Facing issues in making a bash script work

Question

[adnan.haider.ra]

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

Here is the link for RTG Program: https://github.com/RealTimeGenomics/rtg-core

[Michael]

run your script with the following line:

#!/bin/bash
set -eux

That way you can easily see what's going wrong, always use set -eu

Answer 1

[Tej Sowpati]

As far as I can see, there are several syntax errors in your script. Also, I assume you are trying to replace _1.fastq with _2.fastq to get your right fastq file? The syntax you used simply appends _2.fastq, does not substitute. Instead, a simpler although longer approach is as follows.

Step 1: Store your base fastq file names in a file

$ ls /data/reads/NA19240/*_1.fastq | perl -pe 's/_1.fastq//' > file_list

Step 2: Use the following script instead

#!/bin/bash                                                                                                                                                                                                  
for lane_id in `cat file_list`; do
    left_fastq=${lane_id}_1.fastq
    right_fastq=${lane_id}_2.fastq
    rtg format -f fastq -q sanger -o $lane_id -l $left_fastq -r $right_fastq --sam-rg "Blah Blah"
done

What you are essentially doing is having a list of base names, from which you will create your left and right files to run the command. Let me know if this works.

Cheers,

TEJ