HISAT2 "error: Encountered internal HISAT2 exception (#1)"
Having some issue run hisat2. Keep getting error message.
hisat2 -x ../yeast/yeast -U mini.fq -S mini.sam
Could not locate a HISAT2 index corresponding to basename "../yeast/yeast" Error: Encountered internal HISAT2 exception (#1) Command: /usr/local/bin/hisat2-align-s --wrapper basic-0 -x ../yeast/yeast -S mini.sam -U mini.fq (ERR): hisat2-align exited with value 1
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Looks like you have not made the necessary index to use with HISAT2.
see my reply here: A: HISAT error: Encountered internal HISAT2 exception (#1)
It is appreciated that you contribute but please be smart about it. This thread is about missing index files, not memory so your answer does not really applies here.