File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/62/acc023318c3d85c0c95e6ad46fbf1d/.command.log
Size
2.3 KB
Task
DAQ:FASTP (1029_BCAN-T1-TDNA-1_A23MHWWLT4_1;L004)
Attempt

Content

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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/62/acc023318c3d85c0c95e6ad46fbf1d/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/62/acc023318c3d85c0c95e6ad46fbf1d/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/0661beadb497aec7e239ce346c70c2/output/1029_BCAN-T1-TDNA-1_A23MHWWLT4_1_S29_L004_R1_001.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/0661beadb497aec7e239ce346c70c2/output/1029_BCAN-T1-TDNA-1_A23MHWWLT4_1_S29_L004_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: 34145060
total bases: 5155904060
Q20 bases: 4900683534(95.0499%)
Q30 bases: 4637991572(89.955%)
Q40 bases: 4637991572(89.955%)

Read2 before filtering:
total reads: 34145060
total bases: 5155904060
Q20 bases: 4970147967(96.3972%)
Q30 bases: 4707509014(91.3033%)
Q40 bases: 4707509014(91.3033%)

Read1 after filtering:
total reads: 33822316
total bases: 3893368354
Q20 bases: 3830282301(98.3797%)
Q30 bases: 3696020296(94.9312%)
Q40 bases: 3696020296(94.9312%)

Read2 after filtering:
total reads: 33822316
total bases: 3895806569
Q20 bases: 3833792308(98.4082%)
Q30 bases: 3713158086(95.3117%)
Q40 bases: 3713158086(95.3117%)

Filtering result:
reads passed filter: 67644632
reads failed due to low quality: 638266
reads failed due to too many N: 3704
reads failed due to too short: 3518
reads with adapter trimmed: 51294646
bases trimmed due to adapters: 2434000952

Duplication rate: 6.09718%

Insert size peak (evaluated by paired-end reads): 94

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

fastp --in1 1029_BCAN-T1-TDNA-1_A23MHWWLT4_1_S29_L004_R1_001.fastq.gz --in2 1029_BCAN-T1-TDNA-1_A23MHWWLT4_1_S29_L004_R2_001.fastq.gz --out1 1029_BCAN-T1-TDNA-1_A23MHWWLT4_1/1029_BCAN-T1-TDNA-1_A23MHWWLT4_1_R1.fastq.gz --out2 1029_BCAN-T1-TDNA-1_A23MHWWLT4_1/1029_BCAN-T1-TDNA-1_A23MHWWLT4_1_R2.fastq.gz --detect_adapter_for_pe --length_required 15 --json 1029_BCAN-T1-TDNA-1_A23MHWWLT4_1.fastp.json --html 1029_BCAN-T1-TDNA-1_A23MHWWLT4_1.fastp.html --thread 4 
fastp v1.0.1, time used: 147 seconds