Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/61/552ffe6d4da3743650714c6feaf448/output/1029_FRC-T1-TDNA-1_A23MHWWLT4_1_S35_L001_R2_001.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f5/b5cd51e6884e371a9a66959faf26d0/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f5/b5cd51e6884e371a9a66959faf26d0/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/61/552ffe6d4da3743650714c6feaf448/output/1029_FRC-T1-TDNA-1_A23MHWWLT4_1_S35_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: 91486851
total bases: 13814514501
Q20 bases: 13469820836(97.5048%)
Q30 bases: 12837970385(92.931%)
Q40 bases: 12837970385(92.931%)

Read2 before filtering:
total reads: 91486851
total bases: 13814514501
Q20 bases: 13229530854(95.7654%)
Q30 bases: 12234518319(88.5628%)
Q40 bases: 12234518319(88.5628%)

Read1 after filtering:
total reads: 90158880
total bases: 13048170893
Q20 bases: 12790659052(98.0265%)
Q30 bases: 12234947587(93.7675%)
Q40 bases: 12234947587(93.7675%)

Read2 after filtering:
total reads: 90158880
total bases: 13049321973
Q20 bases: 12603434544(96.5831%)
Q30 bases: 11735355623(89.9308%)
Q40 bases: 11735355623(89.9308%)

Filtering result:
reads passed filter: 180317760
reads failed due to low quality: 2633680
reads failed due to too many N: 17872
reads failed due to too short: 4390
reads with adapter trimmed: 30665071
bases trimmed due to adapters: 1134588213

Duplication rate: 14.3692%

Insert size peak (evaluated by paired-end reads): 181

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

fastp --in1 1029_FRC-T1-TDNA-1_A23MHWWLT4_1_S35_L001_R1_001.fastq.gz --in2 1029_FRC-T1-TDNA-1_A23MHWWLT4_1_S35_L001_R2_001.fastq.gz --out1 1029_FRC-T1-TDNA-1_A23MHWWLT4_1/1029_FRC-T1-TDNA-1_A23MHWWLT4_1_R1.fastq.gz --out2 1029_FRC-T1-TDNA-1_A23MHWWLT4_1/1029_FRC-T1-TDNA-1_A23MHWWLT4_1_R2.fastq.gz --detect_adapter_for_pe --length_required 15 --json 1029_FRC-T1-TDNA-1_A23MHWWLT4_1.fastp.json --html 1029_FRC-T1-TDNA-1_A23MHWWLT4_1.fastp.html --thread 4 
fastp v1.0.1, time used: 922 seconds