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thierrygosselin / stackr

stackr: an R package to run stacks software pipeline
http://thierrygosselin.github.io/stackr/
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error in summary_ustacks #23

Closed crisale84 closed 4 years ago

crisale84 commented 4 years ago

Hi Thierry, I am using your stackr to do my pictures, but now I have this error, I run stacks in a cluster, and I am trying to do my summarizes in my local Rstudio, can you help me with this? Thank you for your time

ustacks.summary<- summary_ustacks(

  • ustacks.folder= "./denovo_M1/",

  • parallel.core = parallel::detectCores() -1,

  • filename = "./denovo_M1/",
  • verbose = TRUE) ####################################################################### ##################### stackr::summary_ustacks ######################### ####################################################################### Removing these catalog files from the summary: catalog.alleles.tsv.gz catalog.calls catalog.fa.gz catalog.snps.tsv.gz catalog.tags.tsv.gz Summarizing 8 ustacks (snps, tags, alleles) files...

Summarizing information... | | 0%, ETA NA Error: Argument 1 must have names In addition: Warning message: In .stackr_parallel(X = sample.name, FUN = summarise_ustacks, mc.cores = parallel.core, : scheduled cores encountered errors in user code

thierrygosselin commented 4 years ago

Try this and tell me if you still get an error:

library(stackr)
setwd("YOUR WORKING DIRECTORY")
test1 <- stackr::summary_ustacks(
  ustacks.folder = "./denovo_M1", 
  parallel.core = 1, 
  verbose = TRUE
  )

Depending if this work you could increase the number of core used. The other problem I see is that you're using the same value for the argument ustacks.folder and the filename. In this case filename is pointing towards a directory not the actual name you want...

crisale84 commented 4 years ago

Hi Thierry, now I have this message:

test1 <- stackr::summary_ustacks(

  • ustacks.folder = "./denovo_M1",
  • parallel.core = 1,
  • verbose = TRUE
  • ) ####################################################################### ##################### stackr::summary_ustacks ######################### ####################################################################### Removing these catalog files from the summary: catalog.alleles.tsv.gz catalog.calls catalog.fa.gz catalog.snps.tsv.gz catalog.tags.tsv.gz Summarizing 8 ustacks (snps, tags, alleles) files...

Summarizing information... Error in .setMaxGlobalSize(max.vector.size) : could not find function ".setMaxGlobalSize"

thierrygosselin commented 4 years ago

Read this to fix this issue with R

Feel free to re-open this issue if you still have a problem