[phylocom-user] Taxa file

Ken Whitney kwhitney at rice.edu
Fri Nov 6 13:45:06 PST 2009


Hi Steve,

I'm using v 4.1 in Windows XP.

the command I was using is the same as that in the manual

phylocom comtrait -m 0 -x 2

therefore assuming the default file names.

I tried it using

phylocom comtrait -t traits -s sample

and my files ran for the first time.  Aha!  However, when I tried adding 
in the -m and -x switches to the above command, it wouldn't run 
("phylocom.exe has encountered a problem and needs to close.  We are 
sorry for the inconvenience......Please tell Microsoft about this 
problem").  I then went back to

phylocom comtrait -t traits -s sample

and it wouldn't run.  I then just resubmitted the same line again and 
again; in about 4 of 5 cases I get the above error and on the 5th try it 
ran.  I did this with different configurations of switches being present 
or absent and it seemed to run about every 5th or 6th time.

Sorry for all the confusion.  Maybe there is an issue with how my PC is 
configured?  But we were having the same issue on a different PC as well.

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/



Steven Kembel wrote:
> 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 
>>>>
>>>
>>>
>>>
>>>
>>>
>
>
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>
>



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