Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/58/4acdfb65f2fe4c6a0402360504c045/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/928d434150a22d0ca11301a5843191/output/1047_JG-T1-TDNA-1_A23MHWWLT4_1_S42_L003_R2_001.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/58/4acdfb65f2fe4c6a0402360504c045/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/928d434150a22d0ca11301a5843191/output/1047_JG-T1-TDNA-1_A23MHWWLT4_1_S42_L003_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: 194975992
total bases: 29441374792
Q20 bases: 28789059595(97.7844%)
Q30 bases: 27622033334(93.8205%)
Q40 bases: 27622033334(93.8205%)

Read2 before filtering:
total reads: 194975992
total bases: 29441374792
Q20 bases: 28551787433(96.9784%)
Q30 bases: 26995677042(91.693%)
Q40 bases: 26995677042(91.693%)

Read1 after filtering:
total reads: 193081886
total bases: 27585040503
Q20 bases: 27129277904(98.3478%)
Q30 bases: 26119193022(94.6861%)
Q40 bases: 26119193022(94.6861%)

Read2 after filtering:
total reads: 193081886
total bases: 27588448213
Q20 bases: 26934088001(97.6281%)
Q30 bases: 25608836295(92.8245%)
Q40 bases: 25608836295(92.8245%)

Filtering result:
reads passed filter: 386163772
reads failed due to low quality: 3753144
reads failed due to too many N: 28106
reads failed due to too short: 6962
reads with adapter trimmed: 90569248
bases trimmed due to adapters: 3148312830

Duplication rate: 15.5522%

Insert size peak (evaluated by paired-end reads): 162

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_L003_R1_001.fastq.gz --in2 1047_JG-T1-TDNA-1_A23MHWWLT4_1_S42_L003_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: 2027 seconds