File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/ba77a7b57f238eb481a1d342d9f770/.command.log
Size
2.3 KB
Task
DAQ:FASTP (1029_BICJ-T1-TDNA-1_A23MHWWLT4_1;L003)
Attempt

Content

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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/ba77a7b57f238eb481a1d342d9f770/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/928d434150a22d0ca11301a5843191/output/1029_BICJ-T1-TDNA-1_A23MHWWLT4_1_S22_L003_R2_001.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/ba77a7b57f238eb481a1d342d9f770/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/928d434150a22d0ca11301a5843191/output/1029_BICJ-T1-TDNA-1_A23MHWWLT4_1_S22_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: 61492850
total bases: 9285420350
Q20 bases: 9081747034(97.8065%)
Q30 bases: 8739866096(94.1246%)
Q40 bases: 8739866096(94.1246%)

Read2 before filtering:
total reads: 61492850
total bases: 9285420350
Q20 bases: 9039164933(97.3479%)
Q30 bases: 8621865149(92.8538%)
Q40 bases: 8621865149(92.8538%)

Read1 after filtering:
total reads: 61024183
total bases: 8400989833
Q20 bases: 8281093864(98.5728%)
Q30 bases: 8011554617(95.3644%)
Q40 bases: 8011554617(95.3644%)

Read2 after filtering:
total reads: 61024183
total bases: 8402241652
Q20 bases: 8246782927(98.1498%)
Q30 bases: 7926913678(94.3428%)
Q40 bases: 7926913678(94.3428%)

Filtering result:
reads passed filter: 122048366
reads failed due to low quality: 925104
reads failed due to too many N: 9890
reads failed due to too short: 2340
reads with adapter trimmed: 44411543
bases trimmed due to adapters: 1631024634

Duplication rate: 10.8628%

Insert size peak (evaluated by paired-end reads): 132

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

fastp --in1 1029_BICJ-T1-TDNA-1_A23MHWWLT4_1_S22_L003_R1_001.fastq.gz --in2 1029_BICJ-T1-TDNA-1_A23MHWWLT4_1_S22_L003_R2_001.fastq.gz --out1 1029_BICJ-T1-TDNA-1_A23MHWWLT4_1/1029_BICJ-T1-TDNA-1_A23MHWWLT4_1_R1.fastq.gz --out2 1029_BICJ-T1-TDNA-1_A23MHWWLT4_1/1029_BICJ-T1-TDNA-1_A23MHWWLT4_1_R2.fastq.gz --detect_adapter_for_pe --length_required 15 --json 1029_BICJ-T1-TDNA-1_A23MHWWLT4_1.fastp.json --html 1029_BICJ-T1-TDNA-1_A23MHWWLT4_1.fastp.html --thread 4 
fastp v1.0.1, time used: 721 seconds