[phylocom-user] Taxa file

Steven Kembel steve.kembel at gmail.com
Fri Nov 6 10:14:29 PST 2009


Ken,

What version of Phylocom are you using, and what operating system?
Can you share the exact command you are typing to invoke comtrait and  
get the error message?

Comtrait does not use or look for a file called taxa, that is a  
different function altogether. If you are getting a warning about  
"Cannot find file: taxa" while trying to run comtrait I suspect there  
is some problem with the syntax.... are you specifying the name of the  
traits file after -t and the sample file after -s?

i.e. your invocation of phylocom should look something like:
./phylocom comtrait -t nameOfYourTraitsFile -s nameOfYourSampleFile

Steve
On Nov 5, 2009, at 12:19 PM, Ken Whitney wrote:

> Hi Steve,
>
> Thanks for the quick reply.
> Sorry to be dense about this.  We have working phylo and sample  
> files that produce good output (e.g. in Comstruct).  As far as we  
> can tell, our traits file is as it should be (and we have checked  
> that the taxa match between files, etc.).  So when we couldn't get  
> Comtrait to run using these files, we went back to the traits and  
> sample files from /example_data files.  At first, Comtrait would not  
> run on those either, but when the Taxa file was added back into the  
> folder (it had been missing) they ran.  That's why we assumed it was  
> needed.
> I just tried to run Comtrait again without a taxa file in the folder  
> and I get the error "Cannot find file: taxa" with no output.
>
> Thanks again,
> Ken
>
>
>
>
> ------------------
> Ken Whitney
> Assistant Professor
> Dept. of Ecology and Evolutionary Biology
> Rice University
> Houston, TX 77005 USA
> 713 348 3057
> http://www.ruf.rice.edu/~kwhitney/
>
>
>
> Steven Kembel wrote:
>> Hi Ken,
>>
>> comtrait requires two files to run - a sample file that contains  
>> information on the communities, and a traits file that contains  
>> information on the traits of the taxa in those communities. There  
>> are examples of both formats included in the /example_data  
>> directory of Phylocom 4.1 (named sample and traits, respectively).  
>> Please have a look at those for an example of how the files need to  
>> be formatted, as well as page 8 of the Phylocom manual where the  
>> format of these two files are defined. There is also a tutorial  
>> linked to from the Phylocom homepage that goes through the process  
>> of running the comtrait function:
>>
>> http://bodegaphylo.wikispot.org/Community_Phylogenetics
>>
>> Cheers,
>> Steve
>>
>> On Nov 5, 2009, at 9:42 AM, Ken Whitney wrote:
>>
>>> Hello all,
>>>
>>> We kept crashing Phylocom trying to run Comtrait before finally  
>>> realizing that it won't run without a Taxa file.  I hope we didn't  
>>> miss it, but we can't find any information in the manual on what  
>>> the Taxa file is/contains, and it is not obvious from looking at  
>>> the example Taxa file provided.  Hints?
>>>
>>> Many thanks,
>>> Ken
>>>
>>> -- 
>>> ------------------
>>> Ken Whitney
>>> Assistant Professor
>>> Dept. of Ecology and Evolutionary Biology
>>> Rice University
>>> Houston, TX 77005 USA
>>> 713 348 3057
>>> http://www.ruf.rice.edu/~kwhitney/
>>>
>>> _______________________________________________
>>> phylocom-user mailing list
>>> phylocom-user at lists.phylodiversity.net
>>> http://lists.phylodiversity.net/listinfo.cgi/phylocom-user-phylodiversity.net
>>
>>
>> !DSPAM:5951,4af31a4a213612286784294!
>>
>>




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