I'm running hisat2 (version 2.0.1-beta) on a mac (OS X Yosemite, 10.10.5). It is working well on SRA data that I've downloaded and converted to fastqs. I would like to download data directly from SRA using the --sra-acc option. Here is what I'm running:
time hisat2 -x /Volumes/LaCie/hg38.ref/INDEX --sra-acc SRR3192527 -S /Volumes/LaCie/bams/SRR3192527.sam. However, when I try I get the following error: hisat2-align-s: unrecognized option `--sra-acc'. I've installed the ncbi-ngs-toolkit. Any idea what might be going wrong?