<div dir="ltr"><div>Hi Emmanuel, </div><div><br></div><div>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. </div>
<div><br></div><div><font color="#073763">myPath <- system.file("files/usflu.fasta",package="adegenet")</font></div><div><br></div><div><font color="#38761d"># without the parallel arguement --> same error message you are getting: </font></div>
<div><div><font color="#073763">> obj <- fasta2genlight(myPath, chunk=10) # process 10 sequences at a time</font></div><div><font color="#073763"><br></font></div><div><font color="#000000"> Converting FASTA alignment into a genlight object... </font></div>
<div><font color="#000000"><br></font></div><div><font color="#000000">Loading required package: parallel</font></div><div><font color="#000000"><br></font></div><div><font color="#000000"> Looking for polymorphic positions... </font></div>
<div><font color="#000000">..........</font></div><div><br></div><div><font color="#990000"> </font><font color="#ff0000">Error in mclapply(txt, function(e) strsplit(paste(e[-1], collapse = ""), : </font></div>
<div><font color="#ff0000"> 'mc.cores' > 1 is not supported on Windows </font></div></div><div><font color="#ff0000"><br></font></div><div><font color="#ff0000"><br></font></div><div><br></div><div><font color="#38761d"><b># WITH the parallel=FALSE argument: </b></font></div>
<div><div><font color="#073763">obj <- fasta2genlight(myPath, chunk=10, parallel=FALSE)</font><font color="#38761d"> # process 10 sequences at a time</font></div><div><font color="#073763"><br></font></div><div><font color="#000000"> Converting FASTA alignment into a genlight object... </font></div>
<div><br></div><div><font color="#000000"> Looking for polymorphic positions... </font></div><div><font color="#000000">........................................................................................................................................................................................................................................................................................................................................................................</font></div>
<div><font color="#000000"> Extracting SNPs from the alignment... </font></div><div><font color="#000000">........................................................................................................................................................................................................................................................................................................................................................................</font></div>
<div><font color="#000000"> Building final object... </font></div><div><font color="#000000"><br></font></div><div><font color="#000000">...done.</font></div></div><div><br></div><div><br></div><div><br></div><div><br></div>
<div>Cheers, </div><div>Caitlin. </div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, Jun 9, 2014 at 5:02 PM, Emmanuel WICKER <span dir="ltr"><<a href="mailto:emmanuel.wicker@cirad.fr" target="_blank">emmanuel.wicker@cirad.fr</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Thibaut<br>
I already tested that, but still it doesn't work.<br>
For that command, and also for read.snp of a DNAbin object (same error message)<br>
Cheers<br>
Manu<br>
<br>
----- Mail original -----<br>
De: "Thibaut Jombart" <<a href="mailto:t.jombart@imperial.ac.uk">t.jombart@imperial.ac.uk</a>><br>
À: "Emmanuel WICKER" <<a href="mailto:emmanuel.wicker@cirad.fr">emmanuel.wicker@cirad.fr</a>>, <a href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a><br>
Cc: <a href="mailto:wicker@cirad.fr">wicker@cirad.fr</a><br>
Envoyé: Lundi 9 Juin 2014 19:35:55<br>
Objet: RE: [adegenet-forum] Help: pbm conversion of a fasta alignement to Genlight<br>
<div class="HOEnZb"><div class="h5"><br>
<br>
Hi<br>
<br>
can you try<br>
parallel = FALSE<br>
<br>
as argument?<br>
<br>
Cheers<br>
Thibaut<br>
<br>
________________________________________<br>
From: <a href="mailto:adegenet-forum-bounces@lists.r-forge.r-project.org">adegenet-forum-bounces@lists.r-forge.r-project.org</a> [<a href="mailto:adegenet-forum-bounces@lists.r-forge.r-project.org">adegenet-forum-bounces@lists.r-forge.r-project.org</a>] on behalf of Emmanuel WICKER [<a href="mailto:emmanuel.wicker@cirad.fr">emmanuel.wicker@cirad.fr</a>]<br>
Sent: 09 June 2014 16:23<br>
To: <a href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a><br>
Cc: <a href="mailto:wicker@cirad.fr">wicker@cirad.fr</a><br>
Subject: [adegenet-forum] Help: pbm conversion of a fasta alignement to Genlight<br>
<br>
Hi all<br>
I tried and convert a fasta alignment to a genlight object, and I had the following message:<br>
<br>
<br>
> toto=fasta2genlight("EGL_ARB_originaux_160913_TRIM.fas")#my command<br>
<br>
Converting FASTA alignment into a genlight object...<br>
<br>
Loading required package: parallel<br>
<br>
Looking for polymorphic positions...<br>
..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................<br>
..........<br>
Error in mclapply(txt, function(e) strsplit(paste(e[-1], collapse = ""), :<br>
'mc.cores' > 1 is not supported on Windows<br>
<br>
ANy help ?<br>
I run R under Windows 7, adegenet version 1.4.2<br>
Thank you<br>
Manu<br>
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