-s not recognised

[Loki Snyman]

I have tried to run quite a simple RAxML analysis on a data set consisting of 202 taxa and 572 nucleotides, already aligned and truncated. I have used RAxML several times but I have never had the error message "-s is not recognised as an internal or external command, operable program or batch file"

My code is as follows:

>raxmlHPC.exe -s COI_ML.phy -f a -x 1234 -# 1000 -m GTRGAMMA -n MLTree.tre -o Cs_annulata,Ps_howardii,Or_anopheloides,Ma_titillans -p 1234

Quite simple I think. I then collapsed all sequences to haplotypes only and ended up with 145 taxa and 572 characters, but the problem persists. This is only initial runs on unconcatenated data and I hope to sort it out before I start my full analysis. 

I apologise if this error has been brought to the attention of the group, but I could not find anything.

Anyone with any suggestions?

Cheers, Loki

[Alexandros Stamatakis]

so I assume you are running it on windows?

could it be that there is a line break in the command line before -s?

the command line arguments should be written in one single line

alexis

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Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
of Arizona at Tucson

www.exelixis-lab.org

[Loki Snyman]

It seems to work today, don't know why, but it is resolved. Damn technology...