Error while running run-facets-wrapper.R

[akhileshmishra0908]

I am trying to run run-facets-wrapper.R, using this command -

singularity exec facets-suite-dev.img ./run-facets-wrapper.R --counts-file XP490_V4756-XP490_S4763.snp_pileup.gz --sample-id XP490_V4756-XP490_S4763 --purity-cval 1000 --cval 500 --everything --genome hg38 --normal-depth 25 --facets-lib-path /home2/s204755/R/x86_64-pc-linux-gnu-library/3.6/ --directory ./work

And I am getting this error -

WARNING: ignoring environment value of R_HOME
Reading XP490_V4756-XP490_S4763.snp_pileup.gz
Writing to ./work
Loading required package: pctGCdata
[1] "loaded facets version: 0.6.2"
Error: Discrete value supplied to continuous scale
In addition: Warning message:
In max(mafR.clust[seg$chrom < nX & seg$nhet > min.nhet], na.rm = TRUE) :
no non-missing arguments to max; returning -Inf
Execution halted

Could you please help me resolve this error?

Thanks,

Akhilesh,
UT Southwestern Medical Center
Texas

[kelgalla]

I am getting the same error

[kelgalla]

I found a solution, in run-facets-wrapper.R, use facets::readSnpMatrix instead of facetsSuite version called read_snp_matrix. Be sure to load facets library at the top.