HISAT2 error message :Could not locate a HISAT2 index corresponding to basename "/mnt/c/mkr-index2/mm10_adera/genome"

Question

[Michel Edwar]

I am trying to align mouse genome mm10 using HISAT2 command

hisat2 -x /mnt/c/mkr-index2/mm10_adera/genome  -1 SRR11209326_1.fastq.gz -2 SRR11209326_2.fastq.gz 

I get the error message

HISAT2 error message :Could not locate a HISAT2 index corresponding to basename "/mnt/c/mkr-index2/mm10_adera/genome

the genome folder contains the following files

genome.1.ht2
genome.2.ht2
genome.3.ht2
genome.4.ht2
genome.5.ht2
genome.6.ht2
genome.7.ht2
 genome.8.ht2

[ATpoint]

What is the output of ls /mnt/c/mkr-index2/mm10_adera/?

[Michel Edwar]

genome make_mm10.sh mm10_genome.tar

Answer 1

[ATpoint]

Look, the principle is simple.

Say you have a folder called indexfiles, and in that folder you have genome.1.ht2 and so on, then it is

-x /path/to/indexfiles/genome

It is now on you to give the correct path to the folder and the respective basename on your machine as I cannot see your screen and therefore not determine how you've organized files in folders.