URD
Input saved to /scratch/irc/personal/robrechtc/tmp//Rtmp3yPQfj/input:
data.rds
params.json
Attaching package: ‘dplyr’
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
Attaching package: ‘purrr’
The following object is masked from ‘package:jsonlite’:
flatten
Loading required package: ggplot2
Loading required package: Matrix
Attaching package: ‘Matrix’
The following object is masked from ‘package:tidyr’:
expand
2018-08-03 16:41:41: Filtering cells by number of genes.
2018-08-03 16:41:42: Filtering genes by number of cells.
2018-08-03 16:41:43: Filtering genes by number of counts across entire data.
2018-08-03 16:41:43: Filtering genes by maximum observed expression.
2018-08-03 16:41:43: Creating URD object.
2018-08-03 16:41:44: Determining normalization factors.
2018-08-03 16:41:44: Normalizing and log-transforming the data.
2018-08-03 16:41:46: Finishing setup of the URD object.
2018-08-03 16:41:46: All done.
[1] "destiny determined an optimal global sigma of 19.273"
Error in DiffusionMap(data.use, sigma = sigma.use, k = knn, n_eigs = dcs.store, :
Eigen decomposition not possible if n ≤ n_eigs+1 (And 92 ≤ 201)
Calls: calcDM -> DiffusionMap
Execution halted
Input saved to /scratch/irc/personal/robrechtc/tmp//Rtmp4gIZju/input:
data.rds
params.json
Attaching package: ‘dplyr’
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
Attaching package: ‘purrr’
The following object is masked from ‘package:jsonlite’:
flatten
Loading required package: ggplot2
Loading required package: Matrix
Attaching package: ‘Matrix’
The following object is masked from ‘package:tidyr’:
expand
2018-08-03 16:41:40: Filtering cells by number of genes.
2018-08-03 16:41:40: Filtering genes by number of cells.
2018-08-03 16:41:41: Filtering genes by number of counts across entire data.
2018-08-03 16:41:41: Filtering genes by maximum observed expression.
2018-08-03 16:41:42: Creating URD object.
2018-08-03 16:41:42: Determining normalization factors.
2018-08-03 16:41:42: Normalizing and log-transforming the data.
2018-08-03 16:41:43: Finishing setup of the URD object.
2018-08-03 16:41:43: All done.
[1] "destiny determined an optimal global sigma of 26.112"
Error in DiffusionMap(data.use, sigma = sigma.use, k = knn, n_eigs = dcs.store, :
Eigen decomposition not possible if n ≤ n_eigs+1 (And 94 ≤ 201)
Calls: calcDM -> DiffusionMap
Execution halted
Input saved to /scratch/irc/personal/robrechtc/tmp//Rtmpy96cRF/input:
data.rds
params.json
Attaching package: ‘dplyr’
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
Attaching package: ‘purrr’
The following object is masked from ‘package:jsonlite’:
flatten
Loading required package: ggplot2
Loading required package: Matrix
Attaching package: ‘Matrix’
The following object is masked from ‘package:tidyr’:
expand
2018-08-03 16:40:21: Filtering cells by number of genes.
2018-08-03 16:40:22: Filtering genes by number of cells.
2018-08-03 16:40:23: Filtering genes by number of counts across entire data.
2018-08-03 16:40:23: Filtering genes by maximum observed expression.
2018-08-03 16:40:24: Creating URD object.
2018-08-03 16:40:24: Determining normalization factors.
2018-08-03 16:40:25: Normalizing and log-transforming the data.
2018-08-03 16:40:26: Finishing setup of the URD object.
2018-08-03 16:40:26: All done.
[1] "destiny determined an optimal global sigma of 278.918"
[1] "2018-08-03 16:40:30: Centering and scaling data."
[1] "2018-08-03 16:40:31: Removing genes with no variation."
[1] "2018-08-03 16:40:32: Calculating PCA."
[1] "2018-08-03 16:40:34: Estimating significant PCs."
[1] "Marchenko-Pastur eigenvalue null upper bound: 28.2679823258594"
[1] "8 PCs have larger eigenvalues."
[1] "Storing 16 PCs."
Warning message:
In calcPCA(urd, mp.factor = params$mp.factor) :
Variable genes have not been stored. Using all genes instead.
[1] "Mean pseudotime back (~40 cells) 0.0575971135980438"
[1] "Chance of accepted move to equal pseudotime is 0.793153332609836"
[1] "Mean pseudotime forward (~20 cells) -0.0315725598491618"
[1] "Calculating divergence between 1 and 3 (Pseudotime 0 to 0.769)"
Difference between 1 and 3 always FALSE -- setting breakpoint to end.
[1] "Calculating divergence between 1 and 2 (Pseudotime 0 to 0.571)"
Difference between 1 and 2 always FALSE -- setting breakpoint to end.
[1] "Calculating divergence between 1 and 4 (Pseudotime 0 to 0.752)"
Difference between 1 and 4 always FALSE -- setting breakpoint to end.
[1] "Calculating divergence between 3 and 2 (Pseudotime 0 to 0.571)"
Difference between 3 and 2 always FALSE -- setting breakpoint to end.
[1] "Calculating divergence between 3 and 4 (Pseudotime 0 to 0.752)"
Difference between 3 and 4 always FALSE -- setting breakpoint to end.
[1] "Calculating divergence between 2 and 4 (Pseudotime 0 to 0.571)"
Difference between 2 and 4 always FALSE -- setting breakpoint to end.
[1] "Joining segments 1 and 3 at pseudotime 0.769 to create segment 5"
[1] "Calculating divergence between 2 and 5 (Pseudotime 0 to 0.571)"
Difference between 2 and 5 always FALSE -- setting breakpoint to end.
[1] "Calculating divergence between 4 and 5 (Pseudotime 0 to 0.752)"
Difference between 4 and 5 always FALSE -- setting breakpoint to end.
[1] "Joining segments 4 and 5 at pseudotime 0.752 to create segment 6"
[1] "Calculating divergence between 2 and 6 (Pseudotime 0 to 0.571)"
Difference between 2 and 6 always FALSE -- setting breakpoint to end.
[1] "Joining segments 2 and 6 at pseudotime 0.571 to create segment 7"
[1] "Assigning cells to segments."
[1] "Collapsing short segments."
[1] "Removing singleton segments."
[1] "Reassigning cells to segments."
Error in visit.data[which(object@pseudotime[, pseudotime] > object@tree$segment.pseudotime.limits[segment, :
incorrect number of subscripts on matrix
Calls: buildTree -> assignCellsToSegments
Execution halted
Input saved to /scratch/irc/personal/robrechtc/tmp//RtmprpqUGr/input:
data.rds
params.json
Attaching package: ‘dplyr’
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
Attaching package: ‘purrr’
The following object is masked from ‘package:jsonlite’:
flatten
Loading required package: ggplot2
Loading required package: Matrix
Attaching package: ‘Matrix’
The following object is masked from ‘package:tidyr’:
expand
2018-08-03 16:42:59: Filtering cells by number of genes.
2018-08-03 16:43:01: Filtering genes by number of cells.
2018-08-03 16:43:02: Filtering genes by number of counts across entire data.
2018-08-03 16:43:03: Filtering genes by maximum observed expression.
2018-08-03 16:43:04: Creating URD object.
2018-08-03 16:43:05: Determining normalization factors.
2018-08-03 16:43:06: Normalizing and log-transforming the data.
2018-08-03 16:43:10: Finishing setup of the URD object.
2018-08-03 16:43:11: All done.
[1] "destiny determined an optimal global sigma of 120.53"
[1] "2018-08-03 16:43:25: Centering and scaling data."
[1] "2018-08-03 16:43:26: Removing genes with no variation."
[1] "2018-08-03 16:43:27: Calculating PCA."
[1] "2018-08-03 16:43:34: Estimating significant PCs."
[1] "Marchenko-Pastur eigenvalue null upper bound: 16.543090287518"
[1] "13 PCs have larger eigenvalues."
[1] "Storing 26 PCs."
Warning message:
In calcPCA(urd, mp.factor = params$mp.factor) :
Variable genes have not been stored. Using all genes instead.
[1] "Mean pseudotime back (~40 cells) 0.0578756771930394"
[1] "Chance of accepted move to equal pseudotime is 0.818801551852867"
[1] "Mean pseudotime forward (~20 cells) -0.0293185224818785"
[1] "Calculating divergence between 1 and 2 (Pseudotime 0 to 0.446)"
Difference between 1 and 2 always FALSE -- setting breakpoint to end.
[1] "Calculating divergence between 1 and 3 (Pseudotime 0 to 0.425)"
Difference between 1 and 3 always FALSE -- setting breakpoint to end.
[1] "Calculating divergence between 1 and 6 (Pseudotime 0 to 0.699)"
Difference between 1 and 6 always TRUE -- setting breakpoint to beginning.
[1] "Calculating divergence between 1 and 5 (Pseudotime 0 to 0.677)"
Difference between 1 and 5 always FALSE -- setting breakpoint to end.
[1] "Calculating divergence between 1 and 7 (Pseudotime 0 to 0.699)"
Difference between 1 and 7 always TRUE -- setting breakpoint to beginning.
[1] "Calculating divergence between 1 and 4 (Pseudotime 0 to 0.699)"
Difference between 1 and 4 always FALSE -- setting breakpoint to end.
[1] "Calculating divergence between 1 and 8 (Pseudotime 0 to 0.699)"
Difference between 1 and 8 always FALSE -- setting breakpoint to end.
[1] "Calculating divergence between 2 and 3 (Pseudotime 0 to 0.425)"
Difference between 2 and 3 always FALSE -- setting breakpoint to end.
[1] "Calculating divergence between 2 and 6 (Pseudotime 0 to 0.446)"
Difference between 2 and 6 always FALSE -- setting breakpoint to end.
[1] "Calculating divergence between 2 and 5 (Pseudotime 0 to 0.446)"
Difference between 2 and 5 always FALSE -- setting breakpoint to end.
[1] "Calculating divergence between 2 and 7 (Pseudotime 0 to 0.446)"
Difference between 2 and 7 always FALSE -- setting breakpoint to end.
[1] "Calculating divergence between 2 and 4 (Pseudotime 0 to 0.446)"
Difference between 2 and 4 always FALSE -- setting breakpoint to end.
[1] "Calculating divergence between 2 and 8 (Pseudotime 0 to 0.446)"
Difference between 2 and 8 always FALSE -- setting breakpoint to end.
[1] "Calculating divergence between 3 and 6 (Pseudotime 0 to 0.425)"
Difference between 3 and 6 always FALSE -- setting breakpoint to end.
[1] "Calculating divergence between 3 and 5 (Pseudotime 0 to 0.425)"
Difference between 3 and 5 always FALSE -- setting breakpoint to end.
[1] "Calculating divergence between 3 and 7 (Pseudotime 0 to 0.425)"
Difference between 3 and 7 always FALSE -- setting breakpoint to end.
[1] "Calculating divergence between 3 and 4 (Pseudotime 0 to 0.425)"
Difference between 3 and 4 always FALSE -- setting breakpoint to end.
[1] "Calculating divergence between 3 and 8 (Pseudotime 0 to 0.425)"
Difference between 3 and 8 always FALSE -- setting breakpoint to end.
[1] "Calculating divergence between 6 and 5 (Pseudotime 0 to 0.677)"
Difference between 6 and 5 always TRUE -- setting breakpoint to beginning.
[1] "Calculating divergence between 6 and 7 (Pseudotime 0 to 0.74)"
Difference between 6 and 7 always TRUE -- setting breakpoint to beginning.
[1] "Calculating divergence between 6 and 4 (Pseudotime 0 to 0.74)"
Difference between 6 and 4 always FALSE -- setting breakpoint to end.
[1] "Calculating divergence between 6 and 8 (Pseudotime 0 to 0.74)"
Difference between 6 and 8 always TRUE -- setting breakpoint to beginning.
[1] "Calculating divergence between 5 and 7 (Pseudotime 0 to 0.677)"
Difference between 5 and 7 always TRUE -- setting breakpoint to beginning.
[1] "Calculating divergence between 5 and 4 (Pseudotime 0 to 0.677)"
Difference between 5 and 4 always FALSE -- setting breakpoint to end.
[1] "Calculating divergence between 5 and 8 (Pseudotime 0 to 0.677)"
Difference between 5 and 8 always FALSE -- setting breakpoint to end.
[1] "Calculating divergence between 7 and 4 (Pseudotime 0 to 0.759)"
Difference between 7 and 4 always FALSE -- setting breakpoint to end.
[1] "Calculating divergence between 7 and 8 (Pseudotime 0 to 0.759)"
Difference between 7 and 8 always FALSE -- setting breakpoint to end.
[1] "Calculating divergence between 4 and 8 (Pseudotime 0 to 0.807)"
Difference between 4 and 8 always TRUE -- setting breakpoint to beginning.
[1] "Joining segments 7 and 4 at pseudotime 0.759 to create segment 9"
[1] "Calculating divergence between 1 and 9 (Pseudotime 0 to 0.699)"
Difference between 1 and 9 always FALSE -- setting breakpoint to end.
[1] "Calculating divergence between 2 and 9 (Pseudotime 0 to 0.446)"
Difference between 2 and 9 always FALSE -- setting breakpoint to end.
[1] "Calculating divergence between 3 and 9 (Pseudotime 0 to 0.425)"
Difference between 3 and 9 always FALSE -- setting breakpoint to end.
[1] "Calculating divergence between 6 and 9 (Pseudotime 0 to 0.74)"
Difference between 6 and 9 always FALSE -- setting breakpoint to end.
[1] "Calculating divergence between 5 and 9 (Pseudotime 0 to 0.677)"
Difference between 5 and 9 always FALSE -- setting breakpoint to end.
[1] "Calculating divergence between 8 and 9 (Pseudotime 0 to 0.759)"
Difference between 8 and 9 always TRUE -- setting breakpoint to beginning.
[1] "Joining segments 6 and 9 at pseudotime 0.74 to create segment 10"
[1] "Calculating divergence between 1 and 10 (Pseudotime 0 to 0.699)"
Difference between 1 and 10 always FALSE -- setting breakpoint to end.
[1] "Calculating divergence between 2 and 10 (Pseudotime 0 to 0.446)"
Difference between 2 and 10 always FALSE -- setting breakpoint to end.
[1] "Calculating divergence between 3 and 10 (Pseudotime 0 to 0.425)"
Difference between 3 and 10 always FALSE -- setting breakpoint to end.
[1] "Calculating divergence between 5 and 10 (Pseudotime 0 to 0.677)"
Difference between 5 and 10 always FALSE -- setting breakpoint to end.
[1] "Calculating divergence between 8 and 10 (Pseudotime 0 to 0.74)"
Difference between 8 and 10 always FALSE -- setting breakpoint to end.
[1] "Joining segments 8 and 10 at pseudotime 0.74 to create segment 11"
[1] "Calculating divergence between 1 and 11 (Pseudotime 0 to 0.699)"
Difference between 1 and 11 always FALSE -- setting breakpoint to end.
[1] "Calculating divergence between 2 and 11 (Pseudotime 0 to 0.446)"
Difference between 2 and 11 always FALSE -- setting breakpoint to end.
[1] "Calculating divergence between 3 and 11 (Pseudotime 0 to 0.425)"
Difference between 3 and 11 always FALSE -- setting breakpoint to end.
[1] "Calculating divergence between 5 and 11 (Pseudotime 0 to 0.677)"
Difference between 5 and 11 always FALSE -- setting breakpoint to end.
[1] "Joining segments 1 and 11 at pseudotime 0.699 to create segment 12"
[1] "Calculating divergence between 2 and 12 (Pseudotime 0 to 0.446)"
Difference between 2 and 12 always FALSE -- setting breakpoint to end.
[1] "Calculating divergence between 3 and 12 (Pseudotime 0 to 0.425)"
Difference between 3 and 12 always FALSE -- setting breakpoint to end.
[1] "Calculating divergence between 5 and 12 (Pseudotime 0 to 0.677)"
Difference between 5 and 12 always FALSE -- setting breakpoint to end.
[1] "Joining segments 5 and 12 at pseudotime 0.677 to create segment 13"
[1] "Calculating divergence between 2 and 13 (Pseudotime 0 to 0.446)"
Difference between 2 and 13 always FALSE -- setting breakpoint to end.
[1] "Calculating divergence between 3 and 13 (Pseudotime 0 to 0.425)"
Difference between 3 and 13 always FALSE -- setting breakpoint to end.
[1] "Joining segments 2 and 13 at pseudotime 0.446 to create segment 14"
[1] "Calculating divergence between 3 and 14 (Pseudotime 0 to 0.425)"
Difference between 3 and 14 always FALSE -- setting breakpoint to end.
[1] "Joining segments 3 and 14 at pseudotime 0.425 to create segment 15"
[1] "Assigning cells to segments."
[1] "Collapsing short segments."
[1] "Removing singleton segments."
[1] "Reassigning cells to segments."
[1] "Assigning cells to nodes."
[1] "Laying out tree."
[1] "Adding cells to tree."output saved in /scratch/irc/personal/robrechtc/tmp//RtmprpqUGr/output:
output.rds
Input saved to /scratch/irc/personal/robrechtc/tmp//RtmpwEYKGr/input:
data.rds
params.json
Attaching package: ‘dplyr’
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
Attaching package: ‘purrr’
The following object is masked from ‘package:jsonlite’:
flatten
Loading required package: ggplot2
Loading required package: Matrix
Attaching package: ‘Matrix’
The following object is masked from ‘package:tidyr’:
expand
2018-08-03 16:43:00: Filtering cells by number of genes.
2018-08-03 16:43:01: Filtering genes by number of cells.
2018-08-03 16:43:01: Filtering genes by number of counts across entire data.
2018-08-03 16:43:02: Filtering genes by maximum observed expression.
2018-08-03 16:43:02: Creating URD object.
2018-08-03 16:43:03: Determining normalization factors.
2018-08-03 16:43:05: Normalizing and log-transforming the data.
2018-08-03 16:43:06: Finishing setup of the URD object.
2018-08-03 16:43:06: All done.
[1] "destiny determined an optimal global sigma of 9.815"
[1] "2018-08-03 16:43:15: Centering and scaling data."
[1] "2018-08-03 16:43:16: Removing genes with no variation."
[1] "2018-08-03 16:43:16: Calculating PCA."
[1] "2018-08-03 16:43:16: Estimating significant PCs."
[1] "Marchenko-Pastur eigenvalue null upper bound: 1.86363007667355"
[1] "2 PCs have larger eigenvalues."
[1] "Storing 4 PCs."
Warning message:
In calcPCA(urd, mp.factor = params$mp.factor) :
Variable genes have not been stored. Using all genes instead.
[1] "Mean pseudotime back (~40 cells) 0.040312095105272"
[1] "Chance of accepted move to equal pseudotime is 0.780839619629311"
[1] "Mean pseudotime forward (~20 cells) -0.0228779641981184"
[1] "Calculating divergence between 2 and 1 (Pseudotime 0 to 0.694)"
Difference between 2 and 1 always TRUE -- setting breakpoint to beginning.
[1] "Calculating divergence between 2 and 3 (Pseudotime 0 to 0.608)"
Difference between 2 and 3 always TRUE -- setting breakpoint to beginning.
[1] "Calculating divergence between 2 and 6 (Pseudotime 0 to 0.694)"
Difference between 2 and 6 always FALSE -- setting breakpoint to end.
[1] "Calculating divergence between 2 and 5 (Pseudotime 0 to 0.619)"
Difference between 2 and 5 always TRUE -- setting breakpoint to beginning.
[1] "Calculating divergence between 2 and 4 (Pseudotime 0 to 0.694)"
Difference between 2 and 4 always FALSE -- setting breakpoint to end.
[1] "Calculating divergence between 1 and 3 (Pseudotime 0 to 0.608)"
Difference between 1 and 3 always TRUE -- setting breakpoint to beginning.
[1] "Calculating divergence between 1 and 6 (Pseudotime 0 to 0.713)"
Difference between 1 and 6 always TRUE -- setting breakpoint to beginning.
[1] "Calculating divergence between 1 and 5 (Pseudotime 0 to 0.619)"
Difference between 1 and 5 always TRUE -- setting breakpoint to beginning.
[1] "Calculating divergence between 1 and 4 (Pseudotime 0 to 0.713)"
Difference between 1 and 4 always TRUE -- setting breakpoint to beginning.
[1] "Calculating divergence between 3 and 6 (Pseudotime 0 to 0.608)"
Difference between 3 and 6 always TRUE -- setting breakpoint to beginning.
[1] "Calculating divergence between 3 and 5 (Pseudotime 0 to 0.608)"
Difference between 3 and 5 always FALSE -- setting breakpoint to end.
[1] "Calculating divergence between 3 and 4 (Pseudotime 0 to 0.608)"
Difference between 3 and 4 always TRUE -- setting breakpoint to beginning.
[1] "Calculating divergence between 6 and 5 (Pseudotime 0 to 0.619)"
Difference between 6 and 5 always TRUE -- setting breakpoint to beginning.
[1] "Calculating divergence between 6 and 4 (Pseudotime 0 to 0.714)"
Difference between 6 and 4 always FALSE -- setting breakpoint to end.
[1] "Calculating divergence between 5 and 4 (Pseudotime 0 to 0.619)"
Difference between 5 and 4 always TRUE -- setting breakpoint to beginning.
[1] "Joining segments 6 and 4 at pseudotime 0.714 to create segment 7"
[1] "Calculating divergence between 2 and 7 (Pseudotime 0 to 0.694)"
Difference between 2 and 7 always FALSE -- setting breakpoint to end.
[1] "Calculating divergence between 1 and 7 (Pseudotime 0 to 0.713)"
Difference between 1 and 7 always TRUE -- setting breakpoint to beginning.
[1] "Calculating divergence between 3 and 7 (Pseudotime 0 to 0.608)"
Difference between 3 and 7 always TRUE -- setting breakpoint to beginning.
[1] "Calculating divergence between 5 and 7 (Pseudotime 0 to 0.619)"
Difference between 5 and 7 always TRUE -- setting breakpoint to beginning.
[1] "Joining segments 2 and 7 at pseudotime 0.694 to create segment 8"
[1] "Calculating divergence between 1 and 8 (Pseudotime 0 to 0.694)"
Difference between 1 and 8 always TRUE -- setting breakpoint to beginning.
[1] "Calculating divergence between 3 and 8 (Pseudotime 0 to 0.608)"
Difference between 3 and 8 always TRUE -- setting breakpoint to beginning.
[1] "Calculating divergence between 5 and 8 (Pseudotime 0 to 0.619)"
Difference between 5 and 8 always TRUE -- setting breakpoint to beginning.
[1] "Joining segments 3 and 5 at pseudotime 0.608 to create segment 9"
[1] "Calculating divergence between 1 and 9 (Pseudotime 0 to 0.608)"
Difference between 1 and 9 always TRUE -- setting breakpoint to beginning.
[1] "Calculating divergence between 8 and 9 (Pseudotime 0 to 0.608)"
Difference between 8 and 9 always TRUE -- setting breakpoint to beginning.
[1] "Joining segments 1 and 8 at pseudotime 0 to create segment 10"
[1] "Calculating divergence between 9 and 10 (Pseudotime 0 to 0)"
Difference between 9 and 10 always FALSE -- setting breakpoint to end.
[1] "Joining segments 9 and 10 at pseudotime 0 to create segment 11"
[1] "Assigning cells to segments."
[1] "Collapsing short segments."
[1] "Removing singleton segments."
[1] "Reassigning cells to segments."
[1] "Assigning cells to nodes."
[1] "Laying out tree."
[1] "Adding cells to tree."output saved in /scratch/irc/personal/robrechtc/tmp//RtmpwEYKGr/output:
output.rds
Part of 