what is the consequence of running a command line with -f a -f o?

[Mark Miller]

Hi all,

I have been testing command lines for RAxML on CIPRES, to see if I understand how various options work together.

I created this command line

/opt/raxml/bin/raxmlHPC-HYBRID -T 6 -n result -N autoMRE -s infile.txt -p 12345 -c 25 -m GTRCAT -x 12345 -N 100 -f a -f o

expecting it to fail with a complaint that -f o and -f a are mutually exclusive. However the run deployed and ran to completion.

I am wondering if -f a supercedes -f o, in this command line, and-f o is ignored, or if the -f a analysis is run with the old, slower rapid hill climbing algorithm?

Thanks for any advice.

Mark

[Alexandros Stamatakis]

that's actually a bug, the -f whatever commands should be mutually
exclusive ...

I'll have to adapt raxml to fix this,

alexis

On 24.02.2015 16:58, Mark Miller wrote:
>
> Hi all,
>
> I have been testing command lines for RAxML on CIPRES, to see if I
> understand how various options work together.
> I created this command line
>
> /opt/raxml/bin/raxmlHPC-HYBRID -T 6 -n result -N autoMRE -s infile.txt
> -p 12345 -c 25 -m GTRCAT -x 12345 -N 100 -f a -f o
>
> expecting it to fail with a complaint that -f o and -f a are mutually

> exclusive. However the run deployed and ran to completion.t

>
> I am wondering if -f a supercedes -f o, in this command line, and-f o is
> ignored, or if the -f a analysis is run with the old, slower rapid hill
> climbing algorithm?
>
> Thanks for any advice.
>
> Mark
>
>
>

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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

[Alexandros Stamatakis]

Dear Mark,

RAxML v 8.1.18 (released now) will exit with an error now if -f is
specified multiple times.

Alexis

On 24.02.2015 16:58, Mark Miller wrote:
>