gravatar for Hannah Dixon

2 hours ago by


I am trying to run Hisat2 on FASTA files. Hisat has always worked for me and I've only just encountered this issue now. It seems that Hisat can't read the index files, however I'm pretty sure its not due to typos. I have redownloaded the index files (Drosophila) and also redownloaded hisat2.

I'm running Hisat2-2.1.0 on my MacOS Mojave 10.14.6. This is my command:


hisat2 --dta -x /Users/Desktop/test/reference/bdpg6_tran/genome_tran -1 GCCTTAAC_V300033208_05_R1.fq.gz -2 GCCTTAAC_V300033208_05_R2.fq.gz -S /Users/Desktop/test/data/3_aligned/RNA_5.sam

The error:

Could not locate a HISAT2 index corresponding to basename " /Users/Desktop/test/reference/bdgp6_tran/genome_tran"
Error: Encountered internal HISAT2 exception (#1)
Command: /Users/Apps/hisat2-2.1.0/hisat2-align-s --wrapper basic-0 --dta -x /Users/Desktop/test/reference/bdgp6_tran/genome_tran -S /Users/Desktop/test/data/3_aligned/RNA_5.sam -1 /tmp/10184.inpipe1 -2 /tmp/10184.inpipe2 
(ERR): hisat2-align exited with value 1

Any help is greatly appreciated,


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