Bowtie alignment with 0 mismatches

[Nextgen_student]

Dear all

I would like to align filtered and trimmed RNAseq reads to a reference genome. The reads are between 20-24 nt in lenght.
I am using bowtie-1.2.2.
,
First I made an reference index, and six reference index files were created. bowtie3.rev.1.ebwt, bowtie3.rev.2.ebwt, bowtie3.1.ebwt, bowtie3.2.ebwt. bowtie3.3.ebwt, bowtie3.4.ebwt.
I then run the command from the directory where the reference files from the indexing are located:

cd $PBS_O_WORKDIR
module load bowtie-1.2.2

bowtie -v 0 -x /nlustre/users/motto/TF/bowtie3 -q /nlustre/users/motto/TF/AFI-1_S1out.fastq.gz -S /nlustre/users/motto/TF/AFI-1_S1out2.sam

But then continue to get the following error message:

Could not locate a Bowtie index corresponding to basename "/nlustre/users/motto/TF/bowtie3"
Command: /apps/bowtie-1.2.2/bowtie-align-l --wrapper basic-0 -v 0 -q -S /nlustre/users/motto/TF/margot /nlustre/users/motto/TF/AFI-1_S1out.fastq.gz /nlustre/users/motto/TF/AFI-1_S1out2.sam

It can not find the reference index....can someone please advise?

Kind regards
Margot

[GenomicSeq]

I'm not sure. Maybe this old thread will help. https://www.biostars.org/p/372511/