Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/93/efa91fc1793af7e19448772a3cc5c1/output/1029_IWL-T1-TDNA-1_A23MHWWLT4_1_S7_L008_R2_001.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2a/c79e82133b77ec887328fa40f7dab1/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2a/c79e82133b77ec887328fa40f7dab1/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/93/efa91fc1793af7e19448772a3cc5c1/output/1029_IWL-T1-TDNA-1_A23MHWWLT4_1_S7_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: 43501067
total bases: 6568661117
Q20 bases: 6371062284(96.9918%)
Q30 bases: 6104291489(92.9305%)
Q40 bases: 6104291489(92.9305%)

Read2 before filtering:
total reads: 43501067
total bases: 6568661117
Q20 bases: 6391090035(97.2967%)
Q30 bases: 6089915554(92.7117%)
Q40 bases: 6089915554(92.7117%)

Read1 after filtering:
total reads: 43181713
total bases: 5641410894
Q20 bases: 5553436349(98.4406%)
Q30 bases: 5361478830(95.0379%)
Q40 bases: 5361478830(95.0379%)

Read2 after filtering:
total reads: 43181713
total bases: 5642774044
Q20 bases: 5548337542(98.3264%)
Q30 bases: 5347596330(94.7689%)
Q40 bases: 5347596330(94.7689%)

Filtering result:
reads passed filter: 86363426
reads failed due to low quality: 626998
reads failed due to too many N: 9202
reads failed due to too short: 2508
reads with adapter trimmed: 44260434
bases trimmed due to adapters: 1762334029

Duplication rate: 9.20392%

Insert size peak (evaluated by paired-end reads): 111

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

fastp --in1 1029_IWL-T1-TDNA-1_A23MHWWLT4_1_S7_L008_R1_001.fastq.gz --in2 1029_IWL-T1-TDNA-1_A23MHWWLT4_1_S7_L008_R2_001.fastq.gz --out1 1029_IWL-T1-TDNA-1_A23MHWWLT4_1/1029_IWL-T1-TDNA-1_A23MHWWLT4_1_R1.fastq.gz --out2 1029_IWL-T1-TDNA-1_A23MHWWLT4_1/1029_IWL-T1-TDNA-1_A23MHWWLT4_1_R2.fastq.gz --detect_adapter_for_pe --length_required 15 --json 1029_IWL-T1-TDNA-1_A23MHWWLT4_1.fastp.json --html 1029_IWL-T1-TDNA-1_A23MHWWLT4_1.fastp.html --thread 4 
fastp v1.0.1, time used: 427 seconds