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NBISweden / MrBayes

MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. For documentation and downloading the program, please see the home page:
http://NBISweden.github.io/MrBayes/
GNU General Public License v3.0
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Error executing MrBayes #265

Closed callmcgovern closed 2 years ago

callmcgovern commented 2 years ago

Hello, I am trying to execute a bayesian phylogenetic analysis with Mr Bayes 3.2.7a and I keep getting this error: 

MrBayes > exe /Users/callahanmcgovern/Desktop/UNF/C-Lab/software/bayes/Anag_16S_less.nexus 

   Executing file "/Users/callahanmcgovern/Desktop/UNF/C-Lab/software/bayes/Anag_16S_less.nexus"
   DOS line termination
   Longest line length = 80
   Parsing file
   Expecting NEXUS formatted file
   Reading taxa block
ar   You cannot define nchar in a taxa block
      Error when setting parameter "Nchar" (2)
      The error occurred when reading char. 32-32 on line 4
         in the file '/Users/callahanmcgovern/Desktop/UNF/C-Lab/software/bayes/Anag_16S_less.nexus'

   Returning execution to command line ...

   Error in command "Execute"

MrBayes >

Here is my nexus file below: 

#NEXUS
[ Title ]
begin taxa;
       dimensions ntax=10 nchar=1082;
       format missing=? gap=- matchchar=. datatype=nucleotide;
       matrix
AY423710.1_Geitlerinema_carotinosum
---------------------------------ACCGGATGTGCCCACGGGTGAAAGGCT
TGCTGCCTGAAGAAGAGCTTGCGTCCGATTAGCTAGTTGGTGAGGTAAAGGCTTACCAAG
GCATCGATCGGTAGCTGGTCTGAGAGGATGACCAGCCACACTGGGACTGAGACAAGGCCC
AGACTCCTACGGGAGGCAGCAGTGGGGAATTTTCCGCAATGGGCGAAAGCCTGACGGAGC
AATACCGCGTGAGGGAAGAAGGCTCTTGGGTTGTAAACCTCTTTTCTCAGGGAATAAAAA
AATGAAGGTACCTGAGGAATAAGCATCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACG
GAGGATGCAAGCGTTATCCGGAATGATTGGGCGTAAAGCGTCCGCAGGTGGTACAACAAG
TCTAGTGTCAAAGACCGGGG-CTTAACTCCGGGATGGCGGTGGAAACTGTTGAA-CTAGA
GGG-TCGTAGGGG-TAGAGGG-AATTCCCAGTGTAGCGGTGAAATGCGTAGAGATTGGGA
AGAACATCGGT--GGCGAAGGCGCTCTACTGGACGGCAACTGACACTCAGGGACGAAAGC
TAGGGGAGCGAATGGGATTAGATACCCC-AGTAGTCCTAGCCGTAAACGATGGATACTAG
GTGTGGCTTGTAACAAAACGAGCCGTGCCGTAGCTAACGCGTTAAGTATCCCGCCTGGGG
AGTACGCTCGCAAGAGTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGT
ATGTGG-TTTAATT-CGATGCAAC-GCGAAGAACCTTACCAAGACTTGACATGTTGCGAA
TCCCCTTGAAAGGGGGGAGTGCCTTCGGGAGCGCAAACACAGGTGGTGCATGGCTGTCGT
CAGCTCGTGTCGTG-AGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTCATGTTTAG
TTGCCAATATTAAGTTAGGCACTCTAGACAGACTGCCGGTGACAAACCGGAGGAAGGTGG
GG-ATGACGTCAAGTCAGCATGCCCCTT

GU935345.1_Geitlerinema_sp._Sai001
---------------------------------ACCGGATGTGCCTAAGGGTGAAAGGCT
TGCTGCCTGAAGAAGAGCTTGCGTCCGATTAGCTAGTTGGTGAGGTAAAGGCTTACCAAG
GCATCGATCGGTAGCTGGTCTGAGAGGATGACCAGCCACACTGGGACTGAGACAAGGCCC
AGACTCCTACGGGAGGCAGCAGTGGGGAATTTTCCGCAATGGGCGAAAGCCTGACGGAGC
AATACCGCGTGAGGGAAGAAGGCTCTTGGGTTGTAAACCTCTTTTCTCAGGGAATAAAAA
AATGAAGGTACCTGAGGAATAAGCATCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACG
GAGGATGCAAGCGTTATCCGGAATGATTGGGCGTAAAGCGTCCGCAGGTGGTACAACAAG
TCTAGTGTCAAAGACCGGGG-CTCAACTCCGGAAAGGCGGTGGAAACTGTTGAA-CTAGA
GGG-TCGTAGGGG-TAGAGGG-AATTCCCAGTGTAGCGGTGAAATGCGTAGAGATTGGGA
AGAACATCGGT--GGCGAAGGCGCTCTACTGGACGGCAACTGACACTCAGGGACGAAAGC
TAGGGGAGCGAATGGGATTAGATACCCC-AGTAGTCCTAGCCGTAAACGATGGATACTAG
GTGTGGCTTGTAACAAAACGAGCCGTGCCGTAGCTAACGCGTTAAGTATCCCGCCTGGGG
AGTACGCTCGCAAGAGTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGT
ATGTGG-TTTAATT-CGATGCAAC-GCGAAGAACCTTACCAAGACTTGACATGTTGCGAA
TCCCCTTGAAAGGGGGGAGTGCCTTCGGGAGCGCAAACACAGGTGGTGCATGGCTGTCGT
CAGCTCGTGTCGTG-AGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTCATGTTTAG
TTGCCAATATTAAGTTAGGCACTCTAGACAGACTGCCGGTGACAAACCGGAGGAAGGTGG
GG-ATGACGTCAAGTCAGCATGCCCCTT

JQ712598.1_Geitlerinema_carotinosum_P013_16S_ribosomal_RNA_ge
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
-------------------------TTGGGTTGTAAACCTCTTTTCTCAGGGAATAATAA
AATGAAGGTACCTGAGGAATAAGCATCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACG
GAGGATGCAAGCGTTATCCGGAATGATTGGGCGTAAAGCGTCCGCAGGTGGAACAACAAG
TCTAGTGTCAAAGACCGGGG-CTCAACCCCGGGACGGCGGTGGAAACTGTTGAA-CTAGA
GGG-TCGTAGGGG-TAGAGGG-AATTCCCAGTGTAGCGGTGAAATGCGTAGAGATTGGGA
AGAACATCGGT--GGCGAAGGCGCTCTACTGGACGGCACCTGACACTCAGGGACGAAAGC
TAGGGGAGCGAATGGGATTAGATACCCC-AGTAGTCCTAGCCGTAAACGATGGATACTAG
GTGTGGCTTGTAACAAAACGAGCCGTGCCGTAGCTAACGCGTTAAGTATCCCGCCTGGGG
AGTACGCTCGCAAGAGTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGT
ATGTGG-TTTAATT-CGATGCAAC-GCGAAGAACCTTACCAGGACTTGACATGTCGCGAA
TTCCTCTGAAAGGAGGAAGTGCCTTCGGGAGCGCGAACACAGGTGGTGCATGGCTGTCGT
CAGCTCGTGTCGTG-AGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTCGTGTTTAG
TTGCCAATATTAAGTTAGGCACTCTAGACAGACTGCCGGTGACAAACCGGAGGAAGGTGG
GG-ATGACGTCAAGTCAGCATGCCCCTT

JQ712608.1_Geitlerinema_pseudacutissimum_P005_16S_ribosomal_R
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
----CCGCGTGAGGGA-GAGG-CTCTTGGGTTGTAAACCTCTTTTCTCAGGGAATAAAAA
AATGAAGGTACCTGAGGAATAAGCATCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACG
GAGGATGCAAGCGTTATCCGGAATGATTGGGCGTAAAGCGTCCGCAGGTGGTACAACAAG
TCTAGTGTCAAAGACCGGGG-CTTAACTCCGGGATGGCGGTGGAAACTGTTGAA-CTAGA
GGG-TCGTAGGGG-TAGAGGG-AATTCCCAGTGTAGCGGTGAAATGCGTAGAGATTGGGA
AGAACATCGGT--GGCGAAGGCGCTCTACTGGACGGCAACTGACACTCAGGGACGAAAGC
TAGGGGAGCGAATGGGATTAGATACCCC-AGTAGTCCTAGCCGTAAACGATGGATACTAG
GTGTGGCTTGTAACAAAACGAGCCGTGCCGTAGCTAACGCGTTAAGTATCCCGCCTGGGG
AGTACGCTCGCAAGAGTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGT
ATGTGG-TTTAATTGCGATGCAAC-GCGAAGAACCTTACCAAGACTTGACATGTTGCGAA
TCTCCTTGAAAGGGGAGAGTGCCTTCGGGAGCGCAAACACAGGTGGTGCATGGCTGTCGT
CAGCTCGTGTCGTG-AGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTCATGTTTAG
TTGCCAATATTAAGTTAGGCACTCTAGACAGACTGCCGGTGACAAACCGGAGGAAGGTGG
GG-ATGACGTCAAGTCAGCATGCCCCTT

JQ712614.1_Geitlerinema_pseudacutissimum_P03_16S_ribosomal_RN
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
----CCGCGTGAGGGAG--AGGCTCTTGGGTTGTAAACCTCTTTTCTCAGGGAATAAAAA
AATGAAGGTACCTGAGGAATAAGCATCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACG
GAGGATGCAAGCGTTATCCGGAATGATTGGGCGTAAAGCGTCCGCAGGTGGTACAACAAG
TCTAGTGTCAAAGACCGGGG-CTCAACCCCGGAAAGGCGGTAGAAACTGTTGAA-CTAGA
GGG-TCGTAGGGG-TAGAGGG-AATTCCCAGTGTAGCGGTGAAATGCGTAGAGATTGGGA
AGAACATCGGT--GGCGAAGGCGCTCTACTGGACGGCAACTGACACTCAGGGACGAAAGC
TAGGGGAGCGAATGGGATTAGATACCCC-AGTAGTCCTAGCCGTAAACGATGGATACTAG
GTGTGGCTTGTAACAAAACGAGCCGTGCCGTAGCTAACGCGTTAAGTATCCCGCCTGGGG
AGTACGCTCGCAAGAGTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGT
ATGTGG-TTTAATT-CGATGCAAC-GCGAAGAACCTTACCAAGACTTGACATGTTGCGAA
TCCCCTTGAAAGGGGGGAGTGCCTTCGGGAGCGCAAACACAGGTGGTGCATGGCTGTCGT
CAGCTCGTGTCGTG-AGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTCATGTTTAG
TTGCCAATATTAAGTTAGGCACTCTAGACAGACTGCCGGTGACAAACCGGAGGAAGGTGG
GG-ATGACGTCAAGTCAGCATGCCCCTT

JQ712617.1_Geitlerinema_pseudacutissimum_P004_16S_ribosomal_R
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
----CCGCGTGAGGGA-GAGGGCTCTTGGGTTGTAAACCTCTTTTCTCAGGGAATAAAAA
AATGAAGGTACCTGAGGAATAAGCATCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACG
GAGGATGCAAGCGTTATCCGGAATGATTGGGCGTAAAGCGTCCGCAGGTGGTACAACAAG
TCTAGTGTCAAAGACCGGGG-CTTAACTCCGGGATGGCGGTGGAAACTGTTGAA-CTAGA
GGG-TCGTAGGGG-TAGAGGG-AATTCCCAGTGTAGCGGTGAAATGCGTAGAGATTGGGA
AGAACATCGGT--GGCGAAGGCGCTCTACTGGACGGCAACTGACACTCAGGGACGAAAGC
TAGGGGAGCGAATGGGATTAGATACCCC-AGTAGTCCTAGCCGTAAACGATGGATACTAG
GTGTGGCTTGTAACAAAACGAGCCGTGCCGTAGCTAACGCGTTAAGTATCCCGCCTGGGG
AGTACGCTCGCAAGAGTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGT
ATGTGG-TTTAATT-CGATGCAAC-GCGAAGAACCTTACCAAGACTTGACATGTTGCGAA
TCTCCTTGAAAGGGGAGAGTGCCTTCGGGAGCGCAAACACAGGTGGTGCATGGCTGTCGT
CAGCTCGTGTCGTG-AGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTCATGTTTAG
TTGCCAATATTAAGTTAGGCACTCTAGACAGACTGCCGGTGACAAACCGGAG-AAGGTGG
GG-ATGACGTCAAGTCAGCATGCCCCTT

KJ705093.1_Geitlerinema_sp._PUPCCC_110.4_16S_ribosomal_RNA_ge
---------------------------------ACCGGATGTGCCTAAGGGTGAAAGGCT
TGCTGCCTGAAGAAGAGCTTGCGTCCGATTAGCTAGTTGGTGAGGTAAAGGCTTACCAAG
GCATCGATCGGTAGCTGGTCTGAGAGGATGACCAGCCACACTGGGACTGAGACAAGGCCC
AGACTCCTACGGGAGGCAGCAGTGGGGAATTTTCCGCAATGGGCGAAAGCCTGACGGAGC
AATACCGCGTGAGGGAAGAAGGCTCTTGGGTTGTAAACCTCTTTTCTCAGGGAATAAAAA
AATGAAGGTACCTGAGGAATAAGCATCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACG
GAGGATGCAAGCGTTATCCGGAATGATTGGGCGTAAAGCGTCCGCAGGTGGTACAACAAG
TCTAGTGTCAAAGACCGGGG-CTCAACCCCGGAAAGGCGGTAGAAACTGTT-GAACTAGA
GGG-TCGTAGGGG-TAGAGGG-AATTCCCAGTGTAGCGGTGAAATGCGTAGAGATTGGGA
AGAACATCGGT--GGCGAAGGCGCTCTACTGGACGGCAACTGACACTCAGGGACCAATGC
TAGGGGAGCGAATGGGATTAGATACCCCCTTTAGTCAC----------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
----------------------------

KP412630.1_Geitlerinema_splendidum_PSE0519C_16S_ribosomal_RNA
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
---------------------------------------------------------GAA
AGTGACGGTACCTGAGGAATCAGCATCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACG
GAGGATGCAAGCGTTATCCGGAATCATTGGGCGTAAAGAGTCCGTAGGTGGCGCATCAAG
TCTGTCGTTAAAGAGCAGGG-CTTAACCCTGGAGAGGCGGTGGAAACTGATGAAGCTAGA
GTA-CGGCAGGGG-TAGAGGG-AATTCCCAGTGTAGCGGTGAAATGCGTAGAGATTGGGA
AGAACACCGGT--GGCGAAAGCGCTCTACTAGACCTGTACTGACACTGAGGGACGAAAGC
TAGGGGAGCGAATGGGATTAGATACCCC-AGTAGTCCTAGCCGTAAACGATGGATACTAG
GTGTTGTCTGTATCGACCCGGACAGTGCCGGAGCTAACGCGTTAAGTATCCCGCCTGGGG
AGTACGCACGCAAGTGTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGT
ATGTGG-TTTAATT-CGATGCAAC-GCGAAGAACCTTACCAGGGCTTGACATGTCGCGAA
TCCCCTTGAAAGGGGGGAGTGCCTTCGGGAGCGCGAACACAGGTGGTGCATGGCTGTCGT
CAGCTCGTGTCGTG-AGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTCGTCCTAAG
TTGCCAGCATTAAGTTGGGCACTCTGAGGAGACTGCCGGTGACAAACCGGAGGAAGGTGG
GG-ATGACGTCAAGTCAGCATGCCCCTT

KT315930.1_Geitlerinema_sp._LD9_16S_ribosomal_RNA_gene_and_16
---------------------------------WCCGGATGTGCCTACGGGTGAAAGGCT
TGCTGCCTGAAGAAGAGCTTGCGTCCGATTAGCTAGTTGGTAAGGTAAAGGCTTACCAAG
GCATCGATCGGTAGCTGGTCTGARAGGATGACCAGCCACACTGGGACTGARACAAGGCCC
ASACTCCTACGGGAGGCAGCAGTGGGGAATTTTCCGCAATGGGCGAAAGCCTGACGGARC
AATACCGCGTGAGGGAAGAAGGCTCTTGGGTTGTAAACCTCTTTTCTCAGGGAATAAAAA
AATGAAGGKACCTGAGGAATAARCATCGGCTAACTCCGKGCCRGCMKCCGCGGTAATACG
GARGATGCRAGCGTTATCCGGAATGATTGGGCGTAAAGCGTCCGCAGGKGGTACAACAAG
TCTAGTGTCAAAGACCGGGG-CTCAACCCCGGAAAGGCGGTGGAAACTGTTGAA-CTAGA
GGG-TCGTAGGGG-TAGAGGG-AATTCCCAGTGTAGCGGTGAAATGCGTAGAGATTGGRA
AGAACATCGGT--GGCGAAGGCGCTCTACTGGACGGCAACTGACACTCAGGGACGAAAGC
TAGGGGAGCGAATGGGATTAGATACCCC-ASTAKTCCTARCCGTAAACGATGGATACTAG
GTGTGGCTTGTAACARAACGAGCCGTGCCGTAGCTAACGCGTTAAGTATCCCGCCTGGGG
RGTACGCTCGCAAGAGTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGT
ATGTGG-TTTAATT-CGATGCAAC-GCGAAGAACCTTACCAAGACTTGACATGTTGCGAA
TCTCCTTGAAAGGGGAGAGTGCCTTCGGGAGCGCAAACACAGGTGGTGCATGGCTGTCGT
CAGCTCGTGTCGTG-AGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTCATGTTTAG
TTGCCAATATTAAGTTAGGCACTCTAGACAGACTGCCGGTGACAAACCGGAGGAAGGTGG
GG-ATGACGTCAAGTCAGCATGCCCCTT

KT315931.1_Anagnostidinema_pseudacutissimum_LD27_16S_ribosoma
-------------------------------------------------------AGGCT
TGCTGCCTGAARAARAGCTTGCGTCCGATTAGCTAGTTGGTAAGGTAAAGGCTTACCAAG
GCATCGATCGGTAGCTGGTCTGARAGGATGACCAGCCACACTGGGACTGARACAAGGCCC
ARACTCCTACGGGAGGCAGCAGTGGGGAATTTTCCGCAATGGGCGAAAGCCTGACGGAGC
AATACCGCGTGAGGGAARAAGGCTCTTGGGTTGTAAACCTCTTTTCTCAGGGAATAAAAA
AATGAAGGTACCTGAGGAATAAGCATCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACG
GAGGATGCAAGCGTTATCCGGAATGATTGGGCGTAAAGCGTCCGCAGGTGGTACAACAAG
TCTAGTGTCAAAGACCGGGG-CTCAACCCCGGAAAGGCGGTGGAAACTGTTGAA-CTAGA
GGG-TCGTAGGGG-TAGAGGG-AATTCCCAGTGTAGCGGTGAAATGCGTAGAGATTGGGA
AGAACATCGGT--GGCGAAGGCGCTCTACTGGACGGCAACTGACACTCAGGGACGAAAGC
TAGGGGAGCGAATGGGATTAGATACCCC-AGTAGTCCTAGCCGTAAACGATGGATACTAG
GTGTGGCTTGTAACAAAACGAGCCGTGCCGTAGCTAACGCGTTAAGTATCCCGCCTGGGG
AGTACGCTCGCAAGAGTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGT
ATGTGG-TTTAATT-CGATGCAAC-GCGAAGAACCTTACCAAGACTTGACATGTTGCGAA
TCTCCTTGAAAGGGGAGAGTGCCTTCGGGAGCGCAAACACAGGTGGTGCATGGCTGTCGT
CAGCTCGTGTCGTG-AGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTCATGTTTAG
TTGCCAATATTAAGTTAGGCACTCTAGACAGACTGCCGGTGACAAACCGGAGGAAGGTGG
GG-ATGACGTCAAGTCAGCATGCCCCTT

;
end;

Thank you so much for your help with this issue!

haigh002 commented 2 years ago

You may have fixed this already, but:

You need a list of taxa in your taxa block. MrBayes is looking for that list. Instead is sees nchar, so it is telling you that you cannot give it the nchar before you give it the taxa list. So: begin taxa; dimensions ntax=10; taxlabels

AY423710.1_Geitlerinema_carotinosum GU935345.1_Geitlerinema_sp._Sai001 JQ712598.1_Geitlerinema_carotinosum_P013_16S_ribosomal_RNA_ge etc.

Also, datatype=Dna instead of datatype=nucleotide

callmcgovern commented 2 years ago

Thank you for your help! This was exactly the problem.

Best, Callahan

On Apr 13, 2022, at 15:55, haigh002 @.***> wrote:

 You may have fixed this already, but:

You need a list of taxa in your taxa block. MrBayes is looking for that list. Instead is sees nchar, so it is telling you that you cannot give it the nchar before you give it the taxa list. So: begin taxa; dimensions ntax=10; taxlabels

AY423710.1_Geitlerinema_carotinosum GU935345.1_Geitlerinema_sp._Sai001 JQ712598.1_Geitlerinema_carotinosum_P013_16S_ribosomal_RNA_ge etc.

Also, datatype=Dna instead of datatype=nucleotide

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