Bowtie2 no build the index

Question

[Corona Cano]

Hello, this is my first time using R to create an index with bowtie2. I'm using R on windows, I've installed Rbowtie2 and Rsamtools with "BiocManager::install()". But when I'm trying to index the genome "Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa" in the folder "Chromosomes" I'm getting this:

Can you help me or give me some advice? Thank you.

[swbarnes2]

Did you read the manual to see exactly how the command bowtie2_build should be used?

[Corona Cano]

Yes, I even tried the following example and got the same thing

[Peter]

do you have access to a cluster, or a linux box? an example command would be:

# what ever the latest version is - not this one bwa-mem2-2.0pre2_x64-linux 

/PATH/TO/bwa-mem2-2.0pre2_x64-linux/bwa-mem2 index  NAME_OF_FILE.fasta

it is so easy, you dont need R to run it

[GenoMax]

Moving this to a comment since it is not answering the question in the original post.

[Carlo Yague]

What is the issue exactly ? To have the function returns NULL is not an a problem on its own. Have you looked in the folder Chromosomes/ if the bowtie2 index is built ? The files should be named yeast.x.bt2 or yeast.x.bt2l (where x is an integer).

[Corona Cano]

I've searched the folder but the index is not built, only the fasta file is there.

[Carlo Yague]

Ok, have you tried to add the option --verbose option instead of --quiet and see if you can get more details about what went wrong ?

[Corona Cano]

Can you explain me how to do it? Thanks

[Carlo Yague]

I don't know how to explain other than that: replace the option (= the text you write in the console when writing the bowtie2_build command) "--quiet" by "--verbose".

[Corona Cano]

I've tried, but I've got the same.

[Carlo Yague]

Do you have python installed ? On Windows, it is said that you need both perl and python installed to make bowtie2-build work:

The bowtie2 wrapper script is a Perl script and the bowtie2-build wrapper script is a Python script [...] On Windows, both Perl and Python do not come pre-installed and they must be downloaded and installed manually. If either Perl or Python are not installed on your system follow the links below to download and install them.

Python: https://www.python.org/downloads/

Perl: https://www.perl.org/get.html