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fhcrc / taxtastic

Create and maintain phylogenetic "reference packages" of biological sequences.
GNU General Public License v3.0
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Entered LG-model (Fasttree) in lines 116 and 150 #119

Closed sachacoesel closed 6 years ago

sachacoesel commented 6 years ago

I needed to make a reference package with FastTree using the LG substitution model (supported by PPLACER), and got the following error msg:

taxtastic.utils.InvalidLogError: GTR model, but no substitution rates found!

I entered the LG-model as an option in lines 116 and 150 and now I can create a reference package on my system.

Here are the first few lines of a fasttree LG log:

Command: FastTree -lg -log LOVref11.aln.lg.tree.log LOVref11.aln.fasta FastTree Version 2.1.9 No SSE3 Alignment: LOVref11.aln.fasta 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: Le-Gascuel 2008, CAT approximation with 20 rate categories Read 2729 sequences, 243 positions

nhoffman commented 6 years ago

Thanks, @sachacoesel! This will be included in the next release.