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Test.respublica.log
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Loading R/3.6.2
Loading requirement: java/current hdf5/1.10.4 gdal/2.4 gsl/2.5 jags/current
SINBAD installation is ok.
[1] "Reading config.general.R for program paths..."
[1] "Reading config.genome.R for genome paths..."
[1] "Reading config.project.R for prroject settings..."
Loading required package: foreach
Loading required package: iterators
Loading required package: snow
starting worker for localhost:11633
starting worker for localhost:11633
Type: EXEC
Type: EXEC
Loading required package: SINBAD
Loading required package: SINBAD
loaded SINBAD and set parent environment
loaded SINBAD and set parent environment
Type: EXEC
Type: EXEC
[1][1] "Batch2___Lane10.fastq.gz"
"Batch1___Lane01.fastq.gz"
[1][1] "perl /mnt/isilon/tan_lab/uzuny/projects/jamboree/package/dependencies//perl/demultiplex_fastq.pl --demux_index_file /mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//demux_index.txt --raw_fastq_file /mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//reads//Batch2___Lane10.fastq.gz --demux_index_length 6 --output_dir /mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//working_dir//demux_fastq/ --output_prefix Batch2___Lane10 --log_dir /mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//working_dir//logs//demux/" "perl /mnt/isilon/tan_lab/uzuny/projects/jamboree/package/dependencies//perl/demultiplex_fastq.pl --demux_index_file /mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//demux_index.txt --raw_fastq_file /mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//reads//Batch1___Lane01.fastq.gz --demux_index_length 6 --output_dir /mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//working_dir//demux_fastq/ --output_prefix Batch1___Lane01 --log_dir /mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//working_dir//logs//demux/"
...
Hello! My name is Demuxer.
I will split your input read file /mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//reads//Batch2___Lane10.fastq.gz based on index at /mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//demux_index.txt
Index length is specified as 6
Output prefix: Batch2___Lane10
Output dir: /mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//working_dir//demux_fastq/
log_dir dir: /mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//working_dir//logs//demux/
...
CGATGT:CGATGT
***CGATGT:CGATGT
/mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//working_dir//demux_fastq//Batch2___Lane10_CGATGT.fastq.gz
GCCAAT:GCCAAT
***GCCAAT:GCCAAT
/mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//working_dir//demux_fastq//Batch2___Lane10_GCCAAT.fastq.gz
ACTTGA:ACTTGA
***ACTTGA:ACTTGA
/mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//working_dir//demux_fastq//Batch2___Lane10_ACTTGA.fastq.gz
...
Hello! My name is Demuxer.
I will split your input read file /mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//reads//Batch1___Lane01.fastq.gz based on index at /mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//demux_index.txt
Index length is specified as 6
Output prefix: Batch1___Lane01
Output dir: /mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//working_dir//demux_fastq/
log_dir dir: /mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//working_dir//logs//demux/
...
CGATGT:CGATGT
***CGATGT:CGATGT
/mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//working_dir//demux_fastq//Batch1___Lane01_CGATGT.fastq.gz
TAGCTT:TAGCTT
***TAGCTT:TAGCTT
/mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//working_dir//demux_fastq//Batch2___Lane10_TAGCTT.fastq.gz
GCCAAT:GCCAAT
***GCCAAT:GCCAAT
/mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//working_dir//demux_fastq//Batch1___Lane01_GCCAAT.fastq.gz
ATCACG:ATCACG
***ATCACG:ATCACG
/mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//working_dir//demux_fastq//Batch2___Lane10_ATCACG.fastq.gz
ACTTGA:ACTTGA
***ACTTGA:ACTTGA
/mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//working_dir//demux_fastq//Batch1___Lane01_ACTTGA.fastq.gz
TGACCA:TGACCA
***TGACCA:TGACCA
/mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//working_dir//demux_fastq//Batch2___Lane10_TGACCA.fastq.gz
TAGCTT:TAGCTT
***TAGCTT:TAGCTT
/mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//working_dir//demux_fastq//Batch1___Lane01_TAGCTT.fastq.gz
CAGATC:CAGATC
***CAGATC:CAGATC
/mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//working_dir//demux_fastq//Batch2___Lane10_CAGATC.fastq.gz
ATCACG:ATCACG
***ATCACG:ATCACG
/mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//working_dir//demux_fastq//Batch1___Lane01_ATCACG.fastq.gz
CTTGTA:CTTGTA
***CTTGTA:CTTGTA
/mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//working_dir//demux_fastq//Batch2___Lane10_CTTGTA.fastq.gz
TGACCA:TGACCA
***TGACCA:TGACCA
/mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//working_dir//demux_fastq//Batch1___Lane01_TGACCA.fastq.gz
8 indeces found.
Processing /mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//reads//Batch2___Lane10.fastq.gz
CAGATC:CAGATC
***CAGATC:CAGATC
/mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//working_dir//demux_fastq//Batch1___Lane01_CAGATC.fastq.gz
CTTGTA:CTTGTA
***CTTGTA:CTTGTA
/mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//working_dir//demux_fastq//Batch1___Lane01_CTTGTA.fastq.gz
8 indeces found.
Processing /mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//reads//Batch1___Lane01.fastq.gz
**********/mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//working_dir//demux_fastq//No_matching_index.Batch2___Lane10.fastq.gz***********
Finished processing /mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//reads//Batch2___Lane10.fastq.gz
**********/mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//working_dir//demux_fastq//No_matching_index.Batch1___Lane01.fastq.gz***********
Finished processing /mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//reads//Batch1___Lane01.fastq.gz
Type: DONE
Type: DONE
[1] "Batch1___Lane01.log"
[1] "Batch2___Lane10.log"
starting worker for localhost:11633
starting worker for localhost:11633
starting worker for localhost:11633
starting worker for localhost:11633
starting worker for localhost:11633
starting worker for localhost:11633
starting worker for localhost:11633
starting worker for localhost:11633
Type: EXEC
Type: EXEC
Type: EXEC
Type: EXEC
Type: EXEC
Type: EXEC
Type: EXEC
Type: EXEC
Loading required package: SINBAD
Loading required package: SINBAD
Loading required package: SINBAD
Loading required package: SINBAD
Loading required package: SINBAD
Loading required package: SINBAD
Loading required package: SINBAD
Loading required package: SINBAD
loaded SINBAD and set parent environment
loaded SINBAD and set parent environment
loaded SINBAD and set parent environment
loaded SINBAD and set parent environment
loaded SINBAD and set parent environment
loaded SINBAD and set parent environment
loaded SINBAD and set parent environment
loaded SINBAD and set parent environment
Type: EXEC
Type: EXEC
Type: EXEC
Type: EXEC
Type: EXEC
Type: EXEC
Type: EXEC
Type: EXEC
Loading required package: BiocGenerics
Loading required package: BiocGenerics
Loading required package: BiocGenerics
Loading required package: BiocGenerics
Loading required package: BiocGenerics
Loading required package: BiocGenerics
Loading required package: BiocGenerics
Loading required package: BiocGenerics
Loading required package: parallel
Loading required package: parallel
Loading required package: parallel
Loading required package: parallel
Loading required package: parallel
Loading required package: parallel
Loading required package: parallel
Loading required package: parallel
Attaching package: ‘parallel’
Attaching package: ‘parallel’
Attaching package: ‘parallel’
Attaching package: ‘parallel’
Attaching package: ‘parallel’
Attaching package: ‘parallel’
Attaching package: ‘parallel’
Attaching package: ‘parallel’
The following objects are masked from ‘package:snow’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, clusterSplit, makeCluster, parApply,
parCapply, parLapply, parRapply, parSapply, splitIndices,
stopCluster
The following objects are masked from ‘package:snow’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, clusterSplit, makeCluster, parApply,
parCapply, parLapply, parRapply, parSapply, splitIndices,
stopCluster
The following objects are masked from ‘package:snow’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, clusterSplit, makeCluster, parApply,
parCapply, parLapply, parRapply, parSapply, splitIndices,
stopCluster
The following objects are masked from ‘package:snow’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, clusterSplit, makeCluster, parApply,
parCapply, parLapply, parRapply, parSapply, splitIndices,
stopCluster
The following objects are masked from ‘package:snow’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, clusterSplit, makeCluster, parApply,
parCapply, parLapply, parRapply, parSapply, splitIndices,
stopCluster
The following objects are masked from ‘package:snow’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, clusterSplit, makeCluster, parApply,
parCapply, parLapply, parRapply, parSapply, splitIndices,
stopCluster
The following objects are masked from ‘package:snow’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, clusterSplit, makeCluster, parApply,
parCapply, parLapply, parRapply, parSapply, splitIndices,
stopCluster
The following objects are masked from ‘package:snow’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, clusterSplit, makeCluster, parApply,
parCapply, parLapply, parRapply, parSapply, splitIndices,
stopCluster
Attaching package: ‘BiocGenerics’
Attaching package: ‘BiocGenerics’
Attaching package: ‘BiocGenerics’
Attaching package: ‘BiocGenerics’
Attaching package: ‘BiocGenerics’
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:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:snow’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parRapply, parSapply
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:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:snow’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parRapply, parSapply
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:snow’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parRapply, parSapply
The following objects are masked from ‘package:snow’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parRapply, parSapply
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:snow’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parRapply, parSapply
The following objects are masked from ‘package:snow’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parRapply, parSapply
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
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, which.max, which.min
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,
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order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
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order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
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order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
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Welcome to Bioconductor
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'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
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'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
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Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
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Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
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Vignettes contain introductory material; view with
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[1][1] "Batch1___Lane01_ATCACG.fastq.gz"
"Batch1___Lane01_CAGATC.fastq.gz"
[1] "Batch1___Lane01_ACTTGA.fastq.gz"
[1] "Batch1___Lane01_GCCAAT.fastq.gz"
[1] "Batch1___Lane01_CTTGTA.fastq.gz"
[1] "Batch1___Lane01_TGACCA.fastq.gz"
[1] "Batch1___Lane01_CGATGT.fastq.gz"
[1] "Batch1___Lane01_TAGCTT.fastq.gz"
Type: EXEC
[1] "Batch2___Lane10_ACTTGA.fastq.gz"
Type: EXEC
[1] "Batch2___Lane10_ATCACG.fastq.gz"
Type: EXEC
[1] "Batch2___Lane10_CAGATC.fastq.gz"
Type: EXEC
[1] "Batch2___Lane10_CGATGT.fastq.gz"
Type: EXEC
[1] "Batch2___Lane10_CTTGTA.fastq.gz"
Type: EXEC
[1] "Batch2___Lane10_GCCAAT.fastq.gz"
Type: EXEC
[1] "Batch2___Lane10_TAGCTT.fastq.gz"
Type: EXEC
[1] "Batch2___Lane10_TGACCA.fastq.gz"
Warning message:
In e$fun(obj, substitute(ex), parent.frame(), e$data) :
already exporting variable(s): demux_fastq_dir, demux_index_file, demux_index_length, raw_fastq_dir
$main_log_dir
[1] "/mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//working_dir//logs/"
$raw_fastq_dir
[1] "/mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//reads/"
$demux_index_file
[1] "/mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//demux_index.txt"
$demux_fastq_dir
[1] "/mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//working_dir//demux_fastq/"
$trimmed_fastq_dir
[1] "/mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//working_dir//trimmed_fastq/"
$alignment_dir
[1] "/mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//working_dir//alignments/"
$methylation_calls_dir
[1] "/mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//working_dir//methylation_calls/"
$summary_dir
[1] "/mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//working_dir//summary/"
$plot_dir
[1] "/mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//working_dir//plots/"
$sample_name
[1] "Test"
$df_demux_reports
Group Total_reads Reads_with_matching_index
Batch1___Lane01 Batch1___Lane01 23189895 22322810
Batch2___Lane10 Batch2___Lane10 11493001 11199406
Reads_without_matching_index CGATGT TAGCTT TGACCA GCCAAT
Batch1___Lane01 867085 2697288 3044397 3047886 2396650
Batch2___Lane10 293595 1072248 1617483 1010357 1565710
CAGATC ACTTGA CTTGTA ATCACG
Batch1___Lane01 2979879 2566893 2422075 3167742
Batch2___Lane10 1622009 1420252 1596971 1294376
$demux_read_counts
Batch1___Lane01_ACTTGA Batch1___Lane01_ATCACG Batch1___Lane01_CAGATC
2566893 3167742 2979879
Batch1___Lane01_CGATGT Batch1___Lane01_CTTGTA Batch1___Lane01_GCCAAT
2697288 2422075 2396650
Batch1___Lane01_TAGCTT Batch1___Lane01_TGACCA Batch2___Lane10_ACTTGA
3044397 3047886 1420252
Batch2___Lane10_ATCACG Batch2___Lane10_CAGATC Batch2___Lane10_CGATGT
1294376 1622009 1072248
Batch2___Lane10_CTTGTA Batch2___Lane10_GCCAAT Batch2___Lane10_TAGCTT
1596971 1565710 1617483
Batch2___Lane10_TGACCA
1010357
attr(,"class")
[1] "Sinbad"
[1] "Trimming fastq files"
[1] "demux_fastq_files :"
[1] "Batch1___Lane01_ACTTGA.fastq.gz" "Batch1___Lane01_ATCACG.fastq.gz"
[3] "Batch1___Lane01_CAGATC.fastq.gz" "Batch1___Lane01_CGATGT.fastq.gz"
[5] "Batch1___Lane01_CTTGTA.fastq.gz" "Batch1___Lane01_GCCAAT.fastq.gz"
[7] "Batch1___Lane01_TAGCTT.fastq.gz" "Batch1___Lane01_TGACCA.fastq.gz"
[9] "Batch2___Lane10_ACTTGA.fastq.gz" "Batch2___Lane10_ATCACG.fastq.gz"
[11] "Batch2___Lane10_CAGATC.fastq.gz" "Batch2___Lane10_CGATGT.fastq.gz"
[13] "Batch2___Lane10_CTTGTA.fastq.gz" "Batch2___Lane10_GCCAAT.fastq.gz"