Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e9/af6afb342ea146b5f21da60283a8c6/output/1029_FRC-T1-TDNA-1_A23MHWWLT4_1_S35_L006_R2_001.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c6/a3ab1ee7206d3d4df8e47df5a1958e/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c6/a3ab1ee7206d3d4df8e47df5a1958e/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e9/af6afb342ea146b5f21da60283a8c6/output/1029_FRC-T1-TDNA-1_A23MHWWLT4_1_S35_L006_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: 87047260
total bases: 13144136260
Q20 bases: 12774016153(97.1841%)
Q30 bases: 12095119549(92.0191%)
Q40 bases: 12095119549(92.0191%)

Read2 before filtering:
total reads: 87047260
total bases: 13144136260
Q20 bases: 12537273526(95.383%)
Q30 bases: 11516379547(87.6161%)
Q40 bases: 11516379547(87.6161%)

Read1 after filtering:
total reads: 85730999
total bases: 12374199087
Q20 bases: 12094592497(97.7404%)
Q30 bases: 11494902375(92.8941%)
Q40 bases: 11494902375(92.8941%)

Read2 after filtering:
total reads: 85730999
total bases: 12375396009
Q20 bases: 11911544999(96.2518%)
Q30 bases: 11021088887(89.0565%)
Q40 bases: 11021088887(89.0565%)

Filtering result:
reads passed filter: 171461998
reads failed due to low quality: 2616822
reads failed due to too many N: 11378
reads failed due to too short: 4322
reads with adapter trimmed: 30838047
bases trimmed due to adapters: 1145387402

Duplication rate: 11.7669%

Insert size peak (evaluated by paired-end reads): 170

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_L006_R1_001.fastq.gz --in2 1029_FRC-T1-TDNA-1_A23MHWWLT4_1_S35_L006_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: 853 seconds