I'm trying to build the genome indexes with the following comand line (Ubuntu 18.04):
home/bowtie2-2.4.4-linux-x86_64/bowtie2-build ReferenceGenome GrCh38_index
where ReferenceGenome is the GrCh38.fa downloaded from NCBI to which I have added chr1_KI270763v1_alt.fa sequence.
The version of bowtie2 I am using is: version 184.108.40.206.
I'm not able to understand why only 4 files are generated (.rev.1.bt2 and .rev.2.bt2 files are not generated); moreover, the .2.bt2 is 0 bytes and the other 3 files are too small.
Can someone help me solving this issue?
Thanks in advance