Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dd/16a48d02202311b18b052643e10898/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dd/16a48d02202311b18b052643e10898/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/93/efa91fc1793af7e19448772a3cc5c1/output/1029_HTI-T1-TDNA-1_A23MHWWLT4_1_S23_L008_R1_001.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/93/efa91fc1793af7e19448772a3cc5c1/output/1029_HTI-T1-TDNA-1_A23MHWWLT4_1_S23_L008_R2_001.fastq.gz
==> STAGING COMPLETE (4 inputs)

Detecting adapter sequence for read1...
>Illumina TruSeq Adapter Read 1
AGATCGGAAGAGCACACGTCTGAACTCCAGTCA

Detecting adapter sequence for read2...
>Illumina TruSeq Adapter Read 2
AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT

Read1 before filtering:
total reads: 92508830
total bases: 13968833330
Q20 bases: 13642147840(97.6613%)
Q30 bases: 13022289652(93.2239%)
Q40 bases: 13022289652(93.2239%)

Read2 before filtering:
total reads: 92508830
total bases: 13968833330
Q20 bases: 13489076904(96.5655%)
Q30 bases: 12645586137(90.5271%)
Q40 bases: 12645586137(90.5271%)

Read1 after filtering:
total reads: 91578977
total bases: 13124358116
Q20 bases: 12872708594(98.0826%)
Q30 bases: 12330831769(93.9538%)
Q40 bases: 12330831769(93.9538%)

Read2 after filtering:
total reads: 91578977
total bases: 13125751776
Q20 bases: 12759777288(97.2118%)
Q30 bases: 12029226544(91.646%)
Q40 bases: 12029226544(91.646%)

Filtering result:
reads passed filter: 183157954
reads failed due to low quality: 1838290
reads failed due to too many N: 19516
reads failed due to too short: 1900
reads with adapter trimmed: 40992609
bases trimmed due to adapters: 1411585084

Duplication rate: 12.0214%

Insert size peak (evaluated by paired-end reads): 152

JSON report: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.fastp.json
HTML report: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.fastp.html

fastp --in1 1029_HTI-T1-TDNA-1_A23MHWWLT4_1_S23_L008_R1_001.fastq.gz --in2 1029_HTI-T1-TDNA-1_A23MHWWLT4_1_S23_L008_R2_001.fastq.gz --out1 1029_HTI-T1-TDNA-1_A23MHWWLT4_1/1029_HTI-T1-TDNA-1_A23MHWWLT4_1_R1.fastq.gz --out2 1029_HTI-T1-TDNA-1_A23MHWWLT4_1/1029_HTI-T1-TDNA-1_A23MHWWLT4_1_R2.fastq.gz --detect_adapter_for_pe --length_required 15 --json 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.fastp.json --html 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.fastp.html --thread 4 
fastp v1.0.1, time used: 1020 seconds