Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/93/efa91fc1793af7e19448772a3cc5c1/output/1029_I9B-T1-TDNA-1_A23MHWWLT4_1_S27_L008_R1_001.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/57/d72cf70925d4756eccbd3b630b07f5/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/57/d72cf70925d4756eccbd3b630b07f5/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/93/efa91fc1793af7e19448772a3cc5c1/output/1029_I9B-T1-TDNA-1_A23MHWWLT4_1_S27_L008_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: 100655283
total bases: 15198947733
Q20 bases: 14780111227(97.2443%)
Q30 bases: 14010276974(92.1793%)
Q40 bases: 14010276974(92.1793%)

Read2 before filtering:
total reads: 100655283
total bases: 15198947733
Q20 bases: 14473480245(95.2269%)
Q30 bases: 13246904155(87.1567%)
Q40 bases: 13246904155(87.1567%)

Read1 after filtering:
total reads: 98923193
total bases: 14401473355
Q20 bases: 14074644976(97.7306%)
Q30 bases: 13391298813(92.9856%)
Q40 bases: 13391298813(92.9856%)

Read2 after filtering:
total reads: 98923193
total bases: 14402715339
Q20 bases: 13842226927(96.1085%)
Q30 bases: 12765437340(88.6322%)
Q40 bases: 12765437340(88.6322%)

Filtering result:
reads passed filter: 197846386
reads failed due to low quality: 3439962
reads failed due to too many N: 20352
reads failed due to too short: 3866
reads with adapter trimmed: 29761156
bases trimmed due to adapters: 1074880832

Duplication rate: 12.9133%

Insert size peak (evaluated by paired-end reads): 181

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_L008_R1_001.fastq.gz --in2 1029_I9B-T1-TDNA-1_A23MHWWLT4_1_S27_L008_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: 1142 seconds