I am using GNU parallel on the following shortbred script. The script is supposed to take two input files and output one .tsv file but I am getting both _1.tsv and _2.tsv files and directories as an output. How do I get the output something like :

SRR059331_dir

SRR059331.tsv

SRR059339_dir

SRR059339.tsv

I did bash for loop and it outputs the above expected results but it is very time consuming. How do I convert this bash script into parallel. This is my bash script:

for i in test_files/*_1.fastq.gz; do
    F=`basename $i _1.fastq.gz`;
    mkdir test_out/"$F"_dir;
    python shortbred/shortbred_quantify.py --markers markers.faa --wgs "$F"_1.fastq.gz "$F"_2.fastq.gz --results test_out/"$F".tsv --tmp test_out/"$F"_dir --usearch ./shortbred/usearch;

done

This is my script so far for GNU parallel

#!/bin/bash

#Create a sub-directory for ShortBRED output
mkdir test_out

time parallel -j 10 \
"python shortbred/shortbred_quantify.py \
--markers markers.faa \
--wgs {1} {2} \
--results test_out/{1/.}.tsv \
--tmp test_out/{1/.}_dir \
--usearch shortbred/usearch" ::: test_files/fastq/*_1.fastq.gz :::+ test_files/fastq/*_2.fastq.gz