Could not locate a HISAT2 index

[hasanalanya]

Hi there,

I am trying to run Hisat2 on FASTA files and, I've encountered an issue. It seems that HISAT2 can't read the index files, however, I'm pretty sure it's not due to typos. I have re-downloaded the index files (h.sapiens) as well.

This is my command:

hisat2 -p 32 -x .../results/hisat2_alignment/grch38 -1 Read1_1_val_1.fq -2 Read1_2_val_2.fq -S .../hisat2_alignment/outputs/Read1_out.sam

(ERR): ".../results/hisat2_alignment/grch38" does not exist
Exiting now ...

However, when I list the documents in grch38 dir, I am able to see the indexes, as follows:

ls ../results/hisat2_alignment/grch38
genome.1.ht2 genome.2.ht2 genome.3.ht2 genome.4.ht2 genome.5.ht2 genome.6.ht2 genome.7.ht2 genome.8.ht2 make_grch38.sh

I would appreciate if you could help me about this issue.

All the best, Hasan

[imzhangyun]

Hello @hasanalanya

Please try hisat2 -p 32 -x ../results/hisat2_alignment/grch38/genome -1 Read1_1_val_1.fq -2 Read1_2_val_2.fq -S .../hisat2_alignment/outputs/Read1_out.sam.

Also, please check the output path -S. You shouldn't use ... in the path.

Best, Leo

[hasanalanya]

Hi @imzhangyun

Many thanks for your prompt response. Yeah, I will try it! Meanwhile, I don't use ... in the path, just didn't want to put the whole path in here.

Best, Hasan