Error in ifelse(wgd, round(ploidy), 2) : object 'ploidy' not found

[YingYa]

Hi,

I am running facets-suite.v2.0.8 with "run-facets-wrapper.R --counts-file normal-VS-tumor.FACETS.pileup.gz --sample-id normal-VS-tumor --directory facets-suite --everything --genome hg38 --purity-cval 2000 --cval 1000", but some sampels were failed.

n = 626733 > max_n{n in table} = 72000 -- using that as asymptotic value. n = 422038 > max_n{n in table} = 72000 -- using that as asymptotic value. n = 217270 > max_n{n in table} = 72000 -- using that as asymptotic value. n = 658014 > max_n{n in table} = 72000 -- using that as asymptotic value. n = 422180 > max_n{n in table} = 72000 -- using that as asymptotic value. n = 217309 > max_n{n in table} = 72000 -- using that as asymptotic value. Error in ifelse(wgd, round(ploidy), 2) : object 'ploidy' not found Calls: %>% -> eval -> eval -> gene_level_changes -> ifelse Execution halted

[asntech]

I'm getting this error also, @YingYa by any chance if you fixed it.

[YingYa]

I used docker://stevekm/facets-suite:2.0.8 to run then, the issue was solved.

[srinipr4]

Hi YingYa, I was having the same issue and tried using the docker image you mentioned above. However, I am getting an error about the R library not being found: /facets-suite/run-facets-wrapper.R: error: the following arguments are required: -fl/--facets-lib-path

Were you able to resolve this?

[asntech]

Feel free to use this one asntech/facets-suite:v2.0.8. More info here

[WangKang-Leo]

acets-suite:2.0.8 When I run facets-suite using the image you mentioned, I received following error: Error in ifelse(wgd, round(ploidy), 2) : object 'ploidy' not found Calls: %>% -> eval -> eval -> gene_level_changes -> ifelse Execution halted

Do you have any ideas?