Bootstrap threshold error

[Michael Forthman]

I'm trying to run a series of raxml analyses on several alignments on a cluster. I've gotten back the following error:

Bootstrap threshold must be set to values between 0.0 and 1.0, you just set it to 15888.000000

My command for raxml:

raxmlHPC-SSE3 -m GTRGAMMA -s reduced_phylip_alignments/uce-3455.phylip -n uce-3455 -d -N 500 -p 733 -b 1629 -w bootstrap_genetrees

I'm not sure how raxml is inferring that bootstrap threshold from my commands. Anyone know what is happening?

Thanks!

[Alexandros Stamatakis]

that's weird based on your command line, which RAxML version are you
using? maybe omitting -w might help?

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

[Michael Forthman]

Very weird indeed. I'm using raxml 8.2.8.

[Alexandros Stamatakis]

okay, please send me the input files to my personal email address and I
will have a look soonish,

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 <http://www.exelixis-lab.org>

[Michael Forthman]

I also tried removing the -w option and I still replicated my errors.

[Alexandros Stamatakis]

okay, also got your email with the input data, will probably get to look
at it this week,

alexis

[Alexandros Stamatakis]

Hi Micheal,

I was not able to reproduce the error with any of the datasets you sent
me by executing them like this:

raxmlHPC-SSE3 -m GTRGAMMA -s uce-171.phylip -d -N 500 -p 733 -b 1629 -n X3
raxmlHPC-SSE3 -m GTRGAMMA -s uce-227.phylip -d -N 500 -p 733 -b 1629 -n X4
raxmlHPC-SSE3 -m GTRGAMMA -s uce-227.phylip -d -N 500 -p 733 -b 1629 -n X5

etc...

What most likely happend is that you confused -b with -B which is
actually used to specify this bootstrap threshold that must be a
floating point number between 0 and 1, whereas in your case it
complained about the larger integer from the random number seed you
passed to it.

Alexis

On 03.08.2016 15:09, Michael Forthman wrote:

[Michael Forthman]

I took a closer look and you are correct! When I echoed the string, it had -b, but the actual command line accidentally had -B. 

Thanks for taking a look