I'm trying to run hisat2 on a fastq file following the given syntax but it is giving me errors:
$ hisat2 -x S_lycopersicum_chromosomes.3.00_ch04.fa -U SRR404331_ch4.fastq -S test.sam
Could not locate a HISAT2 index corresponding to basename "S_lycopersicum_chromosomes.3.00_ch04.fa" Error: Encountered internal HISAT2 exception (#1) Command: /usr/local/bin/hisat2-align-s --wrapper basic-0 -x S_lycopersicum_chromosomes.3.00_ch04.fasta -S test.sam -U SRR404331_ch4.fastq (ERR): hisat2-align exited with value 1
Even tho the files are present in the same directory I'm running the terminal from. I am a newbie so please explain what is wrong here.
Also upon running other .fastq files from the same directory some of them gives me errors of "could not open read file "file.fastq" for reading : skipping. Does it has something to do with my fastq files?