I am trying to index the human genome (GRCh38) using bowtie2-build in Ubuntu. However, it is not able to generate the index .rev files (only 4 files instead of 6).
I use Ubuntu 20.04.4 LTS on Windows, and bowtie2 version 2.4.5. I tried with two different human genomes (from NCBI and Ensembl), both with same results. I also tried with a small genome such as the lambda_virus.fasta, and it creates all the 6 files (including the .rev files). So, I'm not sure if it's a memory problem? Although I have 30 gb of free space. Thank you!
The code I'm using is:
bowtie2-build GRCh38_human_genome.fasta human_genome_index
Output (last three lines):
bmax according to bmaxDivN setting: 784204788 Using parameters --bmax 588153591 --dcv 1024 Doing ahead-of-time memory usage test