Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/61e2f4975020dd38e7235792445d2c/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/61e2f4975020dd38e7235792445d2c/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/928d434150a22d0ca11301a5843191/output/1029_T05-T1-TDNA-1_A23MHWWLT4_1_S19_L003_R2_001.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/928d434150a22d0ca11301a5843191/output/1029_T05-T1-TDNA-1_A23MHWWLT4_1_S19_L003_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: 97970389
total bases: 14793528739
Q20 bases: 14405209849(97.3751%)
Q30 bases: 13683803912(92.4986%)
Q40 bases: 13683803912(92.4986%)

Read2 before filtering:
total reads: 97970389
total bases: 14793528739
Q20 bases: 14109327080(95.375%)
Q30 bases: 12956355611(87.5812%)
Q40 bases: 12956355611(87.5812%)

Read1 after filtering:
total reads: 96248381
total bases: 13995076007
Q20 bases: 13701133621(97.8997%)
Q30 bases: 13066086392(93.362%)
Q40 bases: 13066086392(93.362%)

Read2 after filtering:
total reads: 96248381
total bases: 13996312750
Q20 bases: 13472120105(96.2548%)
Q30 bases: 12459353331(89.0188%)
Q40 bases: 12459353331(89.0188%)

Filtering result:
reads passed filter: 192496762
reads failed due to low quality: 3427596
reads failed due to too many N: 11768
reads failed due to too short: 4652
reads with adapter trimmed: 29398402
bases trimmed due to adapters: 1079734786

Duplication rate: 12.8088%

Insert size peak (evaluated by paired-end reads): 207

JSON report: 1029_T05-T1-TDNA-1_A23MHWWLT4_1.fastp.json
HTML report: 1029_T05-T1-TDNA-1_A23MHWWLT4_1.fastp.html

fastp --in1 1029_T05-T1-TDNA-1_A23MHWWLT4_1_S19_L003_R1_001.fastq.gz --in2 1029_T05-T1-TDNA-1_A23MHWWLT4_1_S19_L003_R2_001.fastq.gz --out1 1029_T05-T1-TDNA-1_A23MHWWLT4_1/1029_T05-T1-TDNA-1_A23MHWWLT4_1_R1.fastq.gz --out2 1029_T05-T1-TDNA-1_A23MHWWLT4_1/1029_T05-T1-TDNA-1_A23MHWWLT4_1_R2.fastq.gz --detect_adapter_for_pe --length_required 15 --json 1029_T05-T1-TDNA-1_A23MHWWLT4_1.fastp.json --html 1029_T05-T1-TDNA-1_A23MHWWLT4_1.fastp.html --thread 4 
fastp v1.0.1, time used: 1194 seconds