gl.blast Error in names(x)

[Claudia Escobar]

Dear group,

I'm finding the following error when running gl.blast - any idea of how can I solve it? or is it a new bug?. I used to apply the function with no problem.

Starting BLASTing

Starting filtering

Error in names(x) <- value :
  'names' attribute [19] must be the same length as the vector [18]

my arguments are as follows:

gl.blast(

  x = gl,
  ref_genome = "data/chloroplasts.fasta",
  task = "megablast",
  Percentage_identity = 95,
  Percentage_overlap = 0.60,
  bitscore = 50,
  number_of_threads = 2,
  verbose = NULL

[Claudia Escobar]

Good day, everyone, 

I installed the dev versions and that error disappear. Thank you, Luis.

However, I've encountered another issue. I can't find the dartRverse equivalent for gl.print.reports() de dartR. Does it exist? 

Warm regards,

Claudia

[Jose Luis Mijangos]

Hi Claudia,

in dartR, the functions gl.list.reports and gl.print.reports were used to list and retrieve the plots from the temporal directory. In dartRverse, those functions were replaced by adding the parameters plot.dir and plot.file in each function so the plots could be saved in a directory specified by the user. 

Cheers,

Luis

[Claudia Escobar]

Thank you, Luis. I couldn't find that option to add the arguments in gl.blast() but I believe it wouldn't work as the function generate several reports, which are needed to be analyzed independently. 

For instance, I need to do this: blast1_df <- as.data.frame(gl.print.reports(1))

Actually, gl.blast() tells you at the end to run gl.list.reports() and gl.print.reports(). So maybe that could be clarified for the next version :)

I installed dartR in order to be able to run the function.

Cheers!

Claudia