First time trying out HISAT2 and I'm having a problem here, even with the pre-made indices for GRCH38.

    $ hisat2 -x /share/projects/RNASeq/data/reference/GRCh38/grch38_tran -1 /home/echang/PANCANCER-030817-JE3-35880845/KTP-10-43736695/KTP-10_S3_L001_R1_001.fastq.gz -2 /home/echang/PANCANCER-030817-JE3-35880845/KTP-10-43736695/KTP-10_S3_L001_R2_001.fastq.gz -S tmp.sam

Error follows 

    Could not locate a HISAT2 index corresponding to basename "/share/projects/RNASeq/data/reference/GRCh38/grch38_tran"
    Error: Encountered internal HISAT2 exception (#1)
    Command: /home/echang/software/hisat2-2.1.0/hisat2-align-s --wrapper basic-0 -S tmp.sam -1 /tmp/31969.inpipe1 -2 /tmp/31969.inpipe2 /share/projects/RNASeq/data/reference/GRCh38/grch38_tran
    (ERR): hisat2-align exited with value 1

The contents of the `grch38_tran`

    $ ls /share/projects/RNASeq/data/reference/GRCh38/grch38_tran
    genome_tran.1.ht2  genome_tran.3.ht2  genome_tran.5.ht2  genome_tran.7.ht2  make_grch38_tran.sh
    genome_tran.2.ht2  genome_tran.4.ht2  genome_tran.6.ht2  genome_tran.8.ht2

I thought perhaps the `genome_tran.*.ht2` needed to change to `grch38_tran.*.ht2`, but it still does not work after renaming. I've since untarred the original file again without change. Was there a step I missed? Where can I find `HISTAT2_INDEXES`?

    -x <hisat2-idx>
    The basename of the index for the reference genome. The basename is the name of any of the index files up to but not including the final .1.ht2 / etc. hisat2 looks for the specified index first in the current directory, then in the directory specified in the HISAT2_INDEXES environment variable.

Your genome index path in hisat2 should be,


    -x /share/projects/RNASeq/data/reference/GRCh38/grch38_tran/genome_tran