Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/93/efa91fc1793af7e19448772a3cc5c1/output/1029_T05-T1-TDNA-1_A23MHWWLT4_1_S19_L008_R2_001.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e0/42e8dd11302f9d1504b2177a3a31a3/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e0/42e8dd11302f9d1504b2177a3a31a3/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/93/efa91fc1793af7e19448772a3cc5c1/output/1029_T05-T1-TDNA-1_A23MHWWLT4_1_S19_L008_R1_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: 99957010
total bases: 15093508510
Q20 bases: 14687591445(97.3107%)
Q30 bases: 13938919542(92.3504%)
Q40 bases: 13938919542(92.3504%)

Read2 before filtering:
total reads: 99957010
total bases: 15093508510
Q20 bases: 14394947668(95.3718%)
Q30 bases: 13208231683(87.5094%)
Q40 bases: 13208231683(87.5094%)

Read1 after filtering:
total reads: 98257839
total bases: 14311590384
Q20 bases: 13999494445(97.8193%)
Q30 bases: 13336226027(93.1848%)
Q40 bases: 13336226027(93.1848%)

Read2 after filtering:
total reads: 98257839
total bases: 14312768443
Q20 bases: 13769857339(96.2068%)
Q30 bases: 12720403203(88.8745%)
Q40 bases: 12720403203(88.8745%)

Filtering result:
reads passed filter: 196515678
reads failed due to low quality: 3375222
reads failed due to too many N: 18594
reads failed due to too short: 4526
reads with adapter trimmed: 28710448
bases trimmed due to adapters: 1053530440

Duplication rate: 13.9533%

Insert size peak (evaluated by paired-end reads): 199

JSON report: 1029_T05-T1-TDNA-1_A23MHWWLT4_1.fastp.json
HTML report: 1029_T05-T1-TDNA-1_A23MHWWLT4_1.fastp.html

fastp --in1 1029_T05-T1-TDNA-1_A23MHWWLT4_1_S19_L008_R1_001.fastq.gz --in2 1029_T05-T1-TDNA-1_A23MHWWLT4_1_S19_L008_R2_001.fastq.gz --out1 1029_T05-T1-TDNA-1_A23MHWWLT4_1/1029_T05-T1-TDNA-1_A23MHWWLT4_1_R1.fastq.gz --out2 1029_T05-T1-TDNA-1_A23MHWWLT4_1/1029_T05-T1-TDNA-1_A23MHWWLT4_1_R2.fastq.gz --detect_adapter_for_pe --length_required 15 --json 1029_T05-T1-TDNA-1_A23MHWWLT4_1.fastp.json --html 1029_T05-T1-TDNA-1_A23MHWWLT4_1.fastp.html --thread 4 
fastp v1.0.1, time used: 1204 seconds