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	/Users/telatina/git/dadaist2/data/16S
Output	/Users/telatina/git/dadaist2/output/tests/ref-decipher
Timestamp	20210305 11:28:57
Execution time	1m 17s

Parameters

Parameter	Value
Database	/Users/telatina/git/dadaist2/skip
Metadata	/Users/telatina/git/dadaist2
Threads	/Users/telatina/git/dadaist2/8

Machine details

Timestamp

Event

Processors

RAM

16 Gb

Model Name	MacBook Pro
Model Identifier	MacBookPro16,1
Processor Name	8-Core Intel Core i9
Processor Speed	2.3 GHz
Number of Processors	1
Total Number of Cores	8
L2 Cache (per Core)	256 KB
L3 Cache	16 MB
Hyper-Threading Technology	Enabled
Memory	16 GB
System Firmware Version	1554.60.15.0.0 (iBridge
Serial Number (system)	C02ZL5N9MD6N
Hardware UUID	8E0231F9-97C9-5983-93C9-B5825D7A0E67
Provisioning UDID	8E0231F9-97C9-5983-93C9-B5825D7A0E67
Activation Lock Status	Enabled

Shell command fastp

Executed at 2021-03-05 11:29:09 for 0.66s and returned 0

Command

fastp 
-w 8 
-i "/Users/telatina/git/dadaist2/data/16S/A01_S0_L001_R1_001.fastq.gz" 
-I "/Users/telatina/git/dadaist2/data/16S/A01_S0_L001_R2_001.fastq.gz" 
-o "/var/folders/qf/64kyljyn0njdfbz8nyrgjv8hxrrkbt/T/dadaist2_8OXSgR"/for/A01_R1.fastq.gz 
-O  "/var/folders/qf/64kyljyn0njdfbz8nyrgjv8hxrrkbt/T/dadaist2_8OXSgR"/rev/A01_R2.fastq.gz   
--trim_front1 20 
--trim_front2  20  
--detect_adapter_for_pe 
--disable_quality_filtering 
--n_base_limit  1   
--json "/var/folders/qf/64kyljyn0njdfbz8nyrgjv8hxrrkbt/T/dadaist2_8OXSgR/A01.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: 6137 total bases: 1847237 Q20 bases: 1648961(89.2663%) Q30 bases: 1490142(80.6687%) Read2 before filtering: total reads: 6137 total bases: 1847237 Q20 bases: 1577946(85.422%) Q30 bases: 1382606(74.8472%) Read1 after filtering: total reads: 6105 total bases: 1689825 Q20 bases: 1504522(89.0342%) Q30 bases: 1353780(80.1136%) Read2 aftering filtering: total reads: 6105 total bases: 1689825 Q20 bases: 1439363(85.1782%) Q30 bases: 1251309(74.0496%) Filtering result: reads passed filter: 12210 reads failed due to low quality: 0 reads failed due to too many N: 0 reads failed due to too short: 64 reads with adapter trimmed: 1090 bases trimmed due to adapters: 64672 Duplication rate: 7.27273% Insert size peak (evaluated by paired-end reads): 0 JSON report: /var/folders/qf/64kyljyn0njdfbz8nyrgjv8hxrrkbt/T/dadaist2_8OXSgR/A01.json HTML report: /dev/null fastp -w 8 -i /Users/telatina/git/dadaist2/data/16S/A01_S0_L001_R1_001.fastq.gz -I /Users/telatina/git/dadaist2/data/16S/A01_S0_L001_R2_001.fastq.gz -o /var/folders/qf/64kyljyn0njdfbz8nyrgjv8hxrrkbt/T/dadaist2_8OXSgR/for/A01_R1.fastq.gz -O /var/folders/qf/64kyljyn0njdfbz8nyrgjv8hxrrkbt/T/dadaist2_8OXSgR/rev/A01_R2.fastq.gz --trim_front1 20 --trim_front2 20 --detect_adapter_for_pe --disable_quality_filtering --n_base_limit 1 --json /var/folders/qf/64kyljyn0njdfbz8nyrgjv8hxrrkbt/T/dadaist2_8OXSgR/A01.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 2021-03-05 11:29:10 for 0.63s and returned 0

Command

fastp 
-w 8 
-i "/Users/telatina/git/dadaist2/data/16S/A02_S0_L001_R1_001.fastq.gz" 
-I "/Users/telatina/git/dadaist2/data/16S/A02_S0_L001_R2_001.fastq.gz" 
-o "/var/folders/qf/64kyljyn0njdfbz8nyrgjv8hxrrkbt/T/dadaist2_8OXSgR"/for/A02_R1.fastq.gz 
-O  "/var/folders/qf/64kyljyn0njdfbz8nyrgjv8hxrrkbt/T/dadaist2_8OXSgR"/rev/A02_R2.fastq.gz   
--trim_front1 20 
--trim_front2  20  
--detect_adapter_for_pe 
--disable_quality_filtering 
--n_base_limit  1   
--json "/var/folders/qf/64kyljyn0njdfbz8nyrgjv8hxrrkbt/T/dadaist2_8OXSgR/A02.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: 5414 total bases: 1629614 Q20 bases: 1454370(89.2463%) Q30 bases: 1311878(80.5024%) Read2 before filtering: total reads: 5414 total bases: 1629614 Q20 bases: 1412945(86.7043%) Q30 bases: 1240421(76.1175%) Read1 after filtering: total reads: 5399 total bases: 1508588 Q20 bases: 1338035(88.6945%) Q30 bases: 1200838(79.6001%) Read2 aftering filtering: total reads: 5399 total bases: 1508588 Q20 bases: 1299416(86.1346%) Q30 bases: 1130799(74.9574%) Filtering result: reads passed filter: 10798 reads failed due to low quality: 0 reads failed due to too many N: 0 reads failed due to too short: 30 reads with adapter trimmed: 648 bases trimmed due to adapters: 23266 Duplication rate: 14.6341% Insert size peak (evaluated by paired-end reads): 0 JSON report: /var/folders/qf/64kyljyn0njdfbz8nyrgjv8hxrrkbt/T/dadaist2_8OXSgR/A02.json HTML report: /dev/null fastp -w 8 -i /Users/telatina/git/dadaist2/data/16S/A02_S0_L001_R1_001.fastq.gz -I /Users/telatina/git/dadaist2/data/16S/A02_S0_L001_R2_001.fastq.gz -o /var/folders/qf/64kyljyn0njdfbz8nyrgjv8hxrrkbt/T/dadaist2_8OXSgR/for/A02_R1.fastq.gz -O /var/folders/qf/64kyljyn0njdfbz8nyrgjv8hxrrkbt/T/dadaist2_8OXSgR/rev/A02_R2.fastq.gz --trim_front1 20 --trim_front2 20 --detect_adapter_for_pe --disable_quality_filtering --n_base_limit 1 --json /var/folders/qf/64kyljyn0njdfbz8nyrgjv8hxrrkbt/T/dadaist2_8OXSgR/A02.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 2021-03-05 11:29:11 for 0.70s and returned 0

Command

fastp 
-w 8 
-i "/Users/telatina/git/dadaist2/data/16S/F99_S0_L001_R1_001.fastq.gz" 
-I "/Users/telatina/git/dadaist2/data/16S/F99_S0_L001_R2_001.fastq.gz" 
-o "/var/folders/qf/64kyljyn0njdfbz8nyrgjv8hxrrkbt/T/dadaist2_8OXSgR"/for/F99_R1.fastq.gz 
-O  "/var/folders/qf/64kyljyn0njdfbz8nyrgjv8hxrrkbt/T/dadaist2_8OXSgR"/rev/F99_R2.fastq.gz   
--trim_front1 20 
--trim_front2  20  
--detect_adapter_for_pe 
--disable_quality_filtering 
--n_base_limit  1   
--json "/var/folders/qf/64kyljyn0njdfbz8nyrgjv8hxrrkbt/T/dadaist2_8OXSgR/F99.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: 4553 total bases: 1370453 Q20 bases: 1233254(89.9888%) Q30 bases: 1118036(81.5815%) Read2 before filtering: total reads: 4553 total bases: 1370453 Q20 bases: 1175086(85.7443%) Q30 bases: 1025042(74.7959%) Read1 after filtering: total reads: 4536 total bases: 1267283 Q20 bases: 1134520(89.5238%) Q30 bases: 1023409(80.7562%) Read2 aftering filtering: total reads: 4536 total bases: 1267283 Q20 bases: 1078894(85.1344%) Q30 bases: 932192(73.5583%) Filtering result: reads passed filter: 9072 reads failed due to low quality: 0 reads failed due to too many N: 0 reads failed due to too short: 34 reads with adapter trimmed: 432 bases trimmed due to adapters: 21554 Duplication rate: 10.8911% Insert size peak (evaluated by paired-end reads): 0 JSON report: /var/folders/qf/64kyljyn0njdfbz8nyrgjv8hxrrkbt/T/dadaist2_8OXSgR/F99.json HTML report: /dev/null fastp -w 8 -i /Users/telatina/git/dadaist2/data/16S/F99_S0_L001_R1_001.fastq.gz -I /Users/telatina/git/dadaist2/data/16S/F99_S0_L001_R2_001.fastq.gz -o /var/folders/qf/64kyljyn0njdfbz8nyrgjv8hxrrkbt/T/dadaist2_8OXSgR/for/F99_R1.fastq.gz -O /var/folders/qf/64kyljyn0njdfbz8nyrgjv8hxrrkbt/T/dadaist2_8OXSgR/rev/F99_R2.fastq.gz --trim_front1 20 --trim_front2 20 --detect_adapter_for_pe --disable_quality_filtering --n_base_limit 1 --json /var/folders/qf/64kyljyn0njdfbz8nyrgjv8hxrrkbt/T/dadaist2_8OXSgR/F99.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 2021-03-05 11:29:12 for 21.16s and returned 0

Command

Rscript 
--vanilla /Users/telatina/git/dadaist2/bin/D2-dada.R /var/folders/qf/64kyljyn0njdfbz8nyrgjv8hxrrkbt/T/dadaist2_8OXSgR/for /var/folders/qf/64kyljyn0njdfbz8nyrgjv8hxrrkbt/T/dadaist2_8OXSgR/rev /var/folders/qf/64kyljyn0njdfbz8nyrgjv8hxrrkbt/T/dadaist2_8OXSgR/dada2/dada2.tsv /var/folders/qf/64kyljyn0njdfbz8nyrgjv8hxrrkbt/T/dadaist2_8OXSgR/dada2/stats.tsv /var/folders/qf/64kyljyn0njdfbz8nyrgjv8hxrrkbt/T/dadaist2_8OXSgR/for/filtered /var/folders/qf/64kyljyn0njdfbz8nyrgjv8hxrrkbt/T/dadaist2_8OXSgR/rev/filtered 265 207 0 0 1 1.5 10 consensus 1 8 10000 /var/folders/qf/64kyljyn0njdfbz8nyrgjv8hxrrkbt/T/dadaist2_8OXSgR do_plots skip no 0

Standard output

R version 4.0.3 (2020-10-10) 
#DADA2: 1.18.0 / Rcpp: 1.0.6 / RcppParallel: 5.0.3 
2021-03-05 11:29:20 	[1] Filtering reads ...
2021-03-05 11:29:30 	[2] Learning Error Rates
1579400 total bases in 5960 reads from 3 samples will be used for learning the error rates.
1233720 total bases in 5960 reads from 3 samples will be used for learning the error rates.
2021-03-05 11:29:32 	[3] Denoise remaining samples ...
2021-03-05 11:29:33	[4] Remove chimeras (method = consensus)
2021-03-05 11:29:33 	[5.1] Taxonomy (SKIPPED)
2021-03-05 11:29:33 	[6] Write output
	 *  /var/folders/qf/64kyljyn0njdfbz8nyrgjv8hxrrkbt/T/dadaist2_8OXSgR/dada2/dada2.tsv Standard error
Loading required package: Rcpp

Shell command /Users/telatina/git/dadaist2/bin/dadaist2-assigntax

Executed at 2021-03-05 11:29:33 for 39.05s and returned 0

Command

/Users/telatina/git/dadaist2/bin/dadaist2-assigntax 
-i "/Users/telatina/git/dadaist2/output/tests/ref-decipher/rep-seqs.fasta" 
-o "/var/folders/qf/64kyljyn0njdfbz8nyrgjv8hxrrkbt/T/dadaist2_8OXSgR" 
-r "refs/SILVA_SSU_r138_2019.RData" 
-t "8"

Standard output

Standard error

[35;1m DADAIST2 Assign Taxonomy[0m Input file: /Users/telatina/git/dadaist2/output/tests/ref-decipher/rep-seqs.fasta Reference: refs/SILVA_SSU_r138_2019.RData Output dir: /var/folders/qf/64kyljyn0njdfbz8nyrgjv8hxrrkbt/T/dadaist2_8OXSgR Threads: 8 * Using DECIPHER [2021-03-05 11:29:33] Shell> Rscript --vanilla "/Users/telatina/git/dadaist2/bin/D2-decipher.R" "/Users/telatina/git/dadaist2/output/tests/ref-decipher/rep-seqs.fasta" "refs/SILVA_SSU_r138_2019.RData" "/var/folders/qf/64kyljyn0njdfbz8nyrgjv8hxrrkbt/T/dadaist2_8OXSgR" "8" [2021-03-05 11:30:12] +> Elapsed time: 38.84s; Exit status: 0;

Shell command echo

Executed at 2021-03-05 11:28:58 for 2.91s and returned 0

Command

echo "library(DECIPHER)" | R 
--no-save > /dev/null

Standard output

Standard error

Loading required package: Biostrings Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: ‘S4Vectors’ The following object is masked from ‘package:base’: expand.grid Loading required package: IRanges Loading required package: XVector Attaching package: ‘Biostrings’ The following object is masked from ‘package:base’: strsplit Loading required package: RSQLite

Shell command /Users/telatina/git/dadaist2/bin/dadaist2-assigntax

Executed at 2021-03-05 11:29:01 for 0.19s and returned 0

Command

/Users/telatina/git/dadaist2/bin/dadaist2-assigntax --version

Standard output

dadaist2-assigntax 1.0.5

Standard error

[35;1m DADAIST2 Assign Taxonomy[0m

Shell command Rscript

Executed at 2021-03-05 11:29:01 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 clustalo

Executed at 2021-03-05 11:29:01 for 0.03s and returned 0

Command

clustalo 
--version 2>&1

Standard output

1.2.4

Standard error

Shell command echo

Executed at 2021-03-05 11:29:01 for 7.73s and returned 0

Command

echo "library(dada2)" | R 
--no-save > /dev/null

Standard output

Standard error

Loading required package: Rcpp

Shell command /Users/telatina/git/dadaist2/bin/dadaist2-exporter

Executed at 2021-03-05 11:29:08 for 0.12s and returned 0

Command

/Users/telatina/git/dadaist2/bin/dadaist2-exporter --version

Standard output

dadaist2-exporter 1.0.0

Standard error

Shell command fastp

Executed at 2021-03-05 11:29:09 for 0.02s and returned 0

Command

fastp 
--version 2>&1

Standard output

fastp 0.20.1

Standard error

Shell command fasttree

Executed at 2021-03-05 11:29:09 for 0.14s 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 2021-03-05 11:29:09 for 0.05s and returned 0

Command

fu-primers 
--version 2>&1

Standard output

fu-primers 1.0

Standard error

Shell command /Users/telatina/git/dadaist2/bin/makeSampleSheet

Executed at 2021-03-05 11:29:09 for 0.21s and returned 0

Command

/Users/telatina/git/dadaist2/bin/makeSampleSheet --version

Standard output

makeSampleSheet 1.0.0

Standard error

Dadaist2 0.7.4 execution log

Summary

Parameters

Machine details

Shell command fastp

Shell command fastp

Shell command fastp

Shell command Rscript

Shell command /Users/telatina/git/dadaist2/bin/dadaist2-assigntax

Shell command echo

Shell command /Users/telatina/git/dadaist2/bin/dadaist2-assigntax

Shell command Rscript

Shell command clustalo

Shell command echo

Shell command /Users/telatina/git/dadaist2/bin/dadaist2-exporter

Shell command fastp

Shell command fasttree

Shell command fu-primers

Shell command /Users/telatina/git/dadaist2/bin/makeSampleSheet