File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/74/3f01cac530cf4357cf32ba82108d0e/.command.log
Size
2.3 KB
Task
DAQ:FASTP (1029_BICJ-T1-TDNA-1_A23MHWWLT4_1;L008)
Attempt

Content

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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/93/efa91fc1793af7e19448772a3cc5c1/output/1029_BICJ-T1-TDNA-1_A23MHWWLT4_1_S22_L008_R1_001.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/93/efa91fc1793af7e19448772a3cc5c1/output/1029_BICJ-T1-TDNA-1_A23MHWWLT4_1_S22_L008_R2_001.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/74/3f01cac530cf4357cf32ba82108d0e/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/74/3f01cac530cf4357cf32ba82108d0e/.command.run
==> 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: 61628472
total bases: 9305899272
Q20 bases: 9095715754(97.7414%)
Q30 bases: 8744862895(93.9712%)
Q40 bases: 8744862895(93.9712%)

Read2 before filtering:
total reads: 61628472
total bases: 9305899272
Q20 bases: 9061395117(97.3726%)
Q30 bases: 8638745785(92.8309%)
Q40 bases: 8638745785(92.8309%)

Read1 after filtering:
total reads: 61166908
total bases: 8436905380
Q20 bases: 8310835487(98.5057%)
Q30 bases: 8031656292(95.1967%)
Q40 bases: 8031656292(95.1967%)

Read2 after filtering:
total reads: 61166908
total bases: 8438089262
Q20 bases: 8279301888(98.1182%)
Q30 bases: 7950976567(94.2272%)
Q40 bases: 7950976567(94.2272%)

Filtering result:
reads passed filter: 122333816
reads failed due to low quality: 906872
reads failed due to too many N: 13838
reads failed due to too short: 2418
reads with adapter trimmed: 43667048
bases trimmed due to adapters: 1602281415

Duplication rate: 11.7393%

Insert size peak (evaluated by paired-end reads): 127

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_L008_R1_001.fastq.gz --in2 1029_BICJ-T1-TDNA-1_A23MHWWLT4_1_S22_L008_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: 701 seconds