Possible multiple issues. Do you have a file with no readable name that is 3.1G? It looks like your `bowtie-build` command may have failed part-way. You should capture the stdout/stderr to capture those messages. You are missing `rev` files as you have already discovered.
bowtie2-build GCF_000001405.26_GRCh38_genomic.fna index_base_name (use a name you like) > log.out 2>log.error
Then look at the log files produced.