search

dviraran / SingleR

SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
GNU General Public License v3.0
263 stars 98 forks source link

Error message in CreateSinglerObject #65

Open ChaDuss opened 5 years ago

ChaDuss commented 5 years ago

I am in trouble with the function CreateSinglerObject. I got those "Warning messages" several times with different counts and I don't understand why.

I work with R3.6 and Ubuntu.

singler = CreateSinglerObject(pbmc.raw.data, annot = NULL, project.name = "hay_35_pop", min.genes = 0,

  • technology = "10X", species = "Human", citation = "cool",
  • ref.list = list(ref), normalize.gene.length = F, variable.genes = "de",
  • fine.tune = T, do.signatures = T, clusters = pbmcsmall@active.ident, do.main.types = F,
  • reduce.file.size = T, numCores = SingleR.numCores) [1] "Dimensions of counts data: 18934x2647" [1] "Annotating data with refCD34-..." [1] "Variable genes method: de" [1] "Number of DE genes:1599" [1] "Number of cells: 2647" [1] "Fine-tuning round on top cell types (using 16 CPU cores):" |===================================================================================================================================| 100%, Elapsed 00:07 [1] "Number of DE genes:1599" [1] "Number of clusters: 13" [1] "Fine-tuning round on top cell types (using 16 CPU cores):" |===================================================================================================================================| 100%, Elapsed 00:02 Warning messages: 1: In selectChildren(pids[!fin], -1) : cannot wait for child 6345 as it does not exist 2: In parallel::mccollect(...) : 1 parallel job did not deliver a result 3: In selectChildren(pids[!fin], -1) : cannot wait for child 6363 as it does not exist 4: In parallel::mccollect(...) : 1 parallel job did not deliver a result

Do you know what can I do to fix it ?

Than you very much.

Bests,

dviraran commented 5 years ago

Try using numCores=4 instead of 16. Seems like an issue with the multi threading.

ChaDuss commented 5 years ago

Thanks but it did not work with numCores = 4 or numCores =1 : Warning messages: 1: In selectChildren(pids[!fin], -1) : cannot wait for child 6006 as it does not exist 2: In parallel::mccollect(...) : 1 parallel job did not deliver a result 3: In selectChildren(pids[!fin], -1) : cannot wait for child 6017 as it does not exist 4: In parallel::mccollect(...) : 1 parallel job did not deliver a result

dviraran commented 5 years ago

I tried looking for this error online (https://github.com/HenrikBengtsson/future/issues/218) and it seems its a problem with R 3.5.0. Maybe update R to 3.6.0?

Anyway, according to this thread, these warnings are harmless.