Question: why does my paup4 run end with error "Error(#314): Character type "2 1" is unrecognized." ?
0
gravatar for linningr
4.7 years ago by
linningr0
Canada
linningr0 wrote:

****I'm attempting to run paup4 on a data matrix of 54 taxa, 2422562 characters. I get the following error output:

Data matrix has 54 taxa, 2422562 characters
Valid character-state symbols: abc
Missing data identified by '?'
Gaps identified by '-'

Processing of file "~/WorkingFolder/Work/2014/1114/2014-11-18-RepeatFellers57IsolateTree/7-
PaupRunFellers54Isolates/aReference.rReads.nex" completed.

Error(#314): Character type "2 1" is unrecognized.
Error occurred at line 6 of file /home/rob/WorkingFolder/Work/2014/1114/2014-11-18-
RepeatFellers57IsolateTree/7-PaupRunFellers54Isolates/aReferencerReadspaupmaxParsimony.args

Execution terminated due to errors.

**** My aReferencerReadspaupmaxParsimony.args file is as follows:

#NEXUS

Begin paup;
execute aReference.rReads.nex;

ctype 2_1:;             <----Problem Line 6 Here (my addition)
log file=aReference.rReads.maxParsimony.paup.hsearch.log;

set autoclose=yes;
set criterion=parsimony;
set storebrlens=yes;
set increase=auto;
set root=outgroup;

hsearch addseq=random nreps=100 savereps=yes randomize=addseq swap=TBR hold=1 multrees=yes;

savetrees file=aReference.rReads.maxParsimony.paup.all.tree brlen=yes;
filter best=yes permdel=yes;

savetrees file=aReference.rReads.maxParsimony.paup.best.tree brlen=yes;

log stop;
end;

savetrees file=aReference.rReads.maxParsimony.paup.best.tree.phybrlens format=phylip;
savetrees file=aReference.rReads.maxParsimony.paup.best.tree.nexbrlens format=nexus;

**** I would appreciate any help someone can give me. I've scoured the Internets and the paup manual but am having trouble getting around this. A previous run worked fine.

Thanks in advance, Rob.

EDIT

I'm sorry but I should have added the following from the start and end of the aReference.rReads.nex file:

***start***

#NEXUS
Begin data;
Dimensions ntax=54 nchar=2422562;
Format symbols="abc" gap=-;

Matrix

...

 

***end***

;
end;

Begin Assumptions;
usertype 2x1 stepmatrix = 3
 a b c
[a] - 1 2
[b] 1 - 1
[c] 2 1 -
;
end;

paup4 phylogeny • 2.0k views
ADD COMMENTlink modified 4.7 years ago • written 4.7 years ago by linningr0

I added your extra section as an edit to the orginal question. In general, Q and A websites like biostarts if the section under the question is used only for answers to that question. Clarifications/edits/conversations should appear in comments, or edits to the orginal post.

I also updated my answer to match the edited question

ADD REPLYlink modified 4.7 years ago • written 4.7 years ago by David W4.7k

I think you are correct. The run seems to be going along OK now. I'll also recheck my previous run as well. I'll post how it looks in the morning - it may take some time. Thanks for the help!

ADD REPLYlink written 4.7 years ago by linningr0
2
gravatar for David W
4.7 years ago by
David W4.7k
New Zealand
David W4.7k wrote:

According to the PAUP manual, cytpe can be set to a bunch of pre-defined variables (ordered, unordered, dollo...) or a user-defined matrix. The 2_1 type is not one of the built-in types, so if you want to it you'll first have to define it using 'usertype' 

 

In reference to your edited question -- it seems the matrix has is called 2x1, not 2_1?

ADD COMMENTlink modified 4.7 years ago • written 4.7 years ago by David W4.7k
0
gravatar for linningr
4.7 years ago by
linningr0
Canada
linningr0 wrote:

Thank-you David W from New Zealand. A foolish clerical error on my part which I will not make again. I appreciate your help greatly. R.

ADD COMMENTlink written 4.7 years ago by linningr0
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