Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/61/552ffe6d4da3743650714c6feaf448/output/1029_I9B-T1-TDNA-1_A23MHWWLT4_1_S27_L001_R2_001.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/78/c076f788b4554e07b671883128cc9e/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/78/c076f788b4554e07b671883128cc9e/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/61/552ffe6d4da3743650714c6feaf448/output/1029_I9B-T1-TDNA-1_A23MHWWLT4_1_S27_L001_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: 99691423
total bases: 15053404873
Q20 bases: 14648772926(97.312%)
Q30 bases: 13902593894(92.3551%)
Q40 bases: 13902593894(92.3551%)

Read2 before filtering:
total reads: 99691423
total bases: 15053404873
Q20 bases: 14348342835(95.3163%)
Q30 bases: 13159294395(87.4174%)
Q40 bases: 13159294395(87.4174%)

Read1 after filtering:
total reads: 97954377
total bases: 14258209949
Q20 bases: 13944914364(97.8027%)
Q30 bases: 13285004821(93.1744%)
Q40 bases: 13285004821(93.1744%)

Read2 after filtering:
total reads: 97954377
total bases: 14259451435
Q20 bases: 13719501483(96.2134%)
Q30 bases: 12679873257(88.9226%)
Q40 bases: 12679873257(88.9226%)

Filtering result:
reads passed filter: 195908754
reads failed due to low quality: 3449658
reads failed due to too many N: 20566
reads failed due to too short: 3868
reads with adapter trimmed: 29604085
bases trimmed due to adapters: 1068821298

Duplication rate: 12.9154%

Insert size peak (evaluated by paired-end reads): 185

JSON report: 1029_I9B-T1-TDNA-1_A23MHWWLT4_1.fastp.json
HTML report: 1029_I9B-T1-TDNA-1_A23MHWWLT4_1.fastp.html

fastp --in1 1029_I9B-T1-TDNA-1_A23MHWWLT4_1_S27_L001_R1_001.fastq.gz --in2 1029_I9B-T1-TDNA-1_A23MHWWLT4_1_S27_L001_R2_001.fastq.gz --out1 1029_I9B-T1-TDNA-1_A23MHWWLT4_1/1029_I9B-T1-TDNA-1_A23MHWWLT4_1_R1.fastq.gz --out2 1029_I9B-T1-TDNA-1_A23MHWWLT4_1/1029_I9B-T1-TDNA-1_A23MHWWLT4_1_R2.fastq.gz --detect_adapter_for_pe --length_required 15 --json 1029_I9B-T1-TDNA-1_A23MHWWLT4_1.fastp.json --html 1029_I9B-T1-TDNA-1_A23MHWWLT4_1.fastp.html --thread 4 
fastp v1.0.1, time used: 1009 seconds