Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e9/af6afb342ea146b5f21da60283a8c6/output/1029_HTI-T1-TDNA-1_A23MHWWLT4_1_S23_L006_R1_001.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/e2d626c3620e4b1288a2853cd8f9a8/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/e2d626c3620e4b1288a2853cd8f9a8/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e9/af6afb342ea146b5f21da60283a8c6/output/1029_HTI-T1-TDNA-1_A23MHWWLT4_1_S23_L006_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: 89401632
total bases: 13499646432
Q20 bases: 13156271411(97.4564%)
Q30 bases: 12498934235(92.5871%)
Q40 bases: 12498934235(92.5871%)

Read2 before filtering:
total reads: 89401632
total bases: 13499646432
Q20 bases: 13001555299(96.3103%)
Q30 bases: 12138573510(89.9177%)
Q40 bases: 12138573510(89.9177%)

Read1 after filtering:
total reads: 88452221
total bases: 12643561502
Q20 bases: 12377317223(97.8942%)
Q30 bases: 11802247705(93.3459%)
Q40 bases: 11802247705(93.3459%)

Read2 after filtering:
total reads: 88452221
total bases: 12644989313
Q20 bases: 12266955110(97.0104%)
Q30 bases: 11522272291(91.1212%)
Q40 bases: 11522272291(91.1212%)

Filtering result:
reads passed filter: 176904442
reads failed due to low quality: 1883376
reads failed due to too many N: 13486
reads failed due to too short: 1960
reads with adapter trimmed: 41391696
bases trimmed due to adapters: 1428984202

Duplication rate: 10.0122%

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_L006_R1_001.fastq.gz --in2 1029_HTI-T1-TDNA-1_A23MHWWLT4_1_S23_L006_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: 574 seconds