Hisat2 error not recognising files Trimmed files

Question

[Mickey]

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

[Pierre Lindenbaum]

the path to the fastq file os wrong.

what is the output of

ls *q.gz

[Mickey]

    (osxonly) backup@Air-de-Backup grch38 % ls *q.gz
 1_R1_001.trimmed.fastq.gz   1_R2_001.trimmed.fastq.gz

Hi, looks like its there but for some reason not recognised...doesnt make sense to me

[ATpoint]

Try: hisat2 -x genome -1 $(ls *q.gz | grep 'R1_001') -2 -$(ls *q.gz | grep 'R2_001') -S out.sam

My suspicion is that there is maybe a whitespace before the initial "1"?