ERROR: Too large site ID

1,072 views
Skip to first unread message

des...@amnh.org

unread,
Jul 13, 2018, 11:37:49 AM7/13/18
to IQ-TREE

Hi Guys

In trying to run IQtree with partitioned data (a morphological matrix and a aa dataset). I have been getting this error.

My .phy files are good as they run by themselves in IQtree. and here is my nexus file called test.example.nex

#nexus

begin sets;
    charset part1 = Sc.128.txt: 1-2176;
    charset part2 = Whe.txt : 2177-48718;
    charpartition mine = MK:part1, LG+F+I+G4:part2;
end;

SC.128.txt is the morphological set and Whe.txt is the AA set.

and here is the command I use when trying to run the nexus file.

bin/iqtree -sp test.example.nex

I am probably doing something incredibly stupid,  but what?

thanks for any time you can give to this query.


Heiko Schmidt

unread,
Jul 13, 2018, 12:15:03 PM7/13/18
to IQ-TREE Forum
Dear Rob,

Thanks for your interest in IQ-Tree.

Just from the error message, I would say that 48718 is larger than your actual alignment length.
However, this is guessing, because I cannot check your alignment ;)

Best regards,
Heiko
> --
> You received this message because you are subscribed to the Google Groups "IQ-TREE" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to iqtree+un...@googlegroups.com.
> To post to this group, send email to iqt...@googlegroups.com.
> Visit this group at https://groups.google.com/group/iqtree.
> For more options, visit https://groups.google.com/d/optout.

-----------------------------------------------------------------------------
Heiko Schmidt
Center for Integrative Bioinformatics Vienna (CIBIV)
University of Vienna / Max F. Perutz Laboratories (MFPL)
http://www.cibiv.at/
-----------------------------------------------------------------------------

Robert Desalle

unread,
Jul 13, 2018, 1:19:31 PM7/13/18
to iqt...@googlegroups.com

thank you heiko


actually all i needed to do was change the nex file to


#nexus

begin sets;
    charset part1 = Schier.128.txt: 1-2176;
    charset part2 = Whe.txt : 1-46542;

    charpartition mine = MK:part1, LG+F+I+G4:part2;
end;


my whe file starts at 1 not 2177


but you pointed to the obvious error and indeed mine ws pretty silly


great program. glad you guys did it


rob



From: iqt...@googlegroups.com <iqt...@googlegroups.com> on behalf of Heiko Schmidt <heiko....@univie.ac.at>
Sent: Friday, July 13, 2018 12:15:01 PM
To: IQ-TREE Forum
Subject: Re: [iqtree] ERROR: Too large site ID
 


-----------------------------------------------------------------------------
Heiko Schmidt
Center for Integrative Bioinformatics Vienna (CIBIV)
University of Vienna / Max F. Perutz Laboratories (MFPL)


--
You received this message because you are subscribed to the Google Groups "IQ-TREE" group.
To unsubscribe from this group and stop receiving emails from it, send an email to iqtree+un...@googlegroups.com.
To post to this group, send email to iqt...@googlegroups.com.
Reply all
Reply to author
Forward
0 new messages