Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/95/85ba3e8fbc58872619728bf13b74de/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/95/85ba3e8fbc58872619728bf13b74de/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/0661beadb497aec7e239ce346c70c2/output/1029_BICJ-T1-TDNA-1_A23MHWWLT4_1_S22_L004_R2_001.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/0661beadb497aec7e239ce346c70c2/output/1029_BICJ-T1-TDNA-1_A23MHWWLT4_1_S22_L004_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: 63184974
total bases: 9540931074
Q20 bases: 9320709855(97.6918%)
Q30 bases: 8947468981(93.7798%)
Q40 bases: 8947468981(93.7798%)

Read2 before filtering:
total reads: 63184974
total bases: 9540931074
Q20 bases: 9293218581(97.4037%)
Q30 bases: 8866562301(92.9318%)
Q40 bases: 8866562301(92.9318%)

Read1 after filtering:
total reads: 62708308
total bases: 8619096427
Q20 bases: 8486714310(98.4641%)
Q30 bases: 8190223722(95.0242%)
Q40 bases: 8190223722(95.0242%)

Read2 after filtering:
total reads: 62708308
total bases: 8620350686
Q20 bases: 8461129532(98.153%)
Q30 bases: 8132694565(94.343%)
Q40 bases: 8132694565(94.343%)

Filtering result:
reads passed filter: 125416616
reads failed due to low quality: 943010
reads failed due to too many N: 8114
reads failed due to too short: 2208
reads with adapter trimmed: 46265376
bases trimmed due to adapters: 1703460423

Duplication rate: 10.4997%

Insert size peak (evaluated by paired-end reads): 123

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

fastp --in1 1029_BICJ-T1-TDNA-1_A23MHWWLT4_1_S22_L004_R1_001.fastq.gz --in2 1029_BICJ-T1-TDNA-1_A23MHWWLT4_1_S22_L004_R2_001.fastq.gz --out1 1029_BICJ-T1-TDNA-1_A23MHWWLT4_1/1029_BICJ-T1-TDNA-1_A23MHWWLT4_1_R1.fastq.gz --out2 1029_BICJ-T1-TDNA-1_A23MHWWLT4_1/1029_BICJ-T1-TDNA-1_A23MHWWLT4_1_R2.fastq.gz --detect_adapter_for_pe --length_required 15 --json 1029_BICJ-T1-TDNA-1_A23MHWWLT4_1.fastp.json --html 1029_BICJ-T1-TDNA-1_A23MHWWLT4_1.fastp.html --thread 4 
fastp v1.0.1, time used: 328 seconds