Is Ubuntu different from Linux on a Mac? Sorry if this is a basic question...I am new to this. I am trying to run a bash script that creates a .sh script out of some FASTQ files. This works in the terminal on a Mac OS. I am trying to run it on my Windows laptop and it ignores my escaping of #s and just states that several commands are not found. I have tried using dos2unix and double checked with cat -A file.sh but it hasn't helped.

The code I am trying to run takes all fastq files in a folder and creates a .sh file for SLURM job submissions using their file name (needed for my university's computer cluster, and I need to make 100+ job scripts). So the Mac OS version is as follows:

for FILE in *fastq;    #change file type when needed (e.g., fasta, fastq, fastq.gz)

do echo -e 

#!/bin/bash 

n#SBATCH --partition=nonpre  # Partition (job queue) 

n#SBATCH --requeue                 # Return job to the queue if preempted 

n#SBATCH --job-name=samples      # Assign a short name to your job 

n#SBATCH --nodes=1                 # Number of nodes you require 

n#SBATCH --ntasks=1                # Total # of tasks across all nodes 

n#SBATCH --cpus-per-task=64        # Cores per task (>1 if multithread tasks) 

n#SBATCH --mem=180000              # Real memory (RAM) required (MB) 

n#SBATCH --time=72:00:00           # Total run time limit (HH:MM:SS) 

n#SBATCH --output=slurm.%N.${FILE}.out  # STDOUT output file 

n#SBATCH --error=slurm.%N.${FILE}.err   # STDERR output file (optional) 

n 

n#ADD WHATEVER CODE YOU WANT HERE AS YOUR SLURM JOB SUBMISSION 

n 

nsacct --format=JobID,JobName,NTasks,NNodes,NCPUS,MaxRSS,AveRSS,AveCPU,Elapsed,ExitCode -j $SLURM_JOBID #this will get job run stats from SLURM; use these to help designate memory of future submissions 

> ${FILE}.sh; 

done

When running this on Windows, I get:

Slurm_Generator.sh: line 13: #!/bin/bash: No such file or directory

Slurm_Generator.sh: line 14: 

#SBATCH: command not found

Slurm_Generator.sh: line 16: 

#SBATCH: command not found

Slurm_Generator.sh: line 18: 

#SBATCH: command not found

Slurm_Generator.sh: line 20: 

#SBATCH: command not found

Slurm_Generator.sh: line 22: 

#SBATCH: command not found

Slurm_Generator.sh: line 24: 

#SBATCH: command not found

Slurm_Generator.sh: line 26: 

#SBATCH: command not found

Slurm_Generator.sh: line 28: 

#SBATCH: command not found

Slurm_Generator.sh: line 30: 

#SBATCH: command not found

Slurm_Generator.sh: line 32: 

#SBATCH: command not found

Slurm_Generator.sh: line 35: 

: command not found

Slurm_Generator.sh: line 36: 

#ADD: command not found

Slurm_Generator.sh: line 39: 

: command not found

Slurm_Generator.sh: line 40: 

sacct: command not found

Any help would be appreciated, and some explanation on what the difference is between Ubuntu on Windows vs. the Terminal on Mac. I've tried researching this but I keep finding suggested code with no explanation or it isn't particularly my issue. Thank you!

Edit: I tried running chmod +x script.sh and I will get the above errors. Am I running 'echo' wrong? Even running:
'for FILE in *fastq;
do
echo -e
hello;
done'
says Command 'hello' not found

Edit: Running 'bash file.sh' yields the following:
bash file.sh yields the following (for each of the 5 .fastq files in my directoy):

Slurm_Generator.sh: line 8: #!/bin/bash: No such file or directory

Slurm_Generator.sh: line 9: 

#SBATCH: command not found

Slurm_Generator.sh: line 11: 

#SBATCH: command not found

Slurm_Generator.sh: line 13: 

#SBATCH: command not found

Slurm_Generator.sh: line 15: 

#SBATCH: command not found

Slurm_Generator.sh: line 17: 

#SBATCH: command not found

Slurm_Generator.sh: line 19: 

#SBATCH: command not found

Slurm_Generator.sh: line 21: 

#SBATCH: command not found

Slurm_Generator.sh: line 23: 

#SBATCH: command not found

Slurm_Generator.sh: line 25: 

#SBATCH: command not found

Slurm_Generator.sh: line 27: 

#SBATCH: command not found

Slurm_Generator.sh: line 30: 

: command not found

Slurm_Generator.sh: line 31: 

#ADD: command not found

Slurm_Generator.sh: line 34: 

: command not found

Slurm_Generator.sh: line 35: 

sacct: command not found

If I run cat -A file.sh I see a $ at the end of each line. Even if I get rid of these, I get the same result as above.
Running ls -al script.sh gived: -rwxrwxrwx 1 cerberus cerberus 1209 Jun 16 00:17 Slurm_Generator.sh

Edit:
I changed my script to:

#! /bin/bash

for FILE in *fastq;    #change file type when needed (e.g., fasta, fastq, fastq.gz)

do echo -e 

"

#!/bin/bash

#SBATCH --partition=nonpre  # Partition (job queue)

#SBATCH --requeue              # Return job to the queue if preempted

#SBATCH --job-name=samples     # Assign a short name to your job

#SBATCH --nodes=1              # Number of nodes you require

#SBATCH --ntasks=1             # Total # of tasks across all nodes

#SBATCH --cpus-per-task=64 # Cores per task (>1 if multithread tasks)

#SBATCH --mem=180000           # Real memory (RAM) required (MB)

#SBATCH --time=72:00:00        # Total run time limit (HH:MM:SS)

#SBATCH --output=slurm.%N.${FILE}.out # STDOUT output file

#SBATCH --error=slurm.%N.${FILE}.err  # STDERR output file (optional)



#ADD WHATEVER CODE YOU WANT HERE AS YOUR SLURM JOB SUBMISSION 



sacct --format=JobID,JobName,NTasks,NNodes,NCPUS,MaxRSS,AveRSS,AveCPU,Elapsed,ExitCode -j $SLURM_JOBID #this will get job run stats from SLURM; use these to help designate memory of future subm$" 

> ${FILE}.sh;

done

My new output is the following (which is much better):

#!/bin/bash

#SBATCH --partition=nonpre  # Partition (job queue)

#SBATCH --requeue           # Return job to the queue if preempted

#SBATCH --job-name=samples      # Assign a short name to your job

#SBATCH --nodes=1                 # Number of nodes you require

#SBATCH --ntasks=1                # Total # of tasks across all nodes

#SBATCH --cpus-per-task=64 # Cores per task (>1 if multithread tasks)

#SBATCH --mem=180000              # Real memory (RAM) required (MB)

#SBATCH --time=72:00:00           # Total run time limit (HH:MM:SS)

#SBATCH --output=slurm.%N.Sample1.fastq.out  # STDOUT output file

#SBATCH --error=slurm.%N.Sample1.fastq.er  # STDERR output file (optional)





#ADD WHATEVER CODE YOU WANT HERE AS YOUR SLURM JOB SUBMISSION



sacct --format=JobID,JobName,NTasks,NNodes,NCPUS,MaxRSS,AveRSS,AveCPU,Elapsed,ExitCode -j $SLURM_JOBID #this will get job run stats from SLURM; use these to help designate memory of future submissions

The only issue I am running into is that while it prints this out for each .fastq file, which is what I want, the resulting .sh files that it writes out are blank. So it is not recognizing the > ${File}.sh part of the script.

Thank you everyone!