bash script not a valid identifier

Question

[j_weld]

I am trying to run bash script, but it gives this error ( `$fastq': not a valid identifier).

[GenoMax]

Do you get valid names if you just run this: ls *_R1.fastq.gz | sed 's/_R1.fastq.gz//'

[j_weld]

yes, when I am running ls *_R1.fastq.gz | sed 's/_R1.fastq.gz//' in my fastq folder it gives me names

[hugo.avila]

Hi ! try running your script with "bash -x yr_script.sh", this will expand variables and print commands line by line.

Also, add a '\' :

 kraken2 --db $database \
         --threads 8 --memory-mapping \
         --use-names --confidence 0.1 \
         --report taxonomy_reads/${fastq}_kraken2.tax \
         --paired ${fastq}_R1.fastq.gz ${fastq}_R2.fastq.gz \
         --output taxonomy_reads/${fastq}_kraken2.txt

[j_weld]

Okay, I tried, but it also gives the same line error `$fastq': not a valid identifier

Answer 1

[Ram]

It should be for fastq in, not for $fastq in. Variables don't get the $ when they're being declared/initialized/assigned to.

[j_weld]

I knew that the other way around. But in that case it gives this '*_R1.fastq.gz': 'No such file or directory' , but I tried this on my fastq files and it worked.

[Ram]

Do not delete posts when they've been addressed. If one or more solutions worked, accept them using the green check mark.

Answer 2

[hugo.avila]

#!/bin/bash 
database="kraken2_database"
fastq="fastq_dir" # consider change this variable name, you repeat it in the loop variable (sorry if this is what you wanted to do.)
for fastq in $(ls *_R1.fastq.gz | sed 's/_R1.fastq.gz//') # <---- the problem was the "$fastq"
do
    # also, the '\' are needed
     kraken2 --db $database \
             --threads 8 --memory-mapping \
             --use-names --confidence 0.1 \
             --report taxonomy_reads/${fastq}_kraken2.tax \
             --paired ${fastq}_R1.fastq.gz ${fastq}_R2.fastq.gz \
             --output taxonomy_reads/${fastq}_kraken2.txt
done