I am having issues running the monocle container. I have used slignshot and ran with no issues but once I tried with monocle (either tree or ica), I get the next error:
malignant.model.monocle.ddrtree <- dynwrap::infer_trajectory(malignant.pseudotime,
dynmethods::ti_monocle_ddrtree(reduction_method = "ICA", max_components = 2L,
norm_method = "log", auto_param_selection = TRUE,
filter_features = TRUE, filter_features_mean_expression = 0.1),
verbose = TRUE, mc_cores = 16)
Running singularity exec 'docker://dynverse/ti_monocle_ddrtree:v0.9.9.02' \
echo hi
Running /usr/bin/singularity exec --containall -B \
'/scratch/2174604/RtmpN9Tklm/file94b842fa68c3/:/copy_mount,/scratch/2174604/RtmpN9Tklm/file94b84c2eb69c/tmp:/tmp2' \
'docker://dynverse/ti_monocle_ddrtree:v0.9.9.02' cp /code/definition.yml \
/copy_mount/
Executing 'monocle_ddrtree' on '20200703_085655__data_wrapper__4DmAh8WqNR'
With parameters: list(reduction_method = "ICA", max_components = 2L, norm_method = "log", auto_param_selection = TRUE, filter_features = TRUE, filter_features_mean_expression = 0.1, mc_cores = 16)
inputs: counts
priors :
Input saved to /scratch/2174604/RtmpN9Tklm/file94b847b639c3/ti
Running method using babelwhale
Running /usr/bin/singularity run --containall --pwd /ti/workspace -B \
'/scratch/2174604/RtmpN9Tklm/file94b847b639c3/ti:/ti,/scratch/2174604/RtmpN9Tklm/file94b868336e45/tmp:/tmp2' \
'docker://dynverse/ti_monocle_ddrtree:v0.9.9.02' --dataset /ti/input.h5 \
--output /ti/output.h5
Loading required package: Matrix
Attaching package: ‘Matrix’
The following objects are masked from ‘package:tidyr’:
expand, pack, unpack
Loading required package: Biobase
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 object is masked from ‘package:Matrix’:
which
The following objects are masked from ‘package:dplyr’:
combine, intersect, setdiff, union
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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: ggplot2
Loading required package: VGAM
Loading required package: stats4
Loading required package: splines
Attaching package: ‘VGAM’
The following object is masked from ‘package:tidyr’:
fill
Loading required package: DDRTree
Loading required package: irlba
Removing 119 outliers
Warning messages:
1: In log(ifelse(y == 0, 1, y/mu)) : NaNs produced
2: step size truncated due to divergence
Error: node stack overflow
Execution halted
missing value where TRUE/FALSE needed
Error: Error during trajectory inference, see output above ↑↑↑
Traceback:
1. dynwrap::infer_trajectory(malignant.pseudotime, dynmethods::ti_monocle_ddrtree(reduction_method = "ICA",
. max_components = 2L, norm_method = "log", auto_param_selection = TRUE,
. filter_features = TRUE, filter_features_mean_expression = 0.1),
. verbose = TRUE, mc_cores = 16)
2. stop("Error during trajectory inference, see output above ↑↑↑",
. call. = FALSE)
In another dataset I had the same problem but slightly different reason to stop the pipeline:
Input saved to /scratch/2151233/Rtmp1H4eT4/file351b5e691c00/ti
Running method using babelwhale
Running /usr/bin/singularity run --containall --pwd /ti/workspace -B \
'/scratch/2151233/Rtmp1H4eT4/file351b5e691c00/ti:/ti,/scratch/2151233/Rtmp1H4eT4/file351b4b9faefe/tmp:/tmp2' \
'docker://dynverse/ti_monocle_ica:v0.9.9.01' --dataset /ti/input.h5 \
--output /ti/output.h5 --use_priors all
Loading required package: Matrix
Loading required package: Biobase
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 object is masked from ‘package:Matrix’:
which
The following objects are masked from ‘package:dplyr’:
combine, intersect, setdiff, union
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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: ggplot2
Loading required package: VGAM
Loading required package: stats4
Loading required package: splines
Loading required package: DDRTree
Loading required package: irlba
Removing 9 outliers
[1] 5357
Error in task$priors$start_n + task$priors$end_n :
non-numeric argument to binary operator
Execution halted
Loading required package: Matrix
Loading required package: Biobase
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 object is masked from ‘package:Matrix’:
which
The following objects are masked from ‘package:dplyr’:
combine, intersect, setdiff, union
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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: ggplot2
Loading required package: VGAM
Loading required package: stats4
Loading required package: splines
Loading required package: DDRTree
Loading required package: irlba
Removing 9 outliers
Error in task$priors$start_n + task$priors$end_n :
non-numeric argument to binary operator
Execution halted
Error: Error during trajectory inference, see output above ↑↑↑
Traceback:
1. dynwrap::infer_trajectory(monocytes.pseudotime, dynmethods::ti_monocle_ica(reduction_method = "ICA",
. max_components = 2L, norm_method = "log", filter_features = TRUE,
. filter_features_mean_expression = 0.1), give_priors = c("start_id",
. "end_id"), verbose = TRUE)
2. stop("Error during trajectory inference, see output above ↑↑↑",
. call. = FALSE)
Good day,
I am having issues running the monocle container. I have used slignshot and ran with no issues but once I tried with monocle (either tree or ica), I get the next error:
In another dataset I had the same problem but slightly different reason to stop the pipeline:
What could be the problem?
Thanks in advance