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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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Issue with seqlevelsStyle #80

Closed samhitapn closed 3 years ago

samhitapn commented 3 years ago

I use the following script to run the ichorCNA -

Rscript ../../ltg/software/ichorCNA-0.2.0/scripts/runIchorCNA.R --id sample --WIG sample.wig --gcWig /ifs/data/research/projects/ltg/software/ichorCNA-0.2.0/inst/extdata/gc_hg19_10kb.wig --libdir /ifs/data/research/projects/ltg/software/ichorCNA-0.2.0/ --genomeStyle UCSC But I get the following error : 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

The chromosome numbers in the bam fil eare with chr'n' and hence I used --genomeStyle UCSC as a parameter. Even without that I get the same error.

samhitapn commented 3 years ago

I think I figured the issue, it was a version problem.