ERROR: Nexus file format

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RJ

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Jul 27, 2020, 4:50:19 AM7/27/20
to PartitionFinder
Hello,

I am getting error for the Nexus file format while running analysis on IQTREE web-server. 

I am working with four gene sequences comprising a sequence matrix of a total of 2276 nucleotides. I ran PartitionFinder on the total nucleotide sequence and used the partitioning scheme and substitution models details received by the software in NEXUS format to run ML analysis on IQTREE web server. IQTREE repeatedly giving me this following error!

ERROR: Partition file is not in NEXUS format, assuming RAxML-style partition file...
ERROR: Please specify alignment positions for partitionGTR+G:Subset2, GTR+G:Subset3, GTR+I:Subset4, GTR+G:Subset5, GTR+G:Subset6, GTR+G:Subset7;\
ERROR: end;\
ERROR: \ 
ERROR: }

Below is the alignment partitioning detail that I am using to run the analysis. 

#nexus
begin sets;
charset Subset1 = 1-519;
charset Subset2 = 520-1190;
charset Subset3 = 1191-1906\3;
charset Subset4 = 1192-1906\3;
charset Subset5 = 1193-1906\3;
charset Subset6 = 1907-2276\3;
charset Subset7 = 1908-2276\3 1909-2276\3;
charpartition PartitionFinder = GTR+G:Subset1, K80+G:Subset2, F81:Subset3, GTR+I:Subset4, HKY+G:Subset5, HKY:Subset6, JC:Subset7;
end;

Looking forward for help

RJ

unread,
Jul 27, 2020, 4:50:19 AM7/27/20
to PartitionFinder
Hello Guys,

I am working with four gene sequences comprising a sequence matrix of a total of 2276 nucleotides. I ran PartitionFinder on the total nucleotide sequence and used the partitioning scheme and substitution models details received by the software in NEXUS format to run ML analysis on IQTREE web server. However, IQTREE is repeatedly giving me this following error!

ERROR: Partition file is not in NEXUS format, assuming RAxML-style partition file...
ERROR: Please specify alignment positions for partitionGTR+G:Subset2, GTR+G:Subset3, GTR+I:Subset4, GTR+G:Subset5, GTR+G:Subset6, GTR+G:Subset7;\ ERROR: end;\ ERROR: \ 
ERROR: }

Below is the alignment partitioning detail that I am using to run the analysis.  I request you to kindly guide me through this problem.

#nexus
begin sets;
charset Subset1 = 1-519;
charset Subset2 = 520-1190;
charset Subset3 = 1191-1906\3;
charset Subset4 = 1192-1906\3;
charset Subset5 = 1193-1906\3;
charset Subset6 = 1907-2276\3;
charset Subset7 = 1908-2276\3 1909-2276\3;
charpartition PartitionFinder = GTR+G:Subset1, K80+G:Subset2, F81:Subset3, GTR+I:Subset4, HKY+G:Subset5, HKY:Subset6, JC:Subset7;
end;

Looking forward to hearing from you

RJ

unread,
Jul 27, 2020, 4:50:19 AM7/27/20
to PartitionFinder
Hello Guys,

I am writing this message to seek your help in resolving the error message that I am getting while running analysis on IQTREE web-server. 

I am working with four gene sequences comprising a sequence matrix of a total of 2276 nucleotides. I ran PartitionFinder on the total nucleotide sequence and used the partitioning scheme and substitution models details received by the software in NEXUS format to run ML analysis on IQTREE web server. However, IQTREE is repeatedly giving me this following error!

ERROR: Partition file is not in NEXUS format, assuming RAxML-style partition file...
ERROR: Please specify alignment positions for partitionGTR+G:Subset2, GTR+G:Subset3, GTR+I:Subset4, GTR+G:Subset5, GTR+G:Subset6, GTR+G:Subset7;\
ERROR: end;\
ERROR: \ 
ERROR: }

Below is the alignment partitioning detail that I am using to run the analysis. May I request you to kindly guide me through this problem.
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