BOWTIE2_INDEXES environmental variable error

[jmm1005]

I am trying to align my reads to the hg19 build of the human genome. I downloaded and unzipped the pre-built index from iGenomes in the main directory of my project space. I have two different sets of reads that I want to align in different sub folders of that directory. In my bowtie2 PBS file I have tried to set the BOWTIE2_INDEXES environmental variable to the absolute path to the index files (which I have double checked and the files do exist there), but every time I try and run bowtie2 I get this error:

Could not locate a Bowtie index corresponding to basename "genome"

This is the command I am using to set the variable:

export BOWTIE2_INDEXES=/path/to/projectdirectory/Homo_Sapiens/UCSC/hg19/Sequence/Bowtie2Index/
and in the command line: -x genome

I have also tried putting the path directly in the command line:

-x /path/to/projectdirectory/Homo_Sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome

I still get the same error.

Any ideas as to why it won't work?

[GenoMax]

Verify that there are "read" permissions for "all" on the directory hierarchy with the Bowtie2index and that the index files have similar permissions (/path/to/projectdirectory/Homo_Sapiens/UCSC/hg19/Sequence/Bowtie2Index/). I would just use the "-x" option.