Error when trying to perform bootstrap (RAxML 8.1.3)

[Paul Larson]

Our computing cluster recently upgraded to the newest version of RAxML and the following command which ran fine under the earlier version

raxml -f d -s sep17.phy -n sep17boots -m GTRGAMMAI -q parts.txt -T 5 -p 13241 -b 13241 -# 1000

Now give me the following error.

raxml: evaluateGenericSpecial.c:3433: evaluateIterative: Assertion `partitionLikelihood < 0.0' failed.

Aborted (core dumped)

Am I doing something wrong or is this a bug?

Thanks,

-Paul

[Andre J. Aberer]

Hi Paul,

this is somewhat a shot in the dark, but could you try the exact same
run with an additional
--no-bfgs
?

It may very well be related to the invar model or the bug may only occur
for certain bootstrap replicates...

--
Best regards,
Andre

--
Sent with my mu4e

[Paul Larson]

Thanks for the swift reply

I get the same message with --no-bfgs, and when I exclude Invariant site estimation from the model (with and without --no-bfgs)

-Paul

[Andre J. Aberer]

ok, then I fear, this is a case for Alexis. It may still take a while
until he gets to this.

[Paul Larson]

Ok, thanks again!

 

I will use another version for now.

-Paul 

[Ingo Michalak]

Hey together,

I want to add, that the same happens for my setup: Ubuntu laptop, AVX.PTHREADS version, normal ("-f a") analyses. Older version (8.0.26) works. Full error message:

Time for BS model parameter optimization 0.111993

raxml: evaluateGenericSpecial.c:3433: evaluateIterative: Assertion `partitionLikelihood < 0.0' failed.

Aborted (core dumped)

Best regards

[Alexandros Stamatakis]

dear paul and ingo,

could you send me the input datasets that generate this error please?

thanks,

alexis

--
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

[Christian Wurzb]

I am afraid I need to join here.

I got the same error with or without AVX with:

raxmlHPC-PTHREADS -s DNA.fasta -n out.tree -x 1234567 -p 1234567 -# 1000 -d -f a -m GTRGAMMA -T 2 -u

Time for BS model parameter optimization 11.140697
raxmlHPC-PTHREADS: evaluateGenericSpecial.c:3433: evaluateIterative: Assertion `partitionLikelihood < 0.0' failed.
Aborted (core dumped)

Strangely, when I use -m GTRCAT this error does not occur.

Thanks,
Christian

[Alexandros Stamatakis]

Dear All,

Thanks for reporting, I have a good idea where the error might come
from, but I am completely overloaded right now, i.e., no time to write
code, just use release v8.0.26 that will work (hopefully).

I'll let you know once this is fixed.

Alexis

[Alexandros Stamatakis]

Dear Paul,

I just released version 8.1.4 of RAxML at
https://github.com/stamatak/standard-RAxML/releases this should fix the bug.

I'd appreciate if you could double-check.

Thanks,

Alexis

[Alexandros Stamatakis]

Dear Ingo,

I just released version 8.1.4 of RAxML at
https://github.com/stamatak/standard-RAxML/releases this should fix the bug.

I'd appreciate if you could double-check.

Thanks,

Alexis

[Alexandros Stamatakis]

Dear Christian,

I just released version 8.1.4 of RAxML at
https://github.com/stamatak/standard-RAxML/releases this should fix the bug.

I'd appreciate if you could double-check.

Thanks,

Alexis

On 13.11.2014 14:22, Christian Wurzb wrote:

[Christian Wurzb]

Thanks a lot Alexis, Problem solved!

[Alexandros Stamatakis]

thanks :-)

alexis

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

> >>
> >
>
> --
> 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
>

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[kin onn chan]

Dear Alexis,

I am using your latest release 8.1.18 and got the same error:

evaluateGenericSpecial.c:3433: evaluateIterative: Assertion `partitionLikelihood < 0.0' failed

Should I revert back to 8.1.4? Many thanks in advance

[Alexandros Stamatakis]

Dear Kin,

Could you try the latest release v 8.1.20 first.

If this does not work either, please send me the input data and command
line to my personal email and I will have a look,

Alexis

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