Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6a/e52fa7318db2210fc2ec6dc95bb994/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6a/e52fa7318db2210fc2ec6dc95bb994/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/0661beadb497aec7e239ce346c70c2/output/1136_4XR-T1-TDNA-1_A23MHWWLT4_1_S47_L004_R2_001.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/0661beadb497aec7e239ce346c70c2/output/1136_4XR-T1-TDNA-1_A23MHWWLT4_1_S47_L004_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: 75750432
total bases: 11438315232
Q20 bases: 11141921453(97.4088%)
Q30 bases: 10558808944(92.3109%)
Q40 bases: 10558808944(92.3109%)

Read2 before filtering:
total reads: 75750432
total bases: 11438315232
Q20 bases: 10913672145(95.4133%)
Q30 bases: 10031058450(87.697%)
Q40 bases: 10031058450(87.697%)

Read1 after filtering:
total reads: 74436421
total bases: 10891247591
Q20 bases: 10647085869(97.7582%)
Q30 bases: 10125945664(92.9732%)
Q40 bases: 10125945664(92.9732%)

Read2 after filtering:
total reads: 74436421
total bases: 10891927426
Q20 bases: 10487271752(96.2848%)
Q30 bases: 9708599101(89.1357%)
Q40 bases: 9708599101(89.1357%)

Filtering result:
reads passed filter: 148872842
reads failed due to low quality: 2617668
reads failed due to too many N: 8584
reads failed due to too short: 1770
reads with adapter trimmed: 20125500
bases trimmed due to adapters: 699084037

Duplication rate: 11.4888%

Insert size peak (evaluated by paired-end reads): 204

JSON report: 1136_4XR-T1-TDNA-1_A23MHWWLT4_1.fastp.json
HTML report: 1136_4XR-T1-TDNA-1_A23MHWWLT4_1.fastp.html

fastp --in1 1136_4XR-T1-TDNA-1_A23MHWWLT4_1_S47_L004_R1_001.fastq.gz --in2 1136_4XR-T1-TDNA-1_A23MHWWLT4_1_S47_L004_R2_001.fastq.gz --out1 1136_4XR-T1-TDNA-1_A23MHWWLT4_1/1136_4XR-T1-TDNA-1_A23MHWWLT4_1_R1.fastq.gz --out2 1136_4XR-T1-TDNA-1_A23MHWWLT4_1/1136_4XR-T1-TDNA-1_A23MHWWLT4_1_R2.fastq.gz --detect_adapter_for_pe --length_required 15 --json 1136_4XR-T1-TDNA-1_A23MHWWLT4_1.fastp.json --html 1136_4XR-T1-TDNA-1_A23MHWWLT4_1.fastp.html --thread 4 
fastp v1.0.1, time used: 515 seconds