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 220.127.116.11.
This process is computationally really heavy as it takes about 3 hours to complete. At the end of the process the first 4 files (.1.bt2/.2.bt2/.3.bt2/.4.bt2) seems to be ok while rev.1.bt2 and rev.2.bt2 I think they are incomplete as they are 352.5 MB and 264.3 MB (the rev.bt2 files downloaded from bowtie2 website instead are 982.5 MB and 733.7 MB).
Actually, when I try to align after building the indexes I get the following error:
Error reading _ebwt array: no more data Error: Encountered internal Bowtie 2 exception (#1) (ERR): bowtie2-align exited with value 1
and I think this is related to the fact that the indexes are incomplete. Can someone help me to solve this problem?