WARNING: cut_by_quality5 is deprecated, please use cut_front instead.
Detecting adapter sequence for read1...
>TruSeq2_PE_r
AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAG

Read1 before filtering:
total reads: 2720361
total bases: 391731984
Q20 bases: 376130311(96.0173%)
Q30 bases: 351602807(89.756%)

Read1 after filtering:
total reads: 2695060
total bases: 387115244
Q20 bases: 373234613(96.4143%)
Q30 bases: 349379499(90.2521%)

Filtering result:
reads passed filter: 2695060
reads failed due to low quality: 5533
reads failed due to too many N: 768
reads failed due to too short: 19000
reads with adapter trimmed: 43153
bases trimmed due to adapters: 3408907

Duplication rate (may be overestimated since this is SE data): 32.1713%

JSON report: CypressIslandWA_FG149.json
HTML report: CypressIslandWA_FG149.html

fastp -i CypressIslandWA_FG149.F.fq.gz -o CypressIslandWA_FG149.R1.fq.gz --cut_by_quality5 20 --cut_by_quality3 20 --cut_window_size 5 --cut_mean_quality 15 -q 15 -u 50 -j CypressIslandWA_FG149.json -h CypressIslandWA_FG149.html 
fastp v0.20.0, time used: 29 seconds