ERR): "fastq file.fastq" does not exist. Exiting now ...

[big-boo1]

Hi all,

I am running into this issue when trying to use hisat2, and was hoping someone could point me in the right direction. My code looks like

$ hisat2 -p 8 --dta -q -x SRR8846455_2.fastq -1 SRR8846456_2.fastq -s HighvsLowN1.sam

I am trying to use these 2 fastq files, and output a .sam file. However, whenever I try to run this, I get the error

(ERR): "SRR8846455_2.fastq" does not exist
Exiting now ...

I have tried adding the direct path to the files (/Users/me/fastq), copying/pasting or typing the names, running this inside and outside of my environment, and inside and outside jupyter notebook (I am using the terminal inside jupyter notebook, but it hasn't worked in the normal terminal as well).

When I enter $ ls, the files in question show up, so I know where they are. They should be recognized by my commands but I just can't get them to be used in hisat2.

Do you all have any tips?
Thank you