Missing data analysis vignette

[dollykc]

Hi Dr. Gosselin,
I'm trying tor work through the missing data analysis vignette using the sample data and I'm running into problems. First of all, the vcf file created by the line

writeBin(httr::content(httr::GET("http://datadryad.org/bitstream/handle/10255/dryad.97237/sticklebacks_Danish.vcf?sequence=1"), "raw"), "stickleback_ferchaud_2015.vcf")

generated an empty file. Therefore, I went to Dryad and downloaded sticklebacks_Danish.vcf instead. I also downloaded strata.stickleback.tsv for the strata. I executed this line of code

ibm <- grur::missing_visualization(data = "sticklebacks_Danish.vcf", strata = "strata.stickleback.tsv")

Here is the output where the error message occurs:

Number of duplicate id: 0
radiator Genomic Data Structure (GDS) file: radiator_20230105@1248.gds
Error in dplyr::mutate():
! Problem while computing MISSING_PROP = round(...).
Caused by error in .DynamicClusterCall():
! One of the nodes produced an error: Can not open file 'C:\Test\missing_visualization_20230105@1248\radiator_20230105@1248.gds'. The process cannot access the file because it is being used by another process.
Run rlang::last_error() to see where the error occurred.

rlang::last_error()
Backtrace:

1. grur::missing_visualization(...)
2. SeqArray::seqMissing(gdsfile = gds, per.variant = FALSE, parallel = parallel.core)
3. SeqArray::seqParallel(...)
4. SeqArray::seqParallel(...)
5. SeqArray:::.DynamicClusterCall(...)
6. base::stop("One of the nodes produced an error: ", as.character(dv))

Any help would be appreciated.
Kat

[dollykc]

Hi again Dr. Gosselin,
After looking through previous errors reported and email exchanges, I see that I should've used the command
ibm <- grur::missing_visualization(data = "sticklebacks_Danish.vcf", strata = "strata.stickleback.tsv", parallel.core = 1L)

This seems to have resolved the error mentioned above BUT I've run into another error that I will detail in a separate post.