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PD_tissue_polyA_fastp.log
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nohup: ignoring input
-- Attaching packages --------------------------------------- tidyverse 1.2.1 --
v ggplot2 3.1.1 v purrr 0.3.2
v tibble 2.1.1 v dplyr 0.8.1
v tidyr 0.8.3 v stringr 1.4.0
v readr 1.3.1 v forcats 0.4.0
-- Conflicts ------------------------------------------ tidyverse_conflicts() --
x dplyr::filter() masks stats::filter()
x dplyr::lag() masks stats::lag()
[1] "/data/RNAseq_PD/tissue_polyA_samples/QC/fastp directory already exists.."
[1] "/data/RNAseq_PD/tissue_polyA_samples/QC/multiqc directory already exists.."
Warning message:
`data_frame()` is deprecated, use `tibble()`.
This warning is displayed once per session.
[1] "2019-07-01 09:15:33 - Performing QC and trimming for samples: PD332, PD341, PD732, PDC05, PD566, PD366, PD413, PDC22, PD706, PD415, PD416, PDC34, PD563, PD523, PDC87, PD163, PD678, PD747, PD115, PD666, PDC91, PD294, PD531, PD683, Undetermined"
[1] "2019-07-01 09:15:33 - QC and Trimming: PD332"
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: 161440293
total bases: 16144029300
Q20 bases: 15848144623(98.1672%)
Q30 bases: 15335828041(94.9938%)
Read2 before filtering:
total reads: 161440293
total bases: 16144029300
Q20 bases: 15665624807(97.0366%)
Q30 bases: 14918521488(92.4089%)
Read1 after filtering:
total reads: 159970576
total bases: 15782860659
Q20 bases: 15533301519(98.4188%)
Q30 bases: 15045156252(95.3259%)
Read2 aftering filtering:
total reads: 159970576
total bases: 15784082782
Q20 bases: 15393730332(97.5269%)
Q30 bases: 14682386338(93.0202%)
Filtering result:
reads passed filter: 319941152
reads failed due to low quality: 2695372
reads failed due to too many N: 8904
reads failed due to too short: 235158
reads with adapter trimmed: 32383947
bases trimmed due to adapters: 431774625
reads corrected by overlap analysis: 9207202
bases corrected by overlap analysis: 17913442
Duplication rate: 56.3233%
Insert size peak (evaluated by paired-end reads): 119
JSON report: /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD332_fastp.json
HTML report: /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD332_fastp.html
fastp --in1 /data/RNAseq_PD/tissue_polyA_samples/raw_data/NM3327_PD332_A2B1_GM-T_S1_R1_001.fastq.gz --out1 /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/NM3327_PD332_A2B1_GM-T_S1_R1_001_QC.fastq.gz --in2 /data/RNAseq_PD/tissue_polyA_samples/raw_data/NM3327_PD332_A2B1_GM-T_S1_R3_001.fastq.gz --out2 /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/NM3327_PD332_A2B1_GM-T_S1_R3_001_QC.fastq.gz --detect_adapter_for_pe --qualified_quality_phred 15 --unqualified_percent_limit 40 --n_base_limit 5 --length_required 36 --correction --overlap_len_require 30 --overlap_diff_limit 5 --overrepresentation_analysis --overrepresentation_sampling 20 --html /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD332_fastp.html --json /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD332_fastp.json --report_title PD332 --thread 16
fastp v0.20.0, time used: 1737 seconds
[1] "2019-07-01 09:44:30 - QC and Trimming: PD341"
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: 193260831
total bases: 19326083100
Q20 bases: 19035392445(98.4959%)
Q30 bases: 18475185715(95.5972%)
Read2 before filtering:
total reads: 193260831
total bases: 19326083100
Q20 bases: 18897948630(97.7847%)
Q30 bases: 18157201308(93.9518%)
Read1 after filtering:
total reads: 191978162
total bases: 18871268387
Q20 bases: 18614761270(98.6408%)
Q30 bases: 18076135134(95.7865%)
Read2 aftering filtering:
total reads: 191978162
total bases: 18872258944
Q20 bases: 18520212386(98.1346%)
Q30 bases: 17813382108(94.3892%)
Filtering result:
reads passed filter: 383956324
reads failed due to low quality: 2239254
reads failed due to too many N: 10326
reads failed due to too short: 315758
reads with adapter trimmed: 49167273
bases trimmed due to adapters: 658136941
reads corrected by overlap analysis: 8784378
bases corrected by overlap analysis: 15437046
Duplication rate: 32.8419%
Insert size peak (evaluated by paired-end reads): 116
JSON report: /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD341_fastp.json
HTML report: /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD341_fastp.html
fastp --in1 /data/RNAseq_PD/tissue_polyA_samples/raw_data/NM3328_PD341_A2B2_GM-T_S2_R1_001.fastq.gz --out1 /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/NM3328_PD341_A2B2_GM-T_S2_R1_001_QC.fastq.gz --in2 /data/RNAseq_PD/tissue_polyA_samples/raw_data/NM3328_PD341_A2B2_GM-T_S2_R3_001.fastq.gz --out2 /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/NM3328_PD341_A2B2_GM-T_S2_R3_001_QC.fastq.gz --detect_adapter_for_pe --qualified_quality_phred 15 --unqualified_percent_limit 40 --n_base_limit 5 --length_required 36 --correction --overlap_len_require 30 --overlap_diff_limit 5 --overrepresentation_analysis --overrepresentation_sampling 20 --html /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD341_fastp.html --json /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD341_fastp.json --report_title PD341 --thread 16
fastp v0.20.0, time used: 1949 seconds
[1] "2019-07-01 10:16:59 - QC and Trimming: PD732"
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: 199340601
total bases: 19934060100
Q20 bases: 19644201661(98.5459%)
Q30 bases: 19068242996(95.6566%)
Read2 before filtering:
total reads: 199340601
total bases: 19934060100
Q20 bases: 19479423434(97.7193%)
Q30 bases: 18692206855(93.7702%)
Read1 after filtering:
total reads: 198007695
total bases: 19614595495
Q20 bases: 19353437712(98.6686%)
Q30 bases: 18794380835(95.8183%)
Read2 aftering filtering:
total reads: 198007695
total bases: 19615425915
Q20 bases: 19235806060(98.0647%)
Q30 bases: 18476534738(94.1939%)
Filtering result:
reads passed filter: 396015390
reads failed due to low quality: 2292814
reads failed due to too many N: 11256
reads failed due to too short: 361742
reads with adapter trimmed: 30635901
bases trimmed due to adapters: 375512900
reads corrected by overlap analysis: 8238372
bases corrected by overlap analysis: 13921573
Duplication rate: 28.5424%
Insert size peak (evaluated by paired-end reads): 127
JSON report: /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD732_fastp.json
HTML report: /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD732_fastp.html
fastp --in1 /data/RNAseq_PD/tissue_polyA_samples/raw_data/NM3329_PD732_A2B2_GM-T_S3_R1_001.fastq.gz --out1 /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/NM3329_PD732_A2B2_GM-T_S3_R1_001_QC.fastq.gz --in2 /data/RNAseq_PD/tissue_polyA_samples/raw_data/NM3329_PD732_A2B2_GM-T_S3_R3_001.fastq.gz --out2 /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/NM3329_PD732_A2B2_GM-T_S3_R3_001_QC.fastq.gz --detect_adapter_for_pe --qualified_quality_phred 15 --unqualified_percent_limit 40 --n_base_limit 5 --length_required 36 --correction --overlap_len_require 30 --overlap_diff_limit 5 --overrepresentation_analysis --overrepresentation_sampling 20 --html /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD732_fastp.html --json /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD732_fastp.json --report_title PD732 --thread 16
fastp v0.20.0, time used: 2083 seconds
[1] "2019-07-01 10:51:42 - QC and Trimming: PDC05"
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: 224384050
total bases: 22438405000
Q20 bases: 22111790386(98.5444%)
Q30 bases: 21462397399(95.6503%)
Read2 before filtering:
total reads: 224384050
total bases: 22438405000
Q20 bases: 21988393796(97.9945%)
Q30 bases: 21192068882(94.4455%)
Read1 after filtering:
total reads: 222832687
total bases: 21929414792
Q20 bases: 21636987380(98.6665%)
Q30 bases: 21009785352(95.8064%)
Read2 aftering filtering:
total reads: 222832687
total bases: 21930605184
Q20 bases: 21570511287(98.358%)
Q30 bases: 20814513673(94.9108%)
Filtering result:
reads passed filter: 445665374
reads failed due to low quality: 2594882
reads failed due to too many N: 12382
reads failed due to too short: 495462
reads with adapter trimmed: 54073044
bases trimmed due to adapters: 714023162
reads corrected by overlap analysis: 9436380
bases corrected by overlap analysis: 16072493
Duplication rate: 25.4734%
Insert size peak (evaluated by paired-end reads): 116
JSON report: /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PDC05_fastp.json
HTML report: /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PDC05_fastp.html
fastp --in1 /data/RNAseq_PD/tissue_polyA_samples/raw_data/NM3330_PDC05_A1A2_GM-T_S4_R1_001.fastq.gz --out1 /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/NM3330_PDC05_A1A2_GM-T_S4_R1_001_QC.fastq.gz --in2 /data/RNAseq_PD/tissue_polyA_samples/raw_data/NM3330_PDC05_A1A2_GM-T_S4_R3_001.fastq.gz --out2 /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/NM3330_PDC05_A1A2_GM-T_S4_R3_001_QC.fastq.gz --detect_adapter_for_pe --qualified_quality_phred 15 --unqualified_percent_limit 40 --n_base_limit 5 --length_required 36 --correction --overlap_len_require 30 --overlap_diff_limit 5 --overrepresentation_analysis --overrepresentation_sampling 20 --html /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PDC05_fastp.html --json /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PDC05_fastp.json --report_title PDC05 --thread 16
fastp v0.20.0, time used: 2219 seconds
[1] "2019-07-01 11:28:41 - QC and Trimming: PD566"
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: 200123521
total bases: 20012352100
Q20 bases: 19633715556(98.108%)
Q30 bases: 19000147733(94.9421%)
Read2 before filtering:
total reads: 200123521
total bases: 20012352100
Q20 bases: 19404113612(96.9607%)
Q30 bases: 18499196611(92.4389%)
Read1 after filtering:
total reads: 197887380
total bases: 19435129604
Q20 bases: 19121835702(98.388%)
Q30 bases: 18523286258(95.3083%)
Read2 aftering filtering:
total reads: 197887380
total bases: 19437017687
Q20 bases: 18962654081(97.5595%)
Q30 bases: 18110430522(93.1749%)
Filtering result:
reads passed filter: 395774760
reads failed due to low quality: 3972078
reads failed due to too many N: 11000
reads failed due to too short: 489204
reads with adapter trimmed: 50861043
bases trimmed due to adapters: 708929467
reads corrected by overlap analysis: 12518806
bases corrected by overlap analysis: 24703612
Duplication rate: 41.4287%
Insert size peak (evaluated by paired-end reads): 116
JSON report: /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD566_fastp.json
HTML report: /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD566_fastp.html
fastp --in1 /data/RNAseq_PD/tissue_polyA_samples/raw_data/NM3331_PD566_A1B4_GM-T_S5_R1_001.fastq.gz --out1 /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/NM3331_PD566_A1B4_GM-T_S5_R1_001_QC.fastq.gz --in2 /data/RNAseq_PD/tissue_polyA_samples/raw_data/NM3331_PD566_A1B4_GM-T_S5_R3_001.fastq.gz --out2 /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/NM3331_PD566_A1B4_GM-T_S5_R3_001_QC.fastq.gz --detect_adapter_for_pe --qualified_quality_phred 15 --unqualified_percent_limit 40 --n_base_limit 5 --length_required 36 --correction --overlap_len_require 30 --overlap_diff_limit 5 --overrepresentation_analysis --overrepresentation_sampling 20 --html /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD566_fastp.html --json /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD566_fastp.json --report_title PD566 --thread 16
fastp v0.20.0, time used: 2077 seconds
[1] "2019-07-01 12:03:18 - QC and Trimming: PD366"
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: 190011262
total bases: 19001126200
Q20 bases: 18626037499(98.026%)
Q30 bases: 18007502319(94.7707%)
Read2 before filtering:
total reads: 190011262
total bases: 19001126200
Q20 bases: 18435321462(97.0223%)
Q30 bases: 17580370898(92.5228%)
Read1 after filtering:
total reads: 187849609
total bases: 18427872876
Q20 bases: 18120704899(98.3331%)
Q30 bases: 17537795972(95.1699%)
Read2 aftering filtering:
total reads: 187849609
total bases: 18430081253
Q20 bases: 17984931340(97.5847%)
Q30 bases: 17179474357(93.2143%)
Filtering result:
reads passed filter: 375699218
reads failed due to low quality: 3848346
reads failed due to too many N: 10254
reads failed due to too short: 464706
reads with adapter trimmed: 50704112
bases trimmed due to adapters: 716219092
reads corrected by overlap analysis: 12091312
bases corrected by overlap analysis: 23909932
Duplication rate: 39.9825%
Insert size peak (evaluated by paired-end reads): 116
JSON report: /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD366_fastp.json
HTML report: /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD366_fastp.html
fastp --in1 /data/RNAseq_PD/tissue_polyA_samples/raw_data/NM3332_PD366_A2B3_GM-T_S6_R1_001.fastq.gz --out1 /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/NM3332_PD366_A2B3_GM-T_S6_R1_001_QC.fastq.gz --in2 /data/RNAseq_PD/tissue_polyA_samples/raw_data/NM3332_PD366_A2B3_GM-T_S6_R3_001.fastq.gz --out2 /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/NM3332_PD366_A2B3_GM-T_S6_R3_001_QC.fastq.gz --detect_adapter_for_pe --qualified_quality_phred 15 --unqualified_percent_limit 40 --n_base_limit 5 --length_required 36 --correction --overlap_len_require 30 --overlap_diff_limit 5 --overrepresentation_analysis --overrepresentation_sampling 20 --html /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD366_fastp.html --json /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD366_fastp.json --report_title PD366 --thread 16
fastp v0.20.0, time used: 1895 seconds
[1] "2019-07-01 12:34:54 - QC and Trimming: PD413"
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: 200718065
total bases: 20071806500
Q20 bases: 19773977533(98.5162%)
Q30 bases: 19206345674(95.6882%)
Read2 before filtering:
total reads: 200718065
total bases: 20071806500
Q20 bases: 19647342107(97.8853%)
Q30 bases: 18927227039(94.2976%)
Read1 after filtering:
total reads: 199148855
total bases: 19632309672
Q20 bases: 19369196762(98.6598%)
Q30 bases: 18822702836(95.8762%)
Read2 aftering filtering:
total reads: 199148855
total bases: 19633503980
Q20 bases: 19297401226(98.2881%)
Q30 bases: 18613226087(94.8034%)
Filtering result:
reads passed filter: 398297710
reads failed due to low quality: 2714558
reads failed due to too many N: 11242
reads failed due to too short: 412620
reads with adapter trimmed: 42753451
bases trimmed due to adapters: 571981467
reads corrected by overlap analysis: 8571841
bases corrected by overlap analysis: 15112190
Duplication rate: 31.9075%
Insert size peak (evaluated by paired-end reads): 118
JSON report: /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD413_fastp.json
HTML report: /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD413_fastp.html
fastp --in1 /data/RNAseq_PD/tissue_polyA_samples/raw_data/NM3333_PD413_A2B1_GM-T_S7_R1_001.fastq.gz --out1 /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/NM3333_PD413_A2B1_GM-T_S7_R1_001_QC.fastq.gz --in2 /data/RNAseq_PD/tissue_polyA_samples/raw_data/NM3333_PD413_A2B1_GM-T_S7_R3_001.fastq.gz --out2 /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/NM3333_PD413_A2B1_GM-T_S7_R3_001_QC.fastq.gz --detect_adapter_for_pe --qualified_quality_phred 15 --unqualified_percent_limit 40 --n_base_limit 5 --length_required 36 --correction --overlap_len_require 30 --overlap_diff_limit 5 --overrepresentation_analysis --overrepresentation_sampling 20 --html /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD413_fastp.html --json /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD413_fastp.json --report_title PD413 --thread 16
fastp v0.20.0, time used: 2076 seconds
[1] "2019-07-01 13:09:30 - QC and Trimming: PDC22"
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: 189827559
total bases: 18982755900
Q20 bases: 18689380044(98.4545%)
Q30 bases: 18144817649(95.5858%)
Read2 before filtering:
total reads: 189827559
total bases: 18982755900
Q20 bases: 18509297334(97.5058%)
Q30 bases: 17759414848(93.5555%)
Read1 after filtering:
total reads: 187906334
total bases: 18418697984
Q20 bases: 18166253821(98.6294%)
Q30 bases: 17648629915(95.8191%)
Read2 aftering filtering:
total reads: 187906334
total bases: 18420114997
Q20 bases: 18059319328(98.0413%)
Q30 bases: 17356884767(94.2279%)
Filtering result:
reads passed filter: 375812668
reads failed due to low quality: 3220784
reads failed due to too many N: 10302
reads failed due to too short: 611364
reads with adapter trimmed: 53257705
bases trimmed due to adapters: 747965863
reads corrected by overlap analysis: 9824304
bases corrected by overlap analysis: 17737362
Duplication rate: 29.4932%
Insert size peak (evaluated by paired-end reads): 116
JSON report: /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PDC22_fastp.json
HTML report: /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PDC22_fastp.html
fastp --in1 /data/RNAseq_PD/tissue_polyA_samples/raw_data/NM3334_PDC22_A1E3_GM-T_S8_R1_001.fastq.gz --out1 /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/NM3334_PDC22_A1E3_GM-T_S8_R1_001_QC.fastq.gz --in2 /data/RNAseq_PD/tissue_polyA_samples/raw_data/NM3334_PDC22_A1E3_GM-T_S8_R3_001.fastq.gz --out2 /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/NM3334_PDC22_A1E3_GM-T_S8_R3_001_QC.fastq.gz --detect_adapter_for_pe --qualified_quality_phred 15 --unqualified_percent_limit 40 --n_base_limit 5 --length_required 36 --correction --overlap_len_require 30 --overlap_diff_limit 5 --overrepresentation_analysis --overrepresentation_sampling 20 --html /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PDC22_fastp.html --json /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PDC22_fastp.json --report_title PDC22 --thread 16
fastp v0.20.0, time used: 2034 seconds
[1] "2019-07-01 13:43:24 - QC and Trimming: PD706"
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: 186805467
total bases: 18680546700
Q20 bases: 18382254488(98.4032%)
Q30 bases: 17834402762(95.4705%)
Read2 before filtering:
total reads: 186805467
total bases: 18680546700
Q20 bases: 18184209936(97.343%)
Q30 bases: 17421406197(93.2596%)
Read1 after filtering:
total reads: 184899794
total bases: 18267557918
Q20 bases: 18008719802(98.5831%)
Q30 bases: 17483441879(95.7076%)
Read2 aftering filtering:
total reads: 184899794
total bases: 18268808553
Q20 bases: 17883166401(97.8891%)
Q30 bases: 17158931853(93.9247%)
Filtering result:
reads passed filter: 369799588
reads failed due to low quality: 3412244
reads failed due to too many N: 10218
reads failed due to too short: 388884
reads with adapter trimmed: 35794513
bases trimmed due to adapters: 445731056
reads corrected by overlap analysis: 9181835
bases corrected by overlap analysis: 17316280
Duplication rate: 43.5537%
Insert size peak (evaluated by paired-end reads): 119
JSON report: /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD706_fastp.json
HTML report: /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD706_fastp.html
fastp --in1 /data/RNAseq_PD/tissue_polyA_samples/raw_data/NM3335_PD706_A1A1_GM-T_S9_R1_001.fastq.gz --out1 /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/NM3335_PD706_A1A1_GM-T_S9_R1_001_QC.fastq.gz --in2 /data/RNAseq_PD/tissue_polyA_samples/raw_data/NM3335_PD706_A1A1_GM-T_S9_R3_001.fastq.gz --out2 /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/NM3335_PD706_A1A1_GM-T_S9_R3_001_QC.fastq.gz --detect_adapter_for_pe --qualified_quality_phred 15 --unqualified_percent_limit 40 --n_base_limit 5 --length_required 36 --correction --overlap_len_require 30 --overlap_diff_limit 5 --overrepresentation_analysis --overrepresentation_sampling 20 --html /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD706_fastp.html --json /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD706_fastp.json --report_title PD706 --thread 16
fastp v0.20.0, time used: 1720 seconds
[1] "2019-07-01 14:12:04 - QC and Trimming: PD415"
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: 161117201
total bases: 16111720100
Q20 bases: 15844346429(98.3405%)
Q30 bases: 15359168546(95.3292%)
Read2 before filtering:
total reads: 161117201
total bases: 16111720100
Q20 bases: 15723141150(97.5882%)
Q30 bases: 15091009435(93.6648%)
Read1 after filtering:
total reads: 159828542
total bases: 15724151610
Q20 bases: 15493134439(98.5308%)
Q30 bases: 15028663077(95.5769%)
Read2 aftering filtering:
total reads: 159828542
total bases: 15725565972
Q20 bases: 15415859820(98.0306%)
Q30 bases: 14817102789(94.223%)
Filtering result:
reads passed filter: 319657084
reads failed due to low quality: 2296882
reads failed due to too many N: 8768
reads failed due to too short: 271668
reads with adapter trimmed: 37954894
bases trimmed due to adapters: 519171850
reads corrected by overlap analysis: 8144887
bases corrected by overlap analysis: 15508731
Duplication rate: 39.0643%
Insert size peak (evaluated by paired-end reads): 116
JSON report: /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD415_fastp.json
HTML report: /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD415_fastp.html
fastp --in1 /data/RNAseq_PD/tissue_polyA_samples/raw_data/NM3336_PD415_A2B2_GM-T_S10_R1_001.fastq.gz --out1 /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/NM3336_PD415_A2B2_GM-T_S10_R1_001_QC.fastq.gz --in2 /data/RNAseq_PD/tissue_polyA_samples/raw_data/NM3336_PD415_A2B2_GM-T_S10_R3_001.fastq.gz --out2 /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/NM3336_PD415_A2B2_GM-T_S10_R3_001_QC.fastq.gz --detect_adapter_for_pe --qualified_quality_phred 15 --unqualified_percent_limit 40 --n_base_limit 5 --length_required 36 --correction --overlap_len_require 30 --overlap_diff_limit 5 --overrepresentation_analysis --overrepresentation_sampling 20 --html /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD415_fastp.html --json /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD415_fastp.json --report_title PD415 --thread 16
fastp v0.20.0, time used: 1641 seconds
[1] "2019-07-01 14:39:25 - QC and Trimming: PD416"
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: 169933617
total bases: 16993361700
Q20 bases: 16721623313(98.4009%)
Q30 bases: 16222502918(95.4638%)
Read2 before filtering:
total reads: 169933617
total bases: 16993361700
Q20 bases: 16586957301(97.6085%)
Q30 bases: 15918117219(93.6726%)
Read1 after filtering:
total reads: 168618149
total bases: 16622838130
Q20 bases: 16387154488(98.5822%)
Q30 bases: 15908461481(95.7024%)
Read2 aftering filtering:
total reads: 168618149
total bases: 16624122888
Q20 bases: 16298379470(98.0405%)
Q30 bases: 15662223460(94.2138%)
Filtering result:
reads passed filter: 337236298
reads failed due to low quality: 2417768
reads failed due to too many N: 9116
reads failed due to too short: 204052
reads with adapter trimmed: 36490105
bases trimmed due to adapters: 479504462
reads corrected by overlap analysis: 8191339
bases corrected by overlap analysis: 15296917
Duplication rate: 40.6474%
Insert size peak (evaluated by paired-end reads): 116
JSON report: /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD416_fastp.json
HTML report: /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD416_fastp.html
fastp --in1 /data/RNAseq_PD/tissue_polyA_samples/raw_data/NM3337_PD416_A2D3_GM-T_S11_R1_001.fastq.gz --out1 /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/NM3337_PD416_A2D3_GM-T_S11_R1_001_QC.fastq.gz --in2 /data/RNAseq_PD/tissue_polyA_samples/raw_data/NM3337_PD416_A2D3_GM-T_S11_R3_001.fastq.gz --out2 /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/NM3337_PD416_A2D3_GM-T_S11_R3_001_QC.fastq.gz --detect_adapter_for_pe --qualified_quality_phred 15 --unqualified_percent_limit 40 --n_base_limit 5 --length_required 36 --correction --overlap_len_require 30 --overlap_diff_limit 5 --overrepresentation_analysis --overrepresentation_sampling 20 --html /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD416_fastp.html --json /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD416_fastp.json --report_title PD416 --thread 16
fastp v0.20.0, time used: 1663 seconds
[1] "2019-07-01 15:07:09 - QC and Trimming: PDC34"
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: 176276526
total bases: 17627652600
Q20 bases: 17357632178(98.4682%)
Q30 bases: 16839487108(95.5288%)
Read2 before filtering:
total reads: 176276526
total bases: 17627652600
Q20 bases: 17227626348(97.7307%)
Q30 bases: 16530752980(93.7774%)
Read1 after filtering:
total reads: 175187639
total bases: 17276798232
Q20 bases: 17037248385(98.6135%)
Q30 bases: 16536907304(95.7174%)
Read2 aftering filtering:
total reads: 175187639
total bases: 17277717153
Q20 bases: 16945522928(98.0773%)
Q30 bases: 16277064565(94.2084%)
Filtering result:
reads passed filter: 350375278
reads failed due to low quality: 1997228
reads failed due to too many N: 9696
reads failed due to too short: 170850
reads with adapter trimmed: 38619885
bases trimmed due to adapters: 484880883
reads corrected by overlap analysis: 8687710
bases corrected by overlap analysis: 15062370
Duplication rate: 31.4315%
Insert size peak (evaluated by paired-end reads): 116
JSON report: /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PDC34_fastp.json
HTML report: /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PDC34_fastp.html
fastp --in1 /data/RNAseq_PD/tissue_polyA_samples/raw_data/NM3338_PDC34_A1B3_GM-T_S12_R1_001.fastq.gz --out1 /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/NM3338_PDC34_A1B3_GM-T_S12_R1_001_QC.fastq.gz --in2 /data/RNAseq_PD/tissue_polyA_samples/raw_data/NM3338_PDC34_A1B3_GM-T_S12_R3_001.fastq.gz --out2 /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/NM3338_PDC34_A1B3_GM-T_S12_R3_001_QC.fastq.gz --detect_adapter_for_pe --qualified_quality_phred 15 --unqualified_percent_limit 40 --n_base_limit 5 --length_required 36 --correction --overlap_len_require 30 --overlap_diff_limit 5 --overrepresentation_analysis --overrepresentation_sampling 20 --html /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PDC34_fastp.html --json /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PDC34_fastp.json --report_title PDC34 --thread 16
fastp v0.20.0, time used: 1674 seconds
[1] "2019-07-01 15:35:03 - QC and Trimming: PD563"
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: 195575638
total bases: 19557563800
Q20 bases: 19253977112(98.4477%)
Q30 bases: 18689783441(95.5629%)
Read2 before filtering:
total reads: 195575638
total bases: 19557563800
Q20 bases: 19070672753(97.5105%)
Q30 bases: 18290627761(93.522%)
Read1 after filtering:
total reads: 193886926
total bases: 19113218679
Q20 bases: 18848671737(98.6159%)
Q30 bases: 18307389025(95.7839%)
Read2 aftering filtering:
total reads: 193886926
total bases: 19114390589
Q20 bases: 18733536180(98.0075%)
Q30 bases: 17993539147(94.1361%)
Filtering result:
reads passed filter: 387773852
reads failed due to low quality: 3108162
reads failed due to too many N: 10928
reads failed due to too short: 258334
reads with adapter trimmed: 42041485
bases trimmed due to adapters: 552122335
reads corrected by overlap analysis: 9526458
bases corrected by overlap analysis: 17010914
Duplication rate: 35.1888%
Insert size peak (evaluated by paired-end reads): 119
JSON report: /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD563_fastp.json
HTML report: /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD563_fastp.html
fastp --in1 /data/RNAseq_PD/tissue_polyA_samples/raw_data/NM3339_PD563_A1C1_GM-T_S13_R1_001.fastq.gz --out1 /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/NM3339_PD563_A1C1_GM-T_S13_R1_001_QC.fastq.gz --in2 /data/RNAseq_PD/tissue_polyA_samples/raw_data/NM3339_PD563_A1C1_GM-T_S13_R3_001.fastq.gz --out2 /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/NM3339_PD563_A1C1_GM-T_S13_R3_001_QC.fastq.gz --detect_adapter_for_pe --qualified_quality_phred 15 --unqualified_percent_limit 40 --n_base_limit 5 --length_required 36 --correction --overlap_len_require 30 --overlap_diff_limit 5 --overrepresentation_analysis --overrepresentation_sampling 20 --html /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD563_fastp.html --json /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD563_fastp.json --report_title PD563 --thread 16
fastp v0.20.0, time used: 1868 seconds
[1] "2019-07-01 16:06:11 - QC and Trimming: PD523"
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: 177835756
total bases: 17783575600
Q20 bases: 17454708861(98.1507%)
Q30 bases: 16884691699(94.9454%)
Read2 before filtering:
total reads: 177835756
total bases: 17783575600
Q20 bases: 17290421837(97.2269%)
Q30 bases: 16510150926(92.8393%)
Read1 after filtering:
total reads: 176198631
total bases: 17363106306
Q20 bases: 17085743111(98.4026%)
Q30 bases: 16542656962(95.2748%)
Read2 aftering filtering:
total reads: 176198631
total bases: 17364866700
Q20 bases: 16965633312(97.7009%)
Q30 bases: 16222442183(93.4211%)
Filtering result:
reads passed filter: 352397262
reads failed due to low quality: 2989152
reads failed due to too many N: 9610
reads failed due to too short: 275488
reads with adapter trimmed: 38310754
bases trimmed due to adapters: 514383016
reads corrected by overlap analysis: 10433156
bases corrected by overlap analysis: 19598043
Duplication rate: 42.8642%
Insert size peak (evaluated by paired-end reads): 119
JSON report: /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD523_fastp.json
HTML report: /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD523_fastp.html
fastp --in1 /data/RNAseq_PD/tissue_polyA_samples/raw_data/NM3340_PD523_A2B3_GM-T_S14_R1_001.fastq.gz --out1 /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/NM3340_PD523_A2B3_GM-T_S14_R1_001_QC.fastq.gz --in2 /data/RNAseq_PD/tissue_polyA_samples/raw_data/NM3340_PD523_A2B3_GM-T_S14_R3_001.fastq.gz --out2 /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/NM3340_PD523_A2B3_GM-T_S14_R3_001_QC.fastq.gz --detect_adapter_for_pe --qualified_quality_phred 15 --unqualified_percent_limit 40 --n_base_limit 5 --length_required 36 --correction --overlap_len_require 30 --overlap_diff_limit 5 --overrepresentation_analysis --overrepresentation_sampling 20 --html /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD523_fastp.html --json /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD523_fastp.json --report_title PD523 --thread 16
fastp v0.20.0, time used: 1716 seconds
[1] "2019-07-01 16:34:47 - QC and Trimming: PDC87"
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: 191484359
total bases: 19148435900
Q20 bases: 18844509440(98.4128%)
Q30 bases: 18280542492(95.4675%)
Read2 before filtering:
total reads: 191484359
total bases: 19148435900
Q20 bases: 18634012039(97.3135%)
Q30 bases: 17885336664(93.4036%)
Read1 after filtering:
total reads: 189176100
total bases: 18613390902
Q20 bases: 18350843777(98.5895%)
Q30 bases: 17813573828(95.703%)
Read2 aftering filtering:
total reads: 189176100
total bases: 18615086522
Q20 bases: 18240815522(97.9894%)
Q30 bases: 17541438872(94.2324%)
Filtering result:
reads passed filter: 378352200
reads failed due to low quality: 3945804
reads failed due to too many N: 10268
reads failed due to too short: 660446
reads with adapter trimmed: 44505873
bases trimmed due to adapters: 612441936
reads corrected by overlap analysis: 10267595
bases corrected by overlap analysis: 18759351
Duplication rate: 50.9351%
Insert size peak (evaluated by paired-end reads): 119
JSON report: /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PDC87_fastp.json
HTML report: /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PDC87_fastp.html
fastp --in1 /data/RNAseq_PD/tissue_polyA_samples/raw_data/NM3341_PDC87_A1A4_GM-T_S15_R1_001.fastq.gz --out1 /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/NM3341_PDC87_A1A4_GM-T_S15_R1_001_QC.fastq.gz --in2 /data/RNAseq_PD/tissue_polyA_samples/raw_data/NM3341_PDC87_A1A4_GM-T_S15_R3_001.fastq.gz --out2 /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/NM3341_PDC87_A1A4_GM-T_S15_R3_001_QC.fastq.gz --detect_adapter_for_pe --qualified_quality_phred 15 --unqualified_percent_limit 40 --n_base_limit 5 --length_required 36 --correction --overlap_len_require 30 --overlap_diff_limit 5 --overrepresentation_analysis --overrepresentation_sampling 20 --html /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PDC87_fastp.html --json /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PDC87_fastp.json --report_title PDC87 --thread 16
fastp v0.20.0, time used: 1827 seconds
[1] "2019-07-01 17:05:14 - QC and Trimming: PD163"
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: 177373675
total bases: 17737367500
Q20 bases: 17411300778(98.1617%)
Q30 bases: 16856278244(95.0326%)
Read2 before filtering:
total reads: 177373675
total bases: 17737367500
Q20 bases: 17236425826(97.1758%)
Q30 bases: 16458067356(92.7875%)
Read1 after filtering:
total reads: 175636543
total bases: 17278995952
Q20 bases: 17007323074(98.4277%)
Q30 bases: 16481113894(95.3824%)
Read2 aftering filtering:
total reads: 175636543
total bases: 17280754230
Q20 bases: 16881637330(97.6904%)
Q30 bases: 16144827193(93.4266%)
Filtering result:
reads passed filter: 351273086
reads failed due to low quality: 3166306
reads failed due to too many N: 9624
reads failed due to too short: 298334
reads with adapter trimmed: 42169236
bases trimmed due to adapters: 571394881
reads corrected by overlap analysis: 10379981
bases corrected by overlap analysis: 19951623
Duplication rate: 50.1999%
Insert size peak (evaluated by paired-end reads): 119
JSON report: /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD163_fastp.json
HTML report: /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD163_fastp.html
fastp --in1 /data/RNAseq_PD/tissue_polyA_samples/raw_data/NM3342_PD163_A1B1_GM-T_S16_R1_001.fastq.gz --out1 /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/NM3342_PD163_A1B1_GM-T_S16_R1_001_QC.fastq.gz --in2 /data/RNAseq_PD/tissue_polyA_samples/raw_data/NM3342_PD163_A1B1_GM-T_S16_R3_001.fastq.gz --out2 /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/NM3342_PD163_A1B1_GM-T_S16_R3_001_QC.fastq.gz --detect_adapter_for_pe --qualified_quality_phred 15 --unqualified_percent_limit 40 --n_base_limit 5 --length_required 36 --correction --overlap_len_require 30 --overlap_diff_limit 5 --overrepresentation_analysis --overrepresentation_sampling 20 --html /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD163_fastp.html --json /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD163_fastp.json --report_title PD163 --thread 16
fastp v0.20.0, time used: 1850 seconds
[1] "2019-07-01 17:36:04 - QC and Trimming: PD678"
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: 194011252
total bases: 19401125200
Q20 bases: 19044586363(98.1623%)
Q30 bases: 18429556668(94.9922%)
Read2 before filtering:
total reads: 194011252
total bases: 19401125200
Q20 bases: 18830180425(97.0572%)
Q30 bases: 17991330130(92.7334%)
Read1 after filtering:
total reads: 191581437
total bases: 18912834294
Q20 bases: 18610692037(98.4024%)
Q30 bases: 18025357867(95.3075%)
Read2 aftering filtering:
total reads: 191581437
total bases: 18914847317
Q20 bases: 18475973443(97.6797%)
Q30 bases: 17683702055(93.4911%)
Filtering result:
reads passed filter: 383162874
reads failed due to low quality: 4166074
reads failed due to too many N: 10738
reads failed due to too short: 682818
reads with adapter trimmed: 37314138
bases trimmed due to adapters: 491128937
reads corrected by overlap analysis: 10527062
bases corrected by overlap analysis: 20673957
Duplication rate: 41.7992%
Insert size peak (evaluated by paired-end reads): 116
JSON report: /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD678_fastp.json
HTML report: /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD678_fastp.html
fastp --in1 /data/RNAseq_PD/tissue_polyA_samples/raw_data/NM3343_PD678_A1B5_GM-T_S17_R1_001.fastq.gz --out1 /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/NM3343_PD678_A1B5_GM-T_S17_R1_001_QC.fastq.gz --in2 /data/RNAseq_PD/tissue_polyA_samples/raw_data/NM3343_PD678_A1B5_GM-T_S17_R3_001.fastq.gz --out2 /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/NM3343_PD678_A1B5_GM-T_S17_R3_001_QC.fastq.gz --detect_adapter_for_pe --qualified_quality_phred 15 --unqualified_percent_limit 40 --n_base_limit 5 --length_required 36 --correction --overlap_len_require 30 --overlap_diff_limit 5 --overrepresentation_analysis --overrepresentation_sampling 20 --html /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD678_fastp.html --json /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD678_fastp.json --report_title PD678 --thread 16
fastp v0.20.0, time used: 2024 seconds
[1] "2019-07-01 18:09:48 - QC and Trimming: PD747"
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: 170998658
total bases: 17099865800
Q20 bases: 16845033014(98.5097%)
Q30 bases: 16346983339(95.5971%)
Read2 before filtering:
total reads: 170998658
total bases: 17099865800
Q20 bases: 16714774893(97.748%)
Q30 bases: 16050071417(93.8608%)
Read1 after filtering:
total reads: 169863761
total bases: 16791055182
Q20 bases: 16563275462(98.6434%)
Q30 bases: 16081071285(95.7717%)
Read2 aftering filtering:
total reads: 169863761
total bases: 16791913840
Q20 bases: 16475618738(98.1164%)
Q30 bases: 15837809174(94.3181%)
Filtering result:
reads passed filter: 339727522
reads failed due to low quality: 2083156
reads failed due to too many N: 9238
reads failed due to too short: 177400
reads with adapter trimmed: 31625624
bases trimmed due to adapters: 392031516
reads corrected by overlap analysis: 7690544
bases corrected by overlap analysis: 13255327
Duplication rate: 32.1919%
Insert size peak (evaluated by paired-end reads): 118
JSON report: /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD747_fastp.json
HTML report: /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD747_fastp.html
fastp --in1 /data/RNAseq_PD/tissue_polyA_samples/raw_data/NM3344_PD747_A2A9_GM-T_S18_R1_001.fastq.gz --out1 /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/NM3344_PD747_A2A9_GM-T_S18_R1_001_QC.fastq.gz --in2 /data/RNAseq_PD/tissue_polyA_samples/raw_data/NM3344_PD747_A2A9_GM-T_S18_R3_001.fastq.gz --out2 /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/NM3344_PD747_A2A9_GM-T_S18_R3_001_QC.fastq.gz --detect_adapter_for_pe --qualified_quality_phred 15 --unqualified_percent_limit 40 --n_base_limit 5 --length_required 36 --correction --overlap_len_require 30 --overlap_diff_limit 5 --overrepresentation_analysis --overrepresentation_sampling 20 --html /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD747_fastp.html --json /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD747_fastp.json --report_title PD747 --thread 16
fastp v0.20.0, time used: 1640 seconds
[1] "2019-07-01 18:37:08 - QC and Trimming: PD115"
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: 175315012
total bases: 17531501200
Q20 bases: 17226743028(98.2617%)
Q30 bases: 16686597362(95.1807%)
Read2 before filtering:
total reads: 175315012
total bases: 17531501200
Q20 bases: 17010858177(97.0302%)
Q30 bases: 16180473762(92.2937%)
Read1 after filtering:
total reads: 173602474
total bases: 17216645358
Q20 bases: 16956032441(98.4863%)
Q30 bases: 16437891627(95.4767%)
Read2 aftering filtering:
total reads: 173602474
total bases: 17217405800
Q20 bases: 16785837736(97.4934%)
Q30 bases: 15987183477(92.8548%)
Filtering result:
reads passed filter: 347204948
reads failed due to low quality: 3147206
reads failed due to too many N: 9772
reads failed due to too short: 268098
reads with adapter trimmed: 23854239
bases trimmed due to adapters: 287457410
reads corrected by overlap analysis: 8832068
bases corrected by overlap analysis: 16763509
Duplication rate: 56.8041%
Insert size peak (evaluated by paired-end reads): 127
JSON report: /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD115_fastp.json
HTML report: /data/RNAseq_PD/tissue_polyA_samples/QC/fastp/PD115_fastp.html