Hi I am using Salmon quantitation for multiple fastq paired files using following code

salmon_index="human_salmon_index"
fastq_dir="fastq/"
for dir in "${fastq_dir}"/SRR*
do
r1_file=$(find "$dir" -name "*_1.fastq")
r2_file=$(find "$dir" -name "*_2.fastq")
samp=$(basename "$dir")
echo "Processing sample ${samp}"
salmon quant -i "$salmon_index" -l A -1 "$r1_file" -2 "$r2_file" -p 10 -o "salmon_out/${samp}_quant"
done

and getting this error after it iterates over all files and start initial processing steps.

Processing sample SRR27756943_2.fastq Version Info: This is the most recent version of salmon.

salmon (selective-alignment-based) v1.10.0

Exception : [ The following errors were detected with the read files

======================================================

ERROR: file [] does not appear to exist!

Any solution?

Hi I am using Salmon quantitation for multiple fastq paired files using following code

salmon_index="human_salmon_index"
fastq_dir="fastq/"
for dir in "${fastq_dir}"/SRR*
do
r1_file=$(find "$dir" -name "*_1.fastq")
r2_file=$(find "$dir" -name "*_2.fastq")
samp=$(basename "$dir")
echo "Processing sample ${samp}"
salmon quant -i "$salmon_index" -l A -1 "$r1_file" -2 "$r2_file" -p 10 -o "salmon_out/${samp}_quant"
done

and getting this error after it iterates over all files and start initial processing steps.

Processing sample SRR27756943_2.fastq
Version Info: This is the most recent version of salmon.
### salmon (selective-alignment-based) v1.10.0

Exception : [
The following errors were detected with the read files

======================================================

ERROR: file [] does not appear to exist!

Any solution?