Could not locate a HISAT2 index corresponding to basename. Error: Encountered internal HISAT2 exception (#1)

Hi,

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:

pwd
/Users/Desktop/test/data/1_raw

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,

Hannah

assembly hisat2 rna-seq alignment

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updated 3.2 years ago by Ram

• written 6.3 years ago by Hannah Dixon •

Output of ls /Users/Desktop/test/reference/bdgp6_tran/?

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written 6.3 years ago by ATpoint

Output of: ls /Users/Desktop/test/reference/bdgp6_tran/

genome_tran.1.ht2 genome_tran.3.ht2 genome_tran.5.ht2 genome_tran.7.ht2 make_bdgp6_tran.sh genome_tran.2.ht2 genome_tran.4.ht2 genome_tran.6.ht2 genome_tran.8.ht2

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written 6.3 years ago by Hannah Dixon •

There is a discrepancy:

bdpg6_tran => in the hisat2 command you post
bdgp6_tran => in the "could not locate..." error

gp and pg

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written 6.3 years ago by ATpoint

You're right, apologies. Unfortunately I still have the same error with the corrected "bdgp6_tran".

hisat2 --dta -x /Users/Desktop/test/reference/bdgp6_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.sam

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.sam -1 /tmp/11321.inpipe1 -2 /tmp/11321.inpipe2 
(ERR): hisat2-align exited with value 1

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updated 6.3 years ago by GenoMax

• written 6.3 years ago by Hannah Dixon •

1 answer

This must be a typo or so. If you go into the folder with the index and then type pwd, then copy/paste this into the hist command and add /genome_tran, still not working?

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written 6.3 years ago by ATpoint

I copied the printed wd and it worked! Thanks so much for your time!

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written 6.3 years ago by Hannah Dixon •

Glad to hear it works now. It is recommended that you always copy/paste paths and names instead of typing them by hand to avoid exactly these kinds of errors. I learned this the hard way myself ;-)

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written 6.3 years ago by ATpoint