trim
--aligner adapter
--threads 24

-G file:/nas/longleaf/home/dennis/Reference_Files/Atropos_Adapters/5'_anchored_adapters.fa
-g file:/nas/longleaf/home/dennis/Reference_Files/Atropos_Adapters/5'_anchored_adapters.fa
-A file:/nas/longleaf/home/dennis/Reference_Files/Atropos_Adapters/3'_anchored_adapters.fa
-a file:/nas/longleaf/home/dennis/Reference_Files/Atropos_Adapters/3'_anchored_adapters.fa
-o /pine/scr/d/e/dennis/18001/18001_CTGTAGCC_Trim.R1.fastq.gz
-p /pine/scr/d/e/dennis/18001/18001_CTGTAGCC_Trim.R3.fastq.gz
-pe1 /pine/scr/d/e/dennis/18001/H3LFKBGX5_CTGTAGCC_S6_R1_001.fastq.gz
-pe2 /pine/scr/d/e/dennis/18001/H3LFKBGX5_CTGTAGCC_S6_R3_001.fastq.gz
--op-order GAWCQ
--nextseq-trim 1
--error-rate 0.15
--times 3
--quality-cutoff 20
--stats bot
--read-queue-size 500000
--result-queue-size 100000
--report-file /pine/scr/d/e/dennis/18001/Atropos_18001_CTGTAGCC_Trim_Report.txt