Hello,i'm using ichorCNA in TitanCNA snakemake pipeline,my command is
Rscript /gpfs/users/yanghao/software/ichorCNA/scripts/runIchorCNA.R --id tumor_sample_1 --WIG results/readDepth/tumor_sample_1.bin10000.wig --gcWig /gpfs/users/yanghao/software/ichorCNA/inst/extdata/gc_hg19_500kb.wig --mapWig /gpfs/users/yanghao/software/ichorCNA/inst/extdata/map_hg19_500kb.wig --NORMWIG results/readDepth/normal_sample_1.bin10000.wig --ploidy "c(2,3)" --normal "c(0.5)" --maxCN 8 --includeHOMD False --chrs "c(1:22, \"X\")" --chrTrain "c(1:22)" --estimateNormal True --estimatePloidy True --estimateScPrevalence True --scStates "c(1,3)" --centromere /gpfs/users/yanghao/software/ichorCNA/inst/extdata/GRCh37.p13_centromere_UCSC-gapTable.txt --txnE 0.9999 --txnStrength 10000 --fracReadsInChrYForMale 0.001 --plotFileType png --plotYLim "c(-2,4)" --outDir results/ichorCNA/tumor_sample_1/
and output log:
$WIG
[1] "results/readDepth/tumor_sample_1.bin10000.wig"
$NORMWIG
[1] "results/readDepth/normal_sample_1.bin10000.wig"
$gcWig
[1] "/gpfs/users/yanghao/software/ichorCNA/inst/extdata/gc_hg19_500kb.wig"
$mapWig
[1] "/gpfs/users/yanghao/software/ichorCNA/inst/extdata/map_hg19_500kb.wig"
$id
[1] "tumor_sample_1"
$centromere
[1] "/gpfs/users/yanghao/software/ichorCNA/inst/extdata/GRCh37.p13_centromere_UCSC-gapTable.txt"
$rmCentromereFlankLength
[1] 1e+05
$normal
[1] "c(0.5)"
$scStates
[1] "c(1,3)"
$lambda
[1] "NULL"
$lambdaScaleHyperParam
[1] 3
$ploidy
[1] "c(2,3)"
$maxCN
[1] 8
$estimateNormal
[1] TRUE
$estimateScPrevalence
[1] TRUE
$estimatePloidy
[1] TRUE
$maxFracCNASubclone
[1] 0.7
$maxFracGenomeSubclone
[1] 0.5
$minSegmentBins
[1] 50
$altFracThreshold
[1] 0.05
$chrNormalize
[1] "c(1:22)"
$chrTrain
[1] "c(1:22)"
$chrs
[1] "c(1:22, "X")"
$normalizeMaleX
[1] TRUE
$fracReadsInChrYForMale
[1] 0.001
$includeHOMD
[1] FALSE
$txnE
[1] 0.9999
$txnStrength
[1] 10000
$plotFileType
[1] "png"
$plotYLim
[1] "c(-2,4)"
$outDir
[1] "results/ichorCNA/tumor_sample_1/"
$help
[1] FALSE
Loading required package: IRanges
Loading required package: methods
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, cbind, colMeans, colnames,
colSums, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match,
mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort,
table, tapply, union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:base’:
Loading required package: geneplotter
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: lattice
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: XML
Attaching package: ‘ichorCNA’
The following object is masked from ‘package:HMMcopy’:
Loading tumour file:tumor_sample_1
Slurping: results/readDepth/tumor_sample_1.bin10000.wig
Parsing: fixedStep chrom=1 start=1 step=10000 span=10000
Parsing: fixedStep chrom=2 start=1 step=10000 span=10000
Parsing: fixedStep chrom=3 start=1 step=10000 span=10000
Parsing: fixedStep chrom=4 start=1 step=10000 span=10000
Parsing: fixedStep chrom=5 start=1 step=10000 span=10000
Parsing: fixedStep chrom=6 start=1 step=10000 span=10000
Parsing: fixedStep chrom=7 start=1 step=10000 span=10000
Parsing: fixedStep chrom=8 start=1 step=10000 span=10000
Parsing: fixedStep chrom=9 start=1 step=10000 span=10000
Parsing: fixedStep chrom=10 start=1 step=10000 span=10000
Parsing: fixedStep chrom=11 start=1 step=10000 span=10000
Parsing: fixedStep chrom=12 start=1 step=10000 span=10000
Parsing: fixedStep chrom=13 start=1 step=10000 span=10000
Parsing: fixedStep chrom=14 start=1 step=10000 span=10000
Parsing: fixedStep chrom=15 start=1 step=10000 span=10000
Parsing: fixedStep chrom=16 start=1 step=10000 span=10000
Parsing: fixedStep chrom=17 start=1 step=10000 span=10000
Parsing: fixedStep chrom=18 start=1 step=10000 span=10000
Parsing: fixedStep chrom=19 start=1 step=10000 span=10000
Parsing: fixedStep chrom=20 start=1 step=10000 span=10000
Parsing: fixedStep chrom=21 start=1 step=10000 span=10000
Parsing: fixedStep chrom=22 start=1 step=10000 span=10000
Parsing: fixedStep chrom=X start=1 step=10000 span=10000
Parsing: fixedStep chrom=Y start=1 step=10000 span=10000
Sorting by decreasing chromosome size
Reading GC and mappability files
Slurping: /gpfs/users/yanghao/software/ichorCNA/inst/extdata/gc_hg19_500kb.wig
Parsing: fixedStep chrom=1 start=1 step=500000 span=500000
Parsing: fixedStep chrom=2 start=1 step=500000 span=500000
Parsing: fixedStep chrom=3 start=1 step=500000 span=500000
Parsing: fixedStep chrom=4 start=1 step=500000 span=500000
Parsing: fixedStep chrom=5 start=1 step=500000 span=500000
Parsing: fixedStep chrom=6 start=1 step=500000 span=500000
Parsing: fixedStep chrom=7 start=1 step=500000 span=500000
Parsing: fixedStep chrom=8 start=1 step=500000 span=500000
Parsing: fixedStep chrom=9 start=1 step=500000 span=500000
Parsing: fixedStep chrom=10 start=1 step=500000 span=500000
Parsing: fixedStep chrom=11 start=1 step=500000 span=500000
Parsing: fixedStep chrom=12 start=1 step=500000 span=500000
Parsing: fixedStep chrom=13 start=1 step=500000 span=500000
Parsing: fixedStep chrom=14 start=1 step=500000 span=500000
Parsing: fixedStep chrom=15 start=1 step=500000 span=500000
Parsing: fixedStep chrom=16 start=1 step=500000 span=500000
Parsing: fixedStep chrom=17 start=1 step=500000 span=500000
Parsing: fixedStep chrom=18 start=1 step=500000 span=500000
Parsing: fixedStep chrom=19 start=1 step=500000 span=500000
Parsing: fixedStep chrom=20 start=1 step=500000 span=500000
Parsing: fixedStep chrom=21 start=1 step=500000 span=500000
Parsing: fixedStep chrom=22 start=1 step=500000 span=500000
Parsing: fixedStep chrom=X start=1 step=500000 span=500000
Parsing: fixedStep chrom=Y start=1 step=500000 span=500000
Sorting by decreasing chromosome size
Slurping: /gpfs/users/yanghao/software/ichorCNA/inst/extdata/map_hg19_500kb.wig
Parsing: fixedStep chrom=1 start=1 step=500000 span=500000
Parsing: fixedStep chrom=2 start=1 step=500000 span=500000
Parsing: fixedStep chrom=3 start=1 step=500000 span=500000
Parsing: fixedStep chrom=4 start=1 step=500000 span=500000
Parsing: fixedStep chrom=5 start=1 step=500000 span=500000
Parsing: fixedStep chrom=6 start=1 step=500000 span=500000
Parsing: fixedStep chrom=7 start=1 step=500000 span=500000
Parsing: fixedStep chrom=8 start=1 step=500000 span=500000
Parsing: fixedStep chrom=9 start=1 step=500000 span=500000
Parsing: fixedStep chrom=10 start=1 step=500000 span=500000
Parsing: fixedStep chrom=11 start=1 step=500000 span=500000
Parsing: fixedStep chrom=12 start=1 step=500000 span=500000
Parsing: fixedStep chrom=13 start=1 step=500000 span=500000
Parsing: fixedStep chrom=14 start=1 step=500000 span=500000
Parsing: fixedStep chrom=15 start=1 step=500000 span=500000
Parsing: fixedStep chrom=16 start=1 step=500000 span=500000
Parsing: fixedStep chrom=17 start=1 step=500000 span=500000
Parsing: fixedStep chrom=18 start=1 step=500000 span=500000
Parsing: fixedStep chrom=19 start=1 step=500000 span=500000
Parsing: fixedStep chrom=20 start=1 step=500000 span=500000
Parsing: fixedStep chrom=21 start=1 step=500000 span=500000
Parsing: fixedStep chrom=22 start=1 step=500000 span=500000
Parsing: fixedStep chrom=X start=1 step=500000 span=500000
Parsing: fixedStep chrom=Y start=1 step=500000 span=500000
Sorting by decreasing chromosome size
Correcting Tumour
Loading required package: GenomeInfoDb
Error in [[<-
(*tmp*
, name, value = c(-1, -1, 0.598332, 0.539498, 0.594508, :
6087 elements in value to replace 303641 elements
Calls: loadReadCountsFromWig -> $<- -> $<- -> [[<- -> [[<-
Execution halted
Here is my input wig files:
Tumor:https://github.com/haoziyeung/supp_files/blob/master/tumor_sample_1.bin10000.wig
Normal:https://github.com/haoziyeung/supp_files/blob/master/normal_sample_1.bin10000.wig
Thanks a lot.