Killed0.41 seconds: ME NNI round 1 of 34, 1 of 353 splits

Question

[Neel]

Hi, I am trying to running Fast tree & i got this error as well as blank tree.file-

fasttree core_gene_alignment.aln >tree.file
FastTree Version 2.1.10 Double precision (No SSE3)
Alignment: core_gene_alignment.aln
Amino acid distances: BLOSUM45 Joins: balanced Support: SH-like 1000
Search: Normal +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1
TopHits: 1.00*sqrtN close=default refresh=0.80
ML Model: Jones-Taylor-Thorton, CAT approximation with 20 rate categories
WARNING! 100.0% NUCLEOTIDE CHARACTERS -- IS THIS REALLY A PROTEIN ALIGNMENT?
Initial topology in 3530.41 secondsf    352    1 of    355 seqs    300)   
Refining topology: 34 rounds ME-NNIs, 2 rounds ME-SPRs, 17 rounds ML-NNIs
**Killed0.41 seconds: ME NNI round 1 of 34, 1 of 353 splits**   

Thank you

Answer 1

[Mensur Dlakic]

It tells you right there:

WARNING! 100.0% NUCLEOTIDE CHARACTERS -- IS THIS REALLY A PROTEIN ALIGNMENT?

It is unlikely that one can have 355 protein sequences with only ACGT residues. This program works only with protein sequences.