09 05:24:44] Total size of targeted genomic region: 1.68Mb (2.66Mb with 50bp padding).
INFO [2019-02-09 05:24:44] 1.0% of targets contain variants.
INFO [2019-02-09 05:24:44] Removing 0 variants outside intervals.
INFO [2019-02-09 05:24:44] Found SOMATIC annotation in VCF.
INFO [2019-02-09 05:24:44] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2019-02-09 05:24:44] Found SOMATIC annotation in VCF. Setting mapping bias to 0.976.
INFO [2019-02-09 05:24:44] Excluding 0 novel or poor quality variants from segmentation.
INFO [2019-02-09 05:24:44] Sample sex: ?
INFO [2019-02-09 05:24:44] Segmenting data...
INFO [2019-02-09 05:24:44] Loaded provided segmentation file file24bc5e0f31ca.seg.
INFO [2019-02-09 05:24:44] Setting prune.hclust.h parameter to 0.200000.
INFO [2019-02-09 05:24:44] Found 60 segments with median size of 29.97Mb.
INFO [2019-02-09 05:24:44] Using 125 variants.
INFO [2019-02-09 05:24:44] Mean standard deviation of log-ratios: 0.34
INFO [2019-02-09 05:24:44] 2D-grid search of purity and ploidy...
INFO [2019-02-09 05:24:45] Local optima: 0.6/1.9, 0.4/2.1
INFO [2019-02-09 05:24:45] Testing local optimum 1/2 at purity 0.60 and total ploidy 1.90...
INFO [2019-02-09 05:24:47] Testing local optimum 2/2 at purity 0.40 and total ploidy 2.10...
INFO [2019-02-09 05:24:47] Recalibrating log-ratios...
INFO [2019-02-09 05:24:47] Testing local optimum 2/2 at purity 0.40 and total ploidy 2.10...
INFO [2019-02-09 05:24:48] Recalibrating log-ratios...
INFO [2019-02-09 05:24:48] Testing local optimum 2/2 at purity 0.40 and total ploidy 2.10...
INFO [2019-02-09 05:24:48] Recalibrating log-ratios...
INFO [2019-02-09 05:24:48] Testing local optimum 2/2 at purity 0.40 and total ploidy 2.10...
INFO [2019-02-09 05:24:48] Skipping 1 solutions exceeding max.non.clonal (0.20).
INFO [2019-02-09 05:24:48] Fitting variants for local optimum 1/2...
INFO [2019-02-09 05:24:48] Fitting variants for purity 0.60, tumor ploidy 1.76 and contamination 0.01.
INFO [2019-02-09 05:24:49] Fitting variants for purity 0.40, tumor ploidy 1.76 and contamination 0.01.
INFO [2019-02-09 05:24:50] Fitting variants for purity 0.45, tumor ploidy 1.76 and contamination 0.01.
INFO [2019-02-09 05:24:51] Fitting variants for purity 0.50, tumor ploidy 1.76 and contamination 0.01.
INFO [2019-02-09 05:24:52] Fitting variants for purity 0.55, tumor ploidy 1.76 and contamination 0.01.
INFO [2019-02-09 05:24:53] Fitting variants for purity 0.65, tumor ploidy 1.76 and contamination 0.01.
INFO [2019-02-09 05:24:54] Fitting variants for purity 0.70, tumor ploidy 1.76 and contamination 0.01.
INFO [2019-02-09 05:24:55] Optimized purity: 0.65
INFO [2019-02-09 05:24:55] Done.
INFO [2019-02-09 05:24:55] ------------------------------------------------------------
INFO [2019-02-09 05:24:56] Loading coverage data...
INFO [2019-02-09 05:24:57] Mean target coverages: 71X (tumor) 99X (normal).
INFO [2019-02-09 05:24:57] Mean target coverages: 71X (tumor) 43X (normal).
INFO [2019-02-09 05:24:57] ------------------------------------------------------------
INFO [2019-02-09 05:24:57] PureCN 1.13.18
INFO [2019-02-09 05:24:57] ------------------------------------------------------------
INFO [2019-02-09 05:24:58] Using BiocParallel for parallel optimization.
INFO [2019-02-09 05:24:58] Loading coverage files...
INFO [2019-02-09 05:24:58] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2019-02-09 05:24:58] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:24:58] Allosome coverage missing, cannot determine sex.
INFO [2019-02-09 05:24:58] Removing 228 intervals with missing log.ratio.
INFO [2019-02-09 05:24:58] Removing 22 small (< 5bp) intervals.
INFO [2019-02-09 05:24:58] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2019-02-09 05:24:58] No normalDB provided. Provide one for better results.
INFO [2019-02-09 05:24:58] Removing 233 low coverage (< 15.0000X) intervals.
INFO [2019-02-09 05:24:58] Using 9547 intervals (9547 on-target, 0 off-target).
INFO [2019-02-09 05:24:58] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2019-02-09 05:24:58] No interval.file provided. Cannot check if data was GC-normalized. Was it?
INFO [2019-02-09 05:24:58] Sample sex: ?
INFO [2019-02-09 05:24:58] Segmenting data...
INFO [2019-02-09 05:24:58] Interval weights found, will use weighted CBS.
INFO [2019-02-09 05:24:58] Loading pre-computed boundaries for DNAcopy...
INFO [2019-02-09 05:24:58] Setting undo.SD parameter to 1.000000.
Setting multi-figure configuration
INFO [2019-02-09 05:24:59] Found 54 segments with median size of 25.38Mb.
INFO [2019-02-09 05:24:59] Mean standard deviation of log-ratios: 0.37
INFO [2019-02-09 05:24:59] 2D-grid search of purity and ploidy...
INFO [2019-02-09 05:24:59] 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 [2019-02-09 05:25:54] Skipping 3 solutions that converged to the same optima.
INFO [2019-02-09 05:25:54] Skipping 1 solutions exceeding max.non.clonal (0.20).
INFO [2019-02-09 05:25:54] Done.
INFO [2019-02-09 05:25:54] ------------------------------------------------------------
INFO [2019-02-09 05:25:54] Reading C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\RtmpglNOT1\file24bc763a5de2.rds...
FATAL [2019-02-09 05:25:54] runAbsoluteCN was run without a VCF file. 

FATAL [2019-02-09 05:25:54]  

FATAL [2019-02-09 05:25:54] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:25:54] parameters (PureCN 1.13.18). 

FATAL [2019-02-09 05:25:54] runAbsoluteCN was run without a VCF file. 

FATAL [2019-02-09 05:25:54]  

FATAL [2019-02-09 05:25:54] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:25:54] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:25:54] ------------------------------------------------------------
INFO [2019-02-09 05:25:54] PureCN 1.13.18
INFO [2019-02-09 05:25:54] ------------------------------------------------------------
INFO [2019-02-09 05:25:54] Loading coverage files...
FATAL [2019-02-09 05:25:54] Need a normal coverage file if log.ratio and seg.file are not provided. 

FATAL [2019-02-09 05:25:54]  

FATAL [2019-02-09 05:25:54] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:25:54] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:25:54] ------------------------------------------------------------
INFO [2019-02-09 05:25:54] PureCN 1.13.18
INFO [2019-02-09 05:25:54] ------------------------------------------------------------
FATAL [2019-02-09 05:25:54] min.ploidy or max.ploidy not within expected range. 

FATAL [2019-02-09 05:25:54]  

FATAL [2019-02-09 05:25:54] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:25:54] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:25:54] ------------------------------------------------------------
INFO [2019-02-09 05:25:54] PureCN 1.13.18
INFO [2019-02-09 05:25:54] ------------------------------------------------------------
FATAL [2019-02-09 05:25:54] min.ploidy or max.ploidy not within expected range. 

FATAL [2019-02-09 05:25:54]  

FATAL [2019-02-09 05:25:54] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:25:54] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:25:54] ------------------------------------------------------------
INFO [2019-02-09 05:25:54] PureCN 1.13.18
INFO [2019-02-09 05:25:54] ------------------------------------------------------------
INFO [2019-02-09 05:25:54] ------------------------------------------------------------
INFO [2019-02-09 05:25:54] PureCN 1.13.18
INFO [2019-02-09 05:25:54] ------------------------------------------------------------
INFO [2019-02-09 05:25:54] ------------------------------------------------------------
INFO [2019-02-09 05:25:54] PureCN 1.13.18
INFO [2019-02-09 05:25:54] ------------------------------------------------------------
FATAL [2019-02-09 05:25:54] test.num.copy not within expected range. 

FATAL [2019-02-09 05:25:54]  

FATAL [2019-02-09 05:25:54] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:25:54] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:25:54] ------------------------------------------------------------
INFO [2019-02-09 05:25:54] PureCN 1.13.18
INFO [2019-02-09 05:25:54] ------------------------------------------------------------
WARN [2019-02-09 05:25:54] test.num.copy outside recommended range.
FATAL [2019-02-09 05:25:54] max.non.clonal not within expected range or format. 

FATAL [2019-02-09 05:25:54]  

FATAL [2019-02-09 05:25:54] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:25:54] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:25:54] ------------------------------------------------------------
INFO [2019-02-09 05:25:54] PureCN 1.13.18
INFO [2019-02-09 05:25:54] ------------------------------------------------------------
WARN [2019-02-09 05:25:54] test.num.copy outside recommended range.
FATAL [2019-02-09 05:25:54] max.non.clonal not within expected range or format. 

FATAL [2019-02-09 05:25:54]  

FATAL [2019-02-09 05:25:54] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:25:54] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:25:54] ------------------------------------------------------------
INFO [2019-02-09 05:25:54] PureCN 1.13.18
INFO [2019-02-09 05:25:54] ------------------------------------------------------------
FATAL [2019-02-09 05:25:54] test.purity not within expected range. 

FATAL [2019-02-09 05:25:54]  

FATAL [2019-02-09 05:25:54] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:25:54] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:25:54] ------------------------------------------------------------
INFO [2019-02-09 05:25:54] PureCN 1.13.18
INFO [2019-02-09 05:25:54] ------------------------------------------------------------
INFO [2019-02-09 05:25:54] Loading coverage files...
FATAL [2019-02-09 05:25:55] Tumor and normal are identical. This won't give any meaningful results 

FATAL [2019-02-09 05:25:55] and I'm stopping here. 

FATAL [2019-02-09 05:25:55]  

FATAL [2019-02-09 05:25:55] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:25:55] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:25:55] ------------------------------------------------------------
INFO [2019-02-09 05:25:55] PureCN 1.13.18
INFO [2019-02-09 05:25:55] ------------------------------------------------------------
INFO [2019-02-09 05:25:55] Loading coverage files...
FATAL [2019-02-09 05:25:55] Length of log.ratio different from tumor coverage. 

FATAL [2019-02-09 05:25:55]  

FATAL [2019-02-09 05:25:55] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:25:55] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:25:55] ------------------------------------------------------------
INFO [2019-02-09 05:25:55] PureCN 1.13.18
INFO [2019-02-09 05:25:55] ------------------------------------------------------------
FATAL [2019-02-09 05:25:55] prior.purity must have the same length as test.purity. 

FATAL [2019-02-09 05:25:55]  

FATAL [2019-02-09 05:25:55] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:25:55] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:25:55] ------------------------------------------------------------
INFO [2019-02-09 05:25:55] PureCN 1.13.18
INFO [2019-02-09 05:25:55] ------------------------------------------------------------
FATAL [2019-02-09 05:25:55] min.gof not within expected range or format. 

FATAL [2019-02-09 05:25:55]  

FATAL [2019-02-09 05:25:55] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:25:55] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:25:55] ------------------------------------------------------------
INFO [2019-02-09 05:25:55] PureCN 1.13.18
INFO [2019-02-09 05:25:55] ------------------------------------------------------------
FATAL [2019-02-09 05:25:55] prior.purity not within expected range or format. 

FATAL [2019-02-09 05:25:55]  

FATAL [2019-02-09 05:25:55] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:25:55] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:25:55] ------------------------------------------------------------
INFO [2019-02-09 05:25:55] PureCN 1.13.18
INFO [2019-02-09 05:25:55] ------------------------------------------------------------
FATAL [2019-02-09 05:25:55] prior.purity must add to 1. Sum is 1.5 

FATAL [2019-02-09 05:25:55]  

FATAL [2019-02-09 05:25:55] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:25:55] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:25:55] ------------------------------------------------------------
INFO [2019-02-09 05:25:55] PureCN 1.13.18
INFO [2019-02-09 05:25:55] ------------------------------------------------------------
FATAL [2019-02-09 05:25:55] max.homozygous.loss not within expected range or format. 

FATAL [2019-02-09 05:25:55]  

FATAL [2019-02-09 05:25:55] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:25:55] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:25:55] ------------------------------------------------------------
INFO [2019-02-09 05:25:55] PureCN 1.13.18
INFO [2019-02-09 05:25:55] ------------------------------------------------------------
FATAL [2019-02-09 05:25:55] prior.K not within expected range or format. 

FATAL [2019-02-09 05:25:55]  

FATAL [2019-02-09 05:25:55] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:25:55] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:25:55] ------------------------------------------------------------
INFO [2019-02-09 05:25:55] PureCN 1.13.18
INFO [2019-02-09 05:25:55] ------------------------------------------------------------
FATAL [2019-02-09 05:25:55] prior.contamination not within expected range or format. 

FATAL [2019-02-09 05:25:55]  

FATAL [2019-02-09 05:25:55] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:25:55] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:25:55] ------------------------------------------------------------
INFO [2019-02-09 05:25:55] PureCN 1.13.18
INFO [2019-02-09 05:25:55] ------------------------------------------------------------
FATAL [2019-02-09 05:25:55] Iterations not in the expected range from 10 to 250. 

FATAL [2019-02-09 05:25:55]  

FATAL [2019-02-09 05:25:55] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:25:55] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:25:55] ------------------------------------------------------------
INFO [2019-02-09 05:25:55] PureCN 1.13.18
INFO [2019-02-09 05:25:55] ------------------------------------------------------------
FATAL [2019-02-09 05:25:55] Iterations not in the expected range from 10 to 250. 

FATAL [2019-02-09 05:25:55]  

FATAL [2019-02-09 05:25:55] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:25:55] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:25:55] ------------------------------------------------------------
INFO [2019-02-09 05:25:55] PureCN 1.13.18
INFO [2019-02-09 05:25:55] ------------------------------------------------------------
INFO [2019-02-09 05:25:55] Loading coverage files...
FATAL [2019-02-09 05:25:55] Missing tumor.coverage.file requires seg.file or log.ratio and 

FATAL [2019-02-09 05:25:55] interval.file. 

FATAL [2019-02-09 05:25:55]  

FATAL [2019-02-09 05:25:55] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:25:55] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:25:55] ------------------------------------------------------------
INFO [2019-02-09 05:25:55] PureCN 1.13.18
INFO [2019-02-09 05:25:55] ------------------------------------------------------------
INFO [2019-02-09 05:25:56] ------------------------------------------------------------
INFO [2019-02-09 05:25:56] PureCN 1.13.18
INFO [2019-02-09 05:25:56] ------------------------------------------------------------
INFO [2019-02-09 05:25:56] Loading coverage files...
FATAL [2019-02-09 05:25:56] Interval files in normal and tumor different. 

FATAL [2019-02-09 05:25:56]  

FATAL [2019-02-09 05:25:56] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:25:56] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:25:56] ------------------------------------------------------------
INFO [2019-02-09 05:25:56] PureCN 1.13.18
INFO [2019-02-09 05:25:56] ------------------------------------------------------------
INFO [2019-02-09 05:25:56] Loading coverage files...
INFO [2019-02-09 05:25:56] Mean target coverages: 0X (tumor) 99X (normal).
WARN [2019-02-09 05:25:56] Large difference in coverage of tumor and normal.
WARN [2019-02-09 05:25:56] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:25:56] Allosome coverage missing, cannot determine sex.
INFO [2019-02-09 05:25:56] Removing 10049 intervals with missing log.ratio.
WARN [2019-02-09 05:25:56] No normalDB provided. Provide one for better results.
INFO [2019-02-09 05:25:56] Using 0 intervals (0 on-target, 0 off-target).
FATAL [2019-02-09 05:25:56] No intervals passing filters. 

FATAL [2019-02-09 05:25:56]  

FATAL [2019-02-09 05:25:56] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:25:56] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:25:56] ------------------------------------------------------------
INFO [2019-02-09 05:25:56] PureCN 1.13.18
INFO [2019-02-09 05:25:56] ------------------------------------------------------------
INFO [2019-02-09 05:25:56] Loading coverage files...
INFO [2019-02-09 05:25:57] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2019-02-09 05:25:57] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:25:57] Allosome coverage missing, cannot determine sex.
INFO [2019-02-09 05:25:57] Removing 228 intervals with missing log.ratio.
INFO [2019-02-09 05:25:57] Removing 22 small (< 5bp) intervals.
INFO [2019-02-09 05:25:57] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2019-02-09 05:25:57] No normalDB provided. Provide one for better results.
INFO [2019-02-09 05:25:57] Removing 233 low coverage (< 15.0000X) intervals.
INFO [2019-02-09 05:25:57] Using 9547 intervals (9547 on-target, 0 off-target).
INFO [2019-02-09 05:25:57] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2019-02-09 05:25:57] No interval.file provided. Cannot check if data was GC-normalized. Was it?
INFO [2019-02-09 05:25:57] Loading VCF...
INFO [2019-02-09 05:25:57] Found 127 variants in VCF file.
INFO [2019-02-09 05:25:57] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2019-02-09 05:25:57] LIB-02240e4 is tumor in VCF file.
INFO [2019-02-09 05:25:57] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2019-02-09 05:25:58] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2019-02-09 05:25:58] Removing 1 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2019-02-09 05:25:58] Removing 0 low quality variants with BQ < 25.
INFO [2019-02-09 05:25:58] Total size of targeted genomic region: 1.63Mb (2.58Mb with 50bp padding).
INFO [2019-02-09 05:25:58] 1.0% of targets contain variants.
INFO [2019-02-09 05:25:58] Removing 2 variants outside intervals.
INFO [2019-02-09 05:25:58] Found SOMATIC annotation in VCF.
INFO [2019-02-09 05:25:58] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2019-02-09 05:25:58] Found SOMATIC annotation in VCF. Setting mapping bias to 0.973.
INFO [2019-02-09 05:25:58] Excluding 0 novel or poor quality variants from segmentation.
INFO [2019-02-09 05:25:58] Sample sex: ?
INFO [2019-02-09 05:25:58] Segmenting data...
INFO [2019-02-09 05:25:58] Loading pre-computed boundaries for DNAcopy...
INFO [2019-02-09 05:25:58] Setting undo.SD parameter to 1.000000.
INFO [2019-02-09 05:26:00] Setting prune.hclust.h parameter to 0.200000.
INFO [2019-02-09 05:26:00] Found 54 segments with median size of 24.88Mb.
INFO [2019-02-09 05:26:00] Using 123 variants.
INFO [2019-02-09 05:26:00] Mean standard deviation of log-ratios: 0.37
INFO [2019-02-09 05:26:00] 2D-grid search of purity and ploidy...
INFO [2019-02-09 05:26:01] Local optima: 0.62/1.9, 0.3/1.9, 0.32/2
INFO [2019-02-09 05:26:01] Testing local optimum 1/3 at purity 0.62 and total ploidy 1.90...
INFO [2019-02-09 05:26:02] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2019-02-09 05:26:03] Recalibrating log-ratios...
INFO [2019-02-09 05:26:03] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2019-02-09 05:26:03] Recalibrating log-ratios...
INFO [2019-02-09 05:26:03] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2019-02-09 05:26:03] Recalibrating log-ratios...
INFO [2019-02-09 05:26:03] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2019-02-09 05:26:04] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2019-02-09 05:26:04] Recalibrating log-ratios...
INFO [2019-02-09 05:26:04] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2019-02-09 05:26:05] Recalibrating log-ratios...
INFO [2019-02-09 05:26:05] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2019-02-09 05:26:05] Recalibrating log-ratios...
INFO [2019-02-09 05:26:05] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2019-02-09 05:26:05] Skipping 1 solutions that converged to the same optima.
INFO [2019-02-09 05:26:05] Skipping 1 solutions exceeding max.non.clonal (0.20).
INFO [2019-02-09 05:26:05] Fitting variants for local optimum 1/3...
INFO [2019-02-09 05:26:05] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01.
INFO [2019-02-09 05:26:06] Optimized purity: 0.65
INFO [2019-02-09 05:26:06] Done.
INFO [2019-02-09 05:26:06] ------------------------------------------------------------
INFO [2019-02-09 05:26:07] ------------------------------------------------------------
INFO [2019-02-09 05:26:07] PureCN 1.13.18
INFO [2019-02-09 05:26:07] ------------------------------------------------------------
INFO [2019-02-09 05:26:07] Loading coverage files...
INFO [2019-02-09 05:26:07] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2019-02-09 05:26:07] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:26:07] Allosome coverage missing, cannot determine sex.
INFO [2019-02-09 05:26:07] Removing 228 intervals with missing log.ratio.
INFO [2019-02-09 05:26:07] Removing 22 small (< 5bp) intervals.
INFO [2019-02-09 05:26:07] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2019-02-09 05:26:07] No normalDB provided. Provide one for better results.
INFO [2019-02-09 05:26:07] Removing 233 low coverage (< 15.0000X) intervals.
INFO [2019-02-09 05:26:07] Using 9547 intervals (9547 on-target, 0 off-target).
INFO [2019-02-09 05:26:07] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2019-02-09 05:26:07] No interval.file provided. Cannot check if data was GC-normalized. Was it?
INFO [2019-02-09 05:26:07] Loading VCF...
INFO [2019-02-09 05:26:07] Found 127 variants in VCF file.
WARN [2019-02-09 05:26:07] DP FORMAT field contains NAs. Removing 3 variants.
WARN [2019-02-09 05:26:07] DB INFO flag contains NAs
INFO [2019-02-09 05:26:07] 119 (96.0%) variants annotated as likely germline (DB INFO flag).
INFO [2019-02-09 05:26:07] LIB-02240e4 is tumor in VCF file.
INFO [2019-02-09 05:26:07] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2019-02-09 05:26:08] Removing 1 variants with AF < 0.030 or AF >= 0.970 or less than 4 supporting reads or depth < 15.
INFO [2019-02-09 05:26:08] Removing 0 low quality variants with BQ < 25.
INFO [2019-02-09 05:26:08] Total size of targeted genomic region: 1.63Mb (2.58Mb with 50bp padding).
INFO [2019-02-09 05:26:08] 1.0% of targets contain variants.
INFO [2019-02-09 05:26:08] Setting somatic prior probabilities for dbSNP hits to 0.000500 or to 0.500000 otherwise.
INFO [2019-02-09 05:26:08] Excluding 5 novel or poor quality variants from segmentation.
INFO [2019-02-09 05:26:08] Sample sex: ?
INFO [2019-02-09 05:26:08] Segmenting data...
INFO [2019-02-09 05:26:08] Loading pre-computed boundaries for DNAcopy...
INFO [2019-02-09 05:26:08] Setting undo.SD parameter to 1.000000.
Setting multi-figure configuration
INFO [2019-02-09 05:26:10] Setting prune.hclust.h parameter to 0.200000.
INFO [2019-02-09 05:26:10] Found 54 segments with median size of 24.88Mb.
INFO [2019-02-09 05:26:10] Using 123 variants.
INFO [2019-02-09 05:26:10] Mean standard deviation of log-ratios: 0.37
INFO [2019-02-09 05:26:10] 2D-grid search of purity and ploidy...
INFO [2019-02-09 05:26:11] Local optima: 0.62/1.9, 0.3/1.9, 0.32/2
INFO [2019-02-09 05:26:11] Testing local optimum 1/3 at purity 0.62 and total ploidy 1.90...
INFO [2019-02-09 05:26:13] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2019-02-09 05:26:13] Recalibrating log-ratios...
INFO [2019-02-09 05:26:13] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2019-02-09 05:26:14] Recalibrating log-ratios...
INFO [2019-02-09 05:26:14] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2019-02-09 05:26:14] Recalibrating log-ratios...
INFO [2019-02-09 05:26:14] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2019-02-09 05:26:14] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2019-02-09 05:26:15] Recalibrating log-ratios...
INFO [2019-02-09 05:26:15] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2019-02-09 05:26:15] Recalibrating log-ratios...
INFO [2019-02-09 05:26:15] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2019-02-09 05:26:16] Recalibrating log-ratios...
INFO [2019-02-09 05:26:16] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2019-02-09 05:26:16] Skipping 1 solutions that converged to the same optima.
INFO [2019-02-09 05:26:16] Skipping 1 solutions exceeding max.non.clonal (0.20).
INFO [2019-02-09 05:26:16] Fitting variants for local optimum 1/3...
INFO [2019-02-09 05:26:16] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01.
INFO [2019-02-09 05:26:17] Optimized purity: 0.65
INFO [2019-02-09 05:26:17] Done.
INFO [2019-02-09 05:26:17] ------------------------------------------------------------
INFO [2019-02-09 05:26:17] ------------------------------------------------------------
INFO [2019-02-09 05:26:17] PureCN 1.13.18
INFO [2019-02-09 05:26:17] ------------------------------------------------------------
INFO [2019-02-09 05:26:17] Loading coverage files...
INFO [2019-02-09 05:26:17] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2019-02-09 05:26:17] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:26:18] Allosome coverage missing, cannot determine sex.
INFO [2019-02-09 05:26:18] No Gene column in interval.file. You won't get gene-level calls.
INFO [2019-02-09 05:26:18] Removing 228 intervals with missing log.ratio.
INFO [2019-02-09 05:26:18] Removing 15 low/high GC targets.
INFO [2019-02-09 05:26:18] Removing 21 small (< 5bp) intervals.
INFO [2019-02-09 05:26:18] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2019-02-09 05:26:18] No normalDB provided. Provide one for better results.
INFO [2019-02-09 05:26:18] Removing 232 low coverage (< 15.0000X) intervals.
INFO [2019-02-09 05:26:18] Using 9534 intervals (9534 on-target, 0 off-target).
INFO [2019-02-09 05:26:18] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2019-02-09 05:26:18] AT/GC dropout: 1.03 (tumor), 1.03 (normal). 
INFO [2019-02-09 05:26:18] Loading VCF...
INFO [2019-02-09 05:26:18] Found 127 variants in VCF file.
INFO [2019-02-09 05:26:18] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2019-02-09 05:26:18] LIB-02240e4 is tumor in VCF file.
INFO [2019-02-09 05:26:19] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2019-02-09 05:26:19] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2019-02-09 05:26:19] Removing 1 variants with AF < 0.030 or AF >= Inf or less than 4 supporting reads or depth < 15.
INFO [2019-02-09 05:26:19] Removing 0 low quality variants with BQ < 25.
INFO [2019-02-09 05:26:19] Total size of targeted genomic region: 1.63Mb (2.58Mb with 50bp padding).
INFO [2019-02-09 05:26:20] 1.0% of targets contain variants.
INFO [2019-02-09 05:26:20] Removing 2 variants outside intervals.
INFO [2019-02-09 05:26:20] Found SOMATIC annotation in VCF.
INFO [2019-02-09 05:26:20] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2019-02-09 05:26:20] Found SOMATIC annotation in VCF. Setting mapping bias to 0.973.
INFO [2019-02-09 05:26:20] Excluding 0 novel or poor quality variants from segmentation.
INFO [2019-02-09 05:26:20] Sample sex: ?
INFO [2019-02-09 05:26:20] Segmenting data...
INFO [2019-02-09 05:26:20] Using unweighted PSCBS.
INFO [2019-02-09 05:26:20] Setting undo.SD parameter to 1.000000.
INFO [2019-02-09 05:26:41] Setting prune.hclust.h parameter to 0.200000.
INFO [2019-02-09 05:26:41] Found 70 segments with median size of 28.20Mb.
INFO [2019-02-09 05:26:41] Using 123 variants.
INFO [2019-02-09 05:26:41] Mean standard deviation of log-ratios: 0.37
INFO [2019-02-09 05:26:41] 2D-grid search of purity and ploidy...
INFO [2019-02-09 05:26:41] 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 [2019-02-09 05:26:41] Testing local optimum 1/6 at purity 0.65 and total ploidy 1.90...
INFO [2019-02-09 05:26:41] Recalibrating log-ratios...
INFO [2019-02-09 05:26:41] Testing local optimum 1/6 at purity 0.65 and total ploidy 1.90...
INFO [2019-02-09 05:26:42] Recalibrating log-ratios...
INFO [2019-02-09 05:26:42] Testing local optimum 1/6 at purity 0.65 and total ploidy 1.90...
INFO [2019-02-09 05:26:42] Recalibrating log-ratios...
INFO [2019-02-09 05:26:42] Testing local optimum 1/6 at purity 0.65 and total ploidy 1.90...
INFO [2019-02-09 05:26:43] Testing local optimum 2/6 at purity 0.33 and total ploidy 1.90...
INFO [2019-02-09 05:26:43] Recalibrating log-ratios...
INFO [2019-02-09 05:26:43] Testing local optimum 2/6 at purity 0.33 and total ploidy 1.90...
INFO [2019-02-09 05:26:44] Recalibrating log-ratios...
INFO [2019-02-09 05:26:44] Testing local optimum 2/6 at purity 0.33 and total ploidy 1.90...
INFO [2019-02-09 05:26:44] Recalibrating log-ratios...
INFO [2019-02-09 05:26:44] Testing local optimum 2/6 at purity 0.33 and total ploidy 1.90...
INFO [2019-02-09 05:26:44] Testing local optimum 3/6 at purity 0.38 and total ploidy 2.20...
INFO [2019-02-09 05:26:47] Testing local optimum 4/6 at purity 0.27 and total ploidy 2.10...
INFO [2019-02-09 05:26:47] Recalibrating log-ratios...
INFO [2019-02-09 05:26:47] Testing local optimum 4/6 at purity 0.27 and total ploidy 2.10...
INFO [2019-02-09 05:26:47] Recalibrating log-ratios...
INFO [2019-02-09 05:26:47] Testing local optimum 4/6 at purity 0.27 and total ploidy 2.10...
INFO [2019-02-09 05:26:48] Recalibrating log-ratios...
INFO [2019-02-09 05:26:48] Testing local optimum 4/6 at purity 0.27 and total ploidy 2.10...
INFO [2019-02-09 05:26:48] Testing local optimum 5/6 at purity 0.29 and total ploidy 2.00...
INFO [2019-02-09 05:26:49] Recalibrating log-ratios...
INFO [2019-02-09 05:26:49] Testing local optimum 5/6 at purity 0.29 and total ploidy 2.00...
INFO [2019-02-09 05:26:49] Recalibrating log-ratios...
INFO [2019-02-09 05:26:49] Testing local optimum 5/6 at purity 0.29 and total ploidy 2.00...
INFO [2019-02-09 05:26:50] Recalibrating log-ratios...
INFO [2019-02-09 05:26:50] Testing local optimum 5/6 at purity 0.29 and total ploidy 2.00...
INFO [2019-02-09 05:26:50] Testing local optimum 6/6 at purity 0.78 and total ploidy 2.00...
INFO [2019-02-09 05:26:50] Recalibrating log-ratios...
INFO [2019-02-09 05:26:50] Testing local optimum 6/6 at purity 0.78 and total ploidy 2.00...
INFO [2019-02-09 05:26:51] Recalibrating log-ratios...
INFO [2019-02-09 05:26:51] Testing local optimum 6/6 at purity 0.78 and total ploidy 2.00...
INFO [2019-02-09 05:26:51] Recalibrating log-ratios...
INFO [2019-02-09 05:26:51] Testing local optimum 6/6 at purity 0.78 and total ploidy 2.00...
INFO [2019-02-09 05:26:52] Skipping 1 solutions that converged to the same optima.
INFO [2019-02-09 05:26:52] Skipping 4 solutions exceeding max.non.clonal (0.20).
INFO [2019-02-09 05:26:52] Fitting variants for local optimum 3/6...
INFO [2019-02-09 05:26:52] Fitting variants for purity 0.40, tumor ploidy 2.55 and contamination 0.01.
INFO [2019-02-09 05:26:53] Optimized purity: 0.40
INFO [2019-02-09 05:26:53] Done.
INFO [2019-02-09 05:26:53] ------------------------------------------------------------
FATAL [2019-02-09 05:26:53] This function requires gene-level calls. Please add a column 'Gene' 

FATAL [2019-02-09 05:26:53] containing gene symbols to the interval.file. 

FATAL [2019-02-09 05:26:53]  

FATAL [2019-02-09 05:26:53] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:26:53] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:26:54] ------------------------------------------------------------
INFO [2019-02-09 05:26:54] PureCN 1.13.18
INFO [2019-02-09 05:26:54] ------------------------------------------------------------
INFO [2019-02-09 05:26:54] Loading coverage files...
INFO [2019-02-09 05:26:54] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2019-02-09 05:26:54] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:26:54] Allosome coverage missing, cannot determine sex.
INFO [2019-02-09 05:26:54] Removing 228 intervals with missing log.ratio.
INFO [2019-02-09 05:26:54] Removing 22 small (< 5bp) intervals.
INFO [2019-02-09 05:26:54] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2019-02-09 05:26:54] No normalDB provided. Provide one for better results.
INFO [2019-02-09 05:26:54] Removing 233 low coverage (< 15.0000X) intervals.
INFO [2019-02-09 05:26:54] Using 9547 intervals (9547 on-target, 0 off-target).
INFO [2019-02-09 05:26:54] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2019-02-09 05:26:54] No interval.file provided. Cannot check if data was GC-normalized. Was it?
INFO [2019-02-09 05:26:54] Loading VCF...
INFO [2019-02-09 05:26:54] Found 127 variants in VCF file.
INFO [2019-02-09 05:26:54] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
FATAL [2019-02-09 05:26:54] Different chromosome names in coverage and VCF. 

FATAL [2019-02-09 05:26:54]  

FATAL [2019-02-09 05:26:54] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:26:54] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:26:54] ------------------------------------------------------------
INFO [2019-02-09 05:26:54] PureCN 1.13.18
INFO [2019-02-09 05:26:54] ------------------------------------------------------------
INFO [2019-02-09 05:26:55] Loading coverage files...
INFO [2019-02-09 05:26:55] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2019-02-09 05:26:55] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:26:55] Allosome coverage missing, cannot determine sex.
FATAL [2019-02-09 05:26:55] tumor.coverage.file and interval.file do not align. 

FATAL [2019-02-09 05:26:55]  

FATAL [2019-02-09 05:26:55] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:26:55] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:26:55] ------------------------------------------------------------
INFO [2019-02-09 05:26:55] PureCN 1.13.18
INFO [2019-02-09 05:26:55] ------------------------------------------------------------
INFO [2019-02-09 05:26:55] Loading coverage files...
INFO [2019-02-09 05:26:55] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2019-02-09 05:26:55] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:26:55] Allosome coverage missing, cannot determine sex.
INFO [2019-02-09 05:26:56] Removing 228 intervals with missing log.ratio.
INFO [2019-02-09 05:26:56] Removing 15 low/high GC targets.
INFO [2019-02-09 05:26:56] Removing 21 small (< 5bp) intervals.
INFO [2019-02-09 05:26:56] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2019-02-09 05:26:56] No normalDB provided. Provide one for better results.
INFO [2019-02-09 05:26:56] Removing 232 low coverage (< 15.0000X) intervals.
INFO [2019-02-09 05:26:56] Using 9534 intervals (9534 on-target, 0 off-target).
INFO [2019-02-09 05:26:56] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2019-02-09 05:26:56] AT/GC dropout: 1.03 (tumor), 1.03 (normal). 
INFO [2019-02-09 05:26:56] Loading VCF...
INFO [2019-02-09 05:26:56] Found 127 variants in VCF file.
INFO [2019-02-09 05:26:56] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2019-02-09 05:26:57] LIB-02240e4 is tumor in VCF file.
INFO [2019-02-09 05:26:57] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2019-02-09 05:26:57] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2019-02-09 05:26:57] Removing 1 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2019-02-09 05:26:57] Removing 0 low quality variants with BQ < 25.
INFO [2019-02-09 05:26:57] Total size of targeted genomic region: 1.63Mb (2.58Mb with 50bp padding).
INFO [2019-02-09 05:26:57] 1.0% of targets contain variants.
INFO [2019-02-09 05:26:57] Removing 2 variants outside intervals.
INFO [2019-02-09 05:26:57] Found SOMATIC annotation in VCF.
INFO [2019-02-09 05:26:57] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2019-02-09 05:26:57] Found SOMATIC annotation in VCF. Setting mapping bias to 0.973.
INFO [2019-02-09 05:26:57] Excluding 0 novel or poor quality variants from segmentation.
INFO [2019-02-09 05:26:57] Sample sex: ?
INFO [2019-02-09 05:26:57] Segmenting data...
INFO [2019-02-09 05:26:58] Loading pre-computed boundaries for DNAcopy...
INFO [2019-02-09 05:26:58] Setting undo.SD parameter to 1.000000.
INFO [2019-02-09 05:26:59] Setting prune.hclust.h parameter to 0.200000.
INFO [2019-02-09 05:26:59] Found 54 segments with median size of 24.88Mb.
INFO [2019-02-09 05:26:59] Using 123 variants.
INFO [2019-02-09 05:26:59] Mean standard deviation of log-ratios: 0.37
INFO [2019-02-09 05:26:59] 2D-grid search of purity and ploidy...
INFO [2019-02-09 05:27:00] Local optima: 0.63/1.9, 0.4/2.1
INFO [2019-02-09 05:27:00] Testing local optimum 1/2 at purity 0.63 and total ploidy 1.90...
INFO [2019-02-09 05:27:02] Testing local optimum 2/2 at purity 0.40 and total ploidy 2.10...
INFO [2019-02-09 05:27:02] Recalibrating log-ratios...
INFO [2019-02-09 05:27:02] Testing local optimum 2/2 at purity 0.40 and total ploidy 2.10...
INFO [2019-02-09 05:27:02] Recalibrating log-ratios...
INFO [2019-02-09 05:27:02] Testing local optimum 2/2 at purity 0.40 and total ploidy 2.10...
INFO [2019-02-09 05:27:03] Recalibrating log-ratios...
INFO [2019-02-09 05:27:03] Testing local optimum 2/2 at purity 0.40 and total ploidy 2.10...
INFO [2019-02-09 05:27:03] Skipping 1 solutions exceeding max.non.clonal (0.20).
INFO [2019-02-09 05:27:03] Fitting variants for local optimum 1/2...
INFO [2019-02-09 05:27:03] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01.
INFO [2019-02-09 05:27:05] Optimized purity: 0.65
INFO [2019-02-09 05:27:05] Done.
INFO [2019-02-09 05:27:05] ------------------------------------------------------------
INFO [2019-02-09 05:27:05] ------------------------------------------------------------
INFO [2019-02-09 05:27:05] PureCN 1.13.18
INFO [2019-02-09 05:27:05] ------------------------------------------------------------
INFO [2019-02-09 05:27:05] Loading coverage files...
INFO [2019-02-09 05:27:05] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2019-02-09 05:27:05] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:27:05] Allosome coverage missing, cannot determine sex.
INFO [2019-02-09 05:27:06] Removing 228 intervals with missing log.ratio.
INFO [2019-02-09 05:27:06] Removing 15 low/high GC targets.
INFO [2019-02-09 05:27:06] Removing 21 small (< 5bp) intervals.
INFO [2019-02-09 05:27:06] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2019-02-09 05:27:06] No normalDB provided. Provide one for better results.
INFO [2019-02-09 05:27:06] Removing 232 low coverage (< 15.0000X) intervals.
INFO [2019-02-09 05:27:06] Using 9534 intervals (9534 on-target, 0 off-target).
INFO [2019-02-09 05:27:06] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2019-02-09 05:27:06] AT/GC dropout: 1.03 (tumor), 1.03 (normal). 
INFO [2019-02-09 05:27:06] Loading VCF...
INFO [2019-02-09 05:27:06] Found 127 variants in VCF file.
INFO [2019-02-09 05:27:06] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2019-02-09 05:27:06] LIB-02240e4 is tumor in VCF file.
INFO [2019-02-09 05:27:06] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2019-02-09 05:27:06] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2019-02-09 05:27:07] Removing 1 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2019-02-09 05:27:07] Removing 0 low quality variants with BQ < 25.
INFO [2019-02-09 05:27:07] Total size of targeted genomic region: 1.63Mb (2.58Mb with 50bp padding).
INFO [2019-02-09 05:27:07] 1.0% of targets contain variants.
INFO [2019-02-09 05:27:07] Removing 2 variants outside intervals.
INFO [2019-02-09 05:27:07] Found SOMATIC annotation in VCF.
INFO [2019-02-09 05:27:07] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2019-02-09 05:27:07] Found SOMATIC annotation in VCF. Setting mapping bias to 0.973.
INFO [2019-02-09 05:27:07] Excluding 0 novel or poor quality variants from segmentation.
INFO [2019-02-09 05:27:07] Sample sex: ?
INFO [2019-02-09 05:27:07] Segmenting data...
INFO [2019-02-09 05:27:08] Loading pre-computed boundaries for DNAcopy...
INFO [2019-02-09 05:27:08] Setting undo.SD parameter to 1.000000.
INFO [2019-02-09 05:27:09] Setting prune.hclust.h parameter to 0.200000.
INFO [2019-02-09 05:27:09] Found 54 segments with median size of 24.88Mb.
INFO [2019-02-09 05:27:10] Using 123 variants.
INFO [2019-02-09 05:27:10] Mean standard deviation of log-ratios: 0.37
INFO [2019-02-09 05:27:10] 2D-grid search of purity and ploidy...
INFO [2019-02-09 05:27:11] Local optima: 0.63/1.9, 0.4/2.1
INFO [2019-02-09 05:27:11] Testing local optimum 1/2 at purity 0.63 and total ploidy 1.90...
INFO [2019-02-09 05:27:12] Testing local optimum 2/2 at purity 0.40 and total ploidy 2.10...
INFO [2019-02-09 05:27:13] Recalibrating log-ratios...
INFO [2019-02-09 05:27:13] Testing local optimum 2/2 at purity 0.40 and total ploidy 2.10...
INFO [2019-02-09 05:27:13] Recalibrating log-ratios...
INFO [2019-02-09 05:27:13] Testing local optimum 2/2 at purity 0.40 and total ploidy 2.10...
INFO [2019-02-09 05:27:13] Recalibrating log-ratios...
INFO [2019-02-09 05:27:13] Testing local optimum 2/2 at purity 0.40 and total ploidy 2.10...
INFO [2019-02-09 05:27:14] Skipping 1 solutions exceeding max.non.clonal (0.20).
INFO [2019-02-09 05:27:14] Fitting variants for local optimum 1/2...
INFO [2019-02-09 05:27:14] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01.
INFO [2019-02-09 05:27:16] Optimized purity: 0.65
INFO [2019-02-09 05:27:16] Done.
INFO [2019-02-09 05:27:16] ------------------------------------------------------------
FATAL [2019-02-09 05:27:17] chr1 not valid chromosome name(s). Valid names are: 

FATAL [2019-02-09 05:27:17] 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22 

FATAL [2019-02-09 05:27:17]  

FATAL [2019-02-09 05:27:17] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:27:17] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:27:17] ------------------------------------------------------------
INFO [2019-02-09 05:27:17] PureCN 1.13.18
INFO [2019-02-09 05:27:17] ------------------------------------------------------------
INFO [2019-02-09 05:27:17] Loading coverage files...
WARN [2019-02-09 05:27:17] Provided sampleid (Sample2) does not match Sample1 found in segmentation.
WARN [2019-02-09 05:27:17] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:27:17] Allosome coverage missing, cannot determine sex.
INFO [2019-02-09 05:27:17] Removing 10 intervals with missing log.ratio.
INFO [2019-02-09 05:27:17] Using 10039 intervals (10039 on-target, 0 off-target).
INFO [2019-02-09 05:27:17] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2019-02-09 05:27:17] Loading VCF...
INFO [2019-02-09 05:27:17] Found 127 variants in VCF file.
INFO [2019-02-09 05:27:17] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2019-02-09 05:27:17] LIB-02240e4 is tumor in VCF file.
INFO [2019-02-09 05:27:17] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2019-02-09 05:27:17] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2019-02-09 05:27:18] Removing 1 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2019-02-09 05:27:18] Removing 0 low quality variants with BQ < 25.
INFO [2019-02-09 05:27:18] Total size of targeted genomic region: 1.71Mb (2.70Mb with 50bp padding).
INFO [2019-02-09 05:27:18] 1.0% of targets contain variants.
INFO [2019-02-09 05:27:18] Removing 0 variants outside intervals.
INFO [2019-02-09 05:27:18] Found SOMATIC annotation in VCF.
INFO [2019-02-09 05:27:18] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2019-02-09 05:27:18] Found SOMATIC annotation in VCF. Setting mapping bias to 0.976.
INFO [2019-02-09 05:27:18] Excluding 0 novel or poor quality variants from segmentation.
INFO [2019-02-09 05:27:18] Sample sex: ?
INFO [2019-02-09 05:27:18] Segmenting data...
INFO [2019-02-09 05:27:18] Loaded provided segmentation file example_seg.txt.
WARN [2019-02-09 05:27:18] Provided sampleid (Sample2) does not match Sample1 found in segmentation.
INFO [2019-02-09 05:27:18] Loading pre-computed boundaries for DNAcopy...
INFO [2019-02-09 05:27:18] Setting undo.SD parameter to 0.000000.
Setting multi-figure configuration
INFO [2019-02-09 05:27:19] Setting prune.hclust.h parameter to 0.200000.
INFO [2019-02-09 05:27:19] Found 54 segments with median size of 24.88Mb.
INFO [2019-02-09 05:27:19] Using 125 variants.
INFO [2019-02-09 05:27:19] Mean standard deviation of log-ratios: 0.40
INFO [2019-02-09 05:27:19] 2D-grid search of purity and ploidy...
INFO [2019-02-09 05:27:20] Local optima: 0.6/1.9, 0.4/2.1
INFO [2019-02-09 05:27:20] Testing local optimum 1/2 at purity 0.60 and total ploidy 1.90...
INFO [2019-02-09 05:27:21] Testing local optimum 2/2 at purity 0.40 and total ploidy 2.10...
INFO [2019-02-09 05:27:21] Recalibrating log-ratios...
INFO [2019-02-09 05:27:21] Testing local optimum 2/2 at purity 0.40 and total ploidy 2.10...
INFO [2019-02-09 05:27:22] Recalibrating log-ratios...
INFO [2019-02-09 05:27:22] Testing local optimum 2/2 at purity 0.40 and total ploidy 2.10...
INFO [2019-02-09 05:27:22] Recalibrating log-ratios...
INFO [2019-02-09 05:27:22] Testing local optimum 2/2 at purity 0.40 and total ploidy 2.10...
INFO [2019-02-09 05:27:23] Skipping 1 solutions exceeding max.non.clonal (0.20).
INFO [2019-02-09 05:27:23] Fitting variants for local optimum 1/2...
INFO [2019-02-09 05:27:23] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01.
INFO [2019-02-09 05:27:24] Optimized purity: 0.65
INFO [2019-02-09 05:27:24] Done.
INFO [2019-02-09 05:27:24] ------------------------------------------------------------
WARN [2019-02-09 05:27:25] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:27:25] Allosome coverage missing, cannot determine sex.
Setting multi-figure configuration
FATAL [2019-02-09 05:27:34] Segmentation file expected with colnames ID, chrom, loc.start, loc.end, 

FATAL [2019-02-09 05:27:34] num.mark, seg.mean 

FATAL [2019-02-09 05:27:34]  

FATAL [2019-02-09 05:27:34] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:27:34] parameters (PureCN 1.13.18). 

FATAL [2019-02-09 05:27:35] seg.file contains multiple samples and sampleid missing. 

FATAL [2019-02-09 05:27:35]  

FATAL [2019-02-09 05:27:35] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:27:35] parameters (PureCN 1.13.18). 

FATAL [2019-02-09 05:27:35] seg.file contains multiple samples and sampleid does not match any. 

FATAL [2019-02-09 05:27:35]  

FATAL [2019-02-09 05:27:35] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:27:35] parameters (PureCN 1.13.18). 

WARN [2019-02-09 05:27:35] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:27:35] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:27:45] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:27:45] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:27:45] Provided sampleid (example_tumor.txt) does not match Sample1 found in segmentation.
WARN [2019-02-09 05:27:51] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:27:51] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:27:52] No normalDB provided. Provide one for better results.
WARN [2019-02-09 05:28:02] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:28:02] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:28:05] Provided sampleid (Sample.1) does not match Sample1 found in segmentation.
Setting multi-figure configuration
WARN [2019-02-09 05:28:14] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:28:14] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:28:14] No normalDB provided. Provide one for better results.
WARN [2019-02-09 05:28:15] Sampleid looks like a normal in VCF, not like a tumor.
WARN [2019-02-09 05:28:23] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:28:23] Allosome coverage missing, cannot determine sex.
FATAL [2019-02-09 05:28:23] normalDB not a valid normalDB object. Use createNormalDatabase to 

FATAL [2019-02-09 05:28:23] create one. 

FATAL [2019-02-09 05:28:23]  

FATAL [2019-02-09 05:28:23] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:28:23] parameters (PureCN 1.13.18). 

WARN [2019-02-09 05:28:24] You are likely not using the correct baits file!
WARN [2019-02-09 05:28:24] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:28:24] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:28:25] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:28:25] Allosome coverage missing, cannot determine sex.
FATAL [2019-02-09 05:28:25] normalDB appears to be empty. 

FATAL [2019-02-09 05:28:25]  

FATAL [2019-02-09 05:28:25] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:28:25] parameters (PureCN 1.13.18). 

WARN [2019-02-09 05:28:26] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:28:26] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:28:26] Intervals in coverage and interval.file have conflicting on/off-target annotation.
FATAL [2019-02-09 05:28:50] min.normals must be >=2. 

FATAL [2019-02-09 05:28:50]  

FATAL [2019-02-09 05:28:50] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:28:50] parameters (PureCN 1.13.18). 

FATAL [2019-02-09 05:28:59] The normal.panel.vcf.file contains only a single sample. 

FATAL [2019-02-09 05:28:59]  

FATAL [2019-02-09 05:28:59] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:28:59] parameters (PureCN 1.13.18). 

== testthat results  ===========================================================
OK: 314 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 310.28    4.75  371.73


R Under development (unstable) (2019-01-10 r75962) -- "Unsuffered Consequences"
Copyright (C) 2019 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.

> 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, 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

Attaching package: 'IRanges'

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

    windows

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, rowsum

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 [2019-02-09 05:29:17] Attempted adding gene symbols to intervals. Heuristics have been used to pick symbols for overlapping genes.
WARN [2019-02-09 05:29:17] Chromosome naming style of txdb file (UCSC) was different from interval file (NCBI).
WARN [2019-02-09 05:29:20] Attempted adding gene symbols to intervals. Heuristics have been used to pick symbols for overlapping genes.
FATAL [2019-02-09 05:29:22] tumor.coverage.file and interval.file do not align. 

FATAL [2019-02-09 05:29:22]  

FATAL [2019-02-09 05:29:22] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:29:22] parameters (PureCN 1.13.18). 

FATAL [2019-02-09 05:29:22] Need either f or purity and ploidy. 

FATAL [2019-02-09 05:29:22]  

FATAL [2019-02-09 05:29:22] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:29:22] parameters (PureCN 1.13.18). 

FATAL [2019-02-09 05:29:22] f not in expected range. 

FATAL [2019-02-09 05:29:22]  

FATAL [2019-02-09 05:29:22] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:29:22] parameters (PureCN 1.13.18). 

FATAL [2019-02-09 05:29:22] coverage not in expected range (>=2) 

FATAL [2019-02-09 05:29:22]  

FATAL [2019-02-09 05:29:22] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:29:22] parameters (PureCN 1.13.18). 

FATAL [2019-02-09 05:29:22] purity not in expected range. 

FATAL [2019-02-09 05:29:22]  

FATAL [2019-02-09 05:29:22] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:29:22] parameters (PureCN 1.13.18). 

FATAL [2019-02-09 05:29:22] ploidy not in expected range. 

FATAL [2019-02-09 05:29:22]  

FATAL [2019-02-09 05:29:22] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:29:22] parameters (PureCN 1.13.18). 

FATAL [2019-02-09 05:29:22] cell.fraction not in expected range. 

FATAL [2019-02-09 05:29:22]  

FATAL [2019-02-09 05:29:22] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:29:22] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:29:25] ------------------------------------------------------------
INFO [2019-02-09 05:29:25] PureCN 1.13.18
INFO [2019-02-09 05:29:25] ------------------------------------------------------------
INFO [2019-02-09 05:29:25] Loading coverage files...
INFO [2019-02-09 05:29:25] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2019-02-09 05:29:25] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:29:25] Allosome coverage missing, cannot determine sex.
INFO [2019-02-09 05:29:25] Removing 228 intervals with missing log.ratio.
INFO [2019-02-09 05:29:25] Removing 22 small (< 5bp) intervals.
INFO [2019-02-09 05:29:25] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2019-02-09 05:29:25] No normalDB provided. Provide one for better results.
INFO [2019-02-09 05:29:25] Removing 233 low coverage (< 15.0000X) intervals.
INFO [2019-02-09 05:29:25] Using 9547 intervals (9547 on-target, 0 off-target).
INFO [2019-02-09 05:29:25] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2019-02-09 05:29:25] No interval.file provided. Cannot check if data was GC-normalized. Was it?
INFO [2019-02-09 05:29:25] Loading VCF...
INFO [2019-02-09 05:29:25] Found 127 variants in VCF file.
INFO [2019-02-09 05:29:25] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2019-02-09 05:29:26] LIB-02240e4 is tumor in VCF file.
INFO [2019-02-09 05:29:26] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2019-02-09 05:29:26] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2019-02-09 05:29:26] Removing 1 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2019-02-09 05:29:27] Removing 0 low quality variants with BQ < 25.
INFO [2019-02-09 05:29:27] Total size of targeted genomic region: 1.63Mb (2.58Mb with 50bp padding).
INFO [2019-02-09 05:29:27] 1.0% of targets contain variants.
INFO [2019-02-09 05:29:27] Removing 2 variants outside intervals.
INFO [2019-02-09 05:29:27] Found SOMATIC annotation in VCF.
INFO [2019-02-09 05:29:27] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2019-02-09 05:29:27] Found SOMATIC annotation in VCF. Setting mapping bias to 0.973.
INFO [2019-02-09 05:29:27] Excluding 0 novel or poor quality variants from segmentation.
INFO [2019-02-09 05:29:27] Sample sex: ?
INFO [2019-02-09 05:29:27] Segmenting data...
INFO [2019-02-09 05:29:27] Loading pre-computed boundaries for DNAcopy...
INFO [2019-02-09 05:29:27] Setting undo.SD parameter to 1.000000.
INFO [2019-02-09 05:29:28] Setting prune.hclust.h parameter to 0.200000.
INFO [2019-02-09 05:29:28] Found 54 segments with median size of 24.88Mb.
INFO [2019-02-09 05:29:28] Using 123 variants.
INFO [2019-02-09 05:29:28] Mean standard deviation of log-ratios: 0.37
INFO [2019-02-09 05:29:28] 2D-grid search of purity and ploidy...
INFO [2019-02-09 05:29:30] Local optima: 0.63/1.9, 0.4/2.2, 0.5/2
INFO [2019-02-09 05:29:30] Testing local optimum 1/3 at purity 0.63 and total ploidy 1.90...
INFO [2019-02-09 05:29:31] Testing local optimum 2/3 at purity 0.40 and total ploidy 2.20...
INFO [2019-02-09 05:29:33] Testing local optimum 3/3 at purity 0.50 and total ploidy 2.00...
INFO [2019-02-09 05:29:34] Skipping 1 solutions that converged to the same optima.
INFO [2019-02-09 05:29:34] Fitting variants for local optimum 1/3...
INFO [2019-02-09 05:29:34] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01.
INFO [2019-02-09 05:29:35] Optimized purity: 0.65
INFO [2019-02-09 05:29:35] Fitting variants for local optimum 2/3...
INFO [2019-02-09 05:29:35] Fitting variants for purity 0.40, tumor ploidy 2.34 and contamination 0.01.
INFO [2019-02-09 05:29:36] Optimized purity: 0.40
INFO [2019-02-09 05:29:36] Done.
INFO [2019-02-09 05:29:36] ------------------------------------------------------------
FATAL [2019-02-09 05:29:37] exclude not a GRanges object. 

FATAL [2019-02-09 05:29:37]  

FATAL [2019-02-09 05:29:37] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:29:37] parameters (PureCN 1.13.18). 

FATAL [2019-02-09 05:29:37] callable not a GRanges object. 

FATAL [2019-02-09 05:29:37]  

FATAL [2019-02-09 05:29:37] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:29:37] parameters (PureCN 1.13.18). 

WARN [2019-02-09 05:29:47] tumor.coverage.file and interval.file do not align.
FATAL [2019-02-09 05:29:48] No gc_bias column in interval.file. 

FATAL [2019-02-09 05:29:48]  

FATAL [2019-02-09 05:29:48] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:29:48] parameters (PureCN 1.13.18). 

FATAL [2019-02-09 05:29:49] Provided coverage is zero, most likely due to a corrupt BAM file. 

FATAL [2019-02-09 05:29:49]  

FATAL [2019-02-09 05:29:49] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:29:49] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:29:55] Reading C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\Rtmp0efuTi\file1f3021ea1488.rds...
INFO [2019-02-09 05:29:55] Reading C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\Rtmp0efuTi\file1f3021ea1488.rds...
INFO [2019-02-09 05:29:56] Reading C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\Rtmp0efuTi\file1f3021ea1488.rds...
INFO [2019-02-09 05:29:56] Reading C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\Rtmp0efuTi\file1f3021ea1488.rds...
INFO [2019-02-09 05:29:56] Reading C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\Rtmp0efuTi\file1f3021ea1488.rds...
INFO [2019-02-09 05:29:56] Reading C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\Rtmp0efuTi\file1f3021ea1488.rds...
FATAL [2019-02-09 05:29:56] Purity or Ploidy not numeric or in expected range. 

FATAL [2019-02-09 05:29:56]  

FATAL [2019-02-09 05:29:56] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:29:56] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:29:56] Reading C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\Rtmp0efuTi\file1f3021ea1488.rds...
INFO [2019-02-09 05:29:57] Reading C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\Rtmp0efuTi\file1f3021ea1488.rds...
FATAL [2019-02-09 05:29:57] 'Failed' column in 

FATAL [2019-02-09 05:29:57] C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\Rtmp0efuTi\file1f3021ea1488.csv 

FATAL [2019-02-09 05:29:57] not logical(1). 

FATAL [2019-02-09 05:29:57]  

FATAL [2019-02-09 05:29:57] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:29:57] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:29:57] 576 on-target bins with low coverage in all samples.
WARN [2019-02-09 05:29:57] You are likely not using the correct baits file!
WARN [2019-02-09 05:29:57] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:29:57] Allosome coverage missing, cannot determine sex.
INFO [2019-02-09 05:29:57] Processing on-target regions...
INFO [2019-02-09 05:29:58] Removing 930 intervals with low coverage in normalDB.
INFO [2019-02-09 05:29:58] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2019-02-09 05:30:01] 576 on-target bins with low coverage in all samples.
WARN [2019-02-09 05:30:01] You are likely not using the correct baits file!
WARN [2019-02-09 05:30:01] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:30:01] Allosome coverage missing, cannot determine sex.
INFO [2019-02-09 05:30:01] Processing on-target regions...
INFO [2019-02-09 05:30:01] Removing 930 intervals with low coverage in normalDB.
INFO [2019-02-09 05:30:01] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2019-02-09 05:30:03] 576 on-target bins with low coverage in all samples.
WARN [2019-02-09 05:30:03] You are likely not using the correct baits file!
WARN [2019-02-09 05:30:03] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:30:03] Allosome coverage missing, cannot determine sex.
INFO [2019-02-09 05:30:03] Processing on-target regions...
INFO [2019-02-09 05:30:04] Removing 930 intervals with low coverage in normalDB.
INFO [2019-02-09 05:30:04] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2019-02-09 05:30:06] 576 on-target bins with low coverage in all samples.
WARN [2019-02-09 05:30:06] You are likely not using the correct baits file!
WARN [2019-02-09 05:30:06] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:30:06] Allosome coverage missing, cannot determine sex.
FATAL [2019-02-09 05:30:06] Length of normal.coverage.files and sex different 

FATAL [2019-02-09 05:30:06]  

FATAL [2019-02-09 05:30:06] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:30:06] parameters (PureCN 1.13.18). 

WARN [2019-02-09 05:30:11] Target intervals were not sorted.
INFO [2019-02-09 05:30:11] 560 on-target bins with low coverage in all samples.
WARN [2019-02-09 05:30:11] You are likely not using the correct baits file!
WARN [2019-02-09 05:30:11] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:30:12] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:30:12] Allosome coverage missing, cannot determine sex.
INFO [2019-02-09 05:30:12] Processing on-target regions...
INFO [2019-02-09 05:30:13] Removing 978 intervals with low coverage in normalDB.
INFO [2019-02-09 05:30:13] Removing 11 intervals with zero coverage in more than 3% of normalDB.
FATAL [2019-02-09 05:30:14] tumor.coverage.file and normalDB do not align. 

FATAL [2019-02-09 05:30:14]  

FATAL [2019-02-09 05:30:14] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:30:14] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:30:14] ------------------------------------------------------------
INFO [2019-02-09 05:30:14] PureCN 1.13.18
INFO [2019-02-09 05:30:14] ------------------------------------------------------------
INFO [2019-02-09 05:30:14] Loading coverage files...
INFO [2019-02-09 05:30:15] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2019-02-09 05:30:15] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:30:15] Allosome coverage missing, cannot determine sex.
INFO [2019-02-09 05:30:15] Removing 228 intervals with missing log.ratio.
FATAL [2019-02-09 05:30:15] normalDB incompatible with this PureCN version. Please re-run 

FATAL [2019-02-09 05:30:15] NormalDB.R. 

FATAL [2019-02-09 05:30:15]  

FATAL [2019-02-09 05:30:15] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:30:15] parameters (PureCN 1.13.18). 

FATAL [2019-02-09 05:30:15] normalDB incompatible with this PureCN version. Please re-run 

FATAL [2019-02-09 05:30:15] NormalDB.R. 

FATAL [2019-02-09 05:30:15]  

FATAL [2019-02-09 05:30:15] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:30:15] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:30:16] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2019-02-09 05:30:17] Initial testing for significant sample cross-contamination: unlikely
INFO [2019-02-09 05:30:17] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2019-02-09 05:30:17] Removing 16 low quality variants with BQ < 25.
INFO [2019-02-09 05:30:17] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2019-02-09 05:30:17] Initial testing for significant sample cross-contamination: unlikely
INFO [2019-02-09 05:30:18] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2019-02-09 05:30:18] Removing 6 blacklisted variants.
INFO [2019-02-09 05:30:18] Removing 16 low quality variants with BQ < 25.
INFO [2019-02-09 05:30:18] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2019-02-09 05:30:18] Initial testing for significant sample cross-contamination: unlikely
INFO [2019-02-09 05:30:19] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2019-02-09 05:30:19] Removing 16 low quality variants with BQ < 25.
WARN [2019-02-09 05:30:19] MuTect stats file lacks contig and position columns.
INFO [2019-02-09 05:30:19] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2019-02-09 05:30:19] Initial testing for significant sample cross-contamination: unlikely
INFO [2019-02-09 05:30:20] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2019-02-09 05:30:20] Removing 16 low quality variants with BQ < 25.
WARN [2019-02-09 05:30:20] MuTect stats file and VCF file do not align perfectly. Will remove 2325 unmatched variants.
WARN [2019-02-09 05:30:20] MuTect stats file lacks failure_reasons column. Keeping all variants listed in stats file.
INFO [2019-02-09 05:30:20] Removing 0 non heterozygous (in matched normal) germline SNPs.
INFO [2019-02-09 05:30:20] Removing 0 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2019-02-09 05:30:20] Removing 0 low quality variants with BQ < 25.
INFO [2019-02-09 05:30:21] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2019-02-09 05:30:21] Initial testing for significant sample cross-contamination: unlikely
INFO [2019-02-09 05:30:21] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2019-02-09 05:30:21] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2019-02-09 05:30:22] Initial testing for significant sample cross-contamination: unlikely
INFO [2019-02-09 05:30:22] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2019-02-09 05:30:23] Found 11 variants in VCF file.
WARN [2019-02-09 05:30:23] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead.
INFO [2019-02-09 05:30:23] 1 (9.1%) variants annotated as likely germline (DB INFO flag).
INFO [2019-02-09 05:30:26] Found 11 variants in VCF file.
WARN [2019-02-09 05:30:26] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead.
INFO [2019-02-09 05:30:26] 1 (9.1%) variants annotated as likely germline (DB INFO flag).
INFO [2019-02-09 05:30:27] Found 11 variants in VCF file.
WARN [2019-02-09 05:30:27] vcf.file has no DB or POP_AF info field for membership in germline databases. Guessing it based on available dbSNP ID.
INFO [2019-02-09 05:30:27] 1 (9.1%) variants annotated as likely germline (DB INFO flag).
INFO [2019-02-09 05:30:28] Found 1000 variants in VCF file.
INFO [2019-02-09 05:30:28] Removing 2 triallelic sites.
WARN [2019-02-09 05:30:28] DP FORMAT field contains NAs. Removing 44 variants.
INFO [2019-02-09 05:30:28] 954 (100.0%) variants annotated as likely germline (DB INFO flag).
WARN [2019-02-09 05:30:29] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:30:29] Allosome coverage missing, cannot determine sex.
INFO [2019-02-09 05:30:29] Mean coverages: chrX: 108.58, chrY: 108.58, chr1-22: 104.87.
INFO [2019-02-09 05:30:29] Mean coverages: chrX: 108.58, chrY: 2.17, chr1-22: 104.87.
INFO [2019-02-09 05:30:29] Mean coverages: chrX: 108.58, chrY: 5.17, chr1-22: 104.87.
INFO [2019-02-09 05:30:30] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2019-02-09 05:30:30] No germline variants in VCF.
FATAL [2019-02-09 05:30:30] No solution with id hello 

FATAL [2019-02-09 05:30:30]  

FATAL [2019-02-09 05:30:30] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:30:30] parameters (PureCN 1.13.18). 

FATAL [2019-02-09 05:30:30] No solution with id 10 

FATAL [2019-02-09 05:30:30]  

FATAL [2019-02-09 05:30:30] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:30:30] parameters (PureCN 1.13.18). 

FATAL [2019-02-09 05:30:31] all.data and w have different lengths. 

FATAL [2019-02-09 05:30:31]  

FATAL [2019-02-09 05:30:31] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:30:31] parameters (PureCN 1.13.18). 

WARN [2019-02-09 05:30:32] No mappability scores provided.
WARN [2019-02-09 05:30:32] No reptiming scores provided.
INFO [2019-02-09 05:30:32] Calculating GC-content...
WARN [2019-02-09 05:30:32] No mappability scores provided.
WARN [2019-02-09 05:30:32] No reptiming scores provided.
INFO [2019-02-09 05:30:32] Calculating GC-content...
INFO [2019-02-09 05:30:32] Removing 1 targets overlapping with exclude.
WARN [2019-02-09 05:30:32] No mappability scores provided.
WARN [2019-02-09 05:30:32] No reptiming scores provided.
INFO [2019-02-09 05:30:32] Calculating GC-content...
FATAL [2019-02-09 05:30:32] off.target.padding must be negative. 

FATAL [2019-02-09 05:30:32]  

FATAL [2019-02-09 05:30:32] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:30:32] parameters (PureCN 1.13.18). 

FATAL [2019-02-09 05:30:32] Interval coordinates should start at 1, not at 0 

FATAL [2019-02-09 05:30:32]  

FATAL [2019-02-09 05:30:32] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:30:32] parameters (PureCN 1.13.18). 

FATAL [2019-02-09 05:30:33] No off-target regions after filtering for mappability and 

FATAL [2019-02-09 05:30:33] off.target.padding 

FATAL [2019-02-09 05:30:33]  

FATAL [2019-02-09 05:30:33] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:30:33] parameters (PureCN 1.13.18). 

WARN [2019-02-09 05:30:33] No mappability scores provided.
INFO [2019-02-09 05:30:33] Calculating GC-content...
INFO [2019-02-09 05:30:33] Averaging reptiming into bins of size 200...
WARN [2019-02-09 05:30:33] No mappability scores provided.
INFO [2019-02-09 05:30:33] Calculating GC-content...
INFO [2019-02-09 05:30:33] Splitting 1 large targets to an average width of 200.
WARN [2019-02-09 05:30:33] No mappability scores provided.
WARN [2019-02-09 05:30:33] No reptiming scores provided.
INFO [2019-02-09 05:30:33] Calculating GC-content...
WARN [2019-02-09 05:30:33] No mappability scores provided.
WARN [2019-02-09 05:30:34] No reptiming scores provided.
INFO [2019-02-09 05:30:34] Calculating GC-content...
INFO [2019-02-09 05:30:34] Tiling off-target regions to an average width of 200000.
WARN [2019-02-09 05:30:34] No mappability scores provided.
WARN [2019-02-09 05:30:34] No reptiming scores provided.
INFO [2019-02-09 05:30:34] Calculating GC-content...
WARN [2019-02-09 05:30:34] Intervals contain off-target regions. Will not change intervals.
WARN [2019-02-09 05:30:34] No mappability scores provided.
WARN [2019-02-09 05:30:34] No reptiming scores provided.
INFO [2019-02-09 05:30:34] Calculating GC-content...
WARN [2019-02-09 05:30:34] No reptiming scores provided.
INFO [2019-02-09 05:30:34] Calculating GC-content...
WARN [2019-02-09 05:30:35] 1 intervals without mappability score (1 on-target).
INFO [2019-02-09 05:30:35] Removing 1 intervals with low mappability score (<0.50).
WARN [2019-02-09 05:30:35] No reptiming scores provided.
INFO [2019-02-09 05:30:35] Calculating GC-content...
INFO [2019-02-09 05:30:35] Tiling off-target regions to an average width of 200000.
WARN [2019-02-09 05:30:35] No reptiming scores provided.
INFO [2019-02-09 05:30:35] Calculating GC-content...
WARN [2019-02-09 05:30:36] No mappability scores provided.
WARN [2019-02-09 05:30:36] No reptiming scores provided.
INFO [2019-02-09 05:30:36] Calculating GC-content...
WARN [2019-02-09 05:30:36] Chromosome naming style of interval file (NCBI) was different from reference (UCSC).
WARN [2019-02-09 05:30:36] No mappability scores provided.
WARN [2019-02-09 05:30:36] No reptiming scores provided.
INFO [2019-02-09 05:30:36] Calculating GC-content...
FATAL [2019-02-09 05:30:36] Chromosome naming style of interval file unknown, should be UCSC. 

FATAL [2019-02-09 05:30:36]  

FATAL [2019-02-09 05:30:36] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:30:36] parameters (PureCN 1.13.18). 

WARN [2019-02-09 05:30:36] Chromosome naming style of interval file (NCBI) was different from reference (UCSC).
WARN [2019-02-09 05:30:36] Chromosome naming style of mappability file (NCBI) was different from reference (UCSC).
WARN [2019-02-09 05:30:36] No reptiming scores provided.
INFO [2019-02-09 05:30:36] Calculating GC-content...
WARN [2019-02-09 05:30:37] Found small target regions (< 60bp). Will resize them.
WARN [2019-02-09 05:30:37] No mappability scores provided.
WARN [2019-02-09 05:30:37] No reptiming scores provided.
INFO [2019-02-09 05:30:37] Calculating GC-content...
WARN [2019-02-09 05:30:37] Found small target regions (< 60bp). Will drop them.
WARN [2019-02-09 05:30:37] No mappability scores provided.
WARN [2019-02-09 05:30:37] No reptiming scores provided.
INFO [2019-02-09 05:30:37] Calculating GC-content...
WARN [2019-02-09 05:30:37] Found small target regions (< 200bp). Will resize them.
WARN [2019-02-09 05:30:37] No mappability scores provided.
WARN [2019-02-09 05:30:37] No reptiming scores provided.
INFO [2019-02-09 05:30:37] Calculating GC-content...
INFO [2019-02-09 05:30:38] 576 on-target bins with low coverage in all samples.
WARN [2019-02-09 05:30:38] You are likely not using the correct baits file!
WARN [2019-02-09 05:30:38] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:30:38] Allosome coverage missing, cannot determine sex.
INFO [2019-02-09 05:30:38] Processing on-target regions...
INFO [2019-02-09 05:30:38] Removing 930 intervals with low coverage in normalDB.
INFO [2019-02-09 05:30:38] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2019-02-09 05:30:50] Loading coverage data...
INFO [2019-02-09 05:31:22] Mean target coverages: 71X (tumor) 99X (normal).
INFO [2019-02-09 05:31:22] Mean target coverages: 71X (tumor) 43X (normal).
INFO [2019-02-09 05:31:24] Interval weights found, but currently not supported by copynumber. Will simply exclude intervals with low weight.
multipcf finished for chromosome arm 1p 
multipcf finished for chromosome arm 1q 
multipcf finished for chromosome arm 2p 
multipcf finished for chromosome arm 2q 
multipcf finished for chromosome arm 3p 
multipcf finished for chromosome arm 3q 
multipcf finished for chromosome arm 4p 
multipcf finished for chromosome arm 4q 
multipcf finished for chromosome arm 5p 
multipcf finished for chromosome arm 5q 
multipcf finished for chromosome arm 6p 
multipcf finished for chromosome arm 6q 
multipcf finished for chromosome arm 7p 
multipcf finished for chromosome arm 7q 
multipcf finished for chromosome arm 8p 
multipcf finished for chromosome arm 8q 
multipcf finished for chromosome arm 9p 
multipcf finished for chromosome arm 9q 
multipcf finished for chromosome arm 10p 
multipcf finished for chromosome arm 10q 
multipcf finished for chromosome arm 11p 
multipcf finished for chromosome arm 11q 
multipcf finished for chromosome arm 12p 
multipcf finished for chromosome arm 12q 
multipcf finished for chromosome arm 13q 
multipcf finished for chromosome arm 14q 
multipcf finished for chromosome arm 15q 
multipcf finished for chromosome arm 16p 
multipcf finished for chromosome arm 16q 
multipcf finished for chromosome arm 17p 
multipcf finished for chromosome arm 17q 
multipcf finished for chromosome arm 18p 
multipcf finished for chromosome arm 18q 
multipcf finished for chromosome arm 19p 
multipcf finished for chromosome arm 19q 
multipcf finished for chromosome arm 20p 
multipcf finished for chromosome arm 20q 
multipcf finished for chromosome arm 21q 
multipcf finished for chromosome arm 22q 
INFO [2019-02-09 05:31:27] ------------------------------------------------------------
INFO [2019-02-09 05:31:27] PureCN 1.13.18
INFO [2019-02-09 05:31:27] ------------------------------------------------------------
INFO [2019-02-09 05:31:27] Loading coverage files...
INFO [2019-02-09 05:31:27] seg.file and normal.coverage.file provided. Using both.
INFO [2019-02-09 05:31:27] Mean target coverages: 112X (tumor) 105X (normal).
WARN [2019-02-09 05:31:27] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:31:27] Allosome coverage missing, cannot determine sex.
INFO [2019-02-09 05:31:27] Removing 199 intervals with missing log.ratio.
INFO [2019-02-09 05:31:27] Using 9850 intervals (9850 on-target, 0 off-target).
INFO [2019-02-09 05:31:27] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2019-02-09 05:31:27] Loading VCF...
INFO [2019-02-09 05:31:27] Found 127 variants in VCF file.
INFO [2019-02-09 05:31:27] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2019-02-09 05:31:28] LIB-02240e4 is tumor in VCF file.
INFO [2019-02-09 05:31:28] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2019-02-09 05:31:28] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2019-02-09 05:31:28] Removing 1 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2019-02-09 05:31:28] Removing 0 low quality variants with BQ < 25.
INFO [2019-02-09 05:31:28] Total size of targeted genomic region: 1.68Mb (2.66Mb with 50bp padding).
INFO [2019-02-09 05:31:29] 1.0% of targets contain variants.
INFO [2019-02-09 05:31:29] Removing 0 variants outside intervals.
INFO [2019-02-09 05:31:29] Found SOMATIC annotation in VCF.
INFO [2019-02-09 05:31:29] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2019-02-09 05:31:29] Found SOMATIC annotation in VCF. Setting mapping bias to 0.976.
INFO [2019-02-09 05:31:29] Excluding 0 novel or poor quality variants from segmentation.
INFO [2019-02-09 05:31:29] Sample sex: ?
INFO [2019-02-09 05:31:29] Segmenting data...
INFO [2019-02-09 05:31:29] Loaded provided segmentation file file1f30374a570c.seg.
INFO [2019-02-09 05:31:29] Setting prune.hclust.h parameter to 0.200000.
INFO [2019-02-09 05:31:29] Found 60 segments with median size of 29.97Mb.
INFO [2019-02-09 05:31:29] Using 125 variants.
INFO [2019-02-09 05:31:29] Mean standard deviation of log-ratios: 0.34
INFO [2019-02-09 05:31:29] 2D-grid search of purity and ploidy...
INFO [2019-02-09 05:31:30] Local optima: 0.6/1.9, 0.4/2.1
INFO [2019-02-09 05:31:30] Testing local optimum 1/2 at purity 0.60 and total ploidy 1.90...
INFO [2019-02-09 05:31:31] Testing local optimum 2/2 at purity 0.40 and total ploidy 2.10...
INFO [2019-02-09 05:31:31] Recalibrating log-ratios...
INFO [2019-02-09 05:31:31] Testing local optimum 2/2 at purity 0.40 and total ploidy 2.10...
INFO [2019-02-09 05:31:32] Recalibrating log-ratios...
INFO [2019-02-09 05:31:32] Testing local optimum 2/2 at purity 0.40 and total ploidy 2.10...
INFO [2019-02-09 05:31:32] Recalibrating log-ratios...
INFO [2019-02-09 05:31:32] Testing local optimum 2/2 at purity 0.40 and total ploidy 2.10...
INFO [2019-02-09 05:31:33] Skipping 1 solutions exceeding max.non.clonal (0.20).
INFO [2019-02-09 05:31:33] Fitting variants for local optimum 1/2...
INFO [2019-02-09 05:31:33] Fitting variants for purity 0.60, tumor ploidy 1.76 and contamination 0.01.
INFO [2019-02-09 05:31:34] Fitting variants for purity 0.40, tumor ploidy 1.76 and contamination 0.01.
INFO [2019-02-09 05:31:35] Fitting variants for purity 0.45, tumor ploidy 1.76 and contamination 0.01.
INFO [2019-02-09 05:31:36] Fitting variants for purity 0.50, tumor ploidy 1.76 and contamination 0.01.
INFO [2019-02-09 05:31:37] Fitting variants for purity 0.55, tumor ploidy 1.76 and contamination 0.01.
INFO [2019-02-09 05:31:38] Fitting variants for purity 0.65, tumor ploidy 1.76 and contamination 0.01.
INFO [2019-02-09 05:31:39] Fitting variants for purity 0.70, tumor ploidy 1.76 and contamination 0.01.
INFO [2019-02-09 05:31:40] Optimized purity: 0.65
INFO [2019-02-09 05:31:40] Done.
INFO [2019-02-09 05:31:40] ------------------------------------------------------------
INFO [2019-02-09 05:31:56] Loading coverage data...
INFO [2019-02-09 05:31:57] Mean target coverages: 71X (tumor) 99X (normal).
INFO [2019-02-09 05:31:57] Mean target coverages: 71X (tumor) 43X (normal).
INFO [2019-02-09 05:31:58] ------------------------------------------------------------
INFO [2019-02-09 05:31:58] PureCN 1.13.18
INFO [2019-02-09 05:31:58] ------------------------------------------------------------
INFO [2019-02-09 05:31:58] Using BiocParallel for parallel optimization.
INFO [2019-02-09 05:31:58] Loading coverage files...
INFO [2019-02-09 05:31:58] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2019-02-09 05:31:58] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:31:58] Allosome coverage missing, cannot determine sex.
INFO [2019-02-09 05:31:58] Removing 228 intervals with missing log.ratio.
INFO [2019-02-09 05:31:58] Removing 22 small (< 5bp) intervals.
INFO [2019-02-09 05:31:58] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2019-02-09 05:31:58] No normalDB provided. Provide one for better results.
INFO [2019-02-09 05:31:58] Removing 233 low coverage (< 15.0000X) intervals.
INFO [2019-02-09 05:31:58] Using 9547 intervals (9547 on-target, 0 off-target).
INFO [2019-02-09 05:31:58] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2019-02-09 05:31:58] No interval.file provided. Cannot check if data was GC-normalized. Was it?
INFO [2019-02-09 05:31:58] Sample sex: ?
INFO [2019-02-09 05:31:58] Segmenting data...
INFO [2019-02-09 05:31:58] Interval weights found, will use weighted CBS.
INFO [2019-02-09 05:31:58] Loading pre-computed boundaries for DNAcopy...
INFO [2019-02-09 05:31:58] Setting undo.SD parameter to 1.000000.
Setting multi-figure configuration
INFO [2019-02-09 05:31:59] Found 54 segments with median size of 25.38Mb.
INFO [2019-02-09 05:31:59] Mean standard deviation of log-ratios: 0.37
INFO [2019-02-09 05:31:59] 2D-grid search of purity and ploidy...
INFO [2019-02-09 05:31:59] 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 [2019-02-09 05:32:50] Skipping 3 solutions that converged to the same optima.
INFO [2019-02-09 05:32:50] Skipping 1 solutions exceeding max.non.clonal (0.20).
INFO [2019-02-09 05:32:50] Done.
INFO [2019-02-09 05:32:50] ------------------------------------------------------------
INFO [2019-02-09 05:32:50] Reading C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\Rtmp0efuTi\file1f3013f319d0.rds...
FATAL [2019-02-09 05:32:50] runAbsoluteCN was run without a VCF file. 

FATAL [2019-02-09 05:32:50]  

FATAL [2019-02-09 05:32:50] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:32:50] parameters (PureCN 1.13.18). 

FATAL [2019-02-09 05:32:50] runAbsoluteCN was run without a VCF file. 

FATAL [2019-02-09 05:32:50]  

FATAL [2019-02-09 05:32:50] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:32:50] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:32:50] ------------------------------------------------------------
INFO [2019-02-09 05:32:50] PureCN 1.13.18
INFO [2019-02-09 05:32:50] ------------------------------------------------------------
INFO [2019-02-09 05:32:50] Loading coverage files...
FATAL [2019-02-09 05:32:51] Need a normal coverage file if log.ratio and seg.file are not provided. 

FATAL [2019-02-09 05:32:51]  

FATAL [2019-02-09 05:32:51] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:32:51] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:32:51] ------------------------------------------------------------
INFO [2019-02-09 05:32:51] PureCN 1.13.18
INFO [2019-02-09 05:32:51] ------------------------------------------------------------
FATAL [2019-02-09 05:32:51] min.ploidy or max.ploidy not within expected range. 

FATAL [2019-02-09 05:32:51]  

FATAL [2019-02-09 05:32:51] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:32:51] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:32:51] ------------------------------------------------------------
INFO [2019-02-09 05:32:51] PureCN 1.13.18
INFO [2019-02-09 05:32:51] ------------------------------------------------------------
FATAL [2019-02-09 05:32:51] min.ploidy or max.ploidy not within expected range. 

FATAL [2019-02-09 05:32:51]  

FATAL [2019-02-09 05:32:51] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:32:51] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:32:51] ------------------------------------------------------------
INFO [2019-02-09 05:32:51] PureCN 1.13.18
INFO [2019-02-09 05:32:51] ------------------------------------------------------------
INFO [2019-02-09 05:32:51] ------------------------------------------------------------
INFO [2019-02-09 05:32:51] PureCN 1.13.18
INFO [2019-02-09 05:32:51] ------------------------------------------------------------
INFO [2019-02-09 05:32:51] ------------------------------------------------------------
INFO [2019-02-09 05:32:51] PureCN 1.13.18
INFO [2019-02-09 05:32:51] ------------------------------------------------------------
FATAL [2019-02-09 05:32:51] test.num.copy not within expected range. 

FATAL [2019-02-09 05:32:51]  

FATAL [2019-02-09 05:32:51] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:32:51] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:32:51] ------------------------------------------------------------
INFO [2019-02-09 05:32:51] PureCN 1.13.18
INFO [2019-02-09 05:32:51] ------------------------------------------------------------
WARN [2019-02-09 05:32:51] test.num.copy outside recommended range.
FATAL [2019-02-09 05:32:51] max.non.clonal not within expected range or format. 

FATAL [2019-02-09 05:32:51]  

FATAL [2019-02-09 05:32:51] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:32:51] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:32:51] ------------------------------------------------------------
INFO [2019-02-09 05:32:51] PureCN 1.13.18
INFO [2019-02-09 05:32:51] ------------------------------------------------------------
WARN [2019-02-09 05:32:51] test.num.copy outside recommended range.
FATAL [2019-02-09 05:32:51] max.non.clonal not within expected range or format. 

FATAL [2019-02-09 05:32:51]  

FATAL [2019-02-09 05:32:51] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:32:51] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:32:51] ------------------------------------------------------------
INFO [2019-02-09 05:32:51] PureCN 1.13.18
INFO [2019-02-09 05:32:51] ------------------------------------------------------------
FATAL [2019-02-09 05:32:51] test.purity not within expected range. 

FATAL [2019-02-09 05:32:51]  

FATAL [2019-02-09 05:32:51] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:32:51] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:32:51] ------------------------------------------------------------
INFO [2019-02-09 05:32:51] PureCN 1.13.18
INFO [2019-02-09 05:32:51] ------------------------------------------------------------
INFO [2019-02-09 05:32:51] Loading coverage files...
FATAL [2019-02-09 05:32:51] Tumor and normal are identical. This won't give any meaningful results 

FATAL [2019-02-09 05:32:51] and I'm stopping here. 

FATAL [2019-02-09 05:32:51]  

FATAL [2019-02-09 05:32:51] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:32:51] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:32:51] ------------------------------------------------------------
INFO [2019-02-09 05:32:51] PureCN 1.13.18
INFO [2019-02-09 05:32:51] ------------------------------------------------------------
INFO [2019-02-09 05:32:51] Loading coverage files...
FATAL [2019-02-09 05:32:52] Length of log.ratio different from tumor coverage. 

FATAL [2019-02-09 05:32:52]  

FATAL [2019-02-09 05:32:52] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:32:52] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:32:52] ------------------------------------------------------------
INFO [2019-02-09 05:32:52] PureCN 1.13.18
INFO [2019-02-09 05:32:52] ------------------------------------------------------------
FATAL [2019-02-09 05:32:52] prior.purity must have the same length as test.purity. 

FATAL [2019-02-09 05:32:52]  

FATAL [2019-02-09 05:32:52] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:32:52] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:32:52] ------------------------------------------------------------
INFO [2019-02-09 05:32:52] PureCN 1.13.18
INFO [2019-02-09 05:32:52] ------------------------------------------------------------
FATAL [2019-02-09 05:32:52] min.gof not within expected range or format. 

FATAL [2019-02-09 05:32:52]  

FATAL [2019-02-09 05:32:52] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:32:52] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:32:52] ------------------------------------------------------------
INFO [2019-02-09 05:32:52] PureCN 1.13.18
INFO [2019-02-09 05:32:52] ------------------------------------------------------------
FATAL [2019-02-09 05:32:52] prior.purity not within expected range or format. 

FATAL [2019-02-09 05:32:52]  

FATAL [2019-02-09 05:32:52] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:32:52] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:32:52] ------------------------------------------------------------
INFO [2019-02-09 05:32:52] PureCN 1.13.18
INFO [2019-02-09 05:32:52] ------------------------------------------------------------
FATAL [2019-02-09 05:32:52] prior.purity must add to 1. Sum is 1.5 

FATAL [2019-02-09 05:32:52]  

FATAL [2019-02-09 05:32:52] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:32:52] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:32:52] ------------------------------------------------------------
INFO [2019-02-09 05:32:52] PureCN 1.13.18
INFO [2019-02-09 05:32:52] ------------------------------------------------------------
FATAL [2019-02-09 05:32:52] max.homozygous.loss not within expected range or format. 

FATAL [2019-02-09 05:32:52]  

FATAL [2019-02-09 05:32:52] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:32:52] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:32:52] ------------------------------------------------------------
INFO [2019-02-09 05:32:52] PureCN 1.13.18
INFO [2019-02-09 05:32:52] ------------------------------------------------------------
FATAL [2019-02-09 05:32:52] prior.K not within expected range or format. 

FATAL [2019-02-09 05:32:52]  

FATAL [2019-02-09 05:32:52] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:32:52] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:32:52] ------------------------------------------------------------
INFO [2019-02-09 05:32:52] PureCN 1.13.18
INFO [2019-02-09 05:32:52] ------------------------------------------------------------
FATAL [2019-02-09 05:32:52] prior.contamination not within expected range or format. 

FATAL [2019-02-09 05:32:52]  

FATAL [2019-02-09 05:32:52] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:32:52] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:32:52] ------------------------------------------------------------
INFO [2019-02-09 05:32:52] PureCN 1.13.18
INFO [2019-02-09 05:32:52] ------------------------------------------------------------
FATAL [2019-02-09 05:32:52] Iterations not in the expected range from 10 to 250. 

FATAL [2019-02-09 05:32:52]  

FATAL [2019-02-09 05:32:52] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:32:52] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:32:52] ------------------------------------------------------------
INFO [2019-02-09 05:32:52] PureCN 1.13.18
INFO [2019-02-09 05:32:52] ------------------------------------------------------------
FATAL [2019-02-09 05:32:52] Iterations not in the expected range from 10 to 250. 

FATAL [2019-02-09 05:32:52]  

FATAL [2019-02-09 05:32:52] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:32:52] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:32:52] ------------------------------------------------------------
INFO [2019-02-09 05:32:52] PureCN 1.13.18
INFO [2019-02-09 05:32:52] ------------------------------------------------------------
INFO [2019-02-09 05:32:52] Loading coverage files...
FATAL [2019-02-09 05:32:52] Missing tumor.coverage.file requires seg.file or log.ratio and 

FATAL [2019-02-09 05:32:52] interval.file. 

FATAL [2019-02-09 05:32:52]  

FATAL [2019-02-09 05:32:52] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:32:52] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:32:52] ------------------------------------------------------------
INFO [2019-02-09 05:32:52] PureCN 1.13.18
INFO [2019-02-09 05:32:52] ------------------------------------------------------------
INFO [2019-02-09 05:32:52] ------------------------------------------------------------
INFO [2019-02-09 05:32:52] PureCN 1.13.18
INFO [2019-02-09 05:32:52] ------------------------------------------------------------
INFO [2019-02-09 05:32:52] Loading coverage files...
FATAL [2019-02-09 05:32:53] Interval files in normal and tumor different. 

FATAL [2019-02-09 05:32:53]  

FATAL [2019-02-09 05:32:53] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:32:53] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:32:53] ------------------------------------------------------------
INFO [2019-02-09 05:32:53] PureCN 1.13.18
INFO [2019-02-09 05:32:53] ------------------------------------------------------------
INFO [2019-02-09 05:32:53] Loading coverage files...
INFO [2019-02-09 05:32:53] Mean target coverages: 0X (tumor) 99X (normal).
WARN [2019-02-09 05:32:53] Large difference in coverage of tumor and normal.
WARN [2019-02-09 05:32:53] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:32:53] Allosome coverage missing, cannot determine sex.
INFO [2019-02-09 05:32:53] Removing 10049 intervals with missing log.ratio.
WARN [2019-02-09 05:32:53] No normalDB provided. Provide one for better results.
INFO [2019-02-09 05:32:53] Using 0 intervals (0 on-target, 0 off-target).
FATAL [2019-02-09 05:32:53] No intervals passing filters. 

FATAL [2019-02-09 05:32:53]  

FATAL [2019-02-09 05:32:53] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:32:53] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:32:53] ------------------------------------------------------------
INFO [2019-02-09 05:32:53] PureCN 1.13.18
INFO [2019-02-09 05:32:53] ------------------------------------------------------------
INFO [2019-02-09 05:32:53] Loading coverage files...
INFO [2019-02-09 05:32:54] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2019-02-09 05:32:54] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:32:54] Allosome coverage missing, cannot determine sex.
INFO [2019-02-09 05:32:54] Removing 228 intervals with missing log.ratio.
INFO [2019-02-09 05:32:54] Removing 22 small (< 5bp) intervals.
INFO [2019-02-09 05:32:54] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2019-02-09 05:32:54] No normalDB provided. Provide one for better results.
INFO [2019-02-09 05:32:54] Removing 233 low coverage (< 15.0000X) intervals.
INFO [2019-02-09 05:32:54] Using 9547 intervals (9547 on-target, 0 off-target).
INFO [2019-02-09 05:32:54] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2019-02-09 05:32:54] No interval.file provided. Cannot check if data was GC-normalized. Was it?
INFO [2019-02-09 05:32:54] Loading VCF...
INFO [2019-02-09 05:32:54] Found 127 variants in VCF file.
INFO [2019-02-09 05:32:54] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2019-02-09 05:32:54] LIB-02240e4 is tumor in VCF file.
INFO [2019-02-09 05:32:54] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2019-02-09 05:32:55] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2019-02-09 05:32:55] Removing 1 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2019-02-09 05:32:55] Removing 0 low quality variants with BQ < 25.
INFO [2019-02-09 05:32:55] Total size of targeted genomic region: 1.63Mb (2.58Mb with 50bp padding).
INFO [2019-02-09 05:32:55] 1.0% of targets contain variants.
INFO [2019-02-09 05:32:55] Removing 2 variants outside intervals.
INFO [2019-02-09 05:32:55] Found SOMATIC annotation in VCF.
INFO [2019-02-09 05:32:55] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2019-02-09 05:32:55] Found SOMATIC annotation in VCF. Setting mapping bias to 0.973.
INFO [2019-02-09 05:32:55] Excluding 0 novel or poor quality variants from segmentation.
INFO [2019-02-09 05:32:55] Sample sex: ?
INFO [2019-02-09 05:32:55] Segmenting data...
INFO [2019-02-09 05:32:55] Loading pre-computed boundaries for DNAcopy...
INFO [2019-02-09 05:32:55] Setting undo.SD parameter to 1.000000.
INFO [2019-02-09 05:32:56] Setting prune.hclust.h parameter to 0.200000.
INFO [2019-02-09 05:32:56] Found 54 segments with median size of 24.88Mb.
INFO [2019-02-09 05:32:57] Using 123 variants.
INFO [2019-02-09 05:32:57] Mean standard deviation of log-ratios: 0.37
INFO [2019-02-09 05:32:57] 2D-grid search of purity and ploidy...
INFO [2019-02-09 05:32:58] Local optima: 0.62/1.9, 0.3/1.9, 0.32/2
INFO [2019-02-09 05:32:58] Testing local optimum 1/3 at purity 0.62 and total ploidy 1.90...
INFO [2019-02-09 05:32:59] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2019-02-09 05:32:59] Recalibrating log-ratios...
INFO [2019-02-09 05:32:59] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2019-02-09 05:33:00] Recalibrating log-ratios...
INFO [2019-02-09 05:33:00] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2019-02-09 05:33:00] Recalibrating log-ratios...
INFO [2019-02-09 05:33:00] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2019-02-09 05:33:00] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2019-02-09 05:33:01] Recalibrating log-ratios...
INFO [2019-02-09 05:33:01] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2019-02-09 05:33:01] Recalibrating log-ratios...
INFO [2019-02-09 05:33:01] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2019-02-09 05:33:01] Recalibrating log-ratios...
INFO [2019-02-09 05:33:01] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2019-02-09 05:33:02] Skipping 1 solutions that converged to the same optima.
INFO [2019-02-09 05:33:02] Skipping 1 solutions exceeding max.non.clonal (0.20).
INFO [2019-02-09 05:33:02] Fitting variants for local optimum 1/3...
INFO [2019-02-09 05:33:02] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01.
INFO [2019-02-09 05:33:03] Optimized purity: 0.65
INFO [2019-02-09 05:33:03] Done.
INFO [2019-02-09 05:33:03] ------------------------------------------------------------
INFO [2019-02-09 05:33:03] ------------------------------------------------------------
INFO [2019-02-09 05:33:03] PureCN 1.13.18
INFO [2019-02-09 05:33:03] ------------------------------------------------------------
INFO [2019-02-09 05:33:03] Loading coverage files...
INFO [2019-02-09 05:33:03] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2019-02-09 05:33:03] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:33:03] Allosome coverage missing, cannot determine sex.
INFO [2019-02-09 05:33:03] Removing 228 intervals with missing log.ratio.
INFO [2019-02-09 05:33:03] Removing 22 small (< 5bp) intervals.
INFO [2019-02-09 05:33:03] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2019-02-09 05:33:03] No normalDB provided. Provide one for better results.
INFO [2019-02-09 05:33:03] Removing 233 low coverage (< 15.0000X) intervals.
INFO [2019-02-09 05:33:03] Using 9547 intervals (9547 on-target, 0 off-target).
INFO [2019-02-09 05:33:03] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2019-02-09 05:33:03] No interval.file provided. Cannot check if data was GC-normalized. Was it?
INFO [2019-02-09 05:33:03] Loading VCF...
INFO [2019-02-09 05:33:03] Found 127 variants in VCF file.
WARN [2019-02-09 05:33:03] DP FORMAT field contains NAs. Removing 3 variants.
WARN [2019-02-09 05:33:03] DB INFO flag contains NAs
INFO [2019-02-09 05:33:03] 119 (96.0%) variants annotated as likely germline (DB INFO flag).
INFO [2019-02-09 05:33:04] LIB-02240e4 is tumor in VCF file.
INFO [2019-02-09 05:33:04] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2019-02-09 05:33:04] Removing 1 variants with AF < 0.030 or AF >= 0.970 or less than 4 supporting reads or depth < 15.
INFO [2019-02-09 05:33:04] Removing 0 low quality variants with BQ < 25.
INFO [2019-02-09 05:33:04] Total size of targeted genomic region: 1.63Mb (2.58Mb with 50bp padding).
INFO [2019-02-09 05:33:04] 1.0% of targets contain variants.
INFO [2019-02-09 05:33:04] Setting somatic prior probabilities for dbSNP hits to 0.000500 or to 0.500000 otherwise.
INFO [2019-02-09 05:33:04] Excluding 5 novel or poor quality variants from segmentation.
INFO [2019-02-09 05:33:04] Sample sex: ?
INFO [2019-02-09 05:33:04] Segmenting data...
INFO [2019-02-09 05:33:04] Loading pre-computed boundaries for DNAcopy...
INFO [2019-02-09 05:33:04] Setting undo.SD parameter to 1.000000.
Setting multi-figure configuration
INFO [2019-02-09 05:33:06] Setting prune.hclust.h parameter to 0.200000.
INFO [2019-02-09 05:33:06] Found 54 segments with median size of 24.88Mb.
INFO [2019-02-09 05:33:06] Using 123 variants.
INFO [2019-02-09 05:33:06] Mean standard deviation of log-ratios: 0.37
INFO [2019-02-09 05:33:06] 2D-grid search of purity and ploidy...
INFO [2019-02-09 05:33:07] Local optima: 0.62/1.9, 0.3/1.9, 0.32/2
INFO [2019-02-09 05:33:07] Testing local optimum 1/3 at purity 0.62 and total ploidy 1.90...
INFO [2019-02-09 05:33:08] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2019-02-09 05:33:09] Recalibrating log-ratios...
INFO [2019-02-09 05:33:09] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2019-02-09 05:33:09] Recalibrating log-ratios...
INFO [2019-02-09 05:33:09] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2019-02-09 05:33:09] Recalibrating log-ratios...
INFO [2019-02-09 05:33:09] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90...
INFO [2019-02-09 05:33:10] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2019-02-09 05:33:10] Recalibrating log-ratios...
INFO [2019-02-09 05:33:10] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2019-02-09 05:33:10] Recalibrating log-ratios...
INFO [2019-02-09 05:33:10] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2019-02-09 05:33:11] Recalibrating log-ratios...
INFO [2019-02-09 05:33:11] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00...
INFO [2019-02-09 05:33:11] Skipping 1 solutions that converged to the same optima.
INFO [2019-02-09 05:33:11] Skipping 1 solutions exceeding max.non.clonal (0.20).
INFO [2019-02-09 05:33:11] Fitting variants for local optimum 1/3...
INFO [2019-02-09 05:33:11] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01.
INFO [2019-02-09 05:33:12] Optimized purity: 0.65
INFO [2019-02-09 05:33:12] Done.
INFO [2019-02-09 05:33:12] ------------------------------------------------------------
INFO [2019-02-09 05:33:12] ------------------------------------------------------------
INFO [2019-02-09 05:33:12] PureCN 1.13.18
INFO [2019-02-09 05:33:12] ------------------------------------------------------------
INFO [2019-02-09 05:33:12] Loading coverage files...
INFO [2019-02-09 05:33:13] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2019-02-09 05:33:13] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:33:13] Allosome coverage missing, cannot determine sex.
INFO [2019-02-09 05:33:13] No Gene column in interval.file. You won't get gene-level calls.
INFO [2019-02-09 05:33:13] Removing 228 intervals with missing log.ratio.
INFO [2019-02-09 05:33:13] Removing 15 low/high GC targets.
INFO [2019-02-09 05:33:13] Removing 21 small (< 5bp) intervals.
INFO [2019-02-09 05:33:13] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2019-02-09 05:33:13] No normalDB provided. Provide one for better results.
INFO [2019-02-09 05:33:13] Removing 232 low coverage (< 15.0000X) intervals.
INFO [2019-02-09 05:33:13] Using 9534 intervals (9534 on-target, 0 off-target).
INFO [2019-02-09 05:33:13] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2019-02-09 05:33:13] AT/GC dropout: 1.03 (tumor), 1.03 (normal). 
INFO [2019-02-09 05:33:13] Loading VCF...
INFO [2019-02-09 05:33:13] Found 127 variants in VCF file.
INFO [2019-02-09 05:33:14] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2019-02-09 05:33:14] LIB-02240e4 is tumor in VCF file.
INFO [2019-02-09 05:33:14] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2019-02-09 05:33:14] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2019-02-09 05:33:14] Removing 1 variants with AF < 0.030 or AF >= Inf or less than 4 supporting reads or depth < 15.
INFO [2019-02-09 05:33:14] Removing 0 low quality variants with BQ < 25.
INFO [2019-02-09 05:33:14] Total size of targeted genomic region: 1.63Mb (2.58Mb with 50bp padding).
INFO [2019-02-09 05:33:14] 1.0% of targets contain variants.
INFO [2019-02-09 05:33:14] Removing 2 variants outside intervals.
INFO [2019-02-09 05:33:15] Found SOMATIC annotation in VCF.
INFO [2019-02-09 05:33:15] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2019-02-09 05:33:15] Found SOMATIC annotation in VCF. Setting mapping bias to 0.973.
INFO [2019-02-09 05:33:15] Excluding 0 novel or poor quality variants from segmentation.
INFO [2019-02-09 05:33:15] Sample sex: ?
INFO [2019-02-09 05:33:15] Segmenting data...
INFO [2019-02-09 05:33:15] Using unweighted PSCBS.
INFO [2019-02-09 05:33:15] Setting undo.SD parameter to 1.000000.
INFO [2019-02-09 05:33:35] Setting prune.hclust.h parameter to 0.200000.
INFO [2019-02-09 05:33:35] Found 72 segments with median size of 26.71Mb.
INFO [2019-02-09 05:33:35] Using 123 variants.
INFO [2019-02-09 05:33:35] Mean standard deviation of log-ratios: 0.37
INFO [2019-02-09 05:33:35] 2D-grid search of purity and ploidy...
INFO [2019-02-09 05:33:35] 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 [2019-02-09 05:33:35] Testing local optimum 1/6 at purity 0.65 and total ploidy 1.90...
INFO [2019-02-09 05:33:35] Recalibrating log-ratios...
INFO [2019-02-09 05:33:35] Testing local optimum 1/6 at purity 0.65 and total ploidy 1.90...
INFO [2019-02-09 05:33:36] Recalibrating log-ratios...
INFO [2019-02-09 05:33:36] Testing local optimum 1/6 at purity 0.65 and total ploidy 1.90...
INFO [2019-02-09 05:33:36] Recalibrating log-ratios...
INFO [2019-02-09 05:33:36] Testing local optimum 1/6 at purity 0.65 and total ploidy 1.90...
INFO [2019-02-09 05:33:37] Testing local optimum 2/6 at purity 0.33 and total ploidy 1.90...
INFO [2019-02-09 05:33:37] Recalibrating log-ratios...
INFO [2019-02-09 05:33:37] Testing local optimum 2/6 at purity 0.33 and total ploidy 1.90...
INFO [2019-02-09 05:33:38] Recalibrating log-ratios...
INFO [2019-02-09 05:33:38] Testing local optimum 2/6 at purity 0.33 and total ploidy 1.90...
INFO [2019-02-09 05:33:38] Recalibrating log-ratios...
INFO [2019-02-09 05:33:38] Testing local optimum 2/6 at purity 0.33 and total ploidy 1.90...
INFO [2019-02-09 05:33:39] Testing local optimum 3/6 at purity 0.38 and total ploidy 2.20...
INFO [2019-02-09 05:33:41] Testing local optimum 4/6 at purity 0.27 and total ploidy 2.10...
INFO [2019-02-09 05:33:41] Recalibrating log-ratios...
INFO [2019-02-09 05:33:41] Testing local optimum 4/6 at purity 0.27 and total ploidy 2.10...
INFO [2019-02-09 05:33:42] Recalibrating log-ratios...
INFO [2019-02-09 05:33:42] Testing local optimum 4/6 at purity 0.27 and total ploidy 2.10...
INFO [2019-02-09 05:33:43] Recalibrating log-ratios...
INFO [2019-02-09 05:33:43] Testing local optimum 4/6 at purity 0.27 and total ploidy 2.10...
INFO [2019-02-09 05:33:44] Testing local optimum 5/6 at purity 0.29 and total ploidy 2.00...
INFO [2019-02-09 05:33:44] Recalibrating log-ratios...
INFO [2019-02-09 05:33:44] Testing local optimum 5/6 at purity 0.29 and total ploidy 2.00...
INFO [2019-02-09 05:33:45] Recalibrating log-ratios...
INFO [2019-02-09 05:33:45] Testing local optimum 5/6 at purity 0.29 and total ploidy 2.00...
INFO [2019-02-09 05:33:45] Recalibrating log-ratios...
INFO [2019-02-09 05:33:45] Testing local optimum 5/6 at purity 0.29 and total ploidy 2.00...
INFO [2019-02-09 05:33:46] Testing local optimum 6/6 at purity 0.78 and total ploidy 2.00...
INFO [2019-02-09 05:33:46] Recalibrating log-ratios...
INFO [2019-02-09 05:33:46] Testing local optimum 6/6 at purity 0.78 and total ploidy 2.00...
INFO [2019-02-09 05:33:47] Recalibrating log-ratios...
INFO [2019-02-09 05:33:47] Testing local optimum 6/6 at purity 0.78 and total ploidy 2.00...
INFO [2019-02-09 05:33:47] Recalibrating log-ratios...
INFO [2019-02-09 05:33:47] Testing local optimum 6/6 at purity 0.78 and total ploidy 2.00...
INFO [2019-02-09 05:33:47] Skipping 1 solutions that converged to the same optima.
INFO [2019-02-09 05:33:47] Skipping 4 solutions exceeding max.non.clonal (0.20).
INFO [2019-02-09 05:33:47] Fitting variants for local optimum 3/6...
INFO [2019-02-09 05:33:47] Fitting variants for purity 0.40, tumor ploidy 2.55 and contamination 0.01.
INFO [2019-02-09 05:33:49] Optimized purity: 0.40
INFO [2019-02-09 05:33:49] Done.
INFO [2019-02-09 05:33:49] ------------------------------------------------------------
FATAL [2019-02-09 05:33:49] This function requires gene-level calls. Please add a column 'Gene' 

FATAL [2019-02-09 05:33:49] containing gene symbols to the interval.file. 

FATAL [2019-02-09 05:33:49]  

FATAL [2019-02-09 05:33:49] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:33:49] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:33:50] ------------------------------------------------------------
INFO [2019-02-09 05:33:50] PureCN 1.13.18
INFO [2019-02-09 05:33:50] ------------------------------------------------------------
INFO [2019-02-09 05:33:50] Loading coverage files...
INFO [2019-02-09 05:33:50] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2019-02-09 05:33:50] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:33:50] Allosome coverage missing, cannot determine sex.
INFO [2019-02-09 05:33:50] Removing 228 intervals with missing log.ratio.
INFO [2019-02-09 05:33:50] Removing 22 small (< 5bp) intervals.
INFO [2019-02-09 05:33:50] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2019-02-09 05:33:50] No normalDB provided. Provide one for better results.
INFO [2019-02-09 05:33:51] Removing 233 low coverage (< 15.0000X) intervals.
INFO [2019-02-09 05:33:51] Using 9547 intervals (9547 on-target, 0 off-target).
INFO [2019-02-09 05:33:51] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2019-02-09 05:33:51] No interval.file provided. Cannot check if data was GC-normalized. Was it?
INFO [2019-02-09 05:33:51] Loading VCF...
INFO [2019-02-09 05:33:51] Found 127 variants in VCF file.
INFO [2019-02-09 05:33:51] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
FATAL [2019-02-09 05:33:51] Different chromosome names in coverage and VCF. 

FATAL [2019-02-09 05:33:51]  

FATAL [2019-02-09 05:33:51] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:33:51] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:33:51] ------------------------------------------------------------
INFO [2019-02-09 05:33:51] PureCN 1.13.18
INFO [2019-02-09 05:33:51] ------------------------------------------------------------
INFO [2019-02-09 05:33:51] Loading coverage files...
INFO [2019-02-09 05:33:51] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2019-02-09 05:33:51] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:33:51] Allosome coverage missing, cannot determine sex.
FATAL [2019-02-09 05:33:51] tumor.coverage.file and interval.file do not align. 

FATAL [2019-02-09 05:33:51]  

FATAL [2019-02-09 05:33:51] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:33:51] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:33:51] ------------------------------------------------------------
INFO [2019-02-09 05:33:51] PureCN 1.13.18
INFO [2019-02-09 05:33:51] ------------------------------------------------------------
INFO [2019-02-09 05:33:51] Loading coverage files...
INFO [2019-02-09 05:33:51] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2019-02-09 05:33:51] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:33:51] Allosome coverage missing, cannot determine sex.
INFO [2019-02-09 05:33:52] Removing 228 intervals with missing log.ratio.
INFO [2019-02-09 05:33:52] Removing 15 low/high GC targets.
INFO [2019-02-09 05:33:52] Removing 21 small (< 5bp) intervals.
INFO [2019-02-09 05:33:52] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2019-02-09 05:33:52] No normalDB provided. Provide one for better results.
INFO [2019-02-09 05:33:52] Removing 232 low coverage (< 15.0000X) intervals.
INFO [2019-02-09 05:33:52] Using 9534 intervals (9534 on-target, 0 off-target).
INFO [2019-02-09 05:33:53] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2019-02-09 05:33:53] AT/GC dropout: 1.03 (tumor), 1.03 (normal). 
INFO [2019-02-09 05:33:53] Loading VCF...
INFO [2019-02-09 05:33:53] Found 127 variants in VCF file.
INFO [2019-02-09 05:33:53] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2019-02-09 05:33:53] LIB-02240e4 is tumor in VCF file.
INFO [2019-02-09 05:33:53] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2019-02-09 05:33:53] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2019-02-09 05:33:53] Removing 1 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2019-02-09 05:33:53] Removing 0 low quality variants with BQ < 25.
INFO [2019-02-09 05:33:53] Total size of targeted genomic region: 1.63Mb (2.58Mb with 50bp padding).
INFO [2019-02-09 05:33:54] 1.0% of targets contain variants.
INFO [2019-02-09 05:33:54] Removing 2 variants outside intervals.
INFO [2019-02-09 05:33:54] Found SOMATIC annotation in VCF.
INFO [2019-02-09 05:33:54] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2019-02-09 05:33:54] Found SOMATIC annotation in VCF. Setting mapping bias to 0.973.
INFO [2019-02-09 05:33:54] Excluding 0 novel or poor quality variants from segmentation.
INFO [2019-02-09 05:33:54] Sample sex: ?
INFO [2019-02-09 05:33:54] Segmenting data...
INFO [2019-02-09 05:33:54] Loading pre-computed boundaries for DNAcopy...
INFO [2019-02-09 05:33:54] Setting undo.SD parameter to 1.000000.
INFO [2019-02-09 05:33:55] Setting prune.hclust.h parameter to 0.200000.
INFO [2019-02-09 05:33:55] Found 54 segments with median size of 24.88Mb.
INFO [2019-02-09 05:33:55] Using 123 variants.
INFO [2019-02-09 05:33:55] Mean standard deviation of log-ratios: 0.37
INFO [2019-02-09 05:33:55] 2D-grid search of purity and ploidy...
INFO [2019-02-09 05:33:56] Local optima: 0.63/1.9, 0.4/2.1
INFO [2019-02-09 05:33:56] Testing local optimum 1/2 at purity 0.63 and total ploidy 1.90...
INFO [2019-02-09 05:33:57] Testing local optimum 2/2 at purity 0.40 and total ploidy 2.10...
INFO [2019-02-09 05:33:58] Recalibrating log-ratios...
INFO [2019-02-09 05:33:58] Testing local optimum 2/2 at purity 0.40 and total ploidy 2.10...
INFO [2019-02-09 05:33:58] Recalibrating log-ratios...
INFO [2019-02-09 05:33:58] Testing local optimum 2/2 at purity 0.40 and total ploidy 2.10...
INFO [2019-02-09 05:33:59] Recalibrating log-ratios...
INFO [2019-02-09 05:33:59] Testing local optimum 2/2 at purity 0.40 and total ploidy 2.10...
INFO [2019-02-09 05:33:59] Skipping 1 solutions exceeding max.non.clonal (0.20).
INFO [2019-02-09 05:33:59] Fitting variants for local optimum 1/2...
INFO [2019-02-09 05:33:59] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01.
INFO [2019-02-09 05:34:00] Optimized purity: 0.65
INFO [2019-02-09 05:34:00] Done.
INFO [2019-02-09 05:34:00] ------------------------------------------------------------
INFO [2019-02-09 05:34:00] ------------------------------------------------------------
INFO [2019-02-09 05:34:00] PureCN 1.13.18
INFO [2019-02-09 05:34:00] ------------------------------------------------------------
INFO [2019-02-09 05:34:00] Loading coverage files...
INFO [2019-02-09 05:34:01] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2019-02-09 05:34:01] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:34:01] Allosome coverage missing, cannot determine sex.
INFO [2019-02-09 05:34:02] Removing 228 intervals with missing log.ratio.
INFO [2019-02-09 05:34:02] Removing 15 low/high GC targets.
INFO [2019-02-09 05:34:02] Removing 21 small (< 5bp) intervals.
INFO [2019-02-09 05:34:02] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2019-02-09 05:34:02] No normalDB provided. Provide one for better results.
INFO [2019-02-09 05:34:02] Removing 232 low coverage (< 15.0000X) intervals.
INFO [2019-02-09 05:34:02] Using 9534 intervals (9534 on-target, 0 off-target).
INFO [2019-02-09 05:34:02] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2019-02-09 05:34:02] AT/GC dropout: 1.03 (tumor), 1.03 (normal). 
INFO [2019-02-09 05:34:02] Loading VCF...
INFO [2019-02-09 05:34:02] Found 127 variants in VCF file.
INFO [2019-02-09 05:34:02] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2019-02-09 05:34:02] LIB-02240e4 is tumor in VCF file.
INFO [2019-02-09 05:34:02] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2019-02-09 05:34:02] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2019-02-09 05:34:03] Removing 1 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2019-02-09 05:34:03] Removing 0 low quality variants with BQ < 25.
INFO [2019-02-09 05:34:03] Total size of targeted genomic region: 1.63Mb (2.58Mb with 50bp padding).
INFO [2019-02-09 05:34:03] 1.0% of targets contain variants.
INFO [2019-02-09 05:34:03] Removing 2 variants outside intervals.
INFO [2019-02-09 05:34:03] Found SOMATIC annotation in VCF.
INFO [2019-02-09 05:34:03] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2019-02-09 05:34:03] Found SOMATIC annotation in VCF. Setting mapping bias to 0.973.
INFO [2019-02-09 05:34:03] Excluding 0 novel or poor quality variants from segmentation.
INFO [2019-02-09 05:34:03] Sample sex: ?
INFO [2019-02-09 05:34:03] Segmenting data...
INFO [2019-02-09 05:34:03] Loading pre-computed boundaries for DNAcopy...
INFO [2019-02-09 05:34:03] Setting undo.SD parameter to 1.000000.
INFO [2019-02-09 05:34:05] Setting prune.hclust.h parameter to 0.200000.
INFO [2019-02-09 05:34:05] Found 54 segments with median size of 24.88Mb.
INFO [2019-02-09 05:34:05] Using 123 variants.
INFO [2019-02-09 05:34:05] Mean standard deviation of log-ratios: 0.37
INFO [2019-02-09 05:34:05] 2D-grid search of purity and ploidy...
INFO [2019-02-09 05:34:06] Local optima: 0.63/1.9, 0.4/2.1
INFO [2019-02-09 05:34:06] Testing local optimum 1/2 at purity 0.63 and total ploidy 1.90...
INFO [2019-02-09 05:34:07] Testing local optimum 2/2 at purity 0.40 and total ploidy 2.10...
INFO [2019-02-09 05:34:08] Recalibrating log-ratios...
INFO [2019-02-09 05:34:08] Testing local optimum 2/2 at purity 0.40 and total ploidy 2.10...
INFO [2019-02-09 05:34:08] Recalibrating log-ratios...
INFO [2019-02-09 05:34:08] Testing local optimum 2/2 at purity 0.40 and total ploidy 2.10...
INFO [2019-02-09 05:34:09] Recalibrating log-ratios...
INFO [2019-02-09 05:34:09] Testing local optimum 2/2 at purity 0.40 and total ploidy 2.10...
INFO [2019-02-09 05:34:10] Skipping 1 solutions exceeding max.non.clonal (0.20).
INFO [2019-02-09 05:34:10] Fitting variants for local optimum 1/2...
INFO [2019-02-09 05:34:10] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01.
INFO [2019-02-09 05:34:11] Optimized purity: 0.65
INFO [2019-02-09 05:34:11] Done.
INFO [2019-02-09 05:34:11] ------------------------------------------------------------
FATAL [2019-02-09 05:34:11] chr1 not valid chromosome name(s). Valid names are: 

FATAL [2019-02-09 05:34:11] 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22 

FATAL [2019-02-09 05:34:11]  

FATAL [2019-02-09 05:34:11] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:34:11] parameters (PureCN 1.13.18). 

INFO [2019-02-09 05:34:11] ------------------------------------------------------------
INFO [2019-02-09 05:34:11] PureCN 1.13.18
INFO [2019-02-09 05:34:11] ------------------------------------------------------------
INFO [2019-02-09 05:34:11] Loading coverage files...
WARN [2019-02-09 05:34:11] Provided sampleid (Sample2) does not match Sample1 found in segmentation.
WARN [2019-02-09 05:34:11] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:34:11] Allosome coverage missing, cannot determine sex.
INFO [2019-02-09 05:34:11] Removing 10 intervals with missing log.ratio.
INFO [2019-02-09 05:34:11] Using 10039 intervals (10039 on-target, 0 off-target).
INFO [2019-02-09 05:34:11] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2019-02-09 05:34:11] Loading VCF...
INFO [2019-02-09 05:34:12] Found 127 variants in VCF file.
INFO [2019-02-09 05:34:12] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2019-02-09 05:34:12] LIB-02240e4 is tumor in VCF file.
INFO [2019-02-09 05:34:12] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2019-02-09 05:34:12] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2019-02-09 05:34:13] Removing 1 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2019-02-09 05:34:13] Removing 0 low quality variants with BQ < 25.
INFO [2019-02-09 05:34:13] Total size of targeted genomic region: 1.71Mb (2.70Mb with 50bp padding).
INFO [2019-02-09 05:34:13] 1.0% of targets contain variants.
INFO [2019-02-09 05:34:13] Removing 0 variants outside intervals.
INFO [2019-02-09 05:34:13] Found SOMATIC annotation in VCF.
INFO [2019-02-09 05:34:13] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2019-02-09 05:34:13] Found SOMATIC annotation in VCF. Setting mapping bias to 0.976.
INFO [2019-02-09 05:34:13] Excluding 0 novel or poor quality variants from segmentation.
INFO [2019-02-09 05:34:13] Sample sex: ?
INFO [2019-02-09 05:34:13] Segmenting data...
INFO [2019-02-09 05:34:13] Loaded provided segmentation file example_seg.txt.
WARN [2019-02-09 05:34:13] Provided sampleid (Sample2) does not match Sample1 found in segmentation.
INFO [2019-02-09 05:34:13] Loading pre-computed boundaries for DNAcopy...
INFO [2019-02-09 05:34:13] Setting undo.SD parameter to 0.000000.
Setting multi-figure configuration
INFO [2019-02-09 05:34:13] Setting prune.hclust.h parameter to 0.200000.
INFO [2019-02-09 05:34:13] Found 54 segments with median size of 24.88Mb.
INFO [2019-02-09 05:34:14] Using 125 variants.
INFO [2019-02-09 05:34:14] Mean standard deviation of log-ratios: 0.40
INFO [2019-02-09 05:34:14] 2D-grid search of purity and ploidy...
INFO [2019-02-09 05:34:15] Local optima: 0.6/1.9, 0.4/2.1
INFO [2019-02-09 05:34:15] Testing local optimum 1/2 at purity 0.60 and total ploidy 1.90...
INFO [2019-02-09 05:34:16] Testing local optimum 2/2 at purity 0.40 and total ploidy 2.10...
INFO [2019-02-09 05:34:16] Recalibrating log-ratios...
INFO [2019-02-09 05:34:16] Testing local optimum 2/2 at purity 0.40 and total ploidy 2.10...
INFO [2019-02-09 05:34:17] Recalibrating log-ratios...
INFO [2019-02-09 05:34:17] Testing local optimum 2/2 at purity 0.40 and total ploidy 2.10...
INFO [2019-02-09 05:34:17] Recalibrating log-ratios...
INFO [2019-02-09 05:34:17] Testing local optimum 2/2 at purity 0.40 and total ploidy 2.10...
INFO [2019-02-09 05:34:17] Skipping 1 solutions exceeding max.non.clonal (0.20).
INFO [2019-02-09 05:34:17] Fitting variants for local optimum 1/2...
INFO [2019-02-09 05:34:17] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01.
INFO [2019-02-09 05:34:18] Optimized purity: 0.65
INFO [2019-02-09 05:34:18] Done.
INFO [2019-02-09 05:34:18] ------------------------------------------------------------
WARN [2019-02-09 05:34:19] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:34:19] Allosome coverage missing, cannot determine sex.
Setting multi-figure configuration
FATAL [2019-02-09 05:34:29] Segmentation file expected with colnames ID, chrom, loc.start, loc.end, 

FATAL [2019-02-09 05:34:29] num.mark, seg.mean 

FATAL [2019-02-09 05:34:29]  

FATAL [2019-02-09 05:34:29] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:34:29] parameters (PureCN 1.13.18). 

FATAL [2019-02-09 05:34:29] seg.file contains multiple samples and sampleid missing. 

FATAL [2019-02-09 05:34:29]  

FATAL [2019-02-09 05:34:29] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:34:29] parameters (PureCN 1.13.18). 

FATAL [2019-02-09 05:34:29] seg.file contains multiple samples and sampleid does not match any. 

FATAL [2019-02-09 05:34:29]  

FATAL [2019-02-09 05:34:29] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:34:29] parameters (PureCN 1.13.18). 

WARN [2019-02-09 05:34:29] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:34:29] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:34:38] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:34:38] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:34:38] Provided sampleid (example_tumor.txt) does not match Sample1 found in segmentation.
WARN [2019-02-09 05:34:43] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:34:43] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:34:44] No normalDB provided. Provide one for better results.
WARN [2019-02-09 05:34:55] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:34:55] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:34:58] Provided sampleid (Sample.1) does not match Sample1 found in segmentation.
Setting multi-figure configuration
WARN [2019-02-09 05:35:07] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:35:07] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:35:07] No normalDB provided. Provide one for better results.
WARN [2019-02-09 05:35:07] Sampleid looks like a normal in VCF, not like a tumor.
WARN [2019-02-09 05:35:17] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:35:17] Allosome coverage missing, cannot determine sex.
FATAL [2019-02-09 05:35:17] normalDB not a valid normalDB object. Use createNormalDatabase to 

FATAL [2019-02-09 05:35:17] create one. 

FATAL [2019-02-09 05:35:17]  

FATAL [2019-02-09 05:35:17] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:35:17] parameters (PureCN 1.13.18). 

WARN [2019-02-09 05:35:18] You are likely not using the correct baits file!
WARN [2019-02-09 05:35:18] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:35:18] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:35:20] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:35:20] Allosome coverage missing, cannot determine sex.
FATAL [2019-02-09 05:35:20] normalDB appears to be empty. 

FATAL [2019-02-09 05:35:20]  

FATAL [2019-02-09 05:35:20] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:35:20] parameters (PureCN 1.13.18). 

WARN [2019-02-09 05:35:21] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:35:21] Allosome coverage missing, cannot determine sex.
WARN [2019-02-09 05:35:21] Intervals in coverage and interval.file have conflicting on/off-target annotation.
FATAL [2019-02-09 05:35:49] min.normals must be >=2. 

FATAL [2019-02-09 05:35:49]  

FATAL [2019-02-09 05:35:49] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:35:49] parameters (PureCN 1.13.18). 

FATAL [2019-02-09 05:35:59] The normal.panel.vcf.file contains only a single sample. 

FATAL [2019-02-09 05:35:59]  

FATAL [2019-02-09 05:35:59] This is most likely a user error due to invalid input data or 

FATAL [2019-02-09 05:35:59] parameters (PureCN 1.13.18). 

== testthat results  ===========================================================
OK: 312 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 307.26    2.35  419.82

CHECK report for PureCN on tokay2

Summary

Command output

Installation output

Tests output

Example timings