Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/6b64bd665d47775a20aebddbfadc64/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/93/efa91fc1793af7e19448772a3cc5c1/output/1029_FRC-T1-TDNA-1_A23MHWWLT4_1_S35_L008_R1_001.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/6b64bd665d47775a20aebddbfadc64/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/93/efa91fc1793af7e19448772a3cc5c1/output/1029_FRC-T1-TDNA-1_A23MHWWLT4_1_S35_L008_R2_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: 92377718
total bases: 13949035418
Q20 bases: 13591757371(97.4387%)
Q30 bases: 12938808726(92.7577%)
Q40 bases: 12938808726(92.7577%)

Read2 before filtering:
total reads: 92377718
total bases: 13949035418
Q20 bases: 13348590270(95.6954%)
Q30 bases: 12323587432(88.3472%)
Q40 bases: 12323587432(88.3472%)

Read1 after filtering:
total reads: 91059362
total bases: 13180644603
Q20 bases: 12911418789(97.9574%)
Q30 bases: 12334839687(93.583%)
Q40 bases: 12334839687(93.583%)

Read2 after filtering:
total reads: 91059362
total bases: 13181795388
Q20 bases: 12719962740(96.4964%)
Q30 bases: 11821932307(89.6838%)
Q40 bases: 11821932307(89.6838%)

Filtering result:
reads passed filter: 182118724
reads failed due to low quality: 2614632
reads failed due to too many N: 17760
reads failed due to too short: 4320
reads with adapter trimmed: 30826035
bases trimmed due to adapters: 1141620756

Duplication rate: 14.3737%

Insert size peak (evaluated by paired-end reads): 187

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_L008_R1_001.fastq.gz --in2 1029_FRC-T1-TDNA-1_A23MHWWLT4_1_S35_L008_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: 1027 seconds