CODEWITHSUNDEEP
rbioinformaticsvcf-variant-call-format
Pavlo
Pavlo

Reputation: 56

Problem with import of multiVCF by readData from "popgenome" R package

I am trying to import a multiVCF file (created with GATK,~80 individuals (4.3Gb)) into R using the package "popgenome", and "readData". Unfortunately, the import always aborts with the error message: "R encountered a fatal error, session terminated". With a smaller data set it works fine.

I also tried with compressed vcfs (bgzip) – did also not work for me. Do I miss something? Does my PC have not have enough computing resources?

Has anyone had similar experiences or know how to solve this problem? About any advice I would be very grateful.

Kind regards

Pavlo

My code:

 gff3_out = c()
    my_filter = c()
    for(chr in chromosomes){
    my_filter <- list(seqid=chr)  
    gff3_out <- file.path(gff_path, paste(chr,".gff",sep=""))
    export(readGFF("/path/to/my/gff.gff",filter=my_filter), gff3_out)  
    }
    PopGenome::VCF_split_into_scaffolds("my_multiVCF_from_GATK.vcf","scaffoldVCFs2")
    allgenomes <- PopGenome::readData("path/to/data/with_VCFs",format="VCF",gffpath = "path/to/data/gff_data",big.data = TRUE)

My PC:

Windows 10
Intel(R) Core(TM) i7-8565U CPU @ 1.80GHz   1.99 GHz;
RAM 32,0 GB (31,9 GB verwendbar);
Systemtyp   64-Bit-Betriebssystem, x64-basierter Prozessor

Upvotes: 1

Views: 266

Answers (1)

Pavlo
Pavlo

Reputation: 56

I have now tried on another Windows machine/fresh R installation, unfortunately with the same error.

I have also checked under Windows memory usage while the record was being read by readData and gave no indication that a lack of RAM may be the cause of the crash.

After that on Linux server I read the data with the PopGenome and readData and it runs wonderfully.

My temporary solution is - Linux server. However, I still don't know if it's the Windows version of R that the readData can't handle larger data sets, or Windows in general. Maybe someone can answer this question. Actually, it's a shame that you can't use such an attractive R package/function with larger datasets on Windows (at least in my case).

Upvotes: 1

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