Re: [raxml] Potential boostrapping bug

[Alexandros Stamatakis]

Dear Conor,

You are right, I was able to reprodce the error.
I also don't know what is happening here, I will check and get back to you.

Alexis

On 01.08.2017 17:46, Conor Meehan wrote:
> Hi,
>
> I seem to have found a potential bug in RAxML 8.2.11 when trying to do
> bootstrap replicates without building an ML tree.
> The following command will give 10 bootstrap replicates on the alignment:
> raxmlHPC-PTHREADS-AVX -T 4 -m GTRGAMMA -s SNPonly.fasta -p 18161 -b 8095
> -N 10 -n testBoot1
>
> The following gives 10 parsimony trees and appears to ignore the
> bootstrapping command
> raxmlHPC-PTHREADS-AVX -T 4 -m GTRGAMMA -s SNPonly.fasta -p 18161 -N 10
> -n testBoot2 –b 8095
>
> It seems that placing the -b after the -N makes it be ignored or
> something? I can't figure out what is going wrong here. Any help would
> be greatly appreciated.
>
> Thanks,
> Conor
>
> --
> You received this message because you are subscribed to the Google
> Groups "raxml" group.
> To unsubscribe from this group and stop receiving emails from it, send
> an email to raxml+un...@googlegroups.com
> <mailto:raxml+un...@googlegroups.com>.
> For more options, visit https://groups.google.com/d/optout.

--
Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology

www.exelixis-lab.org

[Conor Meehan]

Hi Alexis,

With some extra digging, it seems like the hyphen is not being recognised as a hyphen on the terminal. Some weird copying and pasting between different things seems to have changed it on my computer. When I do a find/replace '-' with BBEdit, it doesn't replace the - before the b. This seems to be the issue. However, what is still odd is that when you use this not hyphen symbol in front of the b, it still puts it in the Raxml.info file as being -b (at the end of the line) but doesnt actually run that option. Still bizarre, but doesnt necessarily seem to be a RAxML bug, more a formatting weirdly on computers bug, perhaps an issue copy/pasting from a pdf.

C

[Alexandros Stamatakis]

Hi Conor,

Thanks for letting me know. RAxML should nonetheless throw an error
message in this case, I shall investigate further.

Alexis

> > an email to raxml+un...@googlegroups.com <javascript:>
> > <mailto:raxml+un...@googlegroups.com <javascript:>>.

> > For more options, visit https://groups.google.com/d/optout

> <https://groups.google.com/d/optout>.

>
> --
> Alexandros (Alexis) Stamatakis
>
> Research Group Leader, Heidelberg Institute for Theoretical Studies
> Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
>

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