SNPS dataset is not producing a bestree output

[vanina v]

Hi, 

I am working with a SNP dataset generated by NGS radseq and my input file does not contain invariant sites.

I m trying to reconstruct the phylogeny using all the raxML versions in CIPRESS but any of them give as a result a BEST TREE output. 

I am selecting YES in the option "Correct for Ascertainment Bias" and I have tried many options without any tree as result.

Are there any of the options specifics for this kind of dataset?

Cheers, 

Vanina

[alexandros...@gmail.com]

Do you get any sort of output or error message? Would be good to also run a local copy of raxml on your computer and see if it works

Alexis

alexis stamatakis

www.exelixis-lab.org

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

Von: vanina v

Datum: Mo., 16. Jan. 2017 11:36

An: raxml;

Betreff:[raxml] SNPS dataset is not producing a bestree output

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[vanina v]

Hi, 

I don`t get any error message. 

I will try using a local copy right now.

Thank you Alexis.

Vanina

[Mark Miller]

Hi Vanina,

Thanks for reporting that.

The most common reason when an output file is missing is that the job "timed out" or hit its max run time before the run completed.

To diagnose that, see the file scheduler_stderr.txt and see if there is a message about reaching the maximum run time.

That will tell you if it timed out.

If so, please clone the job, increase the max run time, and resubmit.

If not, please send me the contents of the file _jobinfo.txt

Best,

Mark

[vanina v]

Hi Mark. 

I don´t see any message of timed out in the file scheduler_stderr.txt. 

the contents of the file  job info is:

Task\ label=filo9

Task\ ID=1079274

Tool=RAXMLHPC2_TGB

created\ on=2017-01-12 06:53:13.0

JobHandle=NGBW-JOB-RAXMLHPC2_TGB-954E00C92C364AA29BF946ED5E5FBDBA

resource=gordon

User\ ID=80174

User\ Name=vanina

email=vanin...@gmail.com

Output=(all_outputfiles,*,UNKNOWN,UNKNOWN,UNKNOWN)

ChargeFactor=1.000000

cores=48

JOBID=2811510.gordon-fe2.local

By the other side, I have run the file in my local computer as Alexis recommended me and it works perfectly. So I suppose the file is not wrong. It is very wear because a friend run a file similar but bigger than mine in CIPRES and it worked for him and then he tried with my file and again it did not work.

Best, 

Vanina

El lunes, 16 de enero de 2017, 11:36:26 (UTC+1), vanina v escribió:

[Alexandros Stamatakis]

mark,

which version of raxml do you have installed?

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

[Mark Miller]

Hi Vanina and Alexis,

We have 8.2.9 installed.

The stdout file ends as follows, it wouldn't imagine this would vary by code version, but then there are always surprises in life!:

Pattern: -----------------------------------------------------------TTTTTTTTTTTTTT--TTTTTTTTTTTT---T---------

Pattern occurs at the following sites of the input alignment:

Site 7856

　

Pattern: -----------------------------------------------------------TTTTTTT----T-T--T-TTT-------TTTTTTTTTTTT-

Pattern occurs at the following sites of the input alignment:

Site 30915

　

For partition No Name Provided you specified that the likelihood score shall be corrected for invariant sites

via an ascertainment bias correction. However, some sites in this partition are already invariant.

This is not allowed, please remove all invariant sites and try again, exiting ...

This seems like an issue with the data set to me.

But please let me know if I am wrong.

Best,

Mark

On Monday, January 16, 2017 at 2:36:26 AM UTC-8, vanina v wrote:

[Alexandros Stamatakis]

yes it is an issue with the dataset, please see previous discussions on
the google group about the ascertainment bias model and how it handles
invariant sites ... there's also a third party script available for
removing these from your alignment ...

alexis