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Error in ifelse(wgd, round(ploidy), 2) : object 'ploidy' not found #46

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YingYa opened this issue Jun 3, 2021 · 5 comments
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@YingYa
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YingYa commented Jun 3, 2021

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
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asntech commented Dec 9, 2021

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

@YingYa
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YingYa commented Dec 10, 2021

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

@srinipr4
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srinipr4 commented Mar 3, 2022

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
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asntech commented Mar 5, 2022

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

@WangKang-Leo
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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?

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