Originally posted by zivlie October 15, 2025
Hello,
I just encountered unexpected behavior in the output of a partition merging run. In other cases, the same input arguments have produced a .best_model.nex file that works fine as input for tree inference. In this case, the best_model.nex (and best_scheme.nex) caused errors in two ways:
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The CharPartition caused a failure: Reading partition model file doli-100.3t-95p.charsets.best_model.nex ... ERROR: ERROR: Error found at line 118, column 107 (file position 50073): ERROR: CharSet uce not found
(Line 118 being the the first model and parameters and the first charset after 'charpartition mymodels=', column 107 being the name of the first charset GTR{1.03847,7.30405,1.18463,0.909962,6.12252}+F{0.281908,0.219077,0.219095,0.27992}+G4{0.496605}: uce-10.nexus_uce-10041.nexus_uce-10222.nexus. . . .
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The actual charsets were formatted with a comma before the positions, e.g. charset uce-10100.nexus_uce-10908.nexus_uce-11150.nexus_uce-12129.nexus = , 41250-42026 353378-354529 450784-451389 840072-840900;
If I manually remove the charpartition section, and remove the extra commas and whitespace, then it runs just fine. However, I would like to know how to avoid this in future.
I've attached the log for the merging run and the .best_model.nex file. The latter is renamed as a .txt file to allow upload here.
This was using version 2.3.1, but I had the same errors when trying to do the inference step on version 2.0.3
doli-100.3t-95p.charsets.best_model.txt
doli-100.3t-95p.charsets.log
Discussed in https://github.com/orgs/iqtree/discussions/494
Originally posted by zivlie October 15, 2025
Hello,
I just encountered unexpected behavior in the output of a partition merging run. In other cases, the same input arguments have produced a .best_model.nex file that works fine as input for tree inference. In this case, the best_model.nex (and best_scheme.nex) caused errors in two ways:
The CharPartition caused a failure:
Reading partition model file doli-100.3t-95p.charsets.best_model.nex ... ERROR: ERROR: Error found at line 118, column 107 (file position 50073): ERROR: CharSet uce not found(Line 118 being the the first model and parameters and the first charset after 'charpartition mymodels=', column 107 being the name of the first charset
GTR{1.03847,7.30405,1.18463,0.909962,6.12252}+F{0.281908,0.219077,0.219095,0.27992}+G4{0.496605}: uce-10.nexus_uce-10041.nexus_uce-10222.nexus. . . .The actual charsets were formatted with a comma before the positions, e.g.
charset uce-10100.nexus_uce-10908.nexus_uce-11150.nexus_uce-12129.nexus = , 41250-42026 353378-354529 450784-451389 840072-840900;If I manually remove the charpartition section, and remove the extra commas and whitespace, then it runs just fine. However, I would like to know how to avoid this in future.
I've attached the log for the merging run and the .best_model.nex file. The latter is renamed as a .txt file to allow upload here.
This was using version 2.3.1, but I had the same errors when trying to do the inference step on version 2.0.3
doli-100.3t-95p.charsets.best_model.txt
doli-100.3t-95p.charsets.log