Could not locate a Bowtie index corresponding to basename

Question

I am new to Bowtie. I am trying to use Bowtie for end to end local alignment. I've got this error message:

Could not locate a Bowtie index corresponding to basename "/bowtie2-index/hg19"

In my installation and in the bowtie2-index/hg19 folder there are six bt2 files. I am using the following command:

/opt/bowtie2/bowtie2-align-s --wrapper basic-0 -p 64 -x /mnt/miczfs/tide/bowtie2-index/hg19 -S /mnt/miczfs/tide/Data/chr2chr3/chr2chr3.sam -1 /mnt/miczfs/tide/Data/chr2chr3/chr2chr3.f1.fastq -2 /mnt/miczfs/tide/Data/chr2chr3/chr2chr3.f2.fastq

Answer 1

This is a perennial question, I guess the documentation isn't explicit enough here. By using -x /mnt/miczfs/tide/bowtie2-index/hg19, you're telling bowtie2 that you have files like /mnt/miczfs/tide/bowtie2-index/hg19.1.bt2 that it should use. You don't specify a folder, you specify a "basename". You probably meant -x /mnt/miczfs/tide/bowtie2-index/hg19/hg19 or something like that.