Re: [Bammds-users] bammds error

[J . Víctor Moreno Mayar]

Hey there, 

It might be some version issue with R or the package itself. A temporal fix would be to remove the skip parameter of that function. You can edit the file called bammds_plot.r so that the line now reads like this:

asd_orig <- as.data.frame(data.table::fread(asd_file, sep="auto", sep2="auto", nrows=nrows,

                                              header="auto", na.strings="NA",

                                              stringsAsFactors=FALSE, verbose=FALSE, autostart=30L,

                                              select=NULL, colClasses=NULL,

                                              integer64=getOption("datatable.integer64")))

Make sure to edit the file that is copied after installing. You find out which one it is by running:

which bammds_plot.r

Hope it helps.

Cheers, 

Víctor  

 

On Thu, Dec 15, 2016 at 3:23 PM, QQ <address@hidden> wrote:

Dear：
      I were puzzled by running bammds software and would need your help. I have installed R, samtools, vcftools , parallel, perl and bammds successfully. When I type " bammds Gus.Ancient.bam HGDP_hg19_one_allele.txt _ _nosum ", it always show the following errors:
     bammds: Warning: Not overwriting tmp/Gus.Subsample,HDGP.Reference.legend.csv
Error in data.table::fread(asd_file, sep = "auto", sep2 = "auto", nrows = nrows,  :
  'skip' must be a length 1 vector of type numeric or integer >=0, or single character search string
Calls: all -> read_data_files -> as.data.frame -> <Anonymous>
Execution halted
        I don't know the reason and I am confused this long time. If you were free, please give me some advices. Thank you!


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José Víctor Moreno Mayar
Centre for GeoGenetics
University of Copenhagen