Error while model testing before generating the tree for a multiple sequence alignment of a gene

[Mohak Sharda]

Hi,

I am trying to run iqtree (version 1.6.5) on a file with a multiple sequence alignment (528 sequences with 190 columns) of a gene in a phylip format (msa was carried out using MUSCLE and trimming was done using BMGE). The command is as follows:

iqtree-1.6.5-Linux/bin/iqtree -s seqs.trimmed.phy -m MFP -mtree -alrt 1000 -bb 1000 -bnni -nt AUTO

I am getting the following error (last line in bold below is the error), during one of the model testing steps:

--------------------------------------------------------------------

|                    FINALIZING TREE SEARCH                        |

--------------------------------------------------------------------

Performs final model parameters optimization

Estimate model parameters (epsilon = 0.010)

1. Initial log-likelihood: -25740.398

Optimal log-likelihood: -25740.387

Rate parameters:  A-C: 1.00000  A-G: 3.86848  A-T: 2.44474  C-G: 2.44474  C-T: 3.65150  G-T: 1.00000

Base frequencies:  A: 0.197  C: 0.254  G: 0.302  T: 0.247

Site proportion and rates:  (0.579,0.325) (0.421,1.929)

Parameters optimization took 1 rounds (0.090 sec)

BEST SCORE FOUND : -25740.387

Testing tree branches by SH-like aLRT with 1000 replicates...

0.697 sec.

Total tree length: 50.369

Total number of iterations: 102

CPU time used for tree search: 48.844 sec (0h:0m:48s)

Wall-clock time used for tree search: 48.851 sec (0h:0m:48s)

Total CPU time used: 50.836 sec (0h:0m:50s)

Total wall-clock time used: 50.844 sec (0h:0m:50s)

3 finished checkpoint entries erased

291  TIM+F+R2      25740.387    745 52970.774    1164510.774  55393.718

ERROR: Too long name ( > 1000) (line 1 column 161823)

There were 207/484 models that were tested for the same file. It was only after TIM+F+R2 (208th model) that the error showed up. Therefore, the files - .contree, .iqtree and .ufboot are not produced. I am trying to figure out the possible reason for the error.

[Minh Bui]

Hi Mohak,

Thanks for reporting this. Can you send me the log file and the alignment via personal email? I’ll have a look.

Minh

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