Facing issues in making a bash script work - linux

Question

I'm new to Bash scripting. My script intended role is to access a provided path and then apply some software (RTG - Real time Genomics) commands on the data provided in that path. However, when i try to execute the bash from CLI, it gives me following error
ERROR:There were invalid input file paths
The path I have provided in the script is accurate. That is, In the original directory, where the program 'RTG' resides, I have made folders accordingly like /data/reads/NA19240 and placed both *_1.fastq and *_2.fastq files inside NA19240.
Here is the script:
#!/bin/bash
for left_fastq in /data/reads/NA19240/*_1.fastq; do
right_fastq=${left_fastq/_1.fastq/_2.fastq}
lane_id=$(basename ${left_fastq/_1.fastq})
rtg format -f fastq -q sanger -o ${lane_id} -l ${left_fastq} -r ${right_fastq} --sam-rg "#RG\tID:${lane_id}\tSM:NA19240\tPL:ILLUMINA"
done
I have tried many workarounds but still not being able to bypass this error. I will be really grateful if you guys can help me fixing this problem. Thanks
After adding set -aux in bash script for debugging purpose, I'm getting following output now
adnan#adnan-VirtualBox[Linux] ./format.sh
+ for left_fastq in '/data/reads/NA19240/*_1.fastq'
+ right_fastq='/data/reads/NA19240/*_2.fastq'
++ basename '/data/reads/NA19240/*'
+ lane_id='*'
+ ./rtg format -f fastq -q sanger -o '*' -l '/data/reads/NA19240/*_1.fastq' -r '/data/reads/NA19240/*_2.fastq' --sam-rg '#RG\tID:*\tSM:NA19240\tPL:ILLUMINA'
Error: File not found: "/data/reads/NA19240/*_1.fastq"
Error: File not found: "/data/reads/NA19240/*_2.fastq"
Error: There were 2 invalid input file paths

Answer 1

You need to set the nullglob option in the script, like so:
shopt -s nullglob
By default, non-matching globs are expanded to themselves. The output you got by setting set -aux indicates that the file glob /data/reads/NA19240/*_1.fastq is getting interpreted literally. The only way this would happen is if there were no files found, and nullglob was disabled.

Answer 2

In the original directory, where the program 'RTG' resides, I have
made folders accordingly like /data/reads/NA19240 and placed both
*_1.fastq and *_2.fastq files inside NA19240.
So you say, your data folders are in the original directory (whatever that may be), but in the script you wrongly specify them to be in the root directory (by the leading /).
Since you start the script in the original directory, just drop the leading / and use a relative path:
for left_fastq in data/reads/NA19240/*_1.fastq