Hisat2 Script Help

Question

[smithkthedale]

Hi,

So, I gave an Arabidopsis cd and inside of it are the files below (download.20220709.154352.zip, hisat.sh, RAW_DATA) The download file is my genome that I got from phytozome:

curl --cookie jgi_session=/api/sessions/e320285f0e13e8973f95c6f5d034bc64 --output download.20220709.160042.zip -d "{\"ids\":{\"Phytozome-322\":[\"569335620d87851ee9726aca\"]}}" -H "Content-Type: application/json" https://files.jgi.doe.gov/filedownload/

I downloaded that file into the ArabiodpsisRNA folder. So my terminal looks like this:

[dalesmith08 ArabidopsisRNA] 
download.20220709.154352.zip hisat.sh RAW_DATA 

To run hisat2 my script is:

for i in $(<samples.txt)
do
hisat2 -p 10 -x ./ArabidospsisRNA/download.20220709.154352.zip -1 ${i}R1.fastq.bz2 -2 ${i}R2.fastq.bz2 -S ${i}sam
done

When I run sbatch hisat2.sh I am getting this error: /var/slurmd/spool/slurmd/job17536270/slurm_script: line 16: samples.txt: No such file or directory

Can someone please fix my script so it works?

[ATpoint]

samples.txt: No such file or directory

The file does not exist in the current directory. Beyond that, unless I miss something, I think you have to unzip that genome folder and provide the path to the basename of the index see manual.

[smithkthedale]

If you look at what is in my linux (shows above) you would see that it is existing in my cd...that's the problem.

[Mensur Dlakic]

If you look at what is in my linux (shows above) you would see that it is existing in my cd...that's the problem.

I already told you in one of earlier posts to learn how to look at what is in front of you, and to follow advice of those who are trying to help you. ATpoint already repeated to you what a computer error message was: No such file or directory. Computers don't play pranks, so when you get a message that there is no file present, that is exactly what it means. But let's use our eyes instead as you suggested. These are the contents of your directory.

download.20220709.154352.zip hisat.sh RAW_DATA

Where exactly do you see samples.txt in that list?