HISAT2 "error: Encountered internal HISAT2 exception (#1)"

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5.0 years ago

zhu.ge • 0

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

hisat2 hisat • 4.9k views

ADD COMMENT • link updated 3.9 years ago by Rks ▴ 30 • written 5.0 years ago by zhu.ge • 0

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Looks like you have not made the necessary index to use with HISAT2.

ADD REPLY • link 5.0 years ago by GenoMax 141k

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see my reply here: A: HISAT error: Encountered internal HISAT2 exception (#1)

ADD REPLY • link 3.9 years ago by Rks ▴ 30

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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.

ADD REPLY • link 3.9 years ago by ATpoint 82k

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