Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/aa/70c8ff25a6a0090ee0bfc2284e33fa/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/aa/70c8ff25a6a0090ee0bfc2284e33fa/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/87/4d24a8043550ff7295820d491d8a43/output/1029_FRC-T1-TDNA-1_A23MHWWLT4_1_S35_L007_R1_001.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/87/4d24a8043550ff7295820d491d8a43/output/1029_FRC-T1-TDNA-1_A23MHWWLT4_1_S35_L007_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: 89567841
total bases: 13524743991
Q20 bases: 13162653880(97.3228%)
Q30 bases: 12501522704(92.4344%)
Q40 bases: 12501522704(92.4344%)

Read2 before filtering:
total reads: 89567841
total bases: 13524743991
Q20 bases: 12914911597(95.491%)
Q30 bases: 11891709426(87.9256%)
Q40 bases: 11891709426(87.9256%)

Read1 after filtering:
total reads: 88205898
total bases: 12753479986
Q20 bases: 12480914327(97.8628%)
Q30 bases: 11898185830(93.2936%)
Q40 bases: 11898185830(93.2936%)

Read2 after filtering:
total reads: 88205898
total bases: 12754669661
Q20 bases: 12290922613(96.3641%)
Q30 bases: 11399638932(89.3762%)
Q40 bases: 11399638932(89.3762%)

Filtering result:
reads passed filter: 176411796
reads failed due to low quality: 2706052
reads failed due to too many N: 13566
reads failed due to too short: 4268
reads with adapter trimmed: 30634050
bases trimmed due to adapters: 1134183067

Duplication rate: 12.8031%

Insert size peak (evaluated by paired-end reads): 177

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_L007_R1_001.fastq.gz --in2 1029_FRC-T1-TDNA-1_A23MHWWLT4_1_S35_L007_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: 992 seconds