Invalid Fasta

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Gonçalo Themudo

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Apr 20, 2021, 8:06:23 AM4/20/21
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Hi,
I am getting some error message that I am not sure how to solve.
Some of my gene families when I try to run SpeciesRax are removed because the program is not able to parse the fasta files.

"Error in family NR1H: Cannot read alignment file (file exists but is invalid)"

I can't see any obvious errors in the fasta files, names are valid, sequences are same length.

Is there any description on what checks are made to see if the fasta file is valid?

Best regards,
Gonçalo

Benoit Morel

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Apr 20, 2021, 9:02:30 AM4/20/21
to GeneRax
Hi Gonçalo,

First, note that if you want to infer a species tree with SpeciesRax and if you already provide some input gene family trees, the alignments won't be used and you can choose not to include them in the families file.

Now, if you want GeneRax/SpeciesRax to infer the gene family trees from the sequences, or if you want to do gene tree correction with GeneRax:
- one possible source of error is that you are providing a substitution model that is not supported (check the format here: https://github.com/amkozlov/raxml-ng/wiki/Input-data#single-model)
- to check that the alignment is correct, you could try to run raxml-ng (https://github.com/amkozlov/raxml-ng) on it. GeneRax and raxml-ng use the same parser, but raxml-ng has a better error reporting (I am working on improving this in GeneRax).
- if it doesn't help, could you please send me one such alignment file and your families file?

Best,
Benoit
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