Error when model testing with amino-acid exchange rate matrix and protein mixture models

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Ales Bucek

May 22, 2019, 5:24:56 AM5/22/19
I run IQTREE 1.6.7 as follows:
iqtree -s ${InputAlignment} -nt ${SLURM_CPUS_PER_TASK} -spp ${PartitioningScheme} -mset LG+G,WAG+G,DCMUT+G,JTT+G,BLOSUM62+G,LG+G+F,WAG+G+F,DCMUT+G+F,JTT+G+F,BLOSUM62+G+F,LG4X -m TESTMERGE -rcluster-max 2000 -rcluster 10 -alrt 1000 -bb 1000 -bnni -pre ${SLURM_JOB_NAME}
which gives me following error:
ERROR: ratefree.cpp:537: double RateFree::optimizeWithEM(): Assertion `score > old_score-0.1' failed.

The same error returns also
iqtree -s ${InputAlignment} -nt ${SLURM_CPUS_PER_TASK} -spp ${PartitioningScheme} -mset BLOSUM62+G+F,LG4X -m TESTMERGE -rcluster-max 2000 -rcluster 10 -alrt 1000 -bb 1000 -bnni -pre ${SLURM_JOB_NAME}

But either
iqtree -s ${InputAlignment} -nt ${SLURM_CPUS_PER_TASK} -spp ${PartitioningScheme} -mset LG+G,WAG+G,DCMUT+G,JTT+G,BLOSUM62+G,LG+G+F,WAG+G+F,DCMUT+G+F,JTT+G+F,BLOSUM62+G+F -m TESTMERGE -rcluster-max 2000 -rcluster 10 -alrt 1000 -bb 1000 -bnni -pre ${SLURM_JOB_NAME}
iqtree -s ${InputAlignment} -nt ${SLURM_CPUS_PER_TASK} -spp ${PartitioningScheme} -m LG4X -alrt 1000 -bb 1000 -bnni -pre ${SLURM_JOB_NAME}
runs without problem.

I'd be thankful for any hints how to run IQTREE with selecting models from a list which includes both amino-acid exchange rate matrices and protein mixture models.

Minh Bui

May 22, 2019, 8:34:14 PM5/22/19
to IQ-TREE, Ales Bucek
Hi Ales,

The problem is that -mset option is supposed to only specify base substitution models, e.g.: 

-mset LG,WAG,…

especially LG4X should not be included here. In your case, please change -mset to:


And add two options:

-mrate G -madd LG4X

to only consider +G and also add LG4X model.

Btw I don’t why you want BLOSUM62 model: it is not an evolutionary model and mainly used with sequence alignment / database search. Therefore I recommend to exclude that model.


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