I have two species tree and a set of gene trees and I'm trying to see which species tree has the best likelihood score using the SpeciesRax method with the strategy EVAL. However, I keep having the error below. I have tried reformatting the alignments several times but I have not figure out what is causing the error. I have also attached a small sample of my database (including a couple of alignments). I hope somebody can help me with this issue.
[00:00:00] GeneRax 2.0.1
Logs will also be printed into GeneRax/generax.log
GeneRax was called as follow:
./generax -f forGeneRax/famFileTest -s forGeneRax/spsTreeOp.newick --si-strategy EVAL
- Output prefix: GeneRax
- Families information: forGeneRax/famFileTest
- Species tree: forGeneRax/spsTreeOp.newick
- You are running GeneRax without MPI (no parallelization)
- Random seed: 123
- Reconciliation model: UndatedDTL
- DTL rates: global rates
- Infer ML reconciliation: ON
- Unrooted reconciliation likelihood: OFF
- Prune species tree mode: OFF
Species tree inference information:
- Species tree Strategy: EVAL
- Quartet branch supports estimation: OFF
- Branch length estimationOFF
- SPR radius: 1
Gene tree correction information:
- Gene tree strategy: SPR
- Max gene SPR radius: 5
[00:00:00] Filtering invalid families...
Error in family OG5149884: Cannot read alignment file (file exists but is invalid)
Error in family OG5160170: Cannot read alignment file (file exists but is invalid)
Error in family OG5171679: Cannot read alignment file (file exists but is invalid)
Error in family OG5172482: Cannot read alignment file (file exists but is invalid)
WARNING!!! Found 4 invalid families (they will be discarded from the analysis)
[00:00:00] Starting species tree initialization...
libc++abi.dylib: terminating with uncaught exception of type LibpllException: Error while reading rooted tree from file GeneRax/species_trees/starting_species_tree.newick.
Error name: FILE_DOES_NOT_EXISTS.
Error help message: File does not exist.
The parsing error was detected at character 1.
Abort trap: 6