Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-07-24 11:42 -0400 (Wed, 24 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4688 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4284 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4455 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4404 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 1591/2248 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
PureCN 2.11.0 (landing page) Markus Riester
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
To the developers/maintainers of the PureCN package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PureCN.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: PureCN |
Version: 2.11.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PureCN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PureCN_2.11.0.tar.gz |
StartedAt: 2024-07-24 00:04:03 -0400 (Wed, 24 Jul 2024) |
EndedAt: 2024-07-24 00:09:04 -0400 (Wed, 24 Jul 2024) |
EllapsedTime: 301.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: PureCN.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PureCN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PureCN_2.11.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/PureCN.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘PureCN/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘PureCN’ version ‘2.11.0’ * checking package namespace information ... OK * checking package dependencies ... NOTE Package which this enhances but not available for checking: ‘genomicsdb’ * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘PureCN’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed callAmplificationsInLowPurity 12.138 0.107 12.251 segmentationPSCBS 8.460 0.129 8.588 filterIntervals 7.077 0.151 7.232 runAbsoluteCN 6.008 0.100 6.109 segmentationHclust 4.984 0.095 5.079 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc/meat/PureCN.Rcheck/00check.log’ for details.
PureCN.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PureCN ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘PureCN’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (PureCN)
PureCN.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(PureCN) Loading required package: DNAcopy Loading required package: VariantAnnotation Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: GenomeInfoDb Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: GenomicRanges Loading required package: SummarizedExperiment Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians Loading required package: Rsamtools Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Attaching package: 'VariantAnnotation' The following object is masked from 'package:base': tabulate > > test_check("PureCN") WARN [2024-07-24 00:07:02] Attempted adding gene symbols to intervals. Heuristics have been used to pick symbols for overlapping genes. WARN [2024-07-24 00:07:02] Chromosome naming style of txdb file (UCSC) was different from interval file (Ensembl). WARN [2024-07-24 00:07:03] Attempted adding gene symbols to intervals. Heuristics have been used to pick symbols for overlapping genes. FATAL [2024-07-24 00:07:05] tumor.coverage.file and interval.file do not align. FATAL [2024-07-24 00:07:05] FATAL [2024-07-24 00:07:05] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:07:05] parameters (PureCN 2.11.0). WARN [2024-07-24 00:07:05] Cannot find all contig lengths while exporting interval file. INFO [2024-07-24 00:07:05] Processing seq1:1-21 (1/3)... INFO [2024-07-24 00:07:05] Processing seq1:1227-1247 (2/3)... INFO [2024-07-24 00:07:05] Processing seq2:594-614 (3/3)... WARN [2024-07-24 00:07:06] Large potential mis-calibration of on- and off-target log2 ratios: 0.26 FATAL [2024-07-24 00:07:06] Need either f or purity and ploidy. FATAL [2024-07-24 00:07:06] FATAL [2024-07-24 00:07:06] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:07:06] parameters (PureCN 2.11.0). FATAL [2024-07-24 00:07:06] f not in expected range. FATAL [2024-07-24 00:07:06] FATAL [2024-07-24 00:07:06] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:07:06] parameters (PureCN 2.11.0). FATAL [2024-07-24 00:07:06] coverage not in expected range (>=2) FATAL [2024-07-24 00:07:06] FATAL [2024-07-24 00:07:06] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:07:06] parameters (PureCN 2.11.0). FATAL [2024-07-24 00:07:06] purity not in expected range. FATAL [2024-07-24 00:07:06] FATAL [2024-07-24 00:07:06] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:07:06] parameters (PureCN 2.11.0). FATAL [2024-07-24 00:07:06] ploidy not in expected range. FATAL [2024-07-24 00:07:06] FATAL [2024-07-24 00:07:06] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:07:06] parameters (PureCN 2.11.0). FATAL [2024-07-24 00:07:06] cell.fraction not in expected range. FATAL [2024-07-24 00:07:06] FATAL [2024-07-24 00:07:06] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:07:06] parameters (PureCN 2.11.0). INFO [2024-07-24 00:07:07] 576 on-target bins with low coverage in all samples. WARN [2024-07-24 00:07:07] You are likely not using the correct baits file! WARN [2024-07-24 00:07:07] Allosome coverage missing, cannot determine sex. WARN [2024-07-24 00:07:07] Allosome coverage missing, cannot determine sex. INFO [2024-07-24 00:07:07] Processing on-target regions... INFO [2024-07-24 00:07:07] Removing 930 intervals with low coverage in normalDB. INFO [2024-07-24 00:07:07] Removing 1 intervals with zero coverage in more than 3% of normalDB. INFO [2024-07-24 00:07:07] Tumor/normal noise ratio: 19.041 WARN [2024-07-24 00:07:07] Extensive noise in tumor compared to normals. INFO [2024-07-24 00:07:21] Tumor/normal noise ratio: 19.041 WARN [2024-07-24 00:07:21] Extensive noise in tumor compared to normals. INFO [2024-07-24 00:07:23] Using BiocParallel for parallel optimization. FATAL [2024-07-24 00:07:27] pvalue.cutoff not within expected range or format. FATAL [2024-07-24 00:07:27] FATAL [2024-07-24 00:07:27] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:07:27] parameters (PureCN 2.11.0). FATAL [2024-07-24 00:07:27] pvalue.cutoff not within expected range or format. FATAL [2024-07-24 00:07:27] FATAL [2024-07-24 00:07:27] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:07:27] parameters (PureCN 2.11.0). FATAL [2024-07-24 00:07:27] percentile.cutoff not in expected range (0 to 100). FATAL [2024-07-24 00:07:27] FATAL [2024-07-24 00:07:27] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:07:27] parameters (PureCN 2.11.0). FATAL [2024-07-24 00:07:27] percentile.cutoff not in expected range (0 to 100). FATAL [2024-07-24 00:07:27] FATAL [2024-07-24 00:07:27] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:07:27] parameters (PureCN 2.11.0). FATAL [2024-07-24 00:07:27] purity not within expected range or format. FATAL [2024-07-24 00:07:27] FATAL [2024-07-24 00:07:27] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:07:27] parameters (PureCN 2.11.0). FATAL [2024-07-24 00:07:27] purity not within expected range or format. FATAL [2024-07-24 00:07:27] FATAL [2024-07-24 00:07:27] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:07:27] parameters (PureCN 2.11.0). INFO [2024-07-24 00:07:27] ------------------------------------------------------------ INFO [2024-07-24 00:07:27] PureCN 2.11.0 INFO [2024-07-24 00:07:27] ------------------------------------------------------------ INFO [2024-07-24 00:07:27] Loading coverage files... INFO [2024-07-24 00:07:27] Mean target coverages: 112X (tumor) 99X (normal). WARN [2024-07-24 00:07:27] Allosome coverage missing, cannot determine sex. WARN [2024-07-24 00:07:27] Allosome coverage missing, cannot determine sex. INFO [2024-07-24 00:07:28] Removing 228 intervals with missing log.ratio. INFO [2024-07-24 00:07:28] Removing 22 small (< 5bp) intervals. INFO [2024-07-24 00:07:28] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2024-07-24 00:07:28] No normalDB provided. Provide one for better results. INFO [2024-07-24 00:07:28] Removing 1724 low count (< 100 total reads) intervals. INFO [2024-07-24 00:07:28] Removing 6 low coverage (< 15.0000X) intervals. INFO [2024-07-24 00:07:28] Using 8050 intervals (8050 on-target, 0 off-target). INFO [2024-07-24 00:07:28] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2024-07-24 00:07:28] No interval.file provided. Cannot check for any GC-biases. INFO [2024-07-24 00:07:28] Loading VCF... INFO [2024-07-24 00:07:28] Found 127 variants in VCF file. INFO [2024-07-24 00:07:28] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2024-07-24 00:07:28] LIB-02240e4 is tumor in VCF file. INFO [2024-07-24 00:07:28] No homozygous variants in VCF, provide unfiltered VCF. INFO [2024-07-24 00:07:28] Removing 1 non heterozygous (in matched normal) germline SNPs. INFO [2024-07-24 00:07:28] Removing 0 low quality variants with non-offset BQ < 25. INFO [2024-07-24 00:07:28] Base quality scores range from 29 to 35 (offset by 1) INFO [2024-07-24 00:07:28] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS. INFO [2024-07-24 00:07:28] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. INFO [2024-07-24 00:07:28] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding). INFO [2024-07-24 00:07:28] 1.2% of targets contain variants. INFO [2024-07-24 00:07:28] Removing 4 variants outside intervals. INFO [2024-07-24 00:07:28] Found SOMATIC annotation in VCF. INFO [2024-07-24 00:07:28] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. INFO [2024-07-24 00:07:28] Found SOMATIC annotation in VCF. Setting mapping bias to 0.972. INFO [2024-07-24 00:07:28] Excluding 0 novel or poor quality variants from segmentation. INFO [2024-07-24 00:07:28] Sample sex: ? INFO [2024-07-24 00:07:28] Segmenting data... INFO [2024-07-24 00:07:28] Loading pre-computed boundaries for DNAcopy... INFO [2024-07-24 00:07:28] Setting undo.SD parameter to 1.000000. INFO [2024-07-24 00:07:29] Setting prune.hclust.h parameter to 0.200000. INFO [2024-07-24 00:07:29] Found 59 segments with median size of 17.67Mb. INFO [2024-07-24 00:07:29] Using 121 variants. INFO [2024-07-24 00:07:29] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30) INFO [2024-07-24 00:07:29] 2D-grid search of purity and ploidy... INFO [2024-07-24 00:07:29] Local optima: 0.63/1.9, 0.5/2 INFO [2024-07-24 00:07:29] Testing local optimum 1/2 at purity 0.63 and total ploidy 1.90... INFO [2024-07-24 00:07:29] Testing local optimum 2/2 at purity 0.50 and total ploidy 2.00... INFO [2024-07-24 00:07:30] Skipping 1 solutions that converged to the same optima. INFO [2024-07-24 00:07:30] Fitting variants with beta model for local optimum 1/2... INFO [2024-07-24 00:07:30] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01. INFO [2024-07-24 00:07:31] Optimized purity: 0.65 INFO [2024-07-24 00:07:31] Done. INFO [2024-07-24 00:07:31] ------------------------------------------------------------ INFO [2024-07-24 00:07:31] Estimating callable regions. FATAL [2024-07-24 00:07:31] exclude not a GRanges object. FATAL [2024-07-24 00:07:31] FATAL [2024-07-24 00:07:31] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:07:31] parameters (PureCN 2.11.0). FATAL [2024-07-24 00:07:31] callable not a GRanges object. FATAL [2024-07-24 00:07:31] FATAL [2024-07-24 00:07:31] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:07:31] parameters (PureCN 2.11.0). WARN [2024-07-24 00:07:34] tumor.coverage.file and interval.file do not align. INFO [2024-07-24 00:07:35] No Gene column in interval.file. You won't get gene-level calls. FATAL [2024-07-24 00:07:35] No gc_bias column in interval.file. FATAL [2024-07-24 00:07:35] FATAL [2024-07-24 00:07:35] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:07:35] parameters (PureCN 2.11.0). FATAL [2024-07-24 00:07:35] Provided coverage is zero, most likely due to a corrupt BAM file. FATAL [2024-07-24 00:07:35] FATAL [2024-07-24 00:07:35] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:07:35] parameters (PureCN 2.11.0). INFO [2024-07-24 00:07:36] No reptiming column in interval.file. INFO [2024-07-24 00:07:37] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpCvWANV/file2239138bec3e.rds... INFO [2024-07-24 00:07:37] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpCvWANV/file2239138bec3e.rds... INFO [2024-07-24 00:07:37] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpCvWANV/file2239138bec3e.rds... INFO [2024-07-24 00:07:37] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpCvWANV/file2239138bec3e.rds... INFO [2024-07-24 00:07:38] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpCvWANV/file2239138bec3e.rds... INFO [2024-07-24 00:07:38] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpCvWANV/file2239138bec3e.rds... FATAL [2024-07-24 00:07:38] Purity or Ploidy not numeric or in expected range. FATAL [2024-07-24 00:07:38] FATAL [2024-07-24 00:07:38] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:07:38] parameters (PureCN 2.11.0). INFO [2024-07-24 00:07:38] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpCvWANV/file2239138bec3e.rds... INFO [2024-07-24 00:07:38] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpCvWANV/file2239138bec3e.rds... FATAL [2024-07-24 00:07:38] 'Failed' column in FATAL [2024-07-24 00:07:38] /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpCvWANV/file2239138bec3e.csv FATAL [2024-07-24 00:07:38] not logical(1). FATAL [2024-07-24 00:07:38] FATAL [2024-07-24 00:07:38] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:07:38] parameters (PureCN 2.11.0). INFO [2024-07-24 00:07:38] 576 on-target bins with low coverage in all samples. WARN [2024-07-24 00:07:38] You are likely not using the correct baits file! WARN [2024-07-24 00:07:38] Allosome coverage missing, cannot determine sex. WARN [2024-07-24 00:07:38] Allosome coverage missing, cannot determine sex. INFO [2024-07-24 00:07:38] Processing on-target regions... INFO [2024-07-24 00:07:39] Removing 930 intervals with low coverage in normalDB. INFO [2024-07-24 00:07:39] Removing 1 intervals with zero coverage in more than 3% of normalDB. INFO [2024-07-24 00:07:40] 576 on-target bins with low coverage in all samples. WARN [2024-07-24 00:07:40] You are likely not using the correct baits file! WARN [2024-07-24 00:07:40] Allosome coverage missing, cannot determine sex. WARN [2024-07-24 00:07:40] Allosome coverage missing, cannot determine sex. INFO [2024-07-24 00:07:40] Processing on-target regions... INFO [2024-07-24 00:07:40] Removing 930 intervals with low coverage in normalDB. INFO [2024-07-24 00:07:40] Removing 1 intervals with zero coverage in more than 3% of normalDB. INFO [2024-07-24 00:07:40] 576 on-target bins with low coverage in all samples. WARN [2024-07-24 00:07:40] You are likely not using the correct baits file! WARN [2024-07-24 00:07:40] Allosome coverage missing, cannot determine sex. WARN [2024-07-24 00:07:40] Allosome coverage missing, cannot determine sex. INFO [2024-07-24 00:07:40] Processing on-target regions... INFO [2024-07-24 00:07:41] Removing 930 intervals with low coverage in normalDB. INFO [2024-07-24 00:07:41] Removing 1 intervals with zero coverage in more than 3% of normalDB. WARN [2024-07-24 00:07:41] Allosome coverage missing, cannot determine sex. INFO [2024-07-24 00:07:41] Sample sex: NA WARN [2024-07-24 00:07:41] Allosome coverage missing, cannot determine sex. INFO [2024-07-24 00:07:41] Sample sex: NA INFO [2024-07-24 00:07:41] 576 on-target bins with low coverage in all samples. WARN [2024-07-24 00:07:41] You are likely not using the correct baits file! WARN [2024-07-24 00:07:41] Allosome coverage missing, cannot determine sex. WARN [2024-07-24 00:07:41] Allosome coverage missing, cannot determine sex. FATAL [2024-07-24 00:07:41] Length of normal.coverage.files and sex different FATAL [2024-07-24 00:07:41] FATAL [2024-07-24 00:07:41] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:07:41] parameters (PureCN 2.11.0). WARN [2024-07-24 00:07:43] Target intervals were not sorted. INFO [2024-07-24 00:07:43] 560 on-target bins with low coverage in all samples. WARN [2024-07-24 00:07:43] You are likely not using the correct baits file! WARN [2024-07-24 00:07:43] Allosome coverage missing, cannot determine sex. WARN [2024-07-24 00:07:43] Allosome coverage missing, cannot determine sex. WARN [2024-07-24 00:07:43] Allosome coverage missing, cannot determine sex. INFO [2024-07-24 00:07:43] Processing on-target regions... INFO [2024-07-24 00:07:43] Removing 978 intervals with low coverage in normalDB. INFO [2024-07-24 00:07:43] Removing 11 intervals with zero coverage in more than 3% of normalDB. FATAL [2024-07-24 00:07:44] tumor.coverage.file and normalDB do not align. FATAL [2024-07-24 00:07:44] FATAL [2024-07-24 00:07:44] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:07:44] parameters (PureCN 2.11.0). FATAL [2024-07-24 00:07:44] At least 2 normal.coverage.files required. FATAL [2024-07-24 00:07:44] FATAL [2024-07-24 00:07:44] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:07:44] parameters (PureCN 2.11.0). INFO [2024-07-24 00:07:44] ------------------------------------------------------------ INFO [2024-07-24 00:07:44] PureCN 2.11.0 INFO [2024-07-24 00:07:44] ------------------------------------------------------------ INFO [2024-07-24 00:07:44] Loading coverage files... INFO [2024-07-24 00:07:45] Mean target coverages: 112X (tumor) 99X (normal). WARN [2024-07-24 00:07:45] Allosome coverage missing, cannot determine sex. WARN [2024-07-24 00:07:45] Allosome coverage missing, cannot determine sex. INFO [2024-07-24 00:07:45] Removing 228 intervals with missing log.ratio. FATAL [2024-07-24 00:07:45] normalDB incompatible with this PureCN version. Please re-run FATAL [2024-07-24 00:07:45] NormalDB.R. FATAL [2024-07-24 00:07:45] FATAL [2024-07-24 00:07:45] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:07:45] parameters (PureCN 2.11.0). FATAL [2024-07-24 00:07:45] normalDB incompatible with this PureCN version. Please re-run FATAL [2024-07-24 00:07:45] NormalDB.R. FATAL [2024-07-24 00:07:45] FATAL [2024-07-24 00:07:45] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:07:45] parameters (PureCN 2.11.0). FATAL [2024-07-24 00:07:45] normal.coverage.files with _coverage.txt and _loess.txt suffix FATAL [2024-07-24 00:07:45] provided. Provide either only GC-normalized or raw coverage files! FATAL [2024-07-24 00:07:45] FATAL [2024-07-24 00:07:45] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:07:45] parameters (PureCN 2.11.0). INFO [2024-07-24 00:07:45] Removing 22 non heterozygous (in matched normal) germline SNPs. INFO [2024-07-24 00:07:45] Removing 19 low quality variants with non-offset BQ < 25. INFO [2024-07-24 00:07:45] Base quality scores range from 24 to 35 (offset by 1) INFO [2024-07-24 00:07:45] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS. INFO [2024-07-24 00:07:45] Initial testing for significant sample cross-contamination: unlikely INFO [2024-07-24 00:07:45] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. INFO [2024-07-24 00:07:45] Removing 22 non heterozygous (in matched normal) germline SNPs. INFO [2024-07-24 00:07:45] Removing 19 low quality variants with non-offset BQ < 25. INFO [2024-07-24 00:07:45] Base quality scores range from 24 to 35 (offset by 1) INFO [2024-07-24 00:07:45] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS. INFO [2024-07-24 00:07:45] Initial testing for significant sample cross-contamination: unlikely INFO [2024-07-24 00:07:45] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. INFO [2024-07-24 00:07:45] Removing 6 blacklisted variants. INFO [2024-07-24 00:07:45] Removing 22 non heterozygous (in matched normal) germline SNPs. INFO [2024-07-24 00:07:45] Removing 19 low quality variants with non-offset BQ < 25. INFO [2024-07-24 00:07:45] Base quality scores range from 24 to 35 (offset by 1) INFO [2024-07-24 00:07:45] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS. INFO [2024-07-24 00:07:46] Initial testing for significant sample cross-contamination: unlikely INFO [2024-07-24 00:07:46] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. WARN [2024-07-24 00:07:46] MuTect stats file lacks contig and position columns. INFO [2024-07-24 00:07:46] Removing 22 non heterozygous (in matched normal) germline SNPs. INFO [2024-07-24 00:07:46] Removing 19 low quality variants with non-offset BQ < 25. INFO [2024-07-24 00:07:46] Base quality scores range from 24 to 35 (offset by 1) INFO [2024-07-24 00:07:46] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS. INFO [2024-07-24 00:07:46] Initial testing for significant sample cross-contamination: unlikely INFO [2024-07-24 00:07:46] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. WARN [2024-07-24 00:07:46] MuTect stats file and VCF file do not align perfectly. Will remove 2325 unmatched variants. WARN [2024-07-24 00:07:46] MuTect stats file lacks failure_reasons column. Keeping all variants listed in stats file. INFO [2024-07-24 00:07:46] Removing 0 non heterozygous (in matched normal) germline SNPs. INFO [2024-07-24 00:07:46] Removing 0 low quality variants with non-offset BQ < 25. INFO [2024-07-24 00:07:46] Base quality scores range from 31 to 33 (offset by 1) INFO [2024-07-24 00:07:46] Minimum number of supporting reads ranges from 3 to 4, depending on coverage and BQS. INFO [2024-07-24 00:07:46] Removing 0 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. INFO [2024-07-24 00:07:46] Removing 22 non heterozygous (in matched normal) germline SNPs. INFO [2024-07-24 00:07:46] Base quality scores range from 7 to 35 (offset by 1) INFO [2024-07-24 00:07:46] Minimum number of supporting reads ranges from 1 to 41, depending on coverage and BQS. INFO [2024-07-24 00:07:46] Initial testing for significant sample cross-contamination: unlikely INFO [2024-07-24 00:07:46] Removing 49 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. INFO [2024-07-24 00:07:46] Removing 22 non heterozygous (in matched normal) germline SNPs. INFO [2024-07-24 00:07:46] Base quality scores range from 7 to 35 (offset by 1) INFO [2024-07-24 00:07:46] Minimum number of supporting reads ranges from 1 to 41, depending on coverage and BQS. INFO [2024-07-24 00:07:46] Initial testing for significant sample cross-contamination: unlikely INFO [2024-07-24 00:07:46] Removing 49 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. INFO [2024-07-24 00:07:46] Removing 22 non heterozygous (in matched normal) germline SNPs. WARN [2024-07-24 00:07:46] Many variants removed by min.base.quality (50) filter. You might want to lower the cutoff. FATAL [2024-07-24 00:07:46] No variants passed filter BQ. FATAL [2024-07-24 00:07:46] FATAL [2024-07-24 00:07:46] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:07:46] parameters (PureCN 2.11.0). INFO [2024-07-24 00:07:47] Found 11 variants in VCF file. WARN [2024-07-24 00:07:47] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead. INFO [2024-07-24 00:07:47] 1 (9.1%) variants annotated as likely germline (DB INFO flag). INFO [2024-07-24 00:07:47] Found 11 variants in VCF file. WARN [2024-07-24 00:07:47] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead. INFO [2024-07-24 00:07:47] 1 (9.1%) variants annotated as likely germline (DB INFO flag). INFO [2024-07-24 00:07:48] Found 11 variants in VCF file. WARN [2024-07-24 00:07:48] vcf.file has no DB or POP_AF info field for membership in germline databases. Guessing it based on available dbSNP ID. INFO [2024-07-24 00:07:48] 1 (9.1%) variants annotated as likely germline (DB INFO flag). INFO [2024-07-24 00:07:48] Found 1000 variants in VCF file. INFO [2024-07-24 00:07:48] Removing 2 triallelic sites. WARN [2024-07-24 00:07:48] Having trouble guessing SOMATIC status... WARN [2024-07-24 00:07:48] DP FORMAT field contains NAs. Removing 44 variants. INFO [2024-07-24 00:07:48] 954 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2024-07-24 00:07:48] Found 12 variants in VCF file. INFO [2024-07-24 00:07:48] Removing 1 triallelic sites. WARN [2024-07-24 00:07:48] DP FORMAT field contains NAs. Removing 1 variants. WARN [2024-07-24 00:07:48] vcf.file has no DB info field for membership in germline databases. Found and used somatic status instead. INFO [2024-07-24 00:07:48] 8 (80.0%) variants annotated as likely germline (DB INFO flag). WARN [2024-07-24 00:07:48] BQ FORMAT field contains NAs. INFO [2024-07-24 00:07:49] Found 2331 variants in VCF file. INFO [2024-07-24 00:07:49] 2282 (97.9%) variants annotated as likely germline (DB INFO flag). INFO [2024-07-24 00:07:49] Found 2331 variants in VCF file. INFO [2024-07-24 00:07:49] 2282 (97.9%) variants annotated as likely germline (DB INFO flag). WARN [2024-07-24 00:07:49] Did not find base quality scores, will use global error rate of 0.0010 instead. INFO [2024-07-24 00:07:49] Removing 21 low quality variants with non-offset BQ < 25. INFO [2024-07-24 00:07:49] Base quality scores range from 24 to 35 (offset by 1) INFO [2024-07-24 00:07:49] Initial testing for significant sample cross-contamination: unlikely INFO [2024-07-24 00:07:49] Removing 89 variants with AF < 0.030 or AF >= 0.970 or insufficient supporting reads or depth < 15. INFO [2024-07-24 00:07:49] Found 2331 variants in VCF file. INFO [2024-07-24 00:07:49] 2282 (97.9%) variants annotated as likely germline (DB INFO flag). WARN [2024-07-24 00:07:49] BQ FORMAT field contains NAs. WARN [2024-07-24 00:07:49] Allosome coverage missing, cannot determine sex. WARN [2024-07-24 00:07:50] Allosome coverage missing, cannot determine sex. INFO [2024-07-24 00:07:50] Mean coverages: chrX: 108.58, chrY: 108.58, chr1-22: 104.87. INFO [2024-07-24 00:07:50] Mean coverages: chrX: 108.58, chrY: 2.17, chr1-22: 104.87. INFO [2024-07-24 00:07:50] Mean coverages: chrX: 108.58, chrY: 5.17, chr1-22: 104.87. INFO [2024-07-24 00:07:50] No homozygous variants in VCF, provide unfiltered VCF. INFO [2024-07-24 00:07:50] No germline variants in VCF. FATAL [2024-07-24 00:07:50] No solution with id hello FATAL [2024-07-24 00:07:50] FATAL [2024-07-24 00:07:50] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:07:50] parameters (PureCN 2.11.0). FATAL [2024-07-24 00:07:50] No solution with id 100 FATAL [2024-07-24 00:07:50] FATAL [2024-07-24 00:07:50] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:07:50] parameters (PureCN 2.11.0). FATAL [2024-07-24 00:07:50] all.data and w have different lengths. FATAL [2024-07-24 00:07:50] FATAL [2024-07-24 00:07:50] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:07:50] parameters (PureCN 2.11.0). INFO [2024-07-24 00:07:51] Splitting 5 large targets to an average width of 400. WARN [2024-07-24 00:07:51] No mappability scores provided. WARN [2024-07-24 00:07:51] No reptiming scores provided. INFO [2024-07-24 00:07:51] Calculating GC-content... INFO [2024-07-24 00:07:51] Splitting 5 large targets to an average width of 400. WARN [2024-07-24 00:07:51] No mappability scores provided. WARN [2024-07-24 00:07:51] No reptiming scores provided. INFO [2024-07-24 00:07:51] Calculating GC-content... INFO [2024-07-24 00:07:51] Splitting 5 large targets to an average width of 400. INFO [2024-07-24 00:07:51] Removing 1 targets overlapping with exclude. WARN [2024-07-24 00:07:51] No mappability scores provided. WARN [2024-07-24 00:07:51] No reptiming scores provided. INFO [2024-07-24 00:07:51] Calculating GC-content... WARN [2024-07-24 00:07:51] Found small target regions (< 100bp). Will resize them. INFO [2024-07-24 00:07:51] Splitting 5 large targets to an average width of 400. FATAL [2024-07-24 00:07:51] off.target.padding must be negative. FATAL [2024-07-24 00:07:51] FATAL [2024-07-24 00:07:51] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:07:51] parameters (PureCN 2.11.0). FATAL [2024-07-24 00:07:51] Interval coordinates should start at 1, not at 0 FATAL [2024-07-24 00:07:51] FATAL [2024-07-24 00:07:51] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:07:51] parameters (PureCN 2.11.0). WARN [2024-07-24 00:07:51] Found small target regions (< 100bp). Will resize them. INFO [2024-07-24 00:07:51] Splitting 5 large targets to an average width of 400. FATAL [2024-07-24 00:07:51] No off-target regions after filtering for mappability and FATAL [2024-07-24 00:07:51] off.target.padding FATAL [2024-07-24 00:07:51] FATAL [2024-07-24 00:07:51] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:07:51] parameters (PureCN 2.11.0). WARN [2024-07-24 00:07:51] Found small target regions (< 100bp). Will resize them. INFO [2024-07-24 00:07:51] Splitting 5 large targets to an average width of 400. WARN [2024-07-24 00:07:51] No mappability scores provided. INFO [2024-07-24 00:07:51] Calculating GC-content... WARN [2024-07-24 00:07:51] Found small target regions (< 100bp). Will resize them. INFO [2024-07-24 00:07:51] Averaging reptiming into bins of size 200... INFO [2024-07-24 00:07:51] Splitting 5 large targets to an average width of 400. WARN [2024-07-24 00:07:51] No mappability scores provided. INFO [2024-07-24 00:07:51] Calculating GC-content... WARN [2024-07-24 00:07:51] Found small target regions (< 100bp). Will resize them. INFO [2024-07-24 00:07:51] Splitting 6 large targets to an average width of 200. WARN [2024-07-24 00:07:51] No mappability scores provided. WARN [2024-07-24 00:07:51] No reptiming scores provided. INFO [2024-07-24 00:07:51] Calculating GC-content... WARN [2024-07-24 00:07:51] Found small target regions (< 100bp). Will resize them. INFO [2024-07-24 00:07:51] Splitting 5 large targets to an average width of 400. WARN [2024-07-24 00:07:51] No mappability scores provided. WARN [2024-07-24 00:07:51] No reptiming scores provided. INFO [2024-07-24 00:07:51] Calculating GC-content... INFO [2024-07-24 00:07:51] Splitting 5 large targets to an average width of 400. INFO [2024-07-24 00:07:52] Tiling off-target regions to an average width of 200000. WARN [2024-07-24 00:07:52] No mappability scores provided. WARN [2024-07-24 00:07:52] No reptiming scores provided. INFO [2024-07-24 00:07:52] Calculating GC-content... WARN [2024-07-24 00:07:52] Intervals contain off-target regions. Will not change intervals. WARN [2024-07-24 00:07:52] No mappability scores provided. WARN [2024-07-24 00:07:52] No reptiming scores provided. INFO [2024-07-24 00:07:52] Calculating GC-content... INFO [2024-07-24 00:07:52] Splitting 5 large targets to an average width of 400. WARN [2024-07-24 00:07:52] No reptiming scores provided. INFO [2024-07-24 00:07:52] Calculating GC-content... WARN [2024-07-24 00:07:52] Found small target regions (< 100bp). Will resize them. INFO [2024-07-24 00:07:52] Splitting 5 large targets to an average width of 400. WARN [2024-07-24 00:07:52] No reptiming scores provided. INFO [2024-07-24 00:07:52] Calculating GC-content... WARN [2024-07-24 00:07:52] Found small target regions (< 100bp). Will resize them. INFO [2024-07-24 00:07:52] Splitting 5 large targets to an average width of 400. WARN [2024-07-24 00:07:52] 1 intervals without mappability score (1 on-target). INFO [2024-07-24 00:07:52] Removing 1 intervals with low mappability score (<0.60). WARN [2024-07-24 00:07:52] No reptiming scores provided. INFO [2024-07-24 00:07:52] Calculating GC-content... WARN [2024-07-24 00:07:52] Found small target regions (< 100bp). Will resize them. INFO [2024-07-24 00:07:52] Splitting 5 large targets to an average width of 400. INFO [2024-07-24 00:07:52] Tiling off-target regions to an average width of 200000. WARN [2024-07-24 00:07:52] No reptiming scores provided. INFO [2024-07-24 00:07:52] Calculating GC-content... INFO [2024-07-24 00:07:53] Splitting 5 large targets to an average width of 400. WARN [2024-07-24 00:07:53] No mappability scores provided. WARN [2024-07-24 00:07:53] No reptiming scores provided. INFO [2024-07-24 00:07:53] Calculating GC-content... WARN [2024-07-24 00:07:53] Chromosome naming style of interval file (Ensembl) was different from reference (UCSC). INFO [2024-07-24 00:07:53] Splitting 5 large targets to an average width of 400. WARN [2024-07-24 00:07:53] No mappability scores provided. WARN [2024-07-24 00:07:53] No reptiming scores provided. INFO [2024-07-24 00:07:53] Calculating GC-content... FATAL [2024-07-24 00:07:53] Chromosome naming style of interval file unknown, should be UCSC. FATAL [2024-07-24 00:07:53] FATAL [2024-07-24 00:07:53] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:07:53] parameters (PureCN 2.11.0). WARN [2024-07-24 00:07:53] Chromosome naming style of interval file (Ensembl) was different from reference (UCSC). WARN [2024-07-24 00:07:53] Chromosome naming style of mappability file (Ensembl) was different from reference (UCSC). INFO [2024-07-24 00:07:53] Splitting 5 large targets to an average width of 400. WARN [2024-07-24 00:07:53] No reptiming scores provided. INFO [2024-07-24 00:07:53] Calculating GC-content... WARN [2024-07-24 00:07:53] Found small target regions (< 60bp). Will resize them. INFO [2024-07-24 00:07:53] Splitting 5 large targets to an average width of 400. WARN [2024-07-24 00:07:53] No mappability scores provided. WARN [2024-07-24 00:07:53] No reptiming scores provided. INFO [2024-07-24 00:07:53] Calculating GC-content... WARN [2024-07-24 00:07:53] Found small target regions (< 60bp). Will drop them. INFO [2024-07-24 00:07:53] Splitting 4 large targets to an average width of 400. WARN [2024-07-24 00:07:53] No mappability scores provided. WARN [2024-07-24 00:07:53] No reptiming scores provided. INFO [2024-07-24 00:07:53] Calculating GC-content... WARN [2024-07-24 00:07:53] Found small target regions (< 200bp). Will resize them. INFO [2024-07-24 00:07:53] Splitting 5 large targets to an average width of 400. WARN [2024-07-24 00:07:53] No mappability scores provided. WARN [2024-07-24 00:07:53] No reptiming scores provided. INFO [2024-07-24 00:07:53] Calculating GC-content... INFO [2024-07-24 00:07:53] Found 20 variants in VCF file. INFO [2024-07-24 00:07:53] 20 (100.0%) variants annotated as likely germline (DB INFO flag). WARN [2024-07-24 00:07:53] Did not find base quality scores, will use global error rate of 0.0010 instead. INFO [2024-07-24 00:07:54] Found 127 variants in VCF file. INFO [2024-07-24 00:07:54] 127 (100.0%) variants annotated as likely germline (DB INFO flag). WARN [2024-07-24 00:07:54] Did not find base quality scores, will use global error rate of 0.0010 instead. INFO [2024-07-24 00:07:54] ------------------------------------------------------------ INFO [2024-07-24 00:07:54] PureCN 2.11.0 INFO [2024-07-24 00:07:54] ------------------------------------------------------------ INFO [2024-07-24 00:07:54] Loading coverage files... INFO [2024-07-24 00:07:54] Mean target coverages: 112X (tumor) 99X (normal). WARN [2024-07-24 00:07:54] Allosome coverage missing, cannot determine sex. WARN [2024-07-24 00:07:54] Allosome coverage missing, cannot determine sex. INFO [2024-07-24 00:07:54] Removing 228 intervals with missing log.ratio. INFO [2024-07-24 00:07:54] Removing 22 small (< 5bp) intervals. INFO [2024-07-24 00:07:54] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2024-07-24 00:07:54] No normalDB provided. Provide one for better results. INFO [2024-07-24 00:07:54] Removing 1724 low count (< 100 total reads) intervals. INFO [2024-07-24 00:07:54] Removing 6 low coverage (< 15.0000X) intervals. INFO [2024-07-24 00:07:54] Using 8050 intervals (8050 on-target, 0 off-target). INFO [2024-07-24 00:07:54] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2024-07-24 00:07:54] No interval.file provided. Cannot check for any GC-biases. INFO [2024-07-24 00:07:54] Loading VCF... INFO [2024-07-24 00:07:54] Found 127 variants in VCF file. INFO [2024-07-24 00:07:54] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2024-07-24 00:07:54] LIB-02240e4 is tumor in VCF file. INFO [2024-07-24 00:07:54] No homozygous variants in VCF, provide unfiltered VCF. INFO [2024-07-24 00:07:54] Removing 1 non heterozygous (in matched normal) germline SNPs. INFO [2024-07-24 00:07:54] Removing 0 low quality variants with non-offset BQ < 25. INFO [2024-07-24 00:07:54] Base quality scores range from 29 to 35 (offset by 1) INFO [2024-07-24 00:07:54] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS. INFO [2024-07-24 00:07:54] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. INFO [2024-07-24 00:07:54] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding). INFO [2024-07-24 00:07:54] 1.2% of targets contain variants. INFO [2024-07-24 00:07:54] Removing 4 variants outside intervals. INFO [2024-07-24 00:07:54] Found SOMATIC annotation in VCF. INFO [2024-07-24 00:07:54] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. INFO [2024-07-24 00:07:54] Found SOMATIC annotation in VCF. Setting mapping bias to 0.972. INFO [2024-07-24 00:07:54] Excluding 0 novel or poor quality variants from segmentation. INFO [2024-07-24 00:07:54] Sample sex: ? INFO [2024-07-24 00:07:54] Segmenting data... INFO [2024-07-24 00:07:54] Loading pre-computed boundaries for DNAcopy... INFO [2024-07-24 00:07:54] Setting undo.SD parameter to 1.000000. INFO [2024-07-24 00:07:55] Setting prune.hclust.h parameter to 0.200000. INFO [2024-07-24 00:07:55] Found 59 segments with median size of 17.67Mb. INFO [2024-07-24 00:07:55] Using 121 variants. INFO [2024-07-24 00:07:55] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30) INFO [2024-07-24 00:07:55] 2D-grid search of purity and ploidy... INFO [2024-07-24 00:07:55] Local optima: 0.65/1.8, 0.52/2 INFO [2024-07-24 00:07:55] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80... INFO [2024-07-24 00:07:55] Testing local optimum 2/2 at purity 0.52 and total ploidy 2.00... INFO [2024-07-24 00:07:56] Skipping 1 solutions that converged to the same optima. INFO [2024-07-24 00:07:56] Fitting variants with beta model for local optimum 1/2... INFO [2024-07-24 00:07:56] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01. INFO [2024-07-24 00:07:57] Optimized purity: 0.65 INFO [2024-07-24 00:07:57] Done. INFO [2024-07-24 00:07:57] ------------------------------------------------------------ FATAL [2024-07-24 00:07:57] log.ratio NULL in .writeLogRatioFileGATK4 FATAL [2024-07-24 00:07:57] FATAL [2024-07-24 00:07:57] This runtime error might be caused by invalid input data or parameters. FATAL [2024-07-24 00:07:57] Please report bug (PureCN 2.11.0). INFO [2024-07-24 00:07:57] Loaded provided segmentation file example_seg.txt (format DNAcopy). INFO [2024-07-24 00:07:57] Re-centering provided segment means (offset -0.0033). INFO [2024-07-24 00:07:57] Loaded provided segmentation file example_gatk4_modelfinal.seg.gz (format GATK4). WARN [2024-07-24 00:07:57] Expecting numeric chromosome names in seg.file, assuming file is properly sorted. INFO [2024-07-24 00:07:57] Re-centering provided segment means (offset -0.0037). INFO [2024-07-24 00:07:57] 576 on-target bins with low coverage in all samples. WARN [2024-07-24 00:07:57] You are likely not using the correct baits file! WARN [2024-07-24 00:07:57] Allosome coverage missing, cannot determine sex. WARN [2024-07-24 00:07:57] Allosome coverage missing, cannot determine sex. INFO [2024-07-24 00:07:57] Processing on-target regions... INFO [2024-07-24 00:07:58] Removing 930 intervals with low coverage in normalDB. INFO [2024-07-24 00:07:58] Removing 1 intervals with zero coverage in more than 3% of normalDB. INFO [2024-07-24 00:07:58] ------------------------------------------------------------ INFO [2024-07-24 00:07:58] PureCN 2.11.0 INFO [2024-07-24 00:07:58] ------------------------------------------------------------ INFO [2024-07-24 00:07:58] Using BiocParallel for parallel optimization. INFO [2024-07-24 00:07:58] Loading coverage files... INFO [2024-07-24 00:07:58] Mean target coverages: 112X (tumor) 99X (normal). WARN [2024-07-24 00:07:58] Allosome coverage missing, cannot determine sex. WARN [2024-07-24 00:07:58] Allosome coverage missing, cannot determine sex. INFO [2024-07-24 00:07:58] Removing 228 intervals with missing log.ratio. INFO [2024-07-24 00:07:58] Removing 705 intervals excluded in normalDB. INFO [2024-07-24 00:07:58] normalDB provided. Setting minimum coverage for segmentation to 0.0015X. INFO [2024-07-24 00:07:58] Removing 1066 low count (< 100 total reads) intervals. INFO [2024-07-24 00:07:58] Using 8050 intervals (8050 on-target, 0 off-target). INFO [2024-07-24 00:07:58] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2024-07-24 00:07:58] No interval.file provided. Cannot check for any GC-biases. INFO [2024-07-24 00:07:58] Sample sex: ? INFO [2024-07-24 00:07:58] Segmenting data... INFO [2024-07-24 00:07:58] Interval weights found, will use weighted CBS. INFO [2024-07-24 00:07:58] Loading pre-computed boundaries for DNAcopy... INFO [2024-07-24 00:07:58] Setting undo.SD parameter to 1.000000. Setting multi-figure configuration INFO [2024-07-24 00:07:59] Found 52 segments with median size of 29.35Mb. INFO [2024-07-24 00:07:59] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30) INFO [2024-07-24 00:07:59] 2D-grid search of purity and ploidy... INFO [2024-07-24 00:07:59] Local optima: 0.65/1.8, 0.52/2 INFO [2024-07-24 00:08:00] Skipping 1 solutions that converged to the same optima. INFO [2024-07-24 00:08:00] Done. INFO [2024-07-24 00:08:00] ------------------------------------------------------------ INFO [2024-07-24 00:08:00] Reading /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpCvWANV/file22394229f350.rds... FATAL [2024-07-24 00:08:00] runAbsoluteCN was run without a VCF file. FATAL [2024-07-24 00:08:00] FATAL [2024-07-24 00:08:00] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:08:00] parameters (PureCN 2.11.0). FATAL [2024-07-24 00:08:00] runAbsoluteCN was run without a VCF file. FATAL [2024-07-24 00:08:00] FATAL [2024-07-24 00:08:00] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:08:00] parameters (PureCN 2.11.0). INFO [2024-07-24 00:08:00] ------------------------------------------------------------ INFO [2024-07-24 00:08:00] PureCN 2.11.0 INFO [2024-07-24 00:08:00] ------------------------------------------------------------ INFO [2024-07-24 00:08:00] Loading coverage files... INFO [2024-07-24 00:08:00] Mean target coverages: 112X (tumor) 99X (normal). WARN [2024-07-24 00:08:00] Allosome coverage missing, cannot determine sex. WARN [2024-07-24 00:08:00] Allosome coverage missing, cannot determine sex. INFO [2024-07-24 00:08:00] Removing 228 intervals with missing log.ratio. INFO [2024-07-24 00:08:00] Removing 705 intervals excluded in normalDB. INFO [2024-07-24 00:08:00] normalDB provided. Setting minimum coverage for segmentation to 0.0015X. INFO [2024-07-24 00:08:00] Removing 1066 low count (< 100 total reads) intervals. INFO [2024-07-24 00:08:00] Using 8050 intervals (8050 on-target, 0 off-target). INFO [2024-07-24 00:08:00] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2024-07-24 00:08:00] No interval.file provided. Cannot check for any GC-biases. INFO [2024-07-24 00:08:00] Sample sex: ? INFO [2024-07-24 00:08:00] Segmenting data... INFO [2024-07-24 00:08:00] Interval weights found, will use weighted PSCBS. FATAL [2024-07-24 00:08:00] segmentationPSCBS requires VCF file. FATAL [2024-07-24 00:08:00] FATAL [2024-07-24 00:08:00] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:08:00] parameters (PureCN 2.11.0). INFO [2024-07-24 00:08:02] ------------------------------------------------------------ INFO [2024-07-24 00:08:02] PureCN 2.11.0 INFO [2024-07-24 00:08:02] ------------------------------------------------------------ INFO [2024-07-24 00:08:02] Loading coverage files... FATAL [2024-07-24 00:08:02] Need a normal coverage file if log.ratio and seg.file are not provided. FATAL [2024-07-24 00:08:02] FATAL [2024-07-24 00:08:02] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:08:02] parameters (PureCN 2.11.0). INFO [2024-07-24 00:08:02] ------------------------------------------------------------ INFO [2024-07-24 00:08:02] PureCN 2.11.0 INFO [2024-07-24 00:08:02] ------------------------------------------------------------ FATAL [2024-07-24 00:08:02] min.ploidy or max.ploidy not within expected range. FATAL [2024-07-24 00:08:02] FATAL [2024-07-24 00:08:02] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:08:02] parameters (PureCN 2.11.0). INFO [2024-07-24 00:08:02] ------------------------------------------------------------ INFO [2024-07-24 00:08:02] PureCN 2.11.0 INFO [2024-07-24 00:08:02] ------------------------------------------------------------ FATAL [2024-07-24 00:08:02] min.ploidy or max.ploidy not within expected range. FATAL [2024-07-24 00:08:02] FATAL [2024-07-24 00:08:02] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:08:02] parameters (PureCN 2.11.0). INFO [2024-07-24 00:08:02] ------------------------------------------------------------ INFO [2024-07-24 00:08:02] PureCN 2.11.0 INFO [2024-07-24 00:08:02] ------------------------------------------------------------ INFO [2024-07-24 00:08:02] ------------------------------------------------------------ INFO [2024-07-24 00:08:02] PureCN 2.11.0 INFO [2024-07-24 00:08:02] ------------------------------------------------------------ INFO [2024-07-24 00:08:02] ------------------------------------------------------------ INFO [2024-07-24 00:08:02] PureCN 2.11.0 INFO [2024-07-24 00:08:02] ------------------------------------------------------------ FATAL [2024-07-24 00:08:02] test.num.copy not within expected range. FATAL [2024-07-24 00:08:02] FATAL [2024-07-24 00:08:02] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:08:02] parameters (PureCN 2.11.0). INFO [2024-07-24 00:08:02] ------------------------------------------------------------ INFO [2024-07-24 00:08:02] PureCN 2.11.0 INFO [2024-07-24 00:08:02] ------------------------------------------------------------ WARN [2024-07-24 00:08:02] test.num.copy outside recommended range. FATAL [2024-07-24 00:08:02] max.non.clonal not within expected range or format. FATAL [2024-07-24 00:08:02] FATAL [2024-07-24 00:08:02] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:08:02] parameters (PureCN 2.11.0). INFO [2024-07-24 00:08:02] ------------------------------------------------------------ INFO [2024-07-24 00:08:02] PureCN 2.11.0 INFO [2024-07-24 00:08:02] ------------------------------------------------------------ WARN [2024-07-24 00:08:02] test.num.copy outside recommended range. FATAL [2024-07-24 00:08:02] max.non.clonal not within expected range or format. FATAL [2024-07-24 00:08:02] FATAL [2024-07-24 00:08:02] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:08:02] parameters (PureCN 2.11.0). INFO [2024-07-24 00:08:02] ------------------------------------------------------------ INFO [2024-07-24 00:08:02] PureCN 2.11.0 INFO [2024-07-24 00:08:02] ------------------------------------------------------------ FATAL [2024-07-24 00:08:02] test.purity not within expected range. FATAL [2024-07-24 00:08:02] FATAL [2024-07-24 00:08:02] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:08:02] parameters (PureCN 2.11.0). INFO [2024-07-24 00:08:02] ------------------------------------------------------------ INFO [2024-07-24 00:08:02] PureCN 2.11.0 INFO [2024-07-24 00:08:02] ------------------------------------------------------------ INFO [2024-07-24 00:08:02] Loading coverage files... FATAL [2024-07-24 00:08:03] Tumor and normal are identical. This won't give any meaningful results FATAL [2024-07-24 00:08:03] and I'm stopping here. FATAL [2024-07-24 00:08:03] FATAL [2024-07-24 00:08:03] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:08:03] parameters (PureCN 2.11.0). INFO [2024-07-24 00:08:03] ------------------------------------------------------------ INFO [2024-07-24 00:08:03] PureCN 2.11.0 INFO [2024-07-24 00:08:03] ------------------------------------------------------------ INFO [2024-07-24 00:08:03] Loading coverage files... FATAL [2024-07-24 00:08:03] Length of log.ratio different from tumor coverage. FATAL [2024-07-24 00:08:03] FATAL [2024-07-24 00:08:03] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:08:03] parameters (PureCN 2.11.0). INFO [2024-07-24 00:08:03] ------------------------------------------------------------ INFO [2024-07-24 00:08:03] PureCN 2.11.0 INFO [2024-07-24 00:08:03] ------------------------------------------------------------ FATAL [2024-07-24 00:08:03] prior.purity must have the same length as test.purity. FATAL [2024-07-24 00:08:03] FATAL [2024-07-24 00:08:03] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:08:03] parameters (PureCN 2.11.0). INFO [2024-07-24 00:08:03] ------------------------------------------------------------ INFO [2024-07-24 00:08:03] PureCN 2.11.0 INFO [2024-07-24 00:08:03] ------------------------------------------------------------ FATAL [2024-07-24 00:08:03] min.gof not within expected range or format. FATAL [2024-07-24 00:08:03] FATAL [2024-07-24 00:08:03] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:08:03] parameters (PureCN 2.11.0). INFO [2024-07-24 00:08:03] ------------------------------------------------------------ INFO [2024-07-24 00:08:03] PureCN 2.11.0 INFO [2024-07-24 00:08:03] ------------------------------------------------------------ FATAL [2024-07-24 00:08:03] prior.purity not within expected range or format. FATAL [2024-07-24 00:08:03] FATAL [2024-07-24 00:08:03] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:08:03] parameters (PureCN 2.11.0). INFO [2024-07-24 00:08:03] ------------------------------------------------------------ INFO [2024-07-24 00:08:03] PureCN 2.11.0 INFO [2024-07-24 00:08:03] ------------------------------------------------------------ FATAL [2024-07-24 00:08:03] prior.purity must add to 1. Sum is 1.5 FATAL [2024-07-24 00:08:03] FATAL [2024-07-24 00:08:03] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:08:03] parameters (PureCN 2.11.0). INFO [2024-07-24 00:08:03] ------------------------------------------------------------ INFO [2024-07-24 00:08:03] PureCN 2.11.0 INFO [2024-07-24 00:08:03] ------------------------------------------------------------ FATAL [2024-07-24 00:08:03] max.homozygous.loss not within expected range or format. FATAL [2024-07-24 00:08:03] FATAL [2024-07-24 00:08:03] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:08:03] parameters (PureCN 2.11.0). INFO [2024-07-24 00:08:03] ------------------------------------------------------------ INFO [2024-07-24 00:08:03] PureCN 2.11.0 INFO [2024-07-24 00:08:03] ------------------------------------------------------------ FATAL [2024-07-24 00:08:03] prior.K not within expected range or format. FATAL [2024-07-24 00:08:03] FATAL [2024-07-24 00:08:03] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:08:03] parameters (PureCN 2.11.0). INFO [2024-07-24 00:08:03] ------------------------------------------------------------ INFO [2024-07-24 00:08:03] PureCN 2.11.0 INFO [2024-07-24 00:08:03] ------------------------------------------------------------ FATAL [2024-07-24 00:08:03] prior.contamination not within expected range or format. FATAL [2024-07-24 00:08:03] FATAL [2024-07-24 00:08:03] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:08:03] parameters (PureCN 2.11.0). INFO [2024-07-24 00:08:03] ------------------------------------------------------------ INFO [2024-07-24 00:08:03] PureCN 2.11.0 INFO [2024-07-24 00:08:03] ------------------------------------------------------------ FATAL [2024-07-24 00:08:03] Iterations not in the expected range from 10 to 250. FATAL [2024-07-24 00:08:03] FATAL [2024-07-24 00:08:03] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:08:03] parameters (PureCN 2.11.0). INFO [2024-07-24 00:08:03] ------------------------------------------------------------ INFO [2024-07-24 00:08:03] PureCN 2.11.0 INFO [2024-07-24 00:08:03] ------------------------------------------------------------ FATAL [2024-07-24 00:08:03] Iterations not in the expected range from 10 to 250. FATAL [2024-07-24 00:08:03] FATAL [2024-07-24 00:08:03] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:08:03] parameters (PureCN 2.11.0). INFO [2024-07-24 00:08:03] ------------------------------------------------------------ INFO [2024-07-24 00:08:03] PureCN 2.11.0 INFO [2024-07-24 00:08:03] ------------------------------------------------------------ INFO [2024-07-24 00:08:03] Loading coverage files... FATAL [2024-07-24 00:08:03] Missing tumor.coverage.file requires seg.file or log.ratio and FATAL [2024-07-24 00:08:03] interval.file. FATAL [2024-07-24 00:08:03] FATAL [2024-07-24 00:08:03] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:08:03] parameters (PureCN 2.11.0). INFO [2024-07-24 00:08:03] ------------------------------------------------------------ INFO [2024-07-24 00:08:03] PureCN 2.11.0 INFO [2024-07-24 00:08:03] ------------------------------------------------------------ INFO [2024-07-24 00:08:03] ------------------------------------------------------------ INFO [2024-07-24 00:08:03] PureCN 2.11.0 INFO [2024-07-24 00:08:03] ------------------------------------------------------------ INFO [2024-07-24 00:08:03] Loading coverage files... FATAL [2024-07-24 00:08:03] Interval files in normal and tumor different. FATAL [2024-07-24 00:08:03] FATAL [2024-07-24 00:08:03] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:08:03] parameters (PureCN 2.11.0). INFO [2024-07-24 00:08:03] ------------------------------------------------------------ INFO [2024-07-24 00:08:03] PureCN 2.11.0 INFO [2024-07-24 00:08:03] ------------------------------------------------------------ INFO [2024-07-24 00:08:03] Loading coverage files... INFO [2024-07-24 00:08:03] Mean target coverages: 0X (tumor) 99X (normal). WARN [2024-07-24 00:08:03] Large difference in coverage of tumor and normal. FATAL [2024-07-24 00:08:03] No finite intervals. FATAL [2024-07-24 00:08:03] FATAL [2024-07-24 00:08:03] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:08:03] parameters (PureCN 2.11.0). INFO [2024-07-24 00:08:03] ------------------------------------------------------------ INFO [2024-07-24 00:08:03] PureCN 2.11.0 INFO [2024-07-24 00:08:03] ------------------------------------------------------------ INFO [2024-07-24 00:08:03] Loading coverage files... INFO [2024-07-24 00:08:04] Mean target coverages: 112X (tumor) 99X (normal). WARN [2024-07-24 00:08:04] Allosome coverage missing, cannot determine sex. WARN [2024-07-24 00:08:04] Allosome coverage missing, cannot determine sex. INFO [2024-07-24 00:08:04] Removing 228 intervals with missing log.ratio. INFO [2024-07-24 00:08:04] Removing 22 small (< 5bp) intervals. INFO [2024-07-24 00:08:04] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2024-07-24 00:08:04] No normalDB provided. Provide one for better results. INFO [2024-07-24 00:08:04] Removing 1724 low count (< 100 total reads) intervals. INFO [2024-07-24 00:08:04] Removing 6 low coverage (< 15.0000X) intervals. INFO [2024-07-24 00:08:04] Using 8050 intervals (8050 on-target, 0 off-target). INFO [2024-07-24 00:08:04] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2024-07-24 00:08:04] No interval.file provided. Cannot check for any GC-biases. INFO [2024-07-24 00:08:04] Loading VCF... INFO [2024-07-24 00:08:04] Found 127 variants in VCF file. INFO [2024-07-24 00:08:04] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2024-07-24 00:08:04] LIB-02240e4 is tumor in VCF file. INFO [2024-07-24 00:08:04] No homozygous variants in VCF, provide unfiltered VCF. INFO [2024-07-24 00:08:04] Removing 1 non heterozygous (in matched normal) germline SNPs. INFO [2024-07-24 00:08:04] Removing 0 low quality variants with non-offset BQ < 25. INFO [2024-07-24 00:08:04] Base quality scores range from 29 to 35 (offset by 1) INFO [2024-07-24 00:08:04] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS. INFO [2024-07-24 00:08:04] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. Error in FileForFormat(resource(con), fileFormat(con)) : Format 'txt' unsupported In addition: Warning message: In for (i in seq_along(extends)) { : closing unused connection 4 (/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/PureCN/extdata/example_gatk4_denoised_cr.tsv.gz) FATAL [2024-07-24 00:08:04] Could not import snp.blacklist FATAL [2024-07-24 00:08:04] /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/PureCN/extdata/example_normal.txt.gz:Error FATAL [2024-07-24 00:08:04] in FileForFormat(resource(con), fileFormat(con)) : Format 'txt' FATAL [2024-07-24 00:08:04] unsupported FATAL [2024-07-24 00:08:04] FATAL [2024-07-24 00:08:04] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:08:04] parameters (PureCN 2.11.0). INFO [2024-07-24 00:08:04] ------------------------------------------------------------ INFO [2024-07-24 00:08:04] PureCN 2.11.0 INFO [2024-07-24 00:08:04] ------------------------------------------------------------ INFO [2024-07-24 00:08:04] Loading coverage files... INFO [2024-07-24 00:08:04] Mean target coverages: 112X (tumor) 99X (normal). WARN [2024-07-24 00:08:04] Allosome coverage missing, cannot determine sex. WARN [2024-07-24 00:08:04] Allosome coverage missing, cannot determine sex. INFO [2024-07-24 00:08:04] Removing 228 intervals with missing log.ratio. INFO [2024-07-24 00:08:04] Removing 22 small (< 5bp) intervals. INFO [2024-07-24 00:08:04] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2024-07-24 00:08:04] No normalDB provided. Provide one for better results. INFO [2024-07-24 00:08:04] Removing 233 low coverage (< 15.0000X) intervals. INFO [2024-07-24 00:08:04] Using 9547 intervals (9547 on-target, 0 off-target). INFO [2024-07-24 00:08:04] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2024-07-24 00:08:04] No interval.file provided. Cannot check for any GC-biases. INFO [2024-07-24 00:08:04] Loading VCF... INFO [2024-07-24 00:08:04] Found 127 variants in VCF file. INFO [2024-07-24 00:08:04] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2024-07-24 00:08:04] LIB-02240e4 is tumor in VCF file. INFO [2024-07-24 00:08:04] No homozygous variants in VCF, provide unfiltered VCF. INFO [2024-07-24 00:08:04] Removing 1 non heterozygous (in matched normal) germline SNPs. INFO [2024-07-24 00:08:04] Removing 0 low quality variants with non-offset BQ < 25. INFO [2024-07-24 00:08:04] Base quality scores range from 29 to 35 (offset by 1) INFO [2024-07-24 00:08:04] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS. INFO [2024-07-24 00:08:05] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. INFO [2024-07-24 00:08:05] Total size of targeted genomic region: 1.63Mb (2.58Mb with 50bp padding). INFO [2024-07-24 00:08:05] 1.0% of targets contain variants. INFO [2024-07-24 00:08:05] Removing 2 variants outside intervals. INFO [2024-07-24 00:08:05] Found SOMATIC annotation in VCF. INFO [2024-07-24 00:08:05] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. INFO [2024-07-24 00:08:05] Found SOMATIC annotation in VCF. Setting mapping bias to 0.973. INFO [2024-07-24 00:08:05] Excluding 0 novel or poor quality variants from segmentation. INFO [2024-07-24 00:08:05] Sample sex: ? INFO [2024-07-24 00:08:05] Segmenting data... INFO [2024-07-24 00:08:05] Loading pre-computed boundaries for DNAcopy... INFO [2024-07-24 00:08:05] Setting undo.SD parameter to 1.000000. INFO [2024-07-24 00:08:05] Setting prune.hclust.h parameter to 0.200000. INFO [2024-07-24 00:08:05] Found 54 segments with median size of 24.88Mb. INFO [2024-07-24 00:08:05] Using 123 variants. INFO [2024-07-24 00:08:05] Mean standard deviation of log-ratios: 0.37 (MAPD: 0.32) INFO [2024-07-24 00:08:05] 2D-grid search of purity and ploidy... INFO [2024-07-24 00:08:06] Local optima: 0.62/1.9, 0.3/1.9, 0.32/2 INFO [2024-07-24 00:08:06] Testing local optimum 1/3 at purity 0.62 and total ploidy 1.90... INFO [2024-07-24 00:08:06] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90... INFO [2024-07-24 00:08:06] Recalibrating log-ratios... INFO [2024-07-24 00:08:06] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90... INFO [2024-07-24 00:08:06] Recalibrating log-ratios... INFO [2024-07-24 00:08:06] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90... INFO [2024-07-24 00:08:06] Recalibrating log-ratios... INFO [2024-07-24 00:08:06] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90... INFO [2024-07-24 00:08:06] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00... INFO [2024-07-24 00:08:07] Recalibrating log-ratios... INFO [2024-07-24 00:08:07] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00... INFO [2024-07-24 00:08:07] Recalibrating log-ratios... INFO [2024-07-24 00:08:07] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00... INFO [2024-07-24 00:08:07] Recalibrating log-ratios... INFO [2024-07-24 00:08:07] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00... INFO [2024-07-24 00:08:07] Skipping 1 solutions that converged to the same optima. INFO [2024-07-24 00:08:07] Skipping 1 solutions exceeding max.non.clonal (0.20): 0.3/1.9 (purity/tumor ploidy) INFO [2024-07-24 00:08:07] Fitting variants with beta model for local optimum 1/3... INFO [2024-07-24 00:08:07] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01. INFO [2024-07-24 00:08:08] Optimized purity: 0.65 INFO [2024-07-24 00:08:08] Done. INFO [2024-07-24 00:08:08] ------------------------------------------------------------ INFO [2024-07-24 00:08:08] ------------------------------------------------------------ INFO [2024-07-24 00:08:08] PureCN 2.11.0 INFO [2024-07-24 00:08:08] ------------------------------------------------------------ INFO [2024-07-24 00:08:08] Loading coverage files... INFO [2024-07-24 00:08:08] Mean target coverages: 112X (tumor) 99X (normal). WARN [2024-07-24 00:08:08] Allosome coverage missing, cannot determine sex. WARN [2024-07-24 00:08:08] Allosome coverage missing, cannot determine sex. INFO [2024-07-24 00:08:08] Removing 228 intervals with missing log.ratio. INFO [2024-07-24 00:08:08] Removing 22 small (< 5bp) intervals. INFO [2024-07-24 00:08:08] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2024-07-24 00:08:08] No normalDB provided. Provide one for better results. INFO [2024-07-24 00:08:08] Removing 1724 low count (< 100 total reads) intervals. INFO [2024-07-24 00:08:08] Removing 6 low coverage (< 15.0000X) intervals. INFO [2024-07-24 00:08:08] Using 8050 intervals (8050 on-target, 0 off-target). INFO [2024-07-24 00:08:08] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2024-07-24 00:08:08] No interval.file provided. Cannot check for any GC-biases. INFO [2024-07-24 00:08:08] Loading VCF... INFO [2024-07-24 00:08:08] Found 127 variants in VCF file. WARN [2024-07-24 00:08:08] DP FORMAT field contains NAs. Removing 3 variants. WARN [2024-07-24 00:08:08] DB INFO flag contains NAs INFO [2024-07-24 00:08:08] 119 (96.0%) variants annotated as likely germline (DB INFO flag). INFO [2024-07-24 00:08:08] LIB-02240e4 is tumor in VCF file. INFO [2024-07-24 00:08:08] No homozygous variants in VCF, provide unfiltered VCF. INFO [2024-07-24 00:08:08] Removing 0 low quality variants with non-offset BQ < 25. INFO [2024-07-24 00:08:08] Base quality scores range from 29 to 35 (offset by 1) INFO [2024-07-24 00:08:08] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS. INFO [2024-07-24 00:08:08] Removing 1 variants with AF < 0.030 or AF >= 0.970 or insufficient supporting reads or depth < 15. INFO [2024-07-24 00:08:08] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding). INFO [2024-07-24 00:08:09] 1.2% of targets contain variants. INFO [2024-07-24 00:08:09] Setting somatic prior probabilities for likely germline hits to 0.000500 or to 0.500000 otherwise. INFO [2024-07-24 00:08:09] Excluding 5 novel or poor quality variants from segmentation. INFO [2024-07-24 00:08:09] Sample sex: ? INFO [2024-07-24 00:08:09] Segmenting data... INFO [2024-07-24 00:08:09] Loading pre-computed boundaries for DNAcopy... INFO [2024-07-24 00:08:09] Setting undo.SD parameter to 1.000000. Setting multi-figure configuration INFO [2024-07-24 00:08:09] Setting prune.hclust.h parameter to 0.200000. INFO [2024-07-24 00:08:09] Found 59 segments with median size of 17.67Mb. INFO [2024-07-24 00:08:09] Using 123 variants. INFO [2024-07-24 00:08:09] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30) INFO [2024-07-24 00:08:09] 2D-grid search of purity and ploidy... INFO [2024-07-24 00:08:10] Local optima: 0.62/1.9, 0.3/1.9, 0.32/2 INFO [2024-07-24 00:08:10] Testing local optimum 1/3 at purity 0.62 and total ploidy 1.90... INFO [2024-07-24 00:08:10] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90... INFO [2024-07-24 00:08:10] Recalibrating log-ratios... INFO [2024-07-24 00:08:10] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90... INFO [2024-07-24 00:08:10] Recalibrating log-ratios... INFO [2024-07-24 00:08:10] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90... INFO [2024-07-24 00:08:10] Recalibrating log-ratios... INFO [2024-07-24 00:08:10] Testing local optimum 2/3 at purity 0.30 and total ploidy 1.90... INFO [2024-07-24 00:08:10] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00... INFO [2024-07-24 00:08:10] Recalibrating log-ratios... INFO [2024-07-24 00:08:10] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00... INFO [2024-07-24 00:08:11] Recalibrating log-ratios... INFO [2024-07-24 00:08:11] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00... INFO [2024-07-24 00:08:11] Recalibrating log-ratios... INFO [2024-07-24 00:08:11] Testing local optimum 3/3 at purity 0.32 and total ploidy 2.00... INFO [2024-07-24 00:08:11] Skipping 2 solutions exceeding max.non.clonal (0.20): 0.3/1.9, 0.35/1.61 (purity/tumor ploidy) INFO [2024-07-24 00:08:11] Fitting variants with beta model for local optimum 1/3... INFO [2024-07-24 00:08:11] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01. INFO [2024-07-24 00:08:12] Optimized purity: 0.65 INFO [2024-07-24 00:08:12] Done. INFO [2024-07-24 00:08:12] ------------------------------------------------------------ INFO [2024-07-24 00:08:12] ------------------------------------------------------------ INFO [2024-07-24 00:08:12] PureCN 2.11.0 INFO [2024-07-24 00:08:12] ------------------------------------------------------------ INFO [2024-07-24 00:08:12] Loading coverage files... INFO [2024-07-24 00:08:12] Mean target coverages: 112X (tumor) 99X (normal). WARN [2024-07-24 00:08:12] Allosome coverage missing, cannot determine sex. WARN [2024-07-24 00:08:12] Allosome coverage missing, cannot determine sex. INFO [2024-07-24 00:08:12] No Gene column in interval.file. You won't get gene-level calls. INFO [2024-07-24 00:08:12] Removing 228 intervals with missing log.ratio. INFO [2024-07-24 00:08:12] Removing 15 low/high GC targets. INFO [2024-07-24 00:08:12] Removing 21 small (< 5bp) intervals. INFO [2024-07-24 00:08:12] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2024-07-24 00:08:12] No normalDB provided. Provide one for better results. INFO [2024-07-24 00:08:12] Removing 1718 low count (< 100 total reads) intervals. INFO [2024-07-24 00:08:12] Removing 6 low coverage (< 15.0000X) intervals. INFO [2024-07-24 00:08:12] Removing 36 low mappability intervals. INFO [2024-07-24 00:08:12] Using 8006 intervals (8006 on-target, 0 off-target). INFO [2024-07-24 00:08:12] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2024-07-24 00:08:12] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio). INFO [2024-07-24 00:08:12] Loading VCF... INFO [2024-07-24 00:08:12] Found 127 variants in VCF file. INFO [2024-07-24 00:08:12] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2024-07-24 00:08:12] LIB-02240e4 is tumor in VCF file. INFO [2024-07-24 00:08:12] No homozygous variants in VCF, provide unfiltered VCF. INFO [2024-07-24 00:08:12] Removing 1 non heterozygous (in matched normal) germline SNPs. INFO [2024-07-24 00:08:12] Removing 0 low quality variants with non-offset BQ < 25. INFO [2024-07-24 00:08:12] Base quality scores range from 29 to 35 (offset by 1) INFO [2024-07-24 00:08:12] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS. INFO [2024-07-24 00:08:13] Removing 1 variants with AF < 0.030 or AF >= Inf or insufficient supporting reads or depth < 15. INFO [2024-07-24 00:08:13] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding). INFO [2024-07-24 00:08:13] 1.2% of targets contain variants. INFO [2024-07-24 00:08:13] Removing 11 variants outside intervals. INFO [2024-07-24 00:08:13] Found SOMATIC annotation in VCF. INFO [2024-07-24 00:08:13] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. INFO [2024-07-24 00:08:13] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970. INFO [2024-07-24 00:08:13] Excluding 0 novel or poor quality variants from segmentation. INFO [2024-07-24 00:08:13] Sample sex: ? INFO [2024-07-24 00:08:13] Segmenting data... INFO [2024-07-24 00:08:13] MAPD of 114 allelic fractions: 0.14 (0.15 adjusted). INFO [2024-07-24 00:08:13] Using unweighted PSCBS. INFO [2024-07-24 00:08:13] Setting undo.SD parameter to 1.000000. INFO [2024-07-24 00:08:18] Setting prune.hclust.h parameter to 0.200000. INFO [2024-07-24 00:08:18] Found 71 segments with median size of 27.72Mb. INFO [2024-07-24 00:08:18] Using 114 variants. INFO [2024-07-24 00:08:18] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30) INFO [2024-07-24 00:08:18] 2D-grid search of purity and ploidy... INFO [2024-07-24 00:08:18] Local optima: 0.65/1.8, 0.38/2.2 INFO [2024-07-24 00:08:18] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80... INFO [2024-07-24 00:08:18] Recalibrating log-ratios... INFO [2024-07-24 00:08:18] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80... INFO [2024-07-24 00:08:18] Recalibrating log-ratios... INFO [2024-07-24 00:08:18] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80... INFO [2024-07-24 00:08:18] Recalibrating log-ratios... INFO [2024-07-24 00:08:18] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80... INFO [2024-07-24 00:08:19] Testing local optimum 2/2 at purity 0.38 and total ploidy 2.20... INFO [2024-07-24 00:08:19] Skipping 1 solutions exceeding max.non.clonal (0.20): 0.65/2.04 (purity/tumor ploidy) INFO [2024-07-24 00:08:19] Fitting variants with beta model for local optimum 2/2... INFO [2024-07-24 00:08:19] Fitting variants for purity 0.40, tumor ploidy 2.53 and contamination 0.01. INFO [2024-07-24 00:08:20] Optimized purity: 0.40 INFO [2024-07-24 00:08:20] Done. INFO [2024-07-24 00:08:20] ------------------------------------------------------------ FATAL [2024-07-24 00:08:20] This function requires gene-level calls. Please add a column 'Gene' FATAL [2024-07-24 00:08:20] containing gene symbols to the interval.file. FATAL [2024-07-24 00:08:20] FATAL [2024-07-24 00:08:20] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:08:20] parameters (PureCN 2.11.0). INFO [2024-07-24 00:08:20] ------------------------------------------------------------ INFO [2024-07-24 00:08:20] PureCN 2.11.0 INFO [2024-07-24 00:08:20] ------------------------------------------------------------ INFO [2024-07-24 00:08:20] Loading coverage files... INFO [2024-07-24 00:08:21] Mean target coverages: 112X (tumor) 99X (normal). WARN [2024-07-24 00:08:21] Allosome coverage missing, cannot determine sex. WARN [2024-07-24 00:08:21] Allosome coverage missing, cannot determine sex. INFO [2024-07-24 00:08:21] Removing 228 intervals with missing log.ratio. INFO [2024-07-24 00:08:21] Removing 22 small (< 5bp) intervals. INFO [2024-07-24 00:08:21] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2024-07-24 00:08:21] No normalDB provided. Provide one for better results. INFO [2024-07-24 00:08:21] Removing 1724 low count (< 100 total reads) intervals. INFO [2024-07-24 00:08:21] Removing 6 low coverage (< 15.0000X) intervals. INFO [2024-07-24 00:08:21] Using 8050 intervals (8050 on-target, 0 off-target). INFO [2024-07-24 00:08:21] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2024-07-24 00:08:21] No interval.file provided. Cannot check for any GC-biases. INFO [2024-07-24 00:08:21] Loading VCF... INFO [2024-07-24 00:08:21] Found 127 variants in VCF file. INFO [2024-07-24 00:08:21] 127 (100.0%) variants annotated as likely germline (DB INFO flag). FATAL [2024-07-24 00:08:21] Different chromosome names in coverage and VCF. FATAL [2024-07-24 00:08:21] FATAL [2024-07-24 00:08:21] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:08:21] parameters (PureCN 2.11.0). INFO [2024-07-24 00:08:21] ------------------------------------------------------------ INFO [2024-07-24 00:08:21] PureCN 2.11.0 INFO [2024-07-24 00:08:21] ------------------------------------------------------------ INFO [2024-07-24 00:08:21] Loading coverage files... INFO [2024-07-24 00:08:21] Mean target coverages: 112X (tumor) 99X (normal). WARN [2024-07-24 00:08:21] Allosome coverage missing, cannot determine sex. WARN [2024-07-24 00:08:21] Allosome coverage missing, cannot determine sex. FATAL [2024-07-24 00:08:21] tumor.coverage.file and interval.file do not align. FATAL [2024-07-24 00:08:21] FATAL [2024-07-24 00:08:21] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:08:21] parameters (PureCN 2.11.0). INFO [2024-07-24 00:08:21] ------------------------------------------------------------ INFO [2024-07-24 00:08:21] PureCN 2.11.0 INFO [2024-07-24 00:08:21] ------------------------------------------------------------ INFO [2024-07-24 00:08:21] Loading coverage files... INFO [2024-07-24 00:08:21] Mean target coverages: 112X (tumor) 99X (normal). WARN [2024-07-24 00:08:21] Allosome coverage missing, cannot determine sex. WARN [2024-07-24 00:08:21] Allosome coverage missing, cannot determine sex. INFO [2024-07-24 00:08:21] Removing 228 intervals with missing log.ratio. INFO [2024-07-24 00:08:21] Removing 15 low/high GC targets. INFO [2024-07-24 00:08:21] Removing 21 small (< 5bp) intervals. INFO [2024-07-24 00:08:21] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2024-07-24 00:08:21] No normalDB provided. Provide one for better results. INFO [2024-07-24 00:08:21] Removing 1718 low count (< 100 total reads) intervals. INFO [2024-07-24 00:08:21] Removing 6 low coverage (< 15.0000X) intervals. INFO [2024-07-24 00:08:21] Removing 36 low mappability intervals. INFO [2024-07-24 00:08:21] Using 8006 intervals (8006 on-target, 0 off-target). INFO [2024-07-24 00:08:21] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2024-07-24 00:08:21] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio). INFO [2024-07-24 00:08:21] Loading VCF... INFO [2024-07-24 00:08:21] Found 127 variants in VCF file. INFO [2024-07-24 00:08:21] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2024-07-24 00:08:22] LIB-02240e4 is tumor in VCF file. INFO [2024-07-24 00:08:22] No homozygous variants in VCF, provide unfiltered VCF. INFO [2024-07-24 00:08:22] Removing 1 non heterozygous (in matched normal) germline SNPs. INFO [2024-07-24 00:08:22] Removing 0 low quality variants with non-offset BQ < 25. INFO [2024-07-24 00:08:22] Base quality scores range from 29 to 35 (offset by 1) INFO [2024-07-24 00:08:22] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS. INFO [2024-07-24 00:08:22] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. INFO [2024-07-24 00:08:22] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding). INFO [2024-07-24 00:08:22] 1.2% of targets contain variants. INFO [2024-07-24 00:08:22] Removing 11 variants outside intervals. INFO [2024-07-24 00:08:22] Found SOMATIC annotation in VCF. INFO [2024-07-24 00:08:22] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. INFO [2024-07-24 00:08:22] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970. INFO [2024-07-24 00:08:22] Excluding 0 novel or poor quality variants from segmentation. INFO [2024-07-24 00:08:22] Sample sex: ? INFO [2024-07-24 00:08:22] Segmenting data... INFO [2024-07-24 00:08:22] Loading pre-computed boundaries for DNAcopy... INFO [2024-07-24 00:08:22] Setting undo.SD parameter to 1.000000. INFO [2024-07-24 00:08:22] Setting prune.hclust.h parameter to 0.200000. INFO [2024-07-24 00:08:22] Found 59 segments with median size of 17.67Mb. INFO [2024-07-24 00:08:22] Using 114 variants. INFO [2024-07-24 00:08:22] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30) INFO [2024-07-24 00:08:22] 2D-grid search of purity and ploidy... INFO [2024-07-24 00:08:23] Local optima: 0.63/1.9 INFO [2024-07-24 00:08:23] Testing local optimum 1/1 at purity 0.63 and total ploidy 1.90... INFO [2024-07-24 00:08:23] Fitting variants with beta model for local optimum 1/1... INFO [2024-07-24 00:08:23] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01. INFO [2024-07-24 00:08:24] Optimized purity: 0.65 INFO [2024-07-24 00:08:24] Done. INFO [2024-07-24 00:08:24] ------------------------------------------------------------ INFO [2024-07-24 00:08:24] ------------------------------------------------------------ INFO [2024-07-24 00:08:24] PureCN 2.11.0 INFO [2024-07-24 00:08:24] ------------------------------------------------------------ INFO [2024-07-24 00:08:24] Loading coverage files... INFO [2024-07-24 00:08:24] Mean target coverages: 112X (tumor) 99X (normal). WARN [2024-07-24 00:08:24] Allosome coverage missing, cannot determine sex. WARN [2024-07-24 00:08:24] Allosome coverage missing, cannot determine sex. INFO [2024-07-24 00:08:24] Removing 228 intervals with missing log.ratio. INFO [2024-07-24 00:08:24] Removing 15 low/high GC targets. INFO [2024-07-24 00:08:24] Removing 21 small (< 5bp) intervals. INFO [2024-07-24 00:08:24] Removing 19 intervals with low total coverage in normal (< 150.00 reads). WARN [2024-07-24 00:08:24] No normalDB provided. Provide one for better results. INFO [2024-07-24 00:08:24] Removing 1718 low count (< 100 total reads) intervals. INFO [2024-07-24 00:08:24] Removing 6 low coverage (< 15.0000X) intervals. INFO [2024-07-24 00:08:24] Removing 36 low mappability intervals. INFO [2024-07-24 00:08:24] Using 8006 intervals (8006 on-target, 0 off-target). INFO [2024-07-24 00:08:24] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2024-07-24 00:08:24] AT/GC dropout: 1.01 (tumor), 1.03 (normal), 0.98 (coverage log-ratio). INFO [2024-07-24 00:08:24] Loading VCF... INFO [2024-07-24 00:08:24] Found 127 variants in VCF file. INFO [2024-07-24 00:08:24] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2024-07-24 00:08:24] LIB-02240e4 is tumor in VCF file. INFO [2024-07-24 00:08:24] No homozygous variants in VCF, provide unfiltered VCF. INFO [2024-07-24 00:08:25] Removing 1 non heterozygous (in matched normal) germline SNPs. INFO [2024-07-24 00:08:25] Removing 0 low quality variants with non-offset BQ < 25. INFO [2024-07-24 00:08:25] Base quality scores range from 29 to 35 (offset by 1) INFO [2024-07-24 00:08:25] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS. INFO [2024-07-24 00:08:25] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. INFO [2024-07-24 00:08:25] Total size of targeted genomic region: 1.51Mb (2.31Mb with 50bp padding). INFO [2024-07-24 00:08:25] 1.2% of targets contain variants. INFO [2024-07-24 00:08:25] Removing 11 variants outside intervals. INFO [2024-07-24 00:08:25] Found SOMATIC annotation in VCF. INFO [2024-07-24 00:08:25] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. INFO [2024-07-24 00:08:25] Found SOMATIC annotation in VCF. Setting mapping bias to 0.970. INFO [2024-07-24 00:08:25] Excluding 0 novel or poor quality variants from segmentation. INFO [2024-07-24 00:08:25] Sample sex: ? INFO [2024-07-24 00:08:25] Segmenting data... INFO [2024-07-24 00:08:25] Loading pre-computed boundaries for DNAcopy... INFO [2024-07-24 00:08:25] Setting undo.SD parameter to 1.000000. INFO [2024-07-24 00:08:25] Setting prune.hclust.h parameter to 0.200000. INFO [2024-07-24 00:08:25] Found 59 segments with median size of 17.67Mb. INFO [2024-07-24 00:08:25] Using 114 variants. INFO [2024-07-24 00:08:25] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30) INFO [2024-07-24 00:08:25] 2D-grid search of purity and ploidy... INFO [2024-07-24 00:08:26] Local optima: 0.63/1.9 INFO [2024-07-24 00:08:26] Testing local optimum 1/1 at purity 0.63 and total ploidy 1.90... INFO [2024-07-24 00:08:26] Fitting variants with beta model for local optimum 1/1... WARN [2024-07-24 00:08:26] Some gene symbols found on multiple chromosomes. Use of approved symbols suggested. INFO [2024-07-24 00:08:26] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01. INFO [2024-07-24 00:08:27] Optimized purity: 0.65 INFO [2024-07-24 00:08:27] Done. INFO [2024-07-24 00:08:27] ------------------------------------------------------------ FATAL [2024-07-24 00:08:27] chr1 not valid chromosome name(s). Valid names are: FATAL [2024-07-24 00:08:27] 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22 FATAL [2024-07-24 00:08:27] FATAL [2024-07-24 00:08:27] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:08:27] parameters (PureCN 2.11.0). INFO [2024-07-24 00:08:27] ------------------------------------------------------------ INFO [2024-07-24 00:08:27] PureCN 2.11.0 INFO [2024-07-24 00:08:27] ------------------------------------------------------------ INFO [2024-07-24 00:08:27] Loading coverage files... WARN [2024-07-24 00:08:27] Provided sampleid (Sample2) does not match Sample1 found in segmentation. WARN [2024-07-24 00:08:27] Allosome coverage missing, cannot determine sex. WARN [2024-07-24 00:08:27] Allosome coverage missing, cannot determine sex. INFO [2024-07-24 00:08:27] Removing 10 intervals with missing log.ratio. INFO [2024-07-24 00:08:27] Using 10039 intervals (10039 on-target, 0 off-target). INFO [2024-07-24 00:08:27] No off-target intervals. If this is hybrid-capture data, consider adding them. INFO [2024-07-24 00:08:27] Loading VCF... INFO [2024-07-24 00:08:27] Found 127 variants in VCF file. INFO [2024-07-24 00:08:27] 127 (100.0%) variants annotated as likely germline (DB INFO flag). INFO [2024-07-24 00:08:27] LIB-02240e4 is tumor in VCF file. INFO [2024-07-24 00:08:27] No homozygous variants in VCF, provide unfiltered VCF. INFO [2024-07-24 00:08:27] Removing 1 non heterozygous (in matched normal) germline SNPs. INFO [2024-07-24 00:08:27] Removing 0 low quality variants with non-offset BQ < 25. INFO [2024-07-24 00:08:27] Base quality scores range from 29 to 35 (offset by 1) INFO [2024-07-24 00:08:27] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS. INFO [2024-07-24 00:08:27] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. INFO [2024-07-24 00:08:28] Total size of targeted genomic region: 1.71Mb (2.70Mb with 50bp padding). INFO [2024-07-24 00:08:28] 1.0% of targets contain variants. INFO [2024-07-24 00:08:28] Removing 0 variants outside intervals. INFO [2024-07-24 00:08:28] Found SOMATIC annotation in VCF. INFO [2024-07-24 00:08:28] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. INFO [2024-07-24 00:08:28] Found SOMATIC annotation in VCF. Setting mapping bias to 0.976. INFO [2024-07-24 00:08:28] Excluding 0 novel or poor quality variants from segmentation. INFO [2024-07-24 00:08:28] Sample sex: ? INFO [2024-07-24 00:08:28] Segmenting data... INFO [2024-07-24 00:08:28] Loaded provided segmentation file example_seg.txt (format DNAcopy). WARN [2024-07-24 00:08:28] Provided sampleid (Sample2) does not match Sample1 found in segmentation. INFO [2024-07-24 00:08:28] Re-centering provided segment means (offset -0.0033). INFO [2024-07-24 00:08:28] Loading pre-computed boundaries for DNAcopy... INFO [2024-07-24 00:08:28] Setting undo.SD parameter to 0.000000. Setting multi-figure configuration INFO [2024-07-24 00:08:28] Setting prune.hclust.h parameter to 0.200000. INFO [2024-07-24 00:08:28] Found 54 segments with median size of 24.88Mb. INFO [2024-07-24 00:08:28] Using 125 variants. INFO [2024-07-24 00:08:28] Mean standard deviation of log-ratios: 0.40 (MAPD: 0.00) INFO [2024-07-24 00:08:28] 2D-grid search of purity and ploidy... INFO [2024-07-24 00:08:28] Local optima: 0.6/1.9 INFO [2024-07-24 00:08:28] Testing local optimum 1/1 at purity 0.60 and total ploidy 1.90... INFO [2024-07-24 00:08:28] Fitting variants with beta model for local optimum 1/1... INFO [2024-07-24 00:08:28] Fitting variants for purity 0.65, tumor ploidy 1.74 and contamination 0.01. INFO [2024-07-24 00:08:29] Optimized purity: 0.65 INFO [2024-07-24 00:08:29] Done. INFO [2024-07-24 00:08:29] ------------------------------------------------------------ WARN [2024-07-24 00:08:29] Allosome coverage missing, cannot determine sex. WARN [2024-07-24 00:08:30] Allosome coverage missing, cannot determine sex. Setting multi-figure configuration FATAL [2024-07-24 00:08:32] Segmentation file expected with colnames ID, chrom, loc.start, loc.end, FATAL [2024-07-24 00:08:32] num.mark, seg.mean FATAL [2024-07-24 00:08:32] FATAL [2024-07-24 00:08:32] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:08:32] parameters (PureCN 2.11.0). FATAL [2024-07-24 00:08:32] seg.file contains multiple samples and sampleid missing. FATAL [2024-07-24 00:08:32] FATAL [2024-07-24 00:08:32] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:08:32] parameters (PureCN 2.11.0). FATAL [2024-07-24 00:08:32] seg.file contains multiple samples and sampleid does not match any. FATAL [2024-07-24 00:08:32] FATAL [2024-07-24 00:08:32] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:08:32] parameters (PureCN 2.11.0). WARN [2024-07-24 00:08:32] Allosome coverage missing, cannot determine sex. WARN [2024-07-24 00:08:32] Allosome coverage missing, cannot determine sex. WARN [2024-07-24 00:08:35] Allosome coverage missing, cannot determine sex. WARN [2024-07-24 00:08:35] Allosome coverage missing, cannot determine sex. WARN [2024-07-24 00:08:35] Provided sampleid (example_tumor.txt.gz) does not match Sample1 found in segmentation. WARN [2024-07-24 00:08:36] Allosome coverage missing, cannot determine sex. WARN [2024-07-24 00:08:36] Allosome coverage missing, cannot determine sex. WARN [2024-07-24 00:08:37] No normalDB provided. Provide one for better results. WARN [2024-07-24 00:08:39] Allosome coverage missing, cannot determine sex. WARN [2024-07-24 00:08:39] Allosome coverage missing, cannot determine sex. WARN [2024-07-24 00:08:40] Provided sampleid (Sample.1) does not match Sample1 found in segmentation. Setting multi-figure configuration WARN [2024-07-24 00:08:42] Allosome coverage missing, cannot determine sex. WARN [2024-07-24 00:08:42] Allosome coverage missing, cannot determine sex. WARN [2024-07-24 00:08:42] No normalDB provided. Provide one for better results. WARN [2024-07-24 00:08:42] Sampleid looks like a normal in VCF, not like a tumor. WARN [2024-07-24 00:08:45] Allosome coverage missing, cannot determine sex. WARN [2024-07-24 00:08:45] Allosome coverage missing, cannot determine sex. FATAL [2024-07-24 00:08:45] normalDB not a valid normalDB object. Use createNormalDatabase to FATAL [2024-07-24 00:08:45] create one. FATAL [2024-07-24 00:08:45] FATAL [2024-07-24 00:08:45] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:08:45] parameters (PureCN 2.11.0). WARN [2024-07-24 00:08:45] You are likely not using the correct baits file! WARN [2024-07-24 00:08:45] Allosome coverage missing, cannot determine sex. WARN [2024-07-24 00:08:45] Allosome coverage missing, cannot determine sex. WARN [2024-07-24 00:08:46] Allosome coverage missing, cannot determine sex. WARN [2024-07-24 00:08:46] Allosome coverage missing, cannot determine sex. FATAL [2024-07-24 00:08:46] normalDB appears to be empty. FATAL [2024-07-24 00:08:46] FATAL [2024-07-24 00:08:46] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:08:46] parameters (PureCN 2.11.0). WARN [2024-07-24 00:08:46] Allosome coverage missing, cannot determine sex. WARN [2024-07-24 00:08:46] Allosome coverage missing, cannot determine sex. WARN [2024-07-24 00:08:46] Intervals in coverage and interval.file have conflicting on/off-target annotation. WARN [2024-07-24 00:08:50] Allosome coverage missing, cannot determine sex. WARN [2024-07-24 00:08:50] Allosome coverage missing, cannot determine sex. FATAL [2024-07-24 00:08:50] Seqlevels missing in provided segmentation: 6 FATAL [2024-07-24 00:08:50] FATAL [2024-07-24 00:08:50] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:08:50] parameters (PureCN 2.11.0). sh: gatk: command not found WARN [2024-07-24 00:08:50] Cannot find gatk binary in path. WARN [2024-07-24 00:08:50] Allosome coverage missing, cannot determine sex. WARN [2024-07-24 00:08:50] Allosome coverage missing, cannot determine sex. WARN [2024-07-24 00:08:50] No normalDB provided. Provide one for better results. FATAL [2024-07-24 00:08:50] segmentationHclust requires an input segmentation. FATAL [2024-07-24 00:08:50] FATAL [2024-07-24 00:08:50] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:08:50] parameters (PureCN 2.11.0). WARN [2024-07-24 00:08:51] Allosome coverage missing, cannot determine sex. WARN [2024-07-24 00:08:51] Allosome coverage missing, cannot determine sex. WARN [2024-07-24 00:08:51] No normalDB provided. Provide one for better results. FATAL [2024-07-24 00:08:59] The normal.panel.vcf.file contains only a single sample. FATAL [2024-07-24 00:08:59] FATAL [2024-07-24 00:08:59] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:08:59] parameters (PureCN 2.11.0). FATAL [2024-07-24 00:08:59] mapping.bias.file must be a file with *.rds suffix. FATAL [2024-07-24 00:08:59] FATAL [2024-07-24 00:08:59] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:08:59] parameters (PureCN 2.11.0). Failed with error: 'there is no package called 'genomicsdb'' In addition: Warning message: In .Internal(vapply(X, FUN, FUN.VALUE, USE.NAMES)) : closing unused connection 5 (/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpCvWANV/file22395240991a.tsv) FATAL [2024-07-24 00:08:59] min.normals (0) must be >= 1. FATAL [2024-07-24 00:08:59] FATAL [2024-07-24 00:08:59] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:08:59] parameters (PureCN 2.11.0). FATAL [2024-07-24 00:08:59] min.normals (10) cannot be larger than min.normals.assign.betafit (3). FATAL [2024-07-24 00:08:59] FATAL [2024-07-24 00:08:59] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:08:59] parameters (PureCN 2.11.0). FATAL [2024-07-24 00:09:00] min.normals.assign.betafit (10) cannot be larger than FATAL [2024-07-24 00:09:00] min.normals.betafit (7). FATAL [2024-07-24 00:09:00] FATAL [2024-07-24 00:09:00] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:09:00] parameters (PureCN 2.11.0). FATAL [2024-07-24 00:09:00] min.normals.betafit (20) cannot be larger than FATAL [2024-07-24 00:09:00] min.normals.position.specific.fit (10). FATAL [2024-07-24 00:09:00] FATAL [2024-07-24 00:09:00] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:09:00] parameters (PureCN 2.11.0). FATAL [2024-07-24 00:09:00] min.betafit.rho not within expected range or format. FATAL [2024-07-24 00:09:00] FATAL [2024-07-24 00:09:00] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:09:00] parameters (PureCN 2.11.0). FATAL [2024-07-24 00:09:00] max.betafit.rho not within expected range or format. FATAL [2024-07-24 00:09:00] FATAL [2024-07-24 00:09:00] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:09:00] parameters (PureCN 2.11.0). FATAL [2024-07-24 00:09:00] min.betafit.rho (0.9) cannot be larger than max.betafit.rho (0.2). FATAL [2024-07-24 00:09:00] FATAL [2024-07-24 00:09:00] This is most likely a user error due to invalid input data or FATAL [2024-07-24 00:09:00] parameters (PureCN 2.11.0). [ FAIL 0 | WARN 13 | SKIP 2 | PASS 404 ] ══ Skipped tests (2) ═══════════════════════════════════════════════════════════ • gatk binary > 4.1.7.0 required (1): 'test_segmentation.R:25:4' • genomicsdb required (1): 'test_setMappingBiasVcf.R:45:5' [ FAIL 0 | WARN 13 | SKIP 2 | PASS 404 ] > > proc.time() user system elapsed 133.617 4.771 126.566
PureCN.Rcheck/PureCN-Ex.timings
name | user | system | elapsed | |
adjustLogRatio | 0.767 | 0.011 | 0.779 | |
annotateTargets | 2.422 | 0.079 | 2.502 | |
bootstrapResults | 0.212 | 0.015 | 0.228 | |
calculateBamCoverageByInterval | 0.070 | 0.001 | 0.072 | |
calculateLogRatio | 0.253 | 0.013 | 0.267 | |
calculateMappingBiasGatk4 | 0.000 | 0.001 | 0.000 | |
calculateMappingBiasVcf | 0.635 | 0.024 | 0.659 | |
calculatePowerDetectSomatic | 0.906 | 0.002 | 0.909 | |
calculateTangentNormal | 0.962 | 0.016 | 0.979 | |
callAlterations | 0.058 | 0.003 | 0.060 | |
callAlterationsFromSegmentation | 0.508 | 0.011 | 0.519 | |
callAmplificationsInLowPurity | 12.138 | 0.107 | 12.251 | |
callCIN | 0.087 | 0.002 | 0.089 | |
callLOH | 0.077 | 0.002 | 0.078 | |
callMutationBurden | 0.572 | 0.017 | 0.590 | |
centromeres | 0.001 | 0.001 | 0.001 | |
correctCoverageBias | 0.561 | 0.016 | 0.576 | |
createCurationFile | 0.152 | 0.003 | 0.155 | |
createNormalDatabase | 0.841 | 0.012 | 0.853 | |
filterIntervals | 7.077 | 0.151 | 7.232 | |
filterVcfBasic | 0.203 | 0.003 | 0.205 | |
filterVcfMuTect | 0.219 | 0.003 | 0.223 | |
filterVcfMuTect2 | 0.205 | 0.002 | 0.206 | |
findFocal | 3.623 | 0.038 | 3.665 | |
getSexFromCoverage | 0.087 | 0.003 | 0.090 | |
getSexFromVcf | 0.090 | 0.002 | 0.091 | |
plotAbs | 0.104 | 0.004 | 0.109 | |
poolCoverage | 0.201 | 0.009 | 0.211 | |
predictSomatic | 0.188 | 0.003 | 0.192 | |
preprocessIntervals | 0.200 | 0.004 | 0.204 | |
processMultipleSamples | 0.854 | 0.015 | 0.869 | |
readAllelicCountsFile | 0.207 | 0.001 | 0.207 | |
readCoverageFile | 0.100 | 0.003 | 0.103 | |
readCurationFile | 0.090 | 0.003 | 0.093 | |
readIntervalFile | 0.059 | 0.002 | 0.061 | |
readLogRatioFile | 0.009 | 0.000 | 0.010 | |
readSegmentationFile | 0.004 | 0.000 | 0.004 | |
runAbsoluteCN | 6.008 | 0.100 | 6.109 | |
segmentationCBS | 2.643 | 0.017 | 2.660 | |
segmentationGATK4 | 0.001 | 0.000 | 0.001 | |
segmentationHclust | 4.984 | 0.095 | 5.079 | |
segmentationPSCBS | 8.460 | 0.129 | 8.588 | |
setMappingBiasVcf | 0.098 | 0.002 | 0.100 | |
setPriorVcf | 0.094 | 0.003 | 0.097 | |