error：Calls: calculateDiffMeth ... simplify2array -> mclapply -> lapply -> FUN -> mcfork

changchuanjun commented 5 months ago

Hello! Thank you for your contribution on methylKit. When I run my script, I meet a problem. Do you know how to solve it? my command is :

Rscript methylation.R --samples_file sample.txt --contrasts contrasts.txt --fmt calmeth --context CHH --window 600 - -step 200 --threads 2 -o CHH_result --dm dmr

the error is : Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : 没有(非NA)案例可用 Calls: calculateDiffMeth ... p.adjusted -> QValuesfun -> SLIMfunc -> lm -> lm.fit 此外: Warning message: In mclapply(cntlist, logReg, vars, treatment = treatment, overdispersion = overdispersion, : scheduled core 1 did not deliver a result, all values of the job will be affected 停止执行

alexg9010 commented 5 months ago

HI @changchuanjun ,

When translating the error message to English it says that there are No (non-NA) cases available.

This indicates NA values in your data are causing the failure of calculateDiffMeth. Some people reported fixing the problem by removing NA values first (https://github.com/al2na/methylKit/issues/206#issuecomment-1303220254).

Best, Alex

changchuanjun commented 4 months ago

@alexg9010 ,thank you for your reply

al2na / methylKit

error：Calls: calculateDiffMeth ... simplify2array -> mclapply -> lapply -> FUN -> mcfork #318