Alignment file exists but is invalid

[Muhammad Sadaqat]

Hi,

 I am Muhammad Sadaqat, a PhD student in Genetics, Genomics, and Bioinformatics from UMR CNRS 6553 ECOBIO, University of Rennes 1, Rennes, France.

First of all, thank you very much for developing such an excellent tool for the Gene Tree Species Tree (GTST) Reconciliation.

I am using the existing data inside the GeneRax directory in the path: data/plants to test GeneRax.

For plants, there are two families with their corresponding alignment, mapping, and genetrees.

I am using the following command:

generax -f families.txt -s speciesTree.newick --geneSearchStrategy SPR -r UndatedDTL -p results

and I got this error:

[00:00:00] GeneRax 2.1.3
Logs will also be printed into results/generax.log
GeneRax was called as follow:
generax -f families.txt -s speciesTree.newick --geneSearchStrategy SPR -r UndatedDTL -p results

General information:
- Output prefix: results
- Families information: families.txt
- Species tree: speciesTree.newick
- MPI Ranks: 1
- Random seed: 123
- Reconciliation model: UndatedDTL
- DTL rates: global rates
- Infer ML reconciliation: ON
- Unrooted reconciliation likelihood: OFF
- Enforcing gene tree root: OFF
- Prune species tree mode: OFF

Gene tree correction information:
- Gene tree search strategy: SPR
- Max gene SPR radius: 5

[00:00:00] Filtering invalid families...

Error in family family_1: Cannot read alignment file (file exists but is invalid)
Error in family family_2: Cannot read alignment file (file exists but is invalid)
WARNING!!! Found 2 invalid families (they will be discarded from the analysis)
[Error] No valid families! Aborting GeneRax

I am attching all the files for your reference.

Looking forward to hearing from you soon.

Thank you in advance.

[Benoit Morel]

Salut Muhammad,

Thanks for your kind feedback :-)

This error message often occures when one uses a DNA model (here GTR+G) in the family file for a protein alignment. Then the parser expects DNA characters and discards the alignment file as invalid. Please try with LG or any protein model you would like to use. If you absolutely need the general reversible model for proteins, I think there is another name (can be found in the raxml-ng documentation) but it is absolutely not recommended for gene tree inference.

Best,

Benoit

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