I am trying to build a Bowtie index from scratch. I have made a local installation of Bowtie in my cluster. The commands I have used to build a local index is "/gpfs/ycga/scratch60/nicoli/ag2646/Bowtie 2.4.2/bowtie2-2.4.2-linux-x86_64/"bowtie2-build "/gpfs/ycga/scratch60/nicoli/ag2646/Bowtie 2.4.2/bowtie2-2.4.2-linux-x86_64/genome.fa" human . The reference genome.fa is NCBI GrCHr38 build.
However, in place of 6 index files, I am getting only 4 .bt2 files but no rev.bt2 files. The terminal window shows Building a SMALL index Reading reference sizes
> Time reading reference sizes: 00:00:21 Calculating joined length > Writing header Reserving space for joined string Joining reference > sequences Time to join reference sequences: 00:00:26 max according > to bmaxDivN setting: 736462266 Using parameters --bmax 552346700 --dcv > 1024 Doing ahead-of-time memory usage test Passed! Constructing > with these parameters: --bmax 552346700 --dcv 1024 Constructing > suffix-array element generator Building DifferenceCoverSample > Building sPrime Building sPrimeOrder V-Sorting samples.
How to generate all 6 index files to build a proper index.