search

abacus-gene / paml

PAML is a program package for model fitting and phylogenetic tree reconstruction using DNA and protein sequence data. Please report only **technical issues** on this repository (e.g., compiling, programs abort or do not run at all, etc.). Problems with input data and general questions should be posted at https://groups.google.com/g/pamlsoftware?pli
GNU General Public License v3.0
103 stars 19 forks source link

Error: you should specify # seqs in the tree file. #37

Closed myoucchent closed 11 months ago

myoucchent commented 11 months ago

Hi, there is an error when I run the mcmctree, counld you give me some help? this is my tree: ((Dicentrarchus_labrax,(Larimichthys_crocea,(Acanthopagrus_latus,Sparus_aurata)))'>2.1',((Epinephelus_lanceolatus,Sander_lucioperca#),(Lates_calcarifer,(Oreochromis_niloticus,(Danio_rerio,(Oryzias_latipes,Oryzias_melastigma))))),(Lateolabrax_maculatus,Micropterus_salmoides));

this is error log: mcmctree mcmctree3.ctl MCMCTREE in paml version 4.10.0, September 2020

Reading options from mcmctree3.ctl.. finetune is deprecated now. Reading master tree.

Error: you should specify # seqs in the tree file.

sabifo4 commented 11 months ago

Hi there!

You may need to add the PHYLIP header in the tree file. As you have 13 tag IDs, then your tree file should have the following:

13  1
((Dicentrarchus_labrax,(Larimichthys_crocea,(Acanthopagrus_latus,Sparus_aurata)))'>2.1',((Epinephelus_lanceolatus,Sander_lucioperca#),(Lates_calcarifer,(Oreochromis_niloticus,(Danio_rerio,(Oryzias_latipes,Oryzias_melastigma))))),(Lateolabrax_maculatus,Micropterus_salmoides));

You may want to check the section on the PAML Wiki with regards to data formatting to make sure your input files are correctly formatted.

Please let me know if that sorted out your issue so that I can close it.

Hope this helps!

myoucchent commented 11 months ago

thank you very much! I select a branch as root seq in my tree. I have solved this problem.