[adegenet-forum] Help: pbm conversion of a fasta alignement to Genlight

[Caitlin Collins]

Hi Emmanuel,

I'm running adegenet on a Windows computer, and I've previously had the
same error message that you're currently experiencing (see below, first
example). For all the instances you have mentioned, however, I usually find
that adding the argument parallel=FALSE does the trick. Would you be able
to copy and paste the following example (the line below starting with
myPath, and then the line from the second example starting with obj) and
then reporting back with the outcome? Thanks very much.

myPath <- system.file("files/usflu.fasta",package="adegenet")

# without the parallel arguement --> same error message you are getting:
> obj <- fasta2genlight(myPath, chunk=10) # process 10 sequences at a time

 Converting FASTA alignment into a genlight object...

Loading required package: parallel

 Looking for polymorphic positions...
..........

 Error in mclapply(txt, function(e) strsplit(paste(e[-1], collapse = ""),
 :
  'mc.cores' > 1 is not supported on Windows



*# WITH the parallel=FALSE argument: *
obj <- fasta2genlight(myPath, chunk=10, parallel=FALSE) # process 10
sequences at a time

 Converting FASTA alignment into a genlight object...

 Looking for polymorphic positions...
........................................................................................................................................................................................................................................................................................................................................................................
 Extracting SNPs from the alignment...
........................................................................................................................................................................................................................................................................................................................................................................
 Building final object...

...done.




Cheers,
Caitlin.


On Mon, Jun 9, 2014 at 5:02 PM, Emmanuel WICKER <emmanuel.wicker at cirad.fr>
wrote:

> Hi Thibaut
> I already tested that, but still it doesn't work.
> For that command, and also for read.snp of a DNAbin object (same error
> message)
> Cheers
> Manu
>
> ----- Mail original -----
> De: "Thibaut Jombart" <t.jombart at imperial.ac.uk>
> À: "Emmanuel WICKER" <emmanuel.wicker at cirad.fr>,
> adegenet-forum at lists.r-forge.r-project.org
> Cc: wicker at cirad.fr
> Envoyé: Lundi 9 Juin 2014 19:35:55
> Objet: RE: [adegenet-forum] Help: pbm conversion of a fasta alignement to
>       Genlight
>
>
> Hi
>
> can you try
> parallel = FALSE
>
> as argument?
>
> Cheers
> Thibaut
>
> ________________________________________
> From: adegenet-forum-bounces at lists.r-forge.r-project.org [
> adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Emmanuel
> WICKER [emmanuel.wicker at cirad.fr]
> Sent: 09 June 2014 16:23
> To: adegenet-forum at lists.r-forge.r-project.org
> Cc: wicker at cirad.fr
> Subject: [adegenet-forum] Help: pbm conversion of a fasta alignement to
> Genlight
>
> Hi all
> I tried and convert a fasta alignment to a genlight object, and I had the
> following message:
>
>
> > toto=fasta2genlight("EGL_ARB_originaux_160913_TRIM.fas")#my command
>
>  Converting FASTA alignment into a genlight object...
>
> Loading required package: parallel
>
>  Looking for polymorphic positions...
>
> ..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
>  ..........
> Error in mclapply(txt, function(e) strsplit(paste(e[-1], collapse = ""),  :
>   'mc.cores' > 1 is not supported on Windows
>
> ANy help ?
> I run R under Windows 7, adegenet version 1.4.2
> Thank you
> Manu
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