Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/61/552ffe6d4da3743650714c6feaf448/output/1029_BICJ-T1-TDNA-1_A23MHWWLT4_1_S22_L001_R2_001.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/ece903b533b8d22cb85187a550da2b/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/ece903b533b8d22cb85187a550da2b/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/61/552ffe6d4da3743650714c6feaf448/output/1029_BICJ-T1-TDNA-1_A23MHWWLT4_1_S22_L001_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: 60408424
total bases: 9121672024
Q20 bases: 8919918237(97.7882%)
Q30 bases: 8584284896(94.1087%)
Q40 bases: 8584284896(94.1087%)

Read2 before filtering:
total reads: 60408424
total bases: 9121672024
Q20 bases: 8885376653(97.4095%)
Q30 bases: 8480292115(92.9686%)
Q40 bases: 8480292115(92.9686%)

Read1 after filtering:
total reads: 59948735
total bases: 8265044138
Q20 bases: 8145663430(98.5556%)
Q30 bases: 7880115948(95.3427%)
Q40 bases: 7880115948(95.3427%)

Read2 after filtering:
total reads: 59948735
total bases: 8266233925
Q20 bases: 8114637464(98.1661%)
Q30 bases: 7802538688(94.3905%)
Q40 bases: 7802538688(94.3905%)

Filtering result:
reads passed filter: 119897470
reads failed due to low quality: 902122
reads failed due to too many N: 15024
reads failed due to too short: 2232
reads with adapter trimmed: 43007580
bases trimmed due to adapters: 1578023404

Duplication rate: 11.5217%

Insert size peak (evaluated by paired-end reads): 126

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_L001_R1_001.fastq.gz --in2 1029_BICJ-T1-TDNA-1_A23MHWWLT4_1_S22_L001_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: 506 seconds