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Test.respublica.old.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:11300
starting worker for localhost:11300
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] "Batch1___Lane01.fastq.gz"
"Batch2___Lane10.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//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/"
"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/"
...
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
GCCAAT:GCCAAT
***GCCAAT:GCCAAT
/mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//working_dir//demux_fastq//Batch1___Lane01_GCCAAT.fastq.gz
...
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
ACTTGA:ACTTGA
***ACTTGA:ACTTGA
/mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//working_dir//demux_fastq//Batch1___Lane01_ACTTGA.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
TAGCTT:TAGCTT
***TAGCTT:TAGCTT
/mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//working_dir//demux_fastq//Batch2___Lane10_TAGCTT.fastq.gz
ATCACG:ATCACG
***ATCACG:ATCACG
/mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//working_dir//demux_fastq//Batch2___Lane10_ATCACG.fastq.gz
TAGCTT:TAGCTT
***TAGCTT:TAGCTT
/mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//working_dir//demux_fastq//Batch1___Lane01_TAGCTT.fastq.gz
ATCACG:ATCACG
***ATCACG:ATCACG
/mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//working_dir//demux_fastq//Batch1___Lane01_ATCACG.fastq.gz
TGACCA:TGACCA
***TGACCA:TGACCA
/mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//working_dir//demux_fastq//Batch2___Lane10_TGACCA.fastq.gz
CAGATC:CAGATC
***CAGATC:CAGATC
/mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//working_dir//demux_fastq//Batch2___Lane10_CAGATC.fastq.gz
TGACCA:TGACCA
***TGACCA:TGACCA
/mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//working_dir//demux_fastq//Batch1___Lane01_TGACCA.fastq.gz
CTTGTA:CTTGTA
***CTTGTA:CTTGTA
/mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//working_dir//demux_fastq//Batch2___Lane10_CTTGTA.fastq.gz
CAGATC:CAGATC
***CAGATC:CAGATC
/mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//working_dir//demux_fastq//Batch1___Lane01_CAGATC.fastq.gz
8 indeces found.
Processing /mnt/isilon/tan_lab/uzuny/projects/jamboree/data/example//reads//Batch2___Lane10.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:11300
starting worker for localhost:11300
starting worker for localhost:11300
starting worker for localhost:11300
starting worker for localhost:11300
starting worker for localhost:11300
starting worker for localhost:11300
starting worker for localhost:11300
starting worker for localhost:11300
starting worker for localhost:11300
starting worker for localhost:11300
starting worker for localhost:11300
starting worker for localhost:11300
starting worker for localhost:11300
starting worker for localhost:11300
starting worker for localhost:11300
Type: EXEC
Type: EXEC
Type: EXEC
Type: EXEC
Type: EXEC
Type: EXEC
Loading required package: SINBAD
Loading required package: SINBAD
Type: EXEC
Loading required package: SINBAD
Type: EXEC
Loading required package: SINBAD
Type: EXEC
Loading required package: SINBAD
Type: EXEC
Loading required package: SINBAD
Loading required package: SINBAD
Loading required package: SINBAD
Type: EXEC
Loading required package: SINBAD
Type: EXEC
Loading required package: SINBAD
Loading required package: SINBAD
Type: EXEC
Loading required package: SINBAD
Type: EXEC
Type: EXEC
Loading required package: SINBAD
Loading required package: SINBAD
Loading required package: SINBAD
Type: EXEC
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
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
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: 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
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’
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
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
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
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
Loading required 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
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
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
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: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:base’:
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order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
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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,
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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: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:base’:
anyDuplicated, append, as.data.frame, basename, cbind, colnames,
dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
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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
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,
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rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Attaching package: ‘BiocGenerics’
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,
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order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
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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
Attaching package: ‘BiocGenerics’
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,
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rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
Attaching package: ‘BiocGenerics’
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: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:base’:
anyDuplicated, append, as.data.frame, basename, cbind, colnames,
dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
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order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
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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,
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rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Attaching package: ‘BiocGenerics’
Loading required package: BiocParallel
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
Loading required package: BiocParallel
Loading required package: BiocParallel
Loading required package: BiocParallel
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: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:stats’:
IQR, mad, sd, var, xtabs
Loading required package: BiocParallel
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,
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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
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, basename, cbind, colnames,
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rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Loading required package: BiocParallel
Attaching package: ‘BiocGenerics’
Loading required package: BiocParallel
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:base’:
anyDuplicated, append, as.data.frame, basename, cbind, colnames,
dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
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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
Loading required package: BiocParallel
Attaching package: ‘BiocGenerics’
Loading required package: BiocParallel
Loading required package: BiocParallel
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
Loading required package: BiocParallel
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,
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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
Loading required package: BiocParallel
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: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: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
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: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: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
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: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: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
Loading required package: BiocParallel
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: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: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
Loading required package: BiocParallel
Loading required package: BiocParallel
Loading required package: BiocParallel
Loading required package: Biostrings
Loading required package: Biostrings
Loading required package: Biostrings
Loading required package: Biostrings
Loading required package: Biostrings
Loading required package: Biostrings
Loading required package: Biostrings
Loading required package: Biostrings
Loading required package: Biostrings
Loading required package: Biostrings
Loading required package: Biostrings
Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: S4Vectors
Loading required package: S4Vectors
Loading required package: S4Vectors
Loading required package: S4Vectors
Loading required package: S4Vectors
Loading required package: S4Vectors
Loading required package: S4Vectors
Loading required package: S4Vectors
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: stats4
Loading required package: stats4
Loading required package: stats4
Loading required package: stats4
Loading required package: stats4
Loading required package: stats4
Loading required package: stats4
Loading required package: S4Vectors
Loading required package: Biostrings
Loading required package: Biostrings
Loading required package: stats4
Loading required package: stats4
Loading required package: Biostrings
Loading required package: Biostrings
Loading required package: stats4
Loading required package: S4Vectors
Loading required package: S4Vectors
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: S4Vectors
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: stats4
Loading required package: stats4
Loading required package: stats4
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:base’:
expand.grid
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:base’:
expand.grid
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:base’:
expand.grid
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:base’:
expand.grid
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:base’:
expand.grid
Loading required package: IRanges
Loading required package: IRanges
Loading required package: IRanges
Loading required package: IRanges
Loading required package: IRanges
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:base’:
expand.grid
Attaching package: ‘S4Vectors’
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:base’:
expand.grid
The following object is masked from ‘package:base’:
expand.grid
Loading required package: IRanges
Loading required package: IRanges
Loading required package: IRanges
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:base’:
expand.grid
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:base’:
expand.grid
Loading required package: IRanges
Loading required package: IRanges
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:base’:
expand.grid
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:base’:
expand.grid
Loading required package: IRanges
Loading required package: IRanges
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:base’:
expand.grid
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:base’:
expand.grid
Loading required package: IRanges
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:base’:
expand.grid