Dadaist2 0.8.0 execution log

This is not a report with the results of the pipeline, but the log of the events occurred to generate it.

×

Summary

This reports contain technical details on the execution of Dadaist2.

Parameter Value
Input /home/ubuntu/volume/16s/mothur-sop/subsample
Output /home/ubuntu/volume/16s/mothur-sop/dadaist_0.8.0/subsample-silva-default
Timestamp 20210408 20:39:21
Execution time 4m 29s


Shell command fastp

Executed at 2021-04-08 20:39:40 for 1.04s and returned 0

'

Command

fastp 
-w 8 
-i "/home/ubuntu/volume/16s/mothur-sop/subsample/F3D0_S188_L001_R1_001.fastq" 
-I "/home/ubuntu/volume/16s/mothur-sop/subsample/F3D0_S188_L001_R2_001.fastq" 
-o "/tmp/dadaist2_oaSFvt"/for/F3D0_R1.fastq.gz 
-O  "/tmp/dadaist2_oaSFvt"/rev/F3D0_R2.fastq.gz   
--trim_front1 20 
--trim_front2  20  
--detect_adapter_for_pe 
--disable_quality_filtering 
--n_base_limit  1   
--json "/tmp/dadaist2_oaSFvt/F3D0.json" 
--html /dev/null  
--trim_tail1 0 
--trim_tail2 0 
--length_required 110

Standard output

Standard error
Detecting adapter sequence for read1...
No adapter detected for read1

Detecting adapter sequence for read2...
No adapter detected for read2

Read1 before filtering:
total reads: 7793
total bases: 1955914
Q20 bases: 1861780(95.1872%)
Q30 bases: 1810170(92.5485%)

Read2 before filtering:
total reads: 7793
total bases: 1953534
Q20 bases: 1726416(88.374%)
Q30 bases: 1614066(82.6229%)

Read1 after filtering:
total reads: 7793
total bases: 1799970
Q20 bases: 1708262(94.905%)
Q30 bases: 1657320(92.0749%)

Read2 aftering filtering:
total reads: 7793
total bases: 1797590
Q20 bases: 1575545(87.6476%)
Q30 bases: 1464970(81.4963%)

Filtering result:
reads passed filter: 15586
reads failed due to low quality: 0
reads failed due to too many N: 0
reads failed due to too short: 0
reads with adapter trimmed: 13896
bases trimmed due to adapters: 168

Duplication rate: 26.3736%

Insert size peak (evaluated by paired-end reads): 253

JSON report: /tmp/dadaist2_oaSFvt/F3D0.json
HTML report: /dev/null

fastp -w 8 -i /home/ubuntu/volume/16s/mothur-sop/subsample/F3D0_S188_L001_R1_001.fastq -I /home/ubuntu/volume/16s/mothur-sop/subsample/F3D0_S188_L001_R2_001.fastq -o /tmp/dadaist2_oaSFvt/for/F3D0_R1.fastq.gz -O /tmp/dadaist2_oaSFvt/rev/F3D0_R2.fastq.gz --trim_front1 20 --trim_front2 20 --detect_adapter_for_pe --disable_quality_filtering --n_base_limit 1 --json /tmp/dadaist2_oaSFvt/F3D0.json --html /dev/null --trim_tail1 0 --trim_tail2 0 --length_required 110 
fastp v0.20.1, time used: 1 seconds


Shell command fastp
Executed at 2021-04-08 20:39:41 for 1.18s and  returned 0 
'
Command
fastp 
-w 8 
-i "/home/ubuntu/volume/16s/mothur-sop/subsample/F3D1_S189_L001_R1_001.fastq" 
-I "/home/ubuntu/volume/16s/mothur-sop/subsample/F3D1_S189_L001_R2_001.fastq" 
-o "/tmp/dadaist2_oaSFvt"/for/F3D1_R1.fastq.gz 
-O  "/tmp/dadaist2_oaSFvt"/rev/F3D1_R2.fastq.gz   
--trim_front1 20 
--trim_front2  20  
--detect_adapter_for_pe 
--disable_quality_filtering 
--n_base_limit  1   
--json "/tmp/dadaist2_oaSFvt/F3D1.json" 
--html /dev/null  
--trim_tail1 0 
--trim_tail2 0 
--length_required 110 


Standard output
Standard error
Detecting adapter sequence for read1...
No adapter detected for read1

Detecting adapter sequence for read2...
No adapter detected for read2

Read1 before filtering:
total reads: 5869
total bases: 1473024
Q20 bases: 1391828(94.4878%)
Q30 bases: 1348464(91.5439%)

Read2 before filtering:
total reads: 5869
total bases: 1471648
Q20 bases: 1308416(88.9082%)
Q30 bases: 1229967(83.5775%)

Read1 after filtering:
total reads: 5869
total bases: 1355643
Q20 bases: 1276325(94.149%)
Q30 bases: 1233521(90.9916%)

Read2 aftering filtering:
total reads: 5869
total bases: 1354268
Q20 bases: 1194849(88.2284%)
Q30 bases: 1117746(82.5351%)

Filtering result:
reads passed filter: 11738
reads failed due to low quality: 0
reads failed due to too many N: 0
reads failed due to too short: 0
reads with adapter trimmed: 10762
bases trimmed due to adapters: 1

Duplication rate: 17.3333%

Insert size peak (evaluated by paired-end reads): 253

JSON report: /tmp/dadaist2_oaSFvt/F3D1.json
HTML report: /dev/null

fastp -w 8 -i /home/ubuntu/volume/16s/mothur-sop/subsample/F3D1_S189_L001_R1_001.fastq -I /home/ubuntu/volume/16s/mothur-sop/subsample/F3D1_S189_L001_R2_001.fastq -o /tmp/dadaist2_oaSFvt/for/F3D1_R1.fastq.gz -O /tmp/dadaist2_oaSFvt/rev/F3D1_R2.fastq.gz --trim_front1 20 --trim_front2 20 --detect_adapter_for_pe --disable_quality_filtering --n_base_limit 1 --json /tmp/dadaist2_oaSFvt/F3D1.json --html /dev/null --trim_tail1 0 --trim_tail2 0 --length_required 110 
fastp v0.20.1, time used: 1 seconds


Shell command fastp
Executed at 2021-04-08 20:39:43 for 0.97s and  returned 0 
'
Command
fastp 
-w 8 
-i "/home/ubuntu/volume/16s/mothur-sop/subsample/F3D141_S207_L001_R1_001.fastq" 
-I "/home/ubuntu/volume/16s/mothur-sop/subsample/F3D141_S207_L001_R2_001.fastq" 
-o "/tmp/dadaist2_oaSFvt"/for/F3D141_R1.fastq.gz 
-O  "/tmp/dadaist2_oaSFvt"/rev/F3D141_R2.fastq.gz   
--trim_front1 20 
--trim_front2  20  
--detect_adapter_for_pe 
--disable_quality_filtering 
--n_base_limit  1   
--json "/tmp/dadaist2_oaSFvt/F3D141.json" 
--html /dev/null  
--trim_tail1 0 
--trim_tail2 0 
--length_required 110 


Standard output
Standard error
Detecting adapter sequence for read1...
No adapter detected for read1

Detecting adapter sequence for read2...
No adapter detected for read2

Read1 before filtering:
total reads: 5958
total bases: 1495347
Q20 bases: 1425359(95.3196%)
Q30 bases: 1388281(92.8401%)

Read2 before filtering:
total reads: 5958
total bases: 1493188
Q20 bases: 1310228(87.747%)
Q30 bases: 1217917(81.5649%)

Read1 after filtering:
total reads: 5958
total bases: 1376183
Q20 bases: 1307756(95.0278%)
Q30 bases: 1271114(92.3652%)

Read2 aftering filtering:
total reads: 5958
total bases: 1374024
Q20 bases: 1194475(86.9326%)
Q30 bases: 1103485(80.3105%)

Filtering result:
reads passed filter: 11916
reads failed due to low quality: 0
reads failed due to too many N: 0
reads failed due to too short: 0
reads with adapter trimmed: 10400
bases trimmed due to adapters: 8

Duplication rate: 10.7143%

Insert size peak (evaluated by paired-end reads): 252

JSON report: /tmp/dadaist2_oaSFvt/F3D141.json
HTML report: /dev/null

fastp -w 8 -i /home/ubuntu/volume/16s/mothur-sop/subsample/F3D141_S207_L001_R1_001.fastq -I /home/ubuntu/volume/16s/mothur-sop/subsample/F3D141_S207_L001_R2_001.fastq -o /tmp/dadaist2_oaSFvt/for/F3D141_R1.fastq.gz -O /tmp/dadaist2_oaSFvt/rev/F3D141_R2.fastq.gz --trim_front1 20 --trim_front2 20 --detect_adapter_for_pe --disable_quality_filtering --n_base_limit 1 --json /tmp/dadaist2_oaSFvt/F3D141.json --html /dev/null --trim_tail1 0 --trim_tail2 0 --length_required 110 
fastp v0.20.1, time used: 1 seconds


Shell command fastp
Executed at 2021-04-08 20:39:44 for 0.90s and  returned 0 
'
Command
fastp 
-w 8 
-i "/home/ubuntu/volume/16s/mothur-sop/subsample/F3D142_S208_L001_R1_001.fastq" 
-I "/home/ubuntu/volume/16s/mothur-sop/subsample/F3D142_S208_L001_R2_001.fastq" 
-o "/tmp/dadaist2_oaSFvt"/for/F3D142_R1.fastq.gz 
-O  "/tmp/dadaist2_oaSFvt"/rev/F3D142_R2.fastq.gz   
--trim_front1 20 
--trim_front2  20  
--detect_adapter_for_pe 
--disable_quality_filtering 
--n_base_limit  1   
--json "/tmp/dadaist2_oaSFvt/F3D142.json" 
--html /dev/null  
--trim_tail1 0 
--trim_tail2 0 
--length_required 110 


Standard output
Standard error
Detecting adapter sequence for read1...
No adapter detected for read1

Detecting adapter sequence for read2...
No adapter detected for read2

Read1 before filtering:
total reads: 3183
total bases: 798912
Q20 bases: 764105(95.6432%)
Q30 bases: 745531(93.3183%)

Read2 before filtering:
total reads: 3183
total bases: 797648
Q20 bases: 691812(86.7315%)
Q30 bases: 638520(80.0503%)

Read1 after filtering:
total reads: 3183
total bases: 735252
Q20 bases: 701177(95.3655%)
Q30 bases: 682849(92.8728%)

Read2 aftering filtering:
total reads: 3183
total bases: 733988
Q20 bases: 630231(85.8639%)
Q30 bases: 577655(78.7009%)

Filtering result:
reads passed filter: 6366
reads failed due to low quality: 0
reads failed due to too many N: 0
reads failed due to too short: 0
reads with adapter trimmed: 5428
bases trimmed due to adapters: 0

Duplication rate: 24%

Insert size peak (evaluated by paired-end reads): 0

JSON report: /tmp/dadaist2_oaSFvt/F3D142.json
HTML report: /dev/null

fastp -w 8 -i /home/ubuntu/volume/16s/mothur-sop/subsample/F3D142_S208_L001_R1_001.fastq -I /home/ubuntu/volume/16s/mothur-sop/subsample/F3D142_S208_L001_R2_001.fastq -o /tmp/dadaist2_oaSFvt/for/F3D142_R1.fastq.gz -O /tmp/dadaist2_oaSFvt/rev/F3D142_R2.fastq.gz --trim_front1 20 --trim_front2 20 --detect_adapter_for_pe --disable_quality_filtering --n_base_limit 1 --json /tmp/dadaist2_oaSFvt/F3D142.json --html /dev/null --trim_tail1 0 --trim_tail2 0 --length_required 110 
fastp v0.20.1, time used: 1 seconds


Shell command fastp
Executed at 2021-04-08 20:39:45 for 0.85s and  returned 0 
'
Command
fastp 
-w 8 
-i "/home/ubuntu/volume/16s/mothur-sop/subsample/F3D143_S209_L001_R1_001.fastq" 
-I "/home/ubuntu/volume/16s/mothur-sop/subsample/F3D143_S209_L001_R2_001.fastq" 
-o "/tmp/dadaist2_oaSFvt"/for/F3D143_R1.fastq.gz 
-O  "/tmp/dadaist2_oaSFvt"/rev/F3D143_R2.fastq.gz   
--trim_front1 20 
--trim_front2  20  
--detect_adapter_for_pe 
--disable_quality_filtering 
--n_base_limit  1   
--json "/tmp/dadaist2_oaSFvt/F3D143.json" 
--html /dev/null  
--trim_tail1 0 
--trim_tail2 0 
--length_required 110 


Standard output
Standard error
Detecting adapter sequence for read1...
No adapter detected for read1

Detecting adapter sequence for read2...
No adapter detected for read2

Read1 before filtering:
total reads: 3178
total bases: 797624
Q20 bases: 761664(95.4916%)
Q30 bases: 742072(93.0353%)

Read2 before filtering:
total reads: 3178
total bases: 796544
Q20 bases: 695494(87.3139%)
Q30 bases: 643987(80.8476%)

Read1 after filtering:
total reads: 3178
total bases: 734064
Q20 bases: 699020(95.226%)
Q30 bases: 679670(92.59%)

Read2 aftering filtering:
total reads: 3178
total bases: 732984
Q20 bases: 633977(86.4926%)
Q30 bases: 583279(79.576%)

Filtering result:
reads passed filter: 6356
reads failed due to low quality: 0
reads failed due to too many N: 0
reads failed due to too short: 0
reads with adapter trimmed: 5474
bases trimmed due to adapters: 0

Duplication rate: 20.7547%

Insert size peak (evaluated by paired-end reads): 252

JSON report: /tmp/dadaist2_oaSFvt/F3D143.json
HTML report: /dev/null

fastp -w 8 -i /home/ubuntu/volume/16s/mothur-sop/subsample/F3D143_S209_L001_R1_001.fastq -I /home/ubuntu/volume/16s/mothur-sop/subsample/F3D143_S209_L001_R2_001.fastq -o /tmp/dadaist2_oaSFvt/for/F3D143_R1.fastq.gz -O /tmp/dadaist2_oaSFvt/rev/F3D143_R2.fastq.gz --trim_front1 20 --trim_front2 20 --detect_adapter_for_pe --disable_quality_filtering --n_base_limit 1 --json /tmp/dadaist2_oaSFvt/F3D143.json --html /dev/null --trim_tail1 0 --trim_tail2 0 --length_required 110 
fastp v0.20.1, time used: 1 seconds


Shell command fastp
Executed at 2021-04-08 20:39:46 for 0.93s and  returned 0 
'
Command
fastp 
-w 8 
-i "/home/ubuntu/volume/16s/mothur-sop/subsample/F3D144_S210_L001_R1_001.fastq" 
-I "/home/ubuntu/volume/16s/mothur-sop/subsample/F3D144_S210_L001_R2_001.fastq" 
-o "/tmp/dadaist2_oaSFvt"/for/F3D144_R1.fastq.gz 
-O  "/tmp/dadaist2_oaSFvt"/rev/F3D144_R2.fastq.gz   
--trim_front1 20 
--trim_front2  20  
--detect_adapter_for_pe 
--disable_quality_filtering 
--n_base_limit  1   
--json "/tmp/dadaist2_oaSFvt/F3D144.json" 
--html /dev/null  
--trim_tail1 0 
--trim_tail2 0 
--length_required 110 


Standard output
Standard error
Detecting adapter sequence for read1...
No adapter detected for read1

Detecting adapter sequence for read2...
No adapter detected for read2

Read1 before filtering:
total reads: 4827
total bases: 1211542
Q20 bases: 1145768(94.5711%)
Q30 bases: 1111861(91.7724%)

Read2 before filtering:
total reads: 4827
total bases: 1209516
Q20 bases: 1028996(85.075%)
Q30 bases: 941297(77.8243%)

Read1 after filtering:
total reads: 4827
total bases: 1114994
Q20 bases: 1050668(94.2308%)
Q30 bases: 1017161(91.2257%)

Read2 aftering filtering:
total reads: 4827
total bases: 1112967
Q20 bases: 936318(84.1281%)
Q30 bases: 849968(76.3696%)

Filtering result:
reads passed filter: 9654
reads failed due to low quality: 0
reads failed due to too many N: 0
reads failed due to too short: 0
reads with adapter trimmed: 7934
bases trimmed due to adapters: 17

Duplication rate: 21.6667%

Insert size peak (evaluated by paired-end reads): 252

JSON report: /tmp/dadaist2_oaSFvt/F3D144.json
HTML report: /dev/null

fastp -w 8 -i /home/ubuntu/volume/16s/mothur-sop/subsample/F3D144_S210_L001_R1_001.fastq -I /home/ubuntu/volume/16s/mothur-sop/subsample/F3D144_S210_L001_R2_001.fastq -o /tmp/dadaist2_oaSFvt/for/F3D144_R1.fastq.gz -O /tmp/dadaist2_oaSFvt/rev/F3D144_R2.fastq.gz --trim_front1 20 --trim_front2 20 --detect_adapter_for_pe --disable_quality_filtering --n_base_limit 1 --json /tmp/dadaist2_oaSFvt/F3D144.json --html /dev/null --trim_tail1 0 --trim_tail2 0 --length_required 110 
fastp v0.20.1, time used: 1 seconds


Shell command fastp
Executed at 2021-04-08 20:39:48 for 0.99s and  returned 0 
'
Command
fastp 
-w 8 
-i "/home/ubuntu/volume/16s/mothur-sop/subsample/F3D145_S211_L001_R1_001.fastq" 
-I "/home/ubuntu/volume/16s/mothur-sop/subsample/F3D145_S211_L001_R2_001.fastq" 
-o "/tmp/dadaist2_oaSFvt"/for/F3D145_R1.fastq.gz 
-O  "/tmp/dadaist2_oaSFvt"/rev/F3D145_R2.fastq.gz   
--trim_front1 20 
--trim_front2  20  
--detect_adapter_for_pe 
--disable_quality_filtering 
--n_base_limit  1   
--json "/tmp/dadaist2_oaSFvt/F3D145.json" 
--html /dev/null  
--trim_tail1 0 
--trim_tail2 0 
--length_required 110 


Standard output
Standard error
Detecting adapter sequence for read1...
No adapter detected for read1

Detecting adapter sequence for read2...
No adapter detected for read2

Read1 before filtering:
total reads: 7377
total bases: 1851563
Q20 bases: 1765537(95.3539%)
Q30 bases: 1720406(92.9164%)

Read2 before filtering:
total reads: 7377
total bases: 1848416
Q20 bases: 1573021(85.101%)
Q30 bases: 1437093(77.7473%)

Read1 after filtering:
total reads: 7377
total bases: 1704022
Q20 bases: 1619936(95.0654%)
Q30 bases: 1575344(92.4486%)

Read2 aftering filtering:
total reads: 7377
total bases: 1700876
Q20 bases: 1430515(84.1046%)
Q30 bases: 1296320(76.2148%)

Filtering result:
reads passed filter: 14754
reads failed due to low quality: 0
reads failed due to too many N: 0
reads failed due to too short: 0
reads with adapter trimmed: 12144
bases trimmed due to adapters: 1

Duplication rate: 31.3953%

Insert size peak (evaluated by paired-end reads): 252

JSON report: /tmp/dadaist2_oaSFvt/F3D145.json
HTML report: /dev/null

fastp -w 8 -i /home/ubuntu/volume/16s/mothur-sop/subsample/F3D145_S211_L001_R1_001.fastq -I /home/ubuntu/volume/16s/mothur-sop/subsample/F3D145_S211_L001_R2_001.fastq -o /tmp/dadaist2_oaSFvt/for/F3D145_R1.fastq.gz -O /tmp/dadaist2_oaSFvt/rev/F3D145_R2.fastq.gz --trim_front1 20 --trim_front2 20 --detect_adapter_for_pe --disable_quality_filtering --n_base_limit 1 --json /tmp/dadaist2_oaSFvt/F3D145.json --html /dev/null --trim_tail1 0 --trim_tail2 0 --length_required 110 
fastp v0.20.1, time used: 1 seconds


Shell command fastp
Executed at 2021-04-08 20:39:49 for 0.89s and  returned 0 
'
Command
fastp 
-w 8 
-i "/home/ubuntu/volume/16s/mothur-sop/subsample/F3D146_S212_L001_R1_001.fastq" 
-I "/home/ubuntu/volume/16s/mothur-sop/subsample/F3D146_S212_L001_R2_001.fastq" 
-o "/tmp/dadaist2_oaSFvt"/for/F3D146_R1.fastq.gz 
-O  "/tmp/dadaist2_oaSFvt"/rev/F3D146_R2.fastq.gz   
--trim_front1 20 
--trim_front2  20  
--detect_adapter_for_pe 
--disable_quality_filtering 
--n_base_limit  1   
--json "/tmp/dadaist2_oaSFvt/F3D146.json" 
--html /dev/null  
--trim_tail1 0 
--trim_tail2 0 
--length_required 110 


Standard output
Standard error
Detecting adapter sequence for read1...
No adapter detected for read1

Detecting adapter sequence for read2...
No adapter detected for read2

Read1 before filtering:
total reads: 5021
total bases: 1260202
Q20 bases: 1195680(94.88%)
Q30 bases: 1161117(92.1374%)

Read2 before filtering:
total reads: 5021
total bases: 1258570
Q20 bases: 1107912(88.0294%)
Q30 bases: 1032060(82.0026%)

Read1 after filtering:
total reads: 5020
total bases: 1159551
Q20 bases: 1096672(94.5773%)
Q30 bases: 1062718(91.6491%)

Read2 aftering filtering:
total reads: 5020
total bases: 1157919
Q20 bases: 1010783(87.2931%)
Q30 bases: 936242(80.8556%)

Filtering result:
reads passed filter: 10040
reads failed due to low quality: 0
reads failed due to too many N: 0
reads failed due to too short: 2
reads with adapter trimmed: 8838
bases trimmed due to adapters: 288

Duplication rate: 14.5455%

Insert size peak (evaluated by paired-end reads): 252

JSON report: /tmp/dadaist2_oaSFvt/F3D146.json
HTML report: /dev/null

fastp -w 8 -i /home/ubuntu/volume/16s/mothur-sop/subsample/F3D146_S212_L001_R1_001.fastq -I /home/ubuntu/volume/16s/mothur-sop/subsample/F3D146_S212_L001_R2_001.fastq -o /tmp/dadaist2_oaSFvt/for/F3D146_R1.fastq.gz -O /tmp/dadaist2_oaSFvt/rev/F3D146_R2.fastq.gz --trim_front1 20 --trim_front2 20 --detect_adapter_for_pe --disable_quality_filtering --n_base_limit 1 --json /tmp/dadaist2_oaSFvt/F3D146.json --html /dev/null --trim_tail1 0 --trim_tail2 0 --length_required 110 
fastp v0.20.1, time used: 1 seconds


Shell command fastp
Executed at 2021-04-08 20:39:50 for 5.32s and  returned 0 
'
Command
fastp 
-w 8 
-i "/home/ubuntu/volume/16s/mothur-sop/subsample/F3D147_S213_L001_R1_001.fastq" 
-I "/home/ubuntu/volume/16s/mothur-sop/subsample/F3D147_S213_L001_R2_001.fastq" 
-o "/tmp/dadaist2_oaSFvt"/for/F3D147_R1.fastq.gz 
-O  "/tmp/dadaist2_oaSFvt"/rev/F3D147_R2.fastq.gz   
--trim_front1 20 
--trim_front2  20  
--detect_adapter_for_pe 
--disable_quality_filtering 
--n_base_limit  1   
--json "/tmp/dadaist2_oaSFvt/F3D147.json" 
--html /dev/null  
--trim_tail1 0 
--trim_tail2 0 
--length_required 110 


Standard output
Standard error
Detecting adapter sequence for read1...
No adapter detected for read1

Detecting adapter sequence for read2...
No adapter detected for read2

Read1 before filtering:
total reads: 17070
total bases: 4284410
Q20 bases: 4095597(95.593%)
Q30 bases: 3993384(93.2073%)

Read2 before filtering:
total reads: 17070
total bases: 4277194
Q20 bases: 3665315(85.6944%)
Q30 bases: 3362295(78.6098%)

Read1 after filtering:
total reads: 17070
total bases: 3942976
Q20 bases: 3759218(95.3396%)
Q30 bases: 3658702(92.7904%)

Read2 aftering filtering:
total reads: 17070
total bases: 3935759
Q20 bases: 3335420(84.7466%)
Q30 bases: 3036422(77.1496%)

Filtering result:
reads passed filter: 34140
reads failed due to low quality: 0
reads failed due to too many N: 0
reads failed due to too short: 0
reads with adapter trimmed: 27206
bases trimmed due to adapters: 69

Duplication rate: 12.3711%

Insert size peak (evaluated by paired-end reads): 252

JSON report: /tmp/dadaist2_oaSFvt/F3D147.json
HTML report: /dev/null

fastp -w 8 -i /home/ubuntu/volume/16s/mothur-sop/subsample/F3D147_S213_L001_R1_001.fastq -I /home/ubuntu/volume/16s/mothur-sop/subsample/F3D147_S213_L001_R2_001.fastq -o /tmp/dadaist2_oaSFvt/for/F3D147_R1.fastq.gz -O /tmp/dadaist2_oaSFvt/rev/F3D147_R2.fastq.gz --trim_front1 20 --trim_front2 20 --detect_adapter_for_pe --disable_quality_filtering --n_base_limit 1 --json /tmp/dadaist2_oaSFvt/F3D147.json --html /dev/null --trim_tail1 0 --trim_tail2 0 --length_required 110 
fastp v0.20.1, time used: 5 seconds


Shell command fastp
Executed at 2021-04-08 20:39:56 for 4.00s and  returned 0 
'
Command
fastp 
-w 8 
-i "/home/ubuntu/volume/16s/mothur-sop/subsample/F3D148_S214_L001_R1_001.fastq" 
-I "/home/ubuntu/volume/16s/mothur-sop/subsample/F3D148_S214_L001_R2_001.fastq" 
-o "/tmp/dadaist2_oaSFvt"/for/F3D148_R1.fastq.gz 
-O  "/tmp/dadaist2_oaSFvt"/rev/F3D148_R2.fastq.gz   
--trim_front1 20 
--trim_front2  20  
--detect_adapter_for_pe 
--disable_quality_filtering 
--n_base_limit  1   
--json "/tmp/dadaist2_oaSFvt/F3D148.json" 
--html /dev/null  
--trim_tail1 0 
--trim_tail2 0 
--length_required 110 


Standard output
Standard error
Detecting adapter sequence for read1...
No adapter detected for read1

Detecting adapter sequence for read2...
No adapter detected for read2

Read1 before filtering:
total reads: 12405
total bases: 3113525
Q20 bases: 2970870(95.4182%)
Q30 bases: 2893974(92.9485%)

Read2 before filtering:
total reads: 12405
total bases: 3108849
Q20 bases: 2712242(87.2426%)
Q30 bases: 2510990(80.7691%)

Read1 after filtering:
total reads: 12405
total bases: 2865381
Q20 bases: 2726448(95.1513%)
Q30 bases: 2650805(92.5114%)

Read2 aftering filtering:
total reads: 12405
total bases: 2860710
Q20 bases: 2471675(86.4008%)
Q30 bases: 2273009(79.4561%)

Filtering result:
reads passed filter: 24810
reads failed due to low quality: 0
reads failed due to too many N: 0
reads failed due to too short: 0
reads with adapter trimmed: 21052
bases trimmed due to adapters: 83

Duplication rate: 9.21053%

Insert size peak (evaluated by paired-end reads): 252

JSON report: /tmp/dadaist2_oaSFvt/F3D148.json
HTML report: /dev/null

fastp -w 8 -i /home/ubuntu/volume/16s/mothur-sop/subsample/F3D148_S214_L001_R1_001.fastq -I /home/ubuntu/volume/16s/mothur-sop/subsample/F3D148_S214_L001_R2_001.fastq -o /tmp/dadaist2_oaSFvt/for/F3D148_R1.fastq.gz -O /tmp/dadaist2_oaSFvt/rev/F3D148_R2.fastq.gz --trim_front1 20 --trim_front2 20 --detect_adapter_for_pe --disable_quality_filtering --n_base_limit 1 --json /tmp/dadaist2_oaSFvt/F3D148.json --html /dev/null --trim_tail1 0 --trim_tail2 0 --length_required 110 
fastp v0.20.1, time used: 4 seconds


Shell command fastp
Executed at 2021-04-08 20:40:00 for 4.33s and  returned 0 
'
Command
fastp 
-w 8 
-i "/home/ubuntu/volume/16s/mothur-sop/subsample/F3D149_S215_L001_R1_001.fastq" 
-I "/home/ubuntu/volume/16s/mothur-sop/subsample/F3D149_S215_L001_R2_001.fastq" 
-o "/tmp/dadaist2_oaSFvt"/for/F3D149_R1.fastq.gz 
-O  "/tmp/dadaist2_oaSFvt"/rev/F3D149_R2.fastq.gz   
--trim_front1 20 
--trim_front2  20  
--detect_adapter_for_pe 
--disable_quality_filtering 
--n_base_limit  1   
--json "/tmp/dadaist2_oaSFvt/F3D149.json" 
--html /dev/null  
--trim_tail1 0 
--trim_tail2 0 
--length_required 110 


Standard output
Standard error
Detecting adapter sequence for read1...
No adapter detected for read1

Detecting adapter sequence for read2...
No adapter detected for read2

Read1 before filtering:
total reads: 13083
total bases: 3283570
Q20 bases: 3126205(95.2075%)
Q30 bases: 3041024(92.6133%)

Read2 before filtering:
total reads: 13083
total bases: 3278781
Q20 bases: 2866585(87.4284%)
Q30 bases: 2658465(81.0809%)

Read1 after filtering:
total reads: 13083
total bases: 3021902
Q20 bases: 2868586(94.9265%)
Q30 bases: 2784863(92.156%)

Read2 aftering filtering:
total reads: 13083
total bases: 3017112
Q20 bases: 2613017(86.6066%)
Q30 bases: 2407686(79.801%)

Filtering result:
reads passed filter: 26166
reads failed due to low quality: 0
reads failed due to too many N: 0
reads failed due to too short: 0
reads with adapter trimmed: 22612
bases trimmed due to adapters: 17

Duplication rate: 13.5417%

Insert size peak (evaluated by paired-end reads): 252

JSON report: /tmp/dadaist2_oaSFvt/F3D149.json
HTML report: /dev/null

fastp -w 8 -i /home/ubuntu/volume/16s/mothur-sop/subsample/F3D149_S215_L001_R1_001.fastq -I /home/ubuntu/volume/16s/mothur-sop/subsample/F3D149_S215_L001_R2_001.fastq -o /tmp/dadaist2_oaSFvt/for/F3D149_R1.fastq.gz -O /tmp/dadaist2_oaSFvt/rev/F3D149_R2.fastq.gz --trim_front1 20 --trim_front2 20 --detect_adapter_for_pe --disable_quality_filtering --n_base_limit 1 --json /tmp/dadaist2_oaSFvt/F3D149.json --html /dev/null --trim_tail1 0 --trim_tail2 0 --length_required 110 
fastp v0.20.1, time used: 4 seconds


Shell command fastp
Executed at 2021-04-08 20:40:05 for 0.93s and  returned 0 
'
Command
fastp 
-w 8 
-i "/home/ubuntu/volume/16s/mothur-sop/subsample/F3D150_S216_L001_R1_001.fastq" 
-I "/home/ubuntu/volume/16s/mothur-sop/subsample/F3D150_S216_L001_R2_001.fastq" 
-o "/tmp/dadaist2_oaSFvt"/for/F3D150_R1.fastq.gz 
-O  "/tmp/dadaist2_oaSFvt"/rev/F3D150_R2.fastq.gz   
--trim_front1 20 
--trim_front2  20  
--detect_adapter_for_pe 
--disable_quality_filtering 
--n_base_limit  1   
--json "/tmp/dadaist2_oaSFvt/F3D150.json" 
--html /dev/null  
--trim_tail1 0 
--trim_tail2 0 
--length_required 110 


Standard output
Standard error
Detecting adapter sequence for read1...
No adapter detected for read1

Detecting adapter sequence for read2...
No adapter detected for read2

Read1 before filtering:
total reads: 5509
total bases: 1382628
Q20 bases: 1318987(95.3971%)
Q30 bases: 1283968(92.8643%)

Read2 before filtering:
total reads: 5509
total bases: 1380722
Q20 bases: 1205351(87.2986%)
Q30 bases: 1117365(80.9261%)

Read1 after filtering:
total reads: 5509
total bases: 1272448
Q20 bases: 1210681(95.1458%)
Q30 bases: 1176308(92.4445%)

Read2 aftering filtering:
total reads: 5509
total bases: 1270542
Q20 bases: 1098380(86.4497%)
Q30 bases: 1011318(79.5974%)

Filtering result:
reads passed filter: 11018
reads failed due to low quality: 0
reads failed due to too many N: 0
reads failed due to too short: 0
reads with adapter trimmed: 9338
bases trimmed due to adapters: 0

Duplication rate: 15.7895%

Insert size peak (evaluated by paired-end reads): 252

JSON report: /tmp/dadaist2_oaSFvt/F3D150.json
HTML report: /dev/null

fastp -w 8 -i /home/ubuntu/volume/16s/mothur-sop/subsample/F3D150_S216_L001_R1_001.fastq -I /home/ubuntu/volume/16s/mothur-sop/subsample/F3D150_S216_L001_R2_001.fastq -o /tmp/dadaist2_oaSFvt/for/F3D150_R1.fastq.gz -O /tmp/dadaist2_oaSFvt/rev/F3D150_R2.fastq.gz --trim_front1 20 --trim_front2 20 --detect_adapter_for_pe --disable_quality_filtering --n_base_limit 1 --json /tmp/dadaist2_oaSFvt/F3D150.json --html /dev/null --trim_tail1 0 --trim_tail2 0 --length_required 110 
fastp v0.20.1, time used: 1 seconds


Shell command fastp
Executed at 2021-04-08 20:40:06 for 5.99s and  returned 0 
'
Command
fastp 
-w 8 
-i "/home/ubuntu/volume/16s/mothur-sop/subsample/F3D2_S190_L001_R1_001.fastq" 
-I "/home/ubuntu/volume/16s/mothur-sop/subsample/F3D2_S190_L001_R2_001.fastq" 
-o "/tmp/dadaist2_oaSFvt"/for/F3D2_R1.fastq.gz 
-O  "/tmp/dadaist2_oaSFvt"/rev/F3D2_R2.fastq.gz   
--trim_front1 20 
--trim_front2  20  
--detect_adapter_for_pe 
--disable_quality_filtering 
--n_base_limit  1   
--json "/tmp/dadaist2_oaSFvt/F3D2.json" 
--html /dev/null  
--trim_tail1 0 
--trim_tail2 0 
--length_required 110 


Standard output
Standard error
Detecting adapter sequence for read1...
No adapter detected for read1

Detecting adapter sequence for read2...
No adapter detected for read2

Read1 before filtering:
total reads: 19620
total bases: 4924442
Q20 bases: 4711317(95.6721%)
Q30 bases: 4596837(93.3474%)

Read2 before filtering:
total reads: 19620
total bases: 4917683
Q20 bases: 4310303(87.6491%)
Q30 bases: 4003016(81.4004%)

Read1 after filtering:
total reads: 19620
total bases: 4532039
Q20 bases: 4324602(95.4229%)
Q30 bases: 4211857(92.9351%)

Read2 aftering filtering:
total reads: 19620
total bases: 4525282
Q20 bases: 3929278(86.8295%)
Q30 bases: 3626015(80.1279%)

Filtering result:
reads passed filter: 39240
reads failed due to low quality: 0
reads failed due to too many N: 0
reads failed due to too short: 0
reads with adapter trimmed: 34966
bases trimmed due to adapters: 4

Duplication rate: 27.7027%

Insert size peak (evaluated by paired-end reads): 252

JSON report: /tmp/dadaist2_oaSFvt/F3D2.json
HTML report: /dev/null

fastp -w 8 -i /home/ubuntu/volume/16s/mothur-sop/subsample/F3D2_S190_L001_R1_001.fastq -I /home/ubuntu/volume/16s/mothur-sop/subsample/F3D2_S190_L001_R2_001.fastq -o /tmp/dadaist2_oaSFvt/for/F3D2_R1.fastq.gz -O /tmp/dadaist2_oaSFvt/rev/F3D2_R2.fastq.gz --trim_front1 20 --trim_front2 20 --detect_adapter_for_pe --disable_quality_filtering --n_base_limit 1 --json /tmp/dadaist2_oaSFvt/F3D2.json --html /dev/null --trim_tail1 0 --trim_tail2 0 --length_required 110 
fastp v0.20.1, time used: 6 seconds


Shell command fastp
Executed at 2021-04-08 20:40:12 for 0.97s and  returned 0 
'
Command
fastp 
-w 8 
-i "/home/ubuntu/volume/16s/mothur-sop/subsample/F3D3_S191_L001_R1_001.fastq" 
-I "/home/ubuntu/volume/16s/mothur-sop/subsample/F3D3_S191_L001_R2_001.fastq" 
-o "/tmp/dadaist2_oaSFvt"/for/F3D3_R1.fastq.gz 
-O  "/tmp/dadaist2_oaSFvt"/rev/F3D3_R2.fastq.gz   
--trim_front1 20 
--trim_front2  20  
--detect_adapter_for_pe 
--disable_quality_filtering 
--n_base_limit  1   
--json "/tmp/dadaist2_oaSFvt/F3D3.json" 
--html /dev/null  
--trim_tail1 0 
--trim_tail2 0 
--length_required 110 


Standard output
Standard error
Detecting adapter sequence for read1...
No adapter detected for read1

Detecting adapter sequence for read2...
No adapter detected for read2

Read1 before filtering:
total reads: 6758
total bases: 1696205
Q20 bases: 1619690(95.489%)
Q30 bases: 1579885(93.1423%)

Read2 before filtering:
total reads: 6758
total bases: 1693513
Q20 bases: 1474137(87.0461%)
Q30 bases: 1363890(80.5361%)

Read1 after filtering:
total reads: 6758
total bases: 1561045
Q20 bases: 1486387(95.2174%)
Q30 bases: 1447131(92.7027%)

Read2 aftering filtering:
total reads: 6758
total bases: 1558353
Q20 bases: 1342978(86.1793%)
Q30 bases: 1234150(79.1958%)

Filtering result:
reads passed filter: 13516
reads failed due to low quality: 0
reads failed due to too many N: 0
reads failed due to too short: 0
reads with adapter trimmed: 11696
bases trimmed due to adapters: 0

Duplication rate: 39.3939%

Insert size peak (evaluated by paired-end reads): 252

JSON report: /tmp/dadaist2_oaSFvt/F3D3.json
HTML report: /dev/null

fastp -w 8 -i /home/ubuntu/volume/16s/mothur-sop/subsample/F3D3_S191_L001_R1_001.fastq -I /home/ubuntu/volume/16s/mothur-sop/subsample/F3D3_S191_L001_R2_001.fastq -o /tmp/dadaist2_oaSFvt/for/F3D3_R1.fastq.gz -O /tmp/dadaist2_oaSFvt/rev/F3D3_R2.fastq.gz --trim_front1 20 --trim_front2 20 --detect_adapter_for_pe --disable_quality_filtering --n_base_limit 1 --json /tmp/dadaist2_oaSFvt/F3D3.json --html /dev/null --trim_tail1 0 --trim_tail2 0 --length_required 110 
fastp v0.20.1, time used: 1 seconds


Shell command fastp
Executed at 2021-04-08 20:40:14 for 0.91s and  returned 0 
'
Command
fastp 
-w 8 
-i "/home/ubuntu/volume/16s/mothur-sop/subsample/F3D5_S193_L001_R1_001.fastq" 
-I "/home/ubuntu/volume/16s/mothur-sop/subsample/F3D5_S193_L001_R2_001.fastq" 
-o "/tmp/dadaist2_oaSFvt"/for/F3D5_R1.fastq.gz 
-O  "/tmp/dadaist2_oaSFvt"/rev/F3D5_R2.fastq.gz   
--trim_front1 20 
--trim_front2  20  
--detect_adapter_for_pe 
--disable_quality_filtering 
--n_base_limit  1   
--json "/tmp/dadaist2_oaSFvt/F3D5.json" 
--html /dev/null  
--trim_tail1 0 
--trim_tail2 0 
--length_required 110 


Standard output
Standard error
Detecting adapter sequence for read1...
No adapter detected for read1

Detecting adapter sequence for read2...
No adapter detected for read2

Read1 before filtering:
total reads: 4448
total bases: 1116401
Q20 bases: 1061302(95.0646%)
Q30 bases: 1031817(92.4235%)

Read2 before filtering:
total reads: 4448
total bases: 1115006
Q20 bases: 973168(87.2792%)
Q30 bases: 904231(81.0965%)

Read1 after filtering:
total reads: 4448
total bases: 1027441
Q20 bases: 973610(94.7607%)
Q30 bases: 944510(91.9284%)

Read2 aftering filtering:
total reads: 4448
total bases: 1026046
Q20 bases: 886769(86.4259%)
Q30 bases: 818680(79.7898%)

Filtering result:
reads passed filter: 8896
reads failed due to low quality: 0
reads failed due to too many N: 0
reads failed due to too short: 0
reads with adapter trimmed: 7716
bases trimmed due to adapters: 0

Duplication rate: 20%

Insert size peak (evaluated by paired-end reads): 253

JSON report: /tmp/dadaist2_oaSFvt/F3D5.json
HTML report: /dev/null

fastp -w 8 -i /home/ubuntu/volume/16s/mothur-sop/subsample/F3D5_S193_L001_R1_001.fastq -I /home/ubuntu/volume/16s/mothur-sop/subsample/F3D5_S193_L001_R2_001.fastq -o /tmp/dadaist2_oaSFvt/for/F3D5_R1.fastq.gz -O /tmp/dadaist2_oaSFvt/rev/F3D5_R2.fastq.gz --trim_front1 20 --trim_front2 20 --detect_adapter_for_pe --disable_quality_filtering --n_base_limit 1 --json /tmp/dadaist2_oaSFvt/F3D5.json --html /dev/null --trim_tail1 0 --trim_tail2 0 --length_required 110 
fastp v0.20.1, time used: 0 seconds


Shell command fastp
Executed at 2021-04-08 20:40:15 for 1.05s and  returned 0 
'
Command
fastp 
-w 8 
-i "/home/ubuntu/volume/16s/mothur-sop/subsample/F3D6_S194_L001_R1_001.fastq" 
-I "/home/ubuntu/volume/16s/mothur-sop/subsample/F3D6_S194_L001_R2_001.fastq" 
-o "/tmp/dadaist2_oaSFvt"/for/F3D6_R1.fastq.gz 
-O  "/tmp/dadaist2_oaSFvt"/rev/F3D6_R2.fastq.gz   
--trim_front1 20 
--trim_front2  20  
--detect_adapter_for_pe 
--disable_quality_filtering 
--n_base_limit  1   
--json "/tmp/dadaist2_oaSFvt/F3D6.json" 
--html /dev/null  
--trim_tail1 0 
--trim_tail2 0 
--length_required 110 


Standard output
Standard error
Detecting adapter sequence for read1...
No adapter detected for read1

Detecting adapter sequence for read2...
No adapter detected for read2

Read1 before filtering:
total reads: 7989
total bases: 2005171
Q20 bases: 1916532(95.5795%)
Q30 bases: 1869292(93.2236%)

Read2 before filtering:
total reads: 7989
total bases: 2002558
Q20 bases: 1760851(87.9301%)
Q30 bases: 1639465(81.8685%)

Read1 after filtering:
total reads: 7989
total bases: 1845388
Q20 bases: 1759084(95.3233%)
Q30 bases: 1712491(92.7984%)

Read2 aftering filtering:
total reads: 7989
total bases: 1842777
Q20 bases: 1605757(87.1379%)
Q30 bases: 1486156(80.6476%)

Filtering result:
reads passed filter: 15978
reads failed due to low quality: 0
reads failed due to too many N: 0
reads failed due to too short: 0
reads with adapter trimmed: 14336
bases trimmed due to adapters: 4

Duplication rate: 64.881%

Insert size peak (evaluated by paired-end reads): 252

JSON report: /tmp/dadaist2_oaSFvt/F3D6.json
HTML report: /dev/null

fastp -w 8 -i /home/ubuntu/volume/16s/mothur-sop/subsample/F3D6_S194_L001_R1_001.fastq -I /home/ubuntu/volume/16s/mothur-sop/subsample/F3D6_S194_L001_R2_001.fastq -o /tmp/dadaist2_oaSFvt/for/F3D6_R1.fastq.gz -O /tmp/dadaist2_oaSFvt/rev/F3D6_R2.fastq.gz --trim_front1 20 --trim_front2 20 --detect_adapter_for_pe --disable_quality_filtering --n_base_limit 1 --json /tmp/dadaist2_oaSFvt/F3D6.json --html /dev/null --trim_tail1 0 --trim_tail2 0 --length_required 110 
fastp v0.20.1, time used: 1 seconds


Shell command fastp
Executed at 2021-04-08 20:40:16 for 0.91s and  returned 0 
'
Command
fastp 
-w 8 
-i "/home/ubuntu/volume/16s/mothur-sop/subsample/F3D7_S195_L001_R1_001.fastq" 
-I "/home/ubuntu/volume/16s/mothur-sop/subsample/F3D7_S195_L001_R2_001.fastq" 
-o "/tmp/dadaist2_oaSFvt"/for/F3D7_R1.fastq.gz 
-O  "/tmp/dadaist2_oaSFvt"/rev/F3D7_R2.fastq.gz   
--trim_front1 20 
--trim_front2  20  
--detect_adapter_for_pe 
--disable_quality_filtering 
--n_base_limit  1   
--json "/tmp/dadaist2_oaSFvt/F3D7.json" 
--html /dev/null  
--trim_tail1 0 
--trim_tail2 0 
--length_required 110 


Standard output
Standard error
Detecting adapter sequence for read1...
No adapter detected for read1

Detecting adapter sequence for read2...
No adapter detected for read2

Read1 before filtering:
total reads: 5129
total bases: 1287342
Q20 bases: 1234208(95.8726%)
Q30 bases: 1206272(93.7025%)

Read2 before filtering:
total reads: 5129
total bases: 1285368
Q20 bases: 1124901(87.5159%)
Q30 bases: 1043858(81.2108%)

Read1 after filtering:
total reads: 5129
total bases: 1184762
Q20 bases: 1133099(95.6394%)
Q30 bases: 1105562(93.3151%)

Read2 aftering filtering:
total reads: 5129
total bases: 1182788
Q20 bases: 1025269(86.6824%)
Q30 bases: 945379(79.928%)

Filtering result:
reads passed filter: 10258
reads failed due to low quality: 0
reads failed due to too many N: 0
reads failed due to too short: 0
reads with adapter trimmed: 9072
bases trimmed due to adapters: 0

Duplication rate: 26.9231%

Insert size peak (evaluated by paired-end reads): 252

JSON report: /tmp/dadaist2_oaSFvt/F3D7.json
HTML report: /dev/null

fastp -w 8 -i /home/ubuntu/volume/16s/mothur-sop/subsample/F3D7_S195_L001_R1_001.fastq -I /home/ubuntu/volume/16s/mothur-sop/subsample/F3D7_S195_L001_R2_001.fastq -o /tmp/dadaist2_oaSFvt/for/F3D7_R1.fastq.gz -O /tmp/dadaist2_oaSFvt/rev/F3D7_R2.fastq.gz --trim_front1 20 --trim_front2 20 --detect_adapter_for_pe --disable_quality_filtering --n_base_limit 1 --json /tmp/dadaist2_oaSFvt/F3D7.json --html /dev/null --trim_tail1 0 --trim_tail2 0 --length_required 110 
fastp v0.20.1, time used: 1 seconds


Shell command fastp
Executed at 2021-04-08 20:40:17 for 0.89s and  returned 0 
'
Command
fastp 
-w 8 
-i "/home/ubuntu/volume/16s/mothur-sop/subsample/F3D8_S196_L001_R1_001.fastq" 
-I "/home/ubuntu/volume/16s/mothur-sop/subsample/F3D8_S196_L001_R2_001.fastq" 
-o "/tmp/dadaist2_oaSFvt"/for/F3D8_R1.fastq.gz 
-O  "/tmp/dadaist2_oaSFvt"/rev/F3D8_R2.fastq.gz   
--trim_front1 20 
--trim_front2  20  
--detect_adapter_for_pe 
--disable_quality_filtering 
--n_base_limit  1   
--json "/tmp/dadaist2_oaSFvt/F3D8.json" 
--html /dev/null  
--trim_tail1 0 
--trim_tail2 0 
--length_required 110 


Standard output
Standard error
Detecting adapter sequence for read1...
No adapter detected for read1

Detecting adapter sequence for read2...
No adapter detected for read2

Read1 before filtering:
total reads: 5294
total bases: 1328727
Q20 bases: 1263542(95.0942%)
Q30 bases: 1229075(92.5002%)

Read2 before filtering:
total reads: 5294
total bases: 1327298
Q20 bases: 1182193(89.0676%)
Q30 bases: 1110909(83.697%)

Read1 after filtering:
total reads: 5294
total bases: 1222846
Q20 bases: 1159215(94.7965%)
Q30 bases: 1125223(92.0167%)

Read2 aftering filtering:
total reads: 5294
total bases: 1221417
Q20 bases: 1079533(88.3837%)
Q30 bases: 1009406(82.6422%)

Filtering result:
reads passed filter: 10588
reads failed due to low quality: 0
reads failed due to too many N: 0
reads failed due to too short: 0
reads with adapter trimmed: 9738
bases trimmed due to adapters: 2

Duplication rate: 25.8824%

Insert size peak (evaluated by paired-end reads): 253

JSON report: /tmp/dadaist2_oaSFvt/F3D8.json
HTML report: /dev/null

fastp -w 8 -i /home/ubuntu/volume/16s/mothur-sop/subsample/F3D8_S196_L001_R1_001.fastq -I /home/ubuntu/volume/16s/mothur-sop/subsample/F3D8_S196_L001_R2_001.fastq -o /tmp/dadaist2_oaSFvt/for/F3D8_R1.fastq.gz -O /tmp/dadaist2_oaSFvt/rev/F3D8_R2.fastq.gz --trim_front1 20 --trim_front2 20 --detect_adapter_for_pe --disable_quality_filtering --n_base_limit 1 --json /tmp/dadaist2_oaSFvt/F3D8.json --html /dev/null --trim_tail1 0 --trim_tail2 0 --length_required 110 
fastp v0.20.1, time used: 1 seconds


Shell command fastp
Executed at 2021-04-08 20:40:19 for 0.96s and  returned 0 
'
Command
fastp 
-w 8 
-i "/home/ubuntu/volume/16s/mothur-sop/subsample/F3D9_S197_L001_R1_001.fastq" 
-I "/home/ubuntu/volume/16s/mothur-sop/subsample/F3D9_S197_L001_R2_001.fastq" 
-o "/tmp/dadaist2_oaSFvt"/for/F3D9_R1.fastq.gz 
-O  "/tmp/dadaist2_oaSFvt"/rev/F3D9_R2.fastq.gz   
--trim_front1 20 
--trim_front2  20  
--detect_adapter_for_pe 
--disable_quality_filtering 
--n_base_limit  1   
--json "/tmp/dadaist2_oaSFvt/F3D9.json" 
--html /dev/null  
--trim_tail1 0 
--trim_tail2 0 
--length_required 110 


Standard output
Standard error
Detecting adapter sequence for read1...
No adapter detected for read1

Detecting adapter sequence for read2...
No adapter detected for read2

Read1 before filtering:
total reads: 7070
total bases: 1774487
Q20 bases: 1694396(95.4865%)
Q30 bases: 1651429(93.0652%)

Read2 before filtering:
total reads: 7070
total bases: 1772522
Q20 bases: 1574025(88.8014%)
Q30 bases: 1476473(83.2979%)

Read1 after filtering:
total reads: 7070
total bases: 1633087
Q20 bases: 1555002(95.2186%)
Q30 bases: 1512624(92.6236%)

Read2 aftering filtering:
total reads: 7070
total bases: 1631122
Q20 bases: 1437046(88.1017%)
Q30 bases: 1341227(82.2273%)

Filtering result:
reads passed filter: 14140
reads failed due to low quality: 0
reads failed due to too many N: 0
reads failed due to too short: 0
reads with adapter trimmed: 12980
bases trimmed due to adapters: 0

Duplication rate: 15.6627%

Insert size peak (evaluated by paired-end reads): 253

JSON report: /tmp/dadaist2_oaSFvt/F3D9.json
HTML report: /dev/null

fastp -w 8 -i /home/ubuntu/volume/16s/mothur-sop/subsample/F3D9_S197_L001_R1_001.fastq -I /home/ubuntu/volume/16s/mothur-sop/subsample/F3D9_S197_L001_R2_001.fastq -o /tmp/dadaist2_oaSFvt/for/F3D9_R1.fastq.gz -O /tmp/dadaist2_oaSFvt/rev/F3D9_R2.fastq.gz --trim_front1 20 --trim_front2 20 --detect_adapter_for_pe --disable_quality_filtering --n_base_limit 1 --json /tmp/dadaist2_oaSFvt/F3D9.json --html /dev/null --trim_tail1 0 --trim_tail2 0 --length_required 110 
fastp v0.20.1, time used: 1 seconds


Shell command fastp
Executed at 2021-04-08 20:40:20 for 0.85s and  returned 0 
'
Command
fastp 
-w 8 
-i "/home/ubuntu/volume/16s/mothur-sop/subsample/Mock_S280_L001_R1_001.fastq" 
-I "/home/ubuntu/volume/16s/mothur-sop/subsample/Mock_S280_L001_R2_001.fastq" 
-o "/tmp/dadaist2_oaSFvt"/for/Mock_R1.fastq.gz 
-O  "/tmp/dadaist2_oaSFvt"/rev/Mock_R2.fastq.gz   
--trim_front1 20 
--trim_front2  20  
--detect_adapter_for_pe 
--disable_quality_filtering 
--n_base_limit  1   
--json "/tmp/dadaist2_oaSFvt/Mock.json" 
--html /dev/null  
--trim_tail1 0 
--trim_tail2 0 
--length_required 110 


Standard output
Standard error
Detecting adapter sequence for read1...
No adapter detected for read1

Detecting adapter sequence for read2...
No adapter detected for read2

Read1 before filtering:
total reads: 4779
total bases: 1199027
Q20 bases: 1129105(94.1684%)
Q30 bases: 1093050(91.1614%)

Read2 before filtering:
total reads: 4779
total bases: 1197710
Q20 bases: 1085627(90.6419%)
Q30 bases: 1035678(86.4715%)

Read1 after filtering:
total reads: 4779
total bases: 1103445
Q20 bases: 1034947(93.7924%)
Q30 bases: 999505(90.5804%)

Read2 aftering filtering:
total reads: 4779
total bases: 1102128
Q20 bases: 993144(90.1115%)
Q30 bases: 944345(85.6838%)

Filtering result:
reads passed filter: 9558
reads failed due to low quality: 0
reads failed due to too many N: 0
reads failed due to too short: 0
reads with adapter trimmed: 9244
bases trimmed due to adapters: 4

Duplication rate: 18.1818%

Insert size peak (evaluated by paired-end reads): 253

JSON report: /tmp/dadaist2_oaSFvt/Mock.json
HTML report: /dev/null

fastp -w 8 -i /home/ubuntu/volume/16s/mothur-sop/subsample/Mock_S280_L001_R1_001.fastq -I /home/ubuntu/volume/16s/mothur-sop/subsample/Mock_S280_L001_R2_001.fastq -o /tmp/dadaist2_oaSFvt/for/Mock_R1.fastq.gz -O /tmp/dadaist2_oaSFvt/rev/Mock_R2.fastq.gz --trim_front1 20 --trim_front2 20 --detect_adapter_for_pe --disable_quality_filtering --n_base_limit 1 --json /tmp/dadaist2_oaSFvt/Mock.json --html /dev/null --trim_tail1 0 --trim_tail2 0 --length_required 110 
fastp v0.20.1, time used: 1 seconds

Shell command Rscript

Executed at 2021-04-08 20:40:21 for 188.01s and returned 0

'

Command

Rscript 
--vanilla /home/ubuntu/volume/dadaist2/bin/D2-dada.R /tmp/dadaist2_oaSFvt/for /tmp/dadaist2_oaSFvt/rev /tmp/dadaist2_oaSFvt/dada2/dada2.tsv /tmp/dadaist2_oaSFvt/dada2/stats.tsv /tmp/dadaist2_oaSFvt/for/filtered /tmp/dadaist2_oaSFvt/rev/filtered 231 215 0 0 1 1.5 10 consensus 1 32 10000 /tmp/dadaist2_oaSFvt do_plots /home/ubuntu/volume/dadaist2/refs/silva_nr_v138_train_set.fa.gz no 0 0

Standard output

R version 4.0.3 (2020-10-10) 
#DADA2: 1.18.0 / Rcpp: 1.0.6 / RcppParallel: 5.0.3 
2021-04-08 20:40:33 	[1] Filtering reads ....................
2021-04-08 20:41:47 	[2] Learning Error Rates
2872947 total bases in 12437 reads from 3 samples will be used for learning the error rates.
2673955 total bases in 12437 reads from 3 samples will be used for learning the error rates.
2021-04-08 20:41:58 	[3] Denoise remaining samples 
 * Sample by sample
2021-04-08 20:42:20	[4] Remove chimeras (method = consensus)
2021-04-08 20:42:20 	[5.1] Taxonomy
2021-04-08 20:43:29 	[6] Write output
	 *  /tmp/dadaist2_oaSFvt/dada2/dada2.tsv 
	 *  /tmp/dadaist2_oaSFvt/taxonomy.tsv 
Standard error
Loading required package: Rcpp
Duplicate sequences in merged output.
Duplicate sequences in merged output.
Duplicate sequences in merged output.
Duplicate sequences in merged output.
Duplicate sequences detected and merged.
Duplicate sequences detected and merged.
Duplicate sequences detected and merged.
Duplicate sequences detected and merged.

Not available.


Shell command Rscript

Executed at 2021-04-08 20:39:22 for 0.01s and returned 0

'

Command

Rscript  
--version 2>&1

Standard output

R scripting front-end version 4.0.3 (2020-10-10)
Standard error


Shell command /home/ubuntu/volume/dadaist2/bin/dadaist2-assigntax
Executed at 2021-04-08 20:39:22 for 0.22s and  returned 0 
'
Command
/home/ubuntu/volume/dadaist2/bin/dadaist2-assigntax --version


Standard output
dadaist2-assigntax 1.1.0
Standard error
 DADAIST2 Assign Taxonomy


Shell command /home/ubuntu/volume/dadaist2/bin/dadaist2-assigntax
Executed at 2021-04-08 20:39:22 for 0.22s and  returned 0 
'
Command
/home/ubuntu/volume/dadaist2/bin/dadaist2-assigntax --version


Standard output
dadaist2-assigntax 1.1.0
Standard error
 DADAIST2 Assign Taxonomy


Shell command clustalo
Executed at 2021-04-08 20:39:22 for 0.01s and  returned 0 
'
Command
clustalo 
--version 2>&1


Standard output
1.2.4
Standard error


Shell command echo
Executed at 2021-04-08 20:39:22 for 17.44s and  returned 0 
'
Command
echo "library(dada2)" | R 
--no-save > /dev/null


Standard output
Standard error
Loading required package: Rcpp


Shell command /home/ubuntu/volume/dadaist2/bin/dadaist2-exporter
Executed at 2021-04-08 20:39:40 for 0.11s and  returned 0 
'
Command
/home/ubuntu/volume/dadaist2/bin/dadaist2-exporter --version


Standard output
dadaist2-exporter 1.4.0
Standard error


Shell command fastp
Executed at 2021-04-08 20:39:40 for 0.01s and  returned 0 
'
Command
fastp 
--version 2>&1


Standard output
fastp 0.20.1
Standard error


Shell command fasttree
Executed at 2021-04-08 20:39:40 for 0.01s and  returned 0 
'
Command
fasttree 2>&1 | head 
-n 1 | cut 
-c 11-


Standard output
FastTree version 2.1.10 Double precision (No SSE3):
Standard error


Shell command fu-primers
Executed at 2021-04-08 20:39:40 for 0.03s and  returned 0 
'
Command
fu-primers 
--version 2>&1


Standard output
fu-primers 1.0
Standard error