Hi im struggling to find the problem with aligning some paired end reads. Essentially, after i trimmed the reads using the trimmomatic to remove adapters i get this error from Hisat2.

 hisat2 -x genome -1 1_R1_001.trimmed.fastq.gz -2 1_R2_001.trimmed.fastq.gz -S output.sam 
Warning: [Errno 2] No such file or directory: '1_R1_001.trimmed.fastq.gz'
(ERR): Read file '1_R1_001.trimmed.fastq.gz' doesn't exist
Exiting now ...

I tried running the same reads with Hisat2 before i trimmed with trimmomatic and it actually works fine, so its something about the trimmed files it does not like i guess, as i have checked the PATH etc and all that seems fine.

Any help welcome, Thanks