[phylocom-user] AOT segmentation fault

Anthony Amend amend at hawaii.edu
Mon Mar 26 10:55:29 PDT 2012


Hello Cam,

Thanks for your help and to everyone else from the group who responded.  Changing the newlines doesn't seem to make a difference (I used text-wrangler and sed unix commands).  Two other people got my files to work and sent me their working copies, but I still get the same segmentation fault using their files. I even upgraded to v 4.2 and compiled it from scratch.  It seems to me like my problem might have something to do with how my machine is configured, but that's as far as my expertise will get me.    

Cheers,

Anthony

On Mar 25, 2012, at 7:00 PM, Cam Webb wrote:

> Dear Anthony,
> 
> I'm afraid I have not been able to duplicate the issue. The traits file had Mac line endings and the others (sample, phylo) had unix ones (at least after saving the dropbox file), but this is not a problem as long as they are consistent within a file.  Please check with a good editor that line endings were consistent within each file - that's all I can think of that may b causing you trouble.  Working files attached.
> 
> Best,
> 
> Cam
> 
> 
> 
> On Fri, 23 Mar 2012, Anthony Amend wrote:
> 
>> Hi Phylocom community,
>> 
>> Sorry for the bother, but I am at my wit's end.
>> 
>> Like the last poster, I've been analyzing my data in Picante, but am interested in working with the AOT functions in phylocom.  Converting my files was a bit of work, but I renamed all of my integer taxon IDS (by prepending QQQ) and named all of my nodes (node1,node2 etc.).
>> 
>> When I try to use aotf in phylocom (4.1) on my mac OS 10.6.8 using the following commands:
>> 
>> phylocom aotf -s phylo.comm -f pruned_phylo.tree -t phylo_traits > aot_out
>> 
>> I get an error reading:
>> 
>> File 'phylo_traits' has mac newlines Segmentation fault
>> 
>> and the output is blank
>> 
>> Changing my newlines to Unix doesn't help things, I just get a different flag.
>> 
>> Interestingly, these same files work for other phylocom functions, like comdist.
>> 
>> I thought that something may be odd with my tree file, so I created versions without node values and without branch lengths (or node values).  But these trees produce the following error:
>> 
>> Abort trap
>> 
>> I've gone through the help forum, but I don't see that anyone else has had this problem.  Any ideas?
>> 
>> My files are posted here:
>> 
>> http://dl.dropbox.com/u/8949385/phylocom_files
>> 
>> Thanks in advance for any advice!
>> 
>> Anthony
>> 
>> 
>> Irvine, CA 92697
>> 
>> 949.824.0532
>> 
>> amend at hawaii.edu
>> 
>> _______________________________________________
>> phylocom-user mailing list
>> phylocom-user at lists.phylodiversity.net
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> <anthony.zip>






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