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broadinstitute / ichorCNA

Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
GNU General Public License v3.0
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The style does not have a compatible entry for the species supported by #82

Open grenaud opened 3 years ago

grenaud commented 3 years ago

Hello, I am trying to run ichorCNA and I get:

`Error in seqlevelsStyle(as.character(x)) :

The style does not have a compatible entry for the species supported by Seqname. Please see genomeStyles() for supported species/style

Calls: loadReadCountsFromWig ... setGenomeStyle -> %in% -> seqlevelsStyle -> seqlevelsStyle`

I tried having wig files both with 'chr1' and '1', any idea what is happening?

gavinha commented 3 years ago

Hi @grenaud

What genome style are you using as input in the congfig.yaml?

grenaud commented 3 years ago

Hello! I am using command line options as such without config.yaml:

Rscript ~/miniconda2/pkgs/r-ichorcna-0.2.0-r36_0/bin/runIchorCNA.R --id myid --WIG input.wig --ploidy "c(2,3)" --normal "c(0.5,0.6,0.7,0.8,0.9)" --maxCN 5 --gcWig [path]/gc_hg19_1000kb.wig --mapWig [path]/map_hg19_1000kb.wig --centromere [path]/GRCh37.p13_centromere_UCSC-gapTable.txt --normalPanel [path]/HD_ULP_PoN_1Mb_median_normAutosome_mapScoreFiltered_median.rds --includeHOMD False --chrs "c(1:22, \"X\")" --chrTrain "c(1:22)" --estimateNormal True --estimatePloidy True --estimateScPrevalence True --normalizeMaleX True --scStates "c(1,3)" --txnE 0.9999 --txnStrength 10000 --outDir outdir

Is this incorrect?