Keep casava option into fastqc after filter of host reads ?
fastqc -o "fastqc_alignment_filter_${replicateId}_logs" --casava --nogroup ${preprocessed_reads_R1} ${preprocessed_reads_R2}
fastqc -o "fastqc_alignment_filter_${replicateId}_logs" --casava --nogroup ${preprocessed_reads_R1} ${preprocessed_reads_R2}