-
Notifications
You must be signed in to change notification settings - Fork 7
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Tree Log-Likelihood -INF Error #50
Comments
Dear Team, |
Hey @kawabata-tomoko, hm, I am a bit confused - let's try to clarify. For your reference sequences, you built an amino acid MSA, and inferred a tree from that, using a protein model (
Or do you have a second MSA for the same sequences, but containing their nucleotides instead of their amino acids, and aligned to that? Either way, using the protein model in EPA-ng, when your query sequences (and the MSA?) are actually nucleotides seems like it could cause an error such as Please check that you are using compatible data and models :-) As for
That is indeed a bit weird - the error message should still be printed, as you got on MacOS. Not sure what's going on there. It could be that EPA-ng was compiled with some older gcc - how did you get or compile EPA-ng? From conda, or did you compile on your own? If the latter, which compiler did you use? Cheers and so long |
Dear @lczech , Thank you for your reply. I apologize for the vagueness of my previous description of the problem. Let me clarify what I did in my workflow. I used both amino acid and nucleic acid sequences from the same genomes. For each genome, I constructed a reference tree using its protein MSA, and then I used its DNA MSA (with the same name) as a reference MSA for the subsequent sequence insertion process. To summarize:
The DNA sequence that I used for the insertion was not the corresponding nucleic acid sequence of the protein, but another conserved gene from the same genome, which I expected to have the same phylogenetic characteristics. For the compilation method, both Linux and MacOS are installed using the Thank you for your time and assistance. Sincerely, |
Hi @kawabata-tomoko, thanks, that makes more sense now :-)
It is totally fine to use a tree build from protein sequences, if that more accurately reflects the phylogenetic relationship of your data (there is always that issue with gene tree vs species tree...). However, you will still need to use model parameters that are optimized for the type of MSA and query sequence data that you are going to place. See here for how to do that. In short, in your case, you want to get the model parameters for a DNA model (of your choice, but Let me know if that helps and solves the issue :-) Cheers and so long |
I hope this message finds you well. I would like to extend my heartfelt gratitude for your previous response. I apologize for the delay in my reply, as I have been preoccupied with various unrelated matters. Your suggestions were incredibly helpful. Ultimately, we implemented the “GTR+G4” parameters to achieve the sequence placement, and we obtained satisfactory results. Once again, thank you for your valuable input. Best regards, |
Hello Team,
When I'm trying to place a sequence into the tree on Linux, I got en error
Aborted (core dumped)
without any error information.And I tried the same data and command on MacOS, core dumped again(with
libc++abi: terminating with uncaught exception of type std::runtime_error: Tree Log-Likelihood -INF!
).the EPA-ng version is
EPA-ng v0.3.8
the command used:
system infos:
running details infos(MacOS):
the query file(has the same length with MSA sequence after aligned with MAFFT:
It's seem like something wrong with my tree or query, I changed another query to place into another tree and everything is OK.
the tree I used in the error situation is build by iqtree2 with command
and the tree is :
After got an error with this tree, I noticed that most nodes have zero confidence. I removed the support , still error.
And I build the tree with Fasttree with
fasttree -intree genus_Acetobacter.treefile ../seq/all_seq.fasta> fast.tre
(transform it to binary tree with ete3:tree.resolve_polytomy()
), still error.What can I do to solve this problem?
Looking forwards to your reply.
Thanks a lot.
the MSA file is uploaded as attachment.
max_16s_ref.txt
The text was updated successfully, but these errors were encountered: