Create Panel of normal #25
Description
Hello @gavinha ,
I'm trying to run create panel of normals, using:
Rscript /usr/local/bin/createPanelOfNormals.R --gcWig R/x86_64-pc-linux-gnu-library/4.0/ichorCNA/extdata/gc_hg38_1000kb.wig --mapWig R/x86_64-pc-linux-gnu-library/4.0/ichorCNA/extdata/map_hg38_1000kb.wig --centromere R/x86_64-pc-linux-gnu-library/4.0/ichorCNA/extdata/GRCh38.GCA_000001405.2_centromere_acen.txt --filelist wig_files_healthy_breast.txt --outfile PoN_output --flankLength 1000000 --chrs "c('chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY')" --genomeStyle "UCSC"
From within singularity: depot.galaxyproject.org-singularity-r-ichorcna-0.5.0--pl5321r42hdfd78af_0.img
And I'm getting no output.
When I'm running within R, I'm getting:
createPanelOfNormals(gcWig="R/x86_64-pc-linux-gnu-library/4.0/ichorCNA/extdata/gc_hg38_1000kb.wig" , mapWig="R/x86_64-pc-linux-gnu-library/4.0/ichorCNA/extdata/map_hg38_1000kb.wig", repTimeWig = NULL, filelist="wig_files_healthy_breast.txt", outfile="PoN_output", centromere="x86_64-pc-linux-gnu-library/4.0/ichorCNA/extdata/GRCh38.GCA_000001405.2_centromere_acen.txt", flankLength = 1000000, chrs = "c('chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22')", genomeStyle = "NCBI", genomeBuild = "hg38", chrNormalize = "c(1:22)", minMapScore = 0.0, maleChrXLogRThres = -0.80, fracReadsInChrYForMale = 0.001, exons.bed = NULL, method = "median", ylim = "c(-2,2)", plotChrPanels = FALSE)
And I'm getting:
Reading GC and mappability files
Parsing: fixedStep chrom=chr1 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr2 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr3 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr4 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr5 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr6 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr7 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr8 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr9 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr10 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr11 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr12 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr13 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr14 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr15 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr16 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr17 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr18 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr19 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr20 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr21 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr22 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chrX start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chrY start=1 step=1000000 span=1000000
Sorting by decreasing chromosome size
Parsing: fixedStep chrom=chr1 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr2 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr3 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr4 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr5 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr6 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr7 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr8 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr9 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr10 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr11 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr12 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr13 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr14 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr15 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr16 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr17 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr18 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr19 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr20 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr21 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr22 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chrX start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chrY start=1 step=1000000 span=1000000
Sorting by decreasing chromosome size
wigToGRanges: WIG file '' not found.
No replication timing wig file input, excluding from correction
Loading normal file: wigs_win_1000000/HU012.01.PL4406.wig
Parsing: fixedStep chrom=chr1 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr2 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr3 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr4 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr5 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr6 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr7 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr8 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr9 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr10 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr11 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr12 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr13 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr14 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr15 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr16 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr17 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr18 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr19 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr20 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr21 start=1 step=1000000 span=1000000
Parsing: fixedStep chrom=chr22 start=1 step=1000000 span=1000000
Sorting by decreasing chromosome size
Removed 152 bins near centromeres.
Applying filter on data...
Correcting for GC bias...
Correcting for mappability bias...
Filtering low uniqueness regions with mappability score < 0
Correcting HU012.01.PL4406 sex: unknown chrYcov: NA chrXMedian:
Error in data.frame(Sample = sid, sex = gender$gender, chrYcov = gender$chrYCovRatio, :
arguments imply differing number of rows: 1, 0