PureCN 1.14.3
Markus Riester
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/PureCN |
| Branch: RELEASE_3_9 |
| Last Commit: 9363655 |
| Last Changed Date: 2019-08-28 10:47:23 -0400 (Wed, 28 Aug 2019) |
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.
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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
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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, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Loading required package: GenomeInfoDb
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, 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 [2019-10-16 04:16:44] Attempted adding gene symbols to intervals. Heuristics have been used to pick symbols for overlapping genes.
WARN [2019-10-16 04:16:45] Chromosome naming style of txdb file (UCSC) was different from interval file (NCBI).
WARN [2019-10-16 04:16:49] Attempted adding gene symbols to intervals. Heuristics have been used to pick symbols for overlapping genes.
FATAL [2019-10-16 04:16:52] tumor.coverage.file and interval.file do not align.
FATAL [2019-10-16 04:16:52]
FATAL [2019-10-16 04:16:52] This is most likely a user error due to invalid input data or
FATAL [2019-10-16 04:16:52] parameters (PureCN 1.14.3).
FATAL [2019-10-16 04:16:52] Need either f or purity and ploidy.
FATAL [2019-10-16 04:16:52]
FATAL [2019-10-16 04:16:52] This is most likely a user error due to invalid input data or
FATAL [2019-10-16 04:16:52] parameters (PureCN 1.14.3).
FATAL [2019-10-16 04:16:52] f not in expected range.
FATAL [2019-10-16 04:16:52]
FATAL [2019-10-16 04:16:52] This is most likely a user error due to invalid input data or
FATAL [2019-10-16 04:16:52] parameters (PureCN 1.14.3).
FATAL [2019-10-16 04:16:52] coverage not in expected range (>=2)
FATAL [2019-10-16 04:16:52]
FATAL [2019-10-16 04:16:52] This is most likely a user error due to invalid input data or
FATAL [2019-10-16 04:16:52] parameters (PureCN 1.14.3).
FATAL [2019-10-16 04:16:52] purity not in expected range.
FATAL [2019-10-16 04:16:52]
FATAL [2019-10-16 04:16:52] This is most likely a user error due to invalid input data or
FATAL [2019-10-16 04:16:52] parameters (PureCN 1.14.3).
FATAL [2019-10-16 04:16:52] ploidy not in expected range.
FATAL [2019-10-16 04:16:52]
FATAL [2019-10-16 04:16:52] This is most likely a user error due to invalid input data or
FATAL [2019-10-16 04:16:52] parameters (PureCN 1.14.3).
FATAL [2019-10-16 04:16:52] cell.fraction not in expected range.
FATAL [2019-10-16 04:16:52]
FATAL [2019-10-16 04:16:52] This is most likely a user error due to invalid input data or
FATAL [2019-10-16 04:16:52] parameters (PureCN 1.14.3).
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
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INFO [2019-10-16 04:16:56] ------------------------------------------------------------
INFO [2019-10-16 04:16:56] PureCN 1.14.3
INFO [2019-10-16 04:16:56] ------------------------------------------------------------
INFO [2019-10-16 04:16:56] Loading coverage files...
INFO [2019-10-16 04:16:57] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2019-10-16 04:16:57] Allosome coverage missing, cannot determine sex.
WARN [2019-10-16 04:16:57] Allosome coverage missing, cannot determine sex.
INFO [2019-10-16 04:16:57] Removing 228 intervals with missing log.ratio.
INFO [2019-10-16 04:16:57] Removing 22 small (< 5bp) intervals.
INFO [2019-10-16 04:16:57] Removing 19 intervals with low total coverage in normal (< 150.00 reads).
WARN [2019-10-16 04:16:57] No normalDB provided. Provide one for better results.
INFO [2019-10-16 04:16:57] Removing 233 low coverage (< 15.0000X) intervals.
INFO [2019-10-16 04:16:57] Using 9547 intervals (9547 on-target, 0 off-target).
INFO [2019-10-16 04:16:57] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2019-10-16 04:16:57] No interval.file provided. Cannot check if data was GC-normalized. Was it?
INFO [2019-10-16 04:16:57] Loading VCF...
INFO [2019-10-16 04:16:57] Found 127 variants in VCF file.
INFO [2019-10-16 04:16:57] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2019-10-16 04:16:57] LIB-02240e4 is tumor in VCF file.
INFO [2019-10-16 04:16:57] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2019-10-16 04:16:57] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2019-10-16 04:16:58] Removing 1 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2019-10-16 04:16:58] Removing 0 low quality variants with BQ < 25.
INFO [2019-10-16 04:16:58] Total size of targeted genomic region: 1.63Mb (2.58Mb with 50bp padding).
INFO [2019-10-16 04:16:58] 1.0% of targets contain variants.
INFO [2019-10-16 04:16:58] Removing 2 variants outside intervals.
INFO [2019-10-16 04:16:58] Found SOMATIC annotation in VCF.
INFO [2019-10-16 04:16:58] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2019-10-16 04:16:59] Found SOMATIC annotation in VCF. Setting mapping bias to 0.973.
INFO [2019-10-16 04:16:59] Excluding 0 novel or poor quality variants from segmentation.
INFO [2019-10-16 04:16:59] Sample sex: ?
INFO [2019-10-16 04:16:59] Segmenting data...
INFO [2019-10-16 04:16:59] Loading pre-computed boundaries for DNAcopy...
INFO [2019-10-16 04:16:59] Setting undo.SD parameter to 1.000000.
INFO [2019-10-16 04:17:00] Setting prune.hclust.h parameter to 0.200000.
INFO [2019-10-16 04:17:00] Found 54 segments with median size of 24.88Mb.
INFO [2019-10-16 04:17:00] Using 123 variants.
INFO [2019-10-16 04:17:00] Mean standard deviation of log-ratios: 0.37
INFO [2019-10-16 04:17:00] 2D-grid search of purity and ploidy...
INFO [2019-10-16 04:17:03] Local optima: 0.63/1.9, 0.4/2.2, 0.5/2
INFO [2019-10-16 04:17:03] Testing local optimum 1/3 at purity 0.63 and total ploidy 1.90...
INFO [2019-10-16 04:17:04] Testing local optimum 2/3 at purity 0.40 and total ploidy 2.20...
INFO [2019-10-16 04:17:06] Testing local optimum 3/3 at purity 0.50 and total ploidy 2.00...
INFO [2019-10-16 04:17:07] Skipping 1 solutions that converged to the same optima.
INFO [2019-10-16 04:17:07] Fitting variants for local optimum 1/3...
INFO [2019-10-16 04:17:07] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01.
INFO [2019-10-16 04:17:09] Optimized purity: 0.65
INFO [2019-10-16 04:17:09] Fitting variants for local optimum 2/3...
INFO [2019-10-16 04:17:09] Fitting variants for purity 0.40, tumor ploidy 2.34 and contamination 0.01.
INFO [2019-10-16 04:17:11] Optimized purity: 0.40
INFO [2019-10-16 04:17:11] Done.
INFO [2019-10-16 04:17:11] ------------------------------------------------------------
FATAL [2019-10-16 04:17:13] exclude not a GRanges object.
FATAL [2019-10-16 04:17:13]
FATAL [2019-10-16 04:17:13] This is most likely a user error due to invalid input data or
FATAL [2019-10-16 04:17:13] parameters (PureCN 1.14.3).
FATAL [2019-10-16 04:17:13] callable not a GRanges object.
FATAL [2019-10-16 04:17:13]
FATAL [2019-10-16 04:17:13] This is most likely a user error due to invalid input data or
FATAL [2019-10-16 04:17:13] parameters (PureCN 1.14.3).
WARN [2019-10-16 04:17:25] tumor.coverage.file and interval.file do not align.
FATAL [2019-10-16 04:17:28] No gc_bias column in interval.file.
FATAL [2019-10-16 04:17:28]
FATAL [2019-10-16 04:17:28] This is most likely a user error due to invalid input data or
FATAL [2019-10-16 04:17:28] parameters (PureCN 1.14.3).
FATAL [2019-10-16 04:17:28] Provided coverage is zero, most likely due to a corrupt BAM file.
FATAL [2019-10-16 04:17:28]
FATAL [2019-10-16 04:17:28] This is most likely a user error due to invalid input data or
FATAL [2019-10-16 04:17:28] parameters (PureCN 1.14.3).
INFO [2019-10-16 04:17:35] Reading /tmp/RtmpFMoIa6/file5c2786210f.rds...
INFO [2019-10-16 04:17:36] Reading /tmp/RtmpFMoIa6/file5c2786210f.rds...
INFO [2019-10-16 04:17:36] Reading /tmp/RtmpFMoIa6/file5c2786210f.rds...
INFO [2019-10-16 04:17:36] Reading /tmp/RtmpFMoIa6/file5c2786210f.rds...
INFO [2019-10-16 04:17:37] Reading /tmp/RtmpFMoIa6/file5c2786210f.rds...
INFO [2019-10-16 04:17:37] Reading /tmp/RtmpFMoIa6/file5c2786210f.rds...
FATAL [2019-10-16 04:17:37] Purity or Ploidy not numeric or in expected range.
FATAL [2019-10-16 04:17:37]
FATAL [2019-10-16 04:17:37] This is most likely a user error due to invalid input data or
FATAL [2019-10-16 04:17:37] parameters (PureCN 1.14.3).
INFO [2019-10-16 04:17:37] Reading /tmp/RtmpFMoIa6/file5c2786210f.rds...
INFO [2019-10-16 04:17:37] Reading /tmp/RtmpFMoIa6/file5c2786210f.rds...
FATAL [2019-10-16 04:17:37] 'Failed' column in /tmp/RtmpFMoIa6/file5c2786210f.csv not logical(1).
FATAL [2019-10-16 04:17:37]
FATAL [2019-10-16 04:17:37] This is most likely a user error due to invalid input data or
FATAL [2019-10-16 04:17:37] parameters (PureCN 1.14.3).
INFO [2019-10-16 04:17:38] 576 on-target bins with low coverage in all samples.
WARN [2019-10-16 04:17:38] You are likely not using the correct baits file!
WARN [2019-10-16 04:17:38] Allosome coverage missing, cannot determine sex.
WARN [2019-10-16 04:17:38] Allosome coverage missing, cannot determine sex.
INFO [2019-10-16 04:17:38] Processing on-target regions...
INFO [2019-10-16 04:17:39] Removing 930 intervals with low coverage in normalDB.
INFO [2019-10-16 04:17:39] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2019-10-16 04:17:42] 576 on-target bins with low coverage in all samples.
WARN [2019-10-16 04:17:42] You are likely not using the correct baits file!
WARN [2019-10-16 04:17:43] Allosome coverage missing, cannot determine sex.
WARN [2019-10-16 04:17:43] Allosome coverage missing, cannot determine sex.
INFO [2019-10-16 04:17:43] Processing on-target regions...
INFO [2019-10-16 04:17:43] Removing 930 intervals with low coverage in normalDB.
INFO [2019-10-16 04:17:43] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2019-10-16 04:17:45] 576 on-target bins with low coverage in all samples.
WARN [2019-10-16 04:17:45] You are likely not using the correct baits file!
WARN [2019-10-16 04:17:45] Allosome coverage missing, cannot determine sex.
WARN [2019-10-16 04:17:45] Allosome coverage missing, cannot determine sex.
INFO [2019-10-16 04:17:45] Processing on-target regions...
INFO [2019-10-16 04:17:46] Removing 930 intervals with low coverage in normalDB.
INFO [2019-10-16 04:17:46] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2019-10-16 04:17:48] 576 on-target bins with low coverage in all samples.
WARN [2019-10-16 04:17:48] You are likely not using the correct baits file!
WARN [2019-10-16 04:17:48] Allosome coverage missing, cannot determine sex.
WARN [2019-10-16 04:17:48] Allosome coverage missing, cannot determine sex.
FATAL [2019-10-16 04:17:48] Length of normal.coverage.files and sex different
FATAL [2019-10-16 04:17:48]
FATAL [2019-10-16 04:17:48] This is most likely a user error due to invalid input data or
FATAL [2019-10-16 04:17:48] parameters (PureCN 1.14.3).
WARN [2019-10-16 04:17:54] Target intervals were not sorted.
INFO [2019-10-16 04:17:54] 560 on-target bins with low coverage in all samples.
WARN [2019-10-16 04:17:54] You are likely not using the correct baits file!
WARN [2019-10-16 04:17:54] Allosome coverage missing, cannot determine sex.
WARN [2019-10-16 04:17:54] Allosome coverage missing, cannot determine sex.
WARN [2019-10-16 04:17:54] Allosome coverage missing, cannot determine sex.
INFO [2019-10-16 04:17:54] Processing on-target regions...
INFO [2019-10-16 04:17:55] Removing 978 intervals with low coverage in normalDB.
INFO [2019-10-16 04:17:55] Removing 11 intervals with zero coverage in more than 3% of normalDB.
FATAL [2019-10-16 04:17:57] tumor.coverage.file and normalDB do not align.
FATAL [2019-10-16 04:17:57]
FATAL [2019-10-16 04:17:57] This is most likely a user error due to invalid input data or
FATAL [2019-10-16 04:17:57] parameters (PureCN 1.14.3).
INFO [2019-10-16 04:17:57] ------------------------------------------------------------
INFO [2019-10-16 04:17:57] PureCN 1.14.3
INFO [2019-10-16 04:17:57] ------------------------------------------------------------
INFO [2019-10-16 04:17:57] Loading coverage files...
INFO [2019-10-16 04:17:57] Mean target coverages: 112X (tumor) 99X (normal).
WARN [2019-10-16 04:17:57] Allosome coverage missing, cannot determine sex.
WARN [2019-10-16 04:17:57] Allosome coverage missing, cannot determine sex.
INFO [2019-10-16 04:17:57] Removing 228 intervals with missing log.ratio.
FATAL [2019-10-16 04:17:58] normalDB incompatible with this PureCN version. Please re-run
FATAL [2019-10-16 04:17:58] NormalDB.R.
FATAL [2019-10-16 04:17:58]
FATAL [2019-10-16 04:17:58] This is most likely a user error due to invalid input data or
FATAL [2019-10-16 04:17:58] parameters (PureCN 1.14.3).
FATAL [2019-10-16 04:17:58] normalDB incompatible with this PureCN version. Please re-run
FATAL [2019-10-16 04:17:58] NormalDB.R.
FATAL [2019-10-16 04:17:58]
FATAL [2019-10-16 04:17:58] This is most likely a user error due to invalid input data or
FATAL [2019-10-16 04:17:58] parameters (PureCN 1.14.3).
INFO [2019-10-16 04:17:58] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2019-10-16 04:17:59] Initial testing for significant sample cross-contamination: unlikely
INFO [2019-10-16 04:17:59] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2019-10-16 04:17:59] Removing 16 low quality variants with BQ < 25.
INFO [2019-10-16 04:17:59] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2019-10-16 04:18:00] Initial testing for significant sample cross-contamination: unlikely
INFO [2019-10-16 04:18:00] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2019-10-16 04:18:00] Removing 6 blacklisted variants.
INFO [2019-10-16 04:18:01] Removing 16 low quality variants with BQ < 25.
INFO [2019-10-16 04:18:01] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2019-10-16 04:18:01] Initial testing for significant sample cross-contamination: unlikely
INFO [2019-10-16 04:18:02] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2019-10-16 04:18:02] Removing 16 low quality variants with BQ < 25.
WARN [2019-10-16 04:18:02] MuTect stats file lacks contig and position columns.
INFO [2019-10-16 04:18:02] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2019-10-16 04:18:03] Initial testing for significant sample cross-contamination: unlikely
INFO [2019-10-16 04:18:03] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2019-10-16 04:18:03] Removing 16 low quality variants with BQ < 25.
WARN [2019-10-16 04:18:03] MuTect stats file and VCF file do not align perfectly. Will remove 2325 unmatched variants.
WARN [2019-10-16 04:18:03] MuTect stats file lacks failure_reasons column. Keeping all variants listed in stats file.
INFO [2019-10-16 04:18:03] Removing 0 non heterozygous (in matched normal) germline SNPs.
INFO [2019-10-16 04:18:04] Removing 0 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2019-10-16 04:18:04] Removing 0 low quality variants with BQ < 25.
INFO [2019-10-16 04:18:04] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2019-10-16 04:18:05] Initial testing for significant sample cross-contamination: unlikely
INFO [2019-10-16 04:18:05] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2019-10-16 04:18:05] Removing 22 non heterozygous (in matched normal) germline SNPs.
INFO [2019-10-16 04:18:06] Initial testing for significant sample cross-contamination: unlikely
INFO [2019-10-16 04:18:06] Removing 48 variants with AF < 0.030 or AF >= 1.000 or less than 4 supporting reads or depth < 15.
INFO [2019-10-16 04:18:06] Found 11 variants in VCF file.
WARN [2019-10-16 04:18:07] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead.
INFO [2019-10-16 04:18:07] 1 (9.1%) variants annotated as likely germline (DB INFO flag).
INFO [2019-10-16 04:18:10] Found 11 variants in VCF file.
WARN [2019-10-16 04:18:11] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead.
INFO [2019-10-16 04:18:11] 1 (9.1%) variants annotated as likely germline (DB INFO flag).
INFO [2019-10-16 04:18:12] Found 11 variants in VCF file.
WARN [2019-10-16 04:18:13] vcf.file has no DB or POP_AF info field for membership in germline databases. Guessing it based on available dbSNP ID.
INFO [2019-10-16 04:18:13] 1 (9.1%) variants annotated as likely germline (DB INFO flag).
INFO [2019-10-16 04:18:13] Found 1000 variants in VCF file.
INFO [2019-10-16 04:18:13] Removing 2 triallelic sites.
WARN [2019-10-16 04:18:14] DP FORMAT field contains NAs. Removing 44 variants.
INFO [2019-10-16 04:18:14] 954 (100.0%) variants annotated as likely germline (DB INFO flag).
WARN [2019-10-16 04:18:14] Allosome coverage missing, cannot determine sex.
WARN [2019-10-16 04:18:15] Allosome coverage missing, cannot determine sex.
INFO [2019-10-16 04:18:15] Mean coverages: chrX: 108.58, chrY: 108.58, chr1-22: 104.87.
INFO [2019-10-16 04:18:15] Mean coverages: chrX: 108.58, chrY: 2.17, chr1-22: 104.87.
INFO [2019-10-16 04:18:15] Mean coverages: chrX: 108.58, chrY: 5.17, chr1-22: 104.87.
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=
INFO [2019-10-16 04:18:15] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2019-10-16 04:18:16] No germline variants in VCF.
FATAL [2019-10-16 04:18:16] No solution with id hello
FATAL [2019-10-16 04:18:16]
FATAL [2019-10-16 04:18:16] This is most likely a user error due to invalid input data or
FATAL [2019-10-16 04:18:16] parameters (PureCN 1.14.3).
FATAL [2019-10-16 04:18:16] No solution with id 10
FATAL [2019-10-16 04:18:16]
FATAL [2019-10-16 04:18:16] This is most likely a user error due to invalid input data or
FATAL [2019-10-16 04:18:16] parameters (PureCN 1.14.3).
FATAL [2019-10-16 04:18:17] all.data and w have different lengths.
FATAL [2019-10-16 04:18:17]
FATAL [2019-10-16 04:18:17] This is most likely a user error due to invalid input data or
FATAL [2019-10-16 04:18:17] parameters (PureCN 1.14.3).
WARN [2019-10-16 04:18:18] No mappability scores provided.
WARN [2019-10-16 04:18:18] No reptiming scores provided.
INFO [2019-10-16 04:18:18] Calculating GC-content...
WARN [2019-10-16 04:18:18] No mappability scores provided.
WARN [2019-10-16 04:18:18] No reptiming scores provided.
INFO [2019-10-16 04:18:18] Calculating GC-content...
INFO [2019-10-16 04:18:18] Removing 1 targets overlapping with exclude.
WARN [2019-10-16 04:18:18] No mappability scores provided.
WARN [2019-10-16 04:18:18] No reptiming scores provided.
INFO [2019-10-16 04:18:18] Calculating GC-content...
FATAL [2019-10-16 04:18:19] off.target.padding must be negative.
FATAL [2019-10-16 04:18:19]
FATAL [2019-10-16 04:18:19] This is most likely a user error due to invalid input data or
FATAL [2019-10-16 04:18:19] parameters (PureCN 1.14.3).
FATAL [2019-10-16 04:18:19] Interval coordinates should start at 1, not at 0
FATAL [2019-10-16 04:18:19]
FATAL [2019-10-16 04:18:19] This is most likely a user error due to invalid input data or
FATAL [2019-10-16 04:18:19] parameters (PureCN 1.14.3).
FATAL [2019-10-16 04:18:19] No off-target regions after filtering for mappability and
FATAL [2019-10-16 04:18:19] off.target.padding
FATAL [2019-10-16 04:18:19]
FATAL [2019-10-16 04:18:19] This is most likely a user error due to invalid input data or
FATAL [2019-10-16 04:18:19] parameters (PureCN 1.14.3).
WARN [2019-10-16 04:18:19] No mappability scores provided.
INFO [2019-10-16 04:18:19] Calculating GC-content...
INFO [2019-10-16 04:18:20] Averaging reptiming into bins of size 200...
WARN [2019-10-16 04:18:20] No mappability scores provided.
INFO [2019-10-16 04:18:20] Calculating GC-content...
INFO [2019-10-16 04:18:20] Splitting 1 large targets to an average width of 200.
WARN [2019-10-16 04:18:20] No mappability scores provided.
WARN [2019-10-16 04:18:20] No reptiming scores provided.
INFO [2019-10-16 04:18:20] Calculating GC-content...
WARN [2019-10-16 04:18:20] No mappability scores provided.
WARN [2019-10-16 04:18:20] No reptiming scores provided.
INFO [2019-10-16 04:18:20] Calculating GC-content...
INFO [2019-10-16 04:18:21] Tiling off-target regions to an average width of 200000.
WARN [2019-10-16 04:18:21] No mappability scores provided.
WARN [2019-10-16 04:18:21] No reptiming scores provided.
INFO [2019-10-16 04:18:21] Calculating GC-content...
WARN [2019-10-16 04:18:21] Intervals contain off-target regions. Will not change intervals.
WARN [2019-10-16 04:18:21] No mappability scores provided.
WARN [2019-10-16 04:18:21] No reptiming scores provided.
INFO [2019-10-16 04:18:21] Calculating GC-content...
WARN [2019-10-16 04:18:22] No reptiming scores provided.
INFO [2019-10-16 04:18:22] Calculating GC-content...
WARN [2019-10-16 04:18:22] No reptiming scores provided.
INFO [2019-10-16 04:18:22] Calculating GC-content...
WARN [2019-10-16 04:18:23] 1 intervals without mappability score (1 on-target).
INFO [2019-10-16 04:18:23] Removing 1 intervals with low mappability score (<0.50).
WARN [2019-10-16 04:18:23] No reptiming scores provided.
INFO [2019-10-16 04:18:23] Calculating GC-content...
INFO [2019-10-16 04:18:23] Tiling off-target regions to an average width of 200000.
WARN [2019-10-16 04:18:23] No reptiming scores provided.
INFO [2019-10-16 04:18:23] Calculating GC-content...
WARN [2019-10-16 04:18:24] No mappability scores provided.
WARN [2019-10-16 04:18:24] No reptiming scores provided.
INFO [2019-10-16 04:18:24] Calculating GC-content...
WARN [2019-10-16 04:18:24] Chromosome naming style of interval file (NCBI) was different from reference (UCSC).
WARN [2019-10-16 04:18:24] No mappability scores provided.
WARN [2019-10-16 04:18:24] No reptiming scores provided.
INFO [2019-10-16 04:18:24] Calculating GC-content...
FATAL [2019-10-16 04:18:24] Chromosome naming style of interval file unknown, should be UCSC.
FATAL [2019-10-16 04:18:24]
FATAL [2019-10-16 04:18:24] This is most likely a user error due to invalid input data or
FATAL [2019-10-16 04:18:24] parameters (PureCN 1.14.3).
WARN [2019-10-16 04:18:25] Chromosome naming style of interval file (NCBI) was different from reference (UCSC).
WARN [2019-10-16 04:18:25] Chromosome naming style of mappability file (NCBI) was different from reference (UCSC).
WARN [2019-10-16 04:18:25] No reptiming scores provided.
INFO [2019-10-16 04:18:25] Calculating GC-content...
WARN [2019-10-16 04:18:25] Found small target regions (< 60bp). Will resize them.
WARN [2019-10-16 04:18:25] No mappability scores provided.
WARN [2019-10-16 04:18:25] No reptiming scores provided.
INFO [2019-10-16 04:18:25] Calculating GC-content...
WARN [2019-10-16 04:18:25] Found small target regions (< 60bp). Will drop them.
WARN [2019-10-16 04:18:25] No mappability scores provided.
WARN [2019-10-16 04:18:25] No reptiming scores provided.
INFO [2019-10-16 04:18:25] Calculating GC-content...
WARN [2019-10-16 04:18:26] Found small target regions (< 200bp). Will resize them.
WARN [2019-10-16 04:18:26] No mappability scores provided.
WARN [2019-10-16 04:18:26] No reptiming scores provided.
INFO [2019-10-16 04:18:26] Calculating GC-content...
INFO [2019-10-16 04:18:26] 576 on-target bins with low coverage in all samples.
WARN [2019-10-16 04:18:26] You are likely not using the correct baits file!
WARN [2019-10-16 04:18:26] Allosome coverage missing, cannot determine sex.
WARN [2019-10-16 04:18:26] Allosome coverage missing, cannot determine sex.
INFO [2019-10-16 04:18:27] Processing on-target regions...
INFO [2019-10-16 04:18:27] Removing 930 intervals with low coverage in normalDB.
INFO [2019-10-16 04:18:27] Removing 1 intervals with zero coverage in more than 3% of normalDB.
INFO [2019-10-16 04:18:29] Loading coverage data...
INFO [2019-10-16 04:18:30] Mean target coverages: 71X (tumor) 99X (normal).
INFO [2019-10-16 04:18:30] Mean target coverages: 71X (tumor) 43X (normal).
INFO [2019-10-16 04:18:32] 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 [2019-10-16 04:18:34] ------------------------------------------------------------
INFO [2019-10-16 04:18:34] PureCN 1.14.3
INFO [2019-10-16 04:18:34] ------------------------------------------------------------
INFO [2019-10-16 04:18:34] Loading coverage files...
INFO [2019-10-16 04:18:34] seg.file and normal.coverage.file provided. Using both.
INFO [2019-10-16 04:18:34] Mean target coverages: 112X (tumor) 105X (normal).
WARN [2019-10-16 04:18:34] Allosome coverage missing, cannot determine sex.
WARN [2019-10-16 04:18:35] Allosome coverage missing, cannot determine sex.
INFO [2019-10-16 04:18:35] Removing 199 intervals with missing log.ratio.
INFO [2019-10-16 04:18:35] Using 9850 intervals (9850 on-target, 0 off-target).
INFO [2019-10-16 04:18:35] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2019-10-16 04:18:35] Loading VCF...
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig="
[W::bcf_hdr_parse] Could not parse header line: ##contig=