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faircloth-lab / phyluce

software for UCE (and general) phylogenomics
http://phyluce.readthedocs.org/
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Error running "align_get_align_summary_data" #165

Closed BenjaminBlanchard closed 5 years ago

BenjaminBlanchard commented 5 years ago

Hello! I'm having a confusing issue running align_get_align_summary_data for the tutorial. I've attached a screenshot of the issue:

Screen Shot 2019-08-07 at 11 57 57 AM

Is the error likely because of the "git fatal" issue at the top? This initially said "fatal: Not a git repository: .git", which I attempted to fix using "git init" as recommended for this error in Stack Overflow, but now it is giving this "git fatal" error. Any thoughts on what this might be?

brantfaircloth commented 5 years ago

Not likely due to the git error, although I'm not sure how you could get in the state where this error is thrown. The actually error may be due to there being an empty alignment in your data set, but it is impossible to know how that may have happened without additional information. You could use LS to look at file sizes of your alignments, then investigate anything that is very short.

BenjaminBlanchard commented 5 years ago

Ok, will do - thanks for the speedy reply!

BenjaminBlanchard commented 5 years ago

You are correct - turns out mafft-nexus-edge-trimmed is empty somehow, don't know why I didn't check this... will investigate why that happened.