Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/93/efa91fc1793af7e19448772a3cc5c1/output/1047_JG-T1-TDNA-1_A23MHWWLT4_1_S42_L008_R1_001.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/54/93c552ba4a292c63ff0f794aa3aa8d/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/54/93c552ba4a292c63ff0f794aa3aa8d/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/93/efa91fc1793af7e19448772a3cc5c1/output/1047_JG-T1-TDNA-1_A23MHWWLT4_1_S42_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: 196632414
total bases: 29691494514
Q20 bases: 29011855821(97.711%)
Q30 bases: 27800762508(93.6321%)
Q40 bases: 27800762508(93.6321%)

Read2 before filtering:
total reads: 196632414
total bases: 29691494514
Q20 bases: 28786682704(96.9526%)
Q30 bases: 27188746360(91.5708%)
Q40 bases: 27188746360(91.5708%)

Read1 after filtering:
total reads: 194745687
total bases: 27869875405
Q20 bases: 27385288475(98.2613%)
Q30 bases: 26329449908(94.4728%)
Q40 bases: 26329449908(94.4728%)

Read2 after filtering:
total reads: 194745687
total bases: 27873178508
Q20 bases: 27197089014(97.5744%)
Q30 bases: 25825595914(92.6539%)
Q40 bases: 25825595914(92.6539%)

Filtering result:
reads passed filter: 389491374
reads failed due to low quality: 3723600
reads failed due to too many N: 42884
reads failed due to too short: 6970
reads with adapter trimmed: 88686196
bases trimmed due to adapters: 3080976173

Duplication rate: 16.3908%

Insert size peak (evaluated by paired-end reads): 168

JSON report: 1047_JG-T1-TDNA-1_A23MHWWLT4_1.fastp.json
HTML report: 1047_JG-T1-TDNA-1_A23MHWWLT4_1.fastp.html

fastp --in1 1047_JG-T1-TDNA-1_A23MHWWLT4_1_S42_L008_R1_001.fastq.gz --in2 1047_JG-T1-TDNA-1_A23MHWWLT4_1_S42_L008_R2_001.fastq.gz --out1 1047_JG-T1-TDNA-1_A23MHWWLT4_1/1047_JG-T1-TDNA-1_A23MHWWLT4_1_R1.fastq.gz --out2 1047_JG-T1-TDNA-1_A23MHWWLT4_1/1047_JG-T1-TDNA-1_A23MHWWLT4_1_R2.fastq.gz --detect_adapter_for_pe --length_required 15 --json 1047_JG-T1-TDNA-1_A23MHWWLT4_1.fastp.json --html 1047_JG-T1-TDNA-1_A23MHWWLT4_1.fastp.html --thread 4 --split_by_lines 400000000 
fastp v1.0.1, time used: 2053 seconds