I am currently learning how to use BiocManager. I was trying to index a .fa file downloaded from NCBI (cropped, because all I want is to get familiarized with the tools).

This is the code I used (just to load bowtie2 and try to use "bowtie2_build")

install.packages("BiocManager")
BiocManager::install("Rbowtie2")
BiocManager::install("Rsamtools") 

library("Rbowtie2")
library("Rsamtools")

bowtie2_build("chromosomes/proof.fa", bt2Index = "chromosomes/yeast")
``

"chromosomes" is a folder from my working directory. The output of the last line in the console is "NULL", and in "files" from Rstudio, it appears a file called "yeast.1.bt2", with 0 B and the date "Jan 1, 1970, 1:00 AM"

I have no idea what I have to do.

Thank you all in advance.

Is proof.fa an actual FASTA file? Have you tried using the demo data that comes with the package? See the vignette under Build Bowtie Index