bowtie2-build problem to index the human genome
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Entering edit mode
8 weeks ago

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:

Input:

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
alignment bowtie linux • 164 views
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Entering edit mode
8 weeks ago

I would recommend downloading prebuilt idices:

http://bowtie-bio.sourceforge.net/bowtie2/index.shtml

you can also use a tool like Refgenie or Go Get Data

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