[phylocom-user] AOT segmentation fault

Cam Webb cwebb at oeb.harvard.edu
Sun Mar 25 19:00:07 PDT 2012

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 



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
> http://lists.phylodiversity.net/listinfo.cgi/phylocom-user-phylodiversity.net
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