File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/e9e10e5c0ca304cb9c0ec4e866d0bb/.command.log
Size
2.3 KB
Task
DAQ:FASTP (1029_BCAN-T1-TDNA-1_A23MHWWLT4_1;L003)
Attempt

Content

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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/928d434150a22d0ca11301a5843191/output/1029_BCAN-T1-TDNA-1_A23MHWWLT4_1_S29_L003_R2_001.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/e9e10e5c0ca304cb9c0ec4e866d0bb/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/e9e10e5c0ca304cb9c0ec4e866d0bb/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/928d434150a22d0ca11301a5843191/output/1029_BCAN-T1-TDNA-1_A23MHWWLT4_1_S29_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: 33257711
total bases: 5021914361
Q20 bases: 4779253152(95.168%)
Q30 bases: 4533830263(90.2809%)
Q40 bases: 4533830263(90.2809%)

Read2 before filtering:
total reads: 33257711
total bases: 5021914361
Q20 bases: 4834555925(96.2692%)
Q30 bases: 4572948786(91.0599%)
Q40 bases: 4572948786(91.0599%)

Read1 after filtering:
total reads: 32939392
total bases: 3797499563
Q20 bases: 3739617371(98.4758%)
Q30 bases: 3616728921(95.2397%)
Q40 bases: 3616728921(95.2397%)

Read2 after filtering:
total reads: 32939392
total bases: 3799912781
Q20 bases: 3737787478(98.3651%)
Q30 bases: 3617156612(95.1905%)
Q40 bases: 3617156612(95.1905%)

Filtering result:
reads passed filter: 65878784
reads failed due to low quality: 628550
reads failed due to too many N: 4622
reads failed due to too short: 3466
reads with adapter trimmed: 49804960
bases trimmed due to adapters: 2359066321

Duplication rate: 6.15303%

Insert size peak (evaluated by paired-end reads): 96

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_L003_R1_001.fastq.gz --in2 1029_BCAN-T1-TDNA-1_A23MHWWLT4_1_S29_L003_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: 313 seconds