Ascertainment Bias Assertion Failed

[William Gearty]

Hi all,

I'm running RAxML on the CIPRES portal (to whom I have also reported this problem).

I was able to run a standard rapid bootstrapping analysis with no problem, even with the correction for ascertainment bias on:

raxmlHPC-HYBRID -T 4 -n AToL_8_26_14 -N autoMRE -s infile.txt -m ASC_MULTIGAMMA -x 22589 -p 48216 -K MK -f a -o Sphenodon_punctatus,Kallimodon_pulchellus,Gephyrosaurus_bridensis --asc-corr lewis

However, I next tried to run the same analysis with a partition file included:

raxmlHPC-HYBRID -T 4 -n AToL_8_26_14_sort -N autoMRE -s infile.txt -m ASC_MULTIGAMMA -q part.txt -p 22654 -x 21476 -K MK -f a -o Sphenodon_punctatus,Kallimodon_pulchellus,Gephyrosaurus_bridensis --asc-corr lewis

The code seems to run fine, starts running a number of bootstraps, but then all of a sudden stops.

The stderr file in CIPRES reports the following error:

raxmlHPC-HYBRID: evaluateGenericSpecial.c:113: ascertainmentBiasSequence: Assertion `0' failed.

Any insight into this potential bug would be very helpful.

Thanks,

Will 

--

William Gearty

people.stanford.edu/wgearty

[Alexandros Stamatakis]

hi william,

I think I know what the problem is, I'll fix it next week, in the
meantime, if you use the sequential version or the MPI version but
without Pthreads it should work,

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

[William Gearty]

Awesome, thanks Alexis!

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William Gearty

people.stanford.edu/wgearty

[Alexandros Stamatakis]

Hi William,

I just committed version 8.2.4, it should solve the problem you reported.

Could you please check and let me know?

Thanks,

Alexis

On 16.09.2015 06:43, William Gearty wrote:

[William Gearty]

Hi Alexis,

Sorry I never got back to you earlier, the quick fix of just using the sequential version did the trick.

I'll check out the new version as soon as possible and will let you know if it works using the P-Threads version.

Thanks,

Will

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William Gearty

PhD Student, Paleobiology

Department of Geological Sciences

Stanford School of Earth, Energy & Environmental Sciences

people.stanford.edu/wgearty

[alexandros...@gmail.com]

No problem, just let me know if the pthreads version now works with your data

Alexis

alexis stamatakis

www.exelixis-lab.org

------ Originalnachricht------

Von: William Gearty

Datum: Fr., 2. Okt. 2015 23:30

An: ra...@googlegroups.com;

Betreff:Re: [raxml] Ascertainment Bias Assertion Failed

[William Gearty]

Hi Alexis,

My apologies for such a late response, but everything works perfectly, now!

Thanks for everything,

Will

[Alexandros Stamatakis]

:-)

alexis

On 20.11.2015 06:23, William Gearty wrote:
> Hi Alexis,
> My apologies for such a late response, but everything works perfectly, now!
> Thanks for everything,
> Will
>
> On Sat, Oct 3, 2015 at 3:20 AM, alexandros...@gmail.com

> <mailto:alexandros...@gmail.com>
> <alexandros...@gmail.com

> <mailto:alexandros...@gmail.com>> wrote:
>
> No problem, just let me know if the pthreads version now works with
> your data
>
>
> Alexis
>
>
> alexis stamatakis
>

> www.exelixis-lab.org <http://www.exelixis-lab.org>
>
>
> ------ Originalnachricht------
>
> *Von: *William Gearty____
>
> *Datum: *Fr., 2. Okt. 2015 23:30
>
> *An: *ra...@googlegroups.com <mailto:ra...@googlegroups.com>;
>
> *Betreff:*Re: [raxml] Ascertainment Bias Assertion Failed

>
>
> Hi Alexis,
> Sorry I never got back to you earlier, the quick fix of just using
> the sequential version did the trick.
> I'll check out the new version as soon as possible and will let you
> know if it works using the P-Threads version.
> Thanks,
> Will
>
> On Fri, Oct 2, 2015 at 6:48 AM, Alexandros Stamatakis
> <alexandros...@gmail.com

> <mailto:alexandros...@gmail.com>> wrote:
>
> Hi William,
>
> I just committed version 8.2.4, it should solve the problem you
> reported.
>
> Could you please check and let me know?
>
> Thanks,
>
> Alexis
>

> <mailto:raxml%2Bunsu...@googlegroups.com>
> <mailto:raxml+un...@googlegroups.com
> <mailto:raxml%2Bunsu...@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
> Adjunct Professor, Dept. of Ecology and Evolutionary Biology,
> University
> of Arizona at Tucson
>

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

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

> William Gearty
> PhD Student, Paleobiology
> Department of Geological Sciences
> Stanford School of Earth, Energy & Environmental Sciences

> <http://people.stanford.edu/wgearty>people.stanford.edu/wgearty

> <http://people.stanford.edu/wgearty>
>
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> William Gearty
> PhD Student, Paleobiology
> Department of Geological Sciences
> Stanford School of Earth, Energy & Environmental Sciences