Hi I am a new user of parallel. I am trying to use it instead of loops to do fastq file trimming using Agilent Agent trimmer. When I run it one by one without using parallel, output is one R1 and one R3 file for each sample as expected. But using the code below produced 4 R1 and 4 R3 files for each sample. Could someone tell me what I have done wrong please?

Input:

cat metatry.txt | parallel java -Xmx5G -jar $Trimmer -fq1 {}R1_001.fastq.gz -fq2 {}R3_001.fastq.gz -xt -out_loc /Trimmed/

Output:

trim -fq1 153_D1_S11_R1_001.fastq.gz -fq2 153_D1_S11_R3_001.fastq.gz -xt -out_loc /Trimmed/

Trimmed file created:
    /Trimmed/153_D1_S11_R1_001.1607137111246_Cut_0.fastq.gz
    /Trimmed/153_D1_S11_R3_001.1607137111246_Cut_0.fastq.gz
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cd /Trimmed/ 

153_D1_S9_R1_001.1607136132795_Cut_0.fastq.gz
153_D1_S9_R1_001.1607136580643_Cut_0.fastq.gz
153_D1_S9_R1_001.1607136902485_Cut_0.fastq.gz
153_D1_S9_R1_001.1607137111246_Cut_0.fastq.gz
153_D1_S9_R3_001.1607136132795_Cut_0.fastq.gz
153_D1_S9_R3_001.1607136580643_Cut_0.fastq.gz
153_D1_S9_R3_001.1607136902485_Cut_0.fastq.gz
153_D1_S9_R3_001.1607137111246_Cut_0.fastq.gz