I am using kneaddata v0.12.0 within a conda environment.
I am attempting to run kneaddata on paired-end reads. However, the output files are only for Read1. I am wondering whether kneaddata is not correctly identifying the paired read files.
kneaddata --input1 SRR689_R1.fastq --input2 SRR689_R2.fastq -db /Volumes/drive/hg_bowtie --output kneaddata_output/SRR689 --trimmomatic /Users/user/opt/anaconda3/envs/knead/share/trimmomatic-0.39-2 --sequencer-source NexteraPE