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error in read.FASTA() function #7

Open Bendlexane opened 2 weeks ago

Bendlexane commented 2 weeks ago

Hi!

I was trying to follow your tutorial on concatipede and while I was running your function concatipede_prepare() i could import the sequences even specifying the right path (read.csv worked fine for some fake data) or changing the fasta format to .fst, .fasta etc.

The issue is related with the ape::read.FASTA() function and the function throws the following error:

concatipede_prepare() Error in if (a != 0) { : missing value where TRUE/FALSE needed In addition: Warning message: In ape::read.FASTA(fasta_files[i]) : failed to read sequences, returns NULL

Is there any way to fix issue?

Best wishes!

tardipede commented 2 weeks ago

Hi, what software did you use to produce the fasta files?

Bendlexane commented 2 weeks ago

Hi!

They were sent me from other collaborators. I renamed them using AliView.

this is the beginning of the file:

A.pungens_BM1 CTGCTATCCA[....]