Open ccruizm opened 4 years ago
Good day,
When using ti_slingshot, I can give start_id and it runs with no issue but once I add end_id, I get the next error:
ti_slingshot
Output with start_id:
Running singularity exec 'docker://dynverse/ti_slingshot:v1.0.3' echo hi Running /usr/bin/singularity exec --containall -B \ '/scratch/2174604/RtmpVRaCmA/file93424d99e843/:/copy_mount,/scratch/2174604/RtmpVRaCmA/file93425b1e0559/tmp:/tmp2' \ 'docker://dynverse/ti_slingshot:v1.0.3' cp /code/definition.yml \ /copy_mount/ Executing 'slingshot' on '20200703_084151__data_wrapper__4DmAh8WqNR' With parameters: list(cluster_method = "pam", ndim = 20L, shrink = 1L, reweight = TRUE, reassign = TRUE, thresh = 0.001, maxit = 10L, stretch = 2L, smoother = "smooth.spline", shrink.method = "cosine", mc_cores = 8) inputs: expression priors : start_id Input saved to /scratch/2174604/RtmpVRaCmA/file93426388f8d3/ti Running method using babelwhale Running /usr/bin/singularity run --containall --pwd /ti/workspace -B \ '/scratch/2174604/RtmpVRaCmA/file93426388f8d3/ti:/ti,/scratch/2174604/RtmpVRaCmA/file93425a1ec615/tmp:/tmp2' \ 'docker://dynverse/ti_slingshot:v1.0.3' --dataset /ti/input.h5 --output \ /ti/output.h5 --use_priors all Warning messages: 1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display 2: 'rgl_init' failed, running with rgl.useNULL = TRUE Using full covariance matrix There were 50 or more warnings (use warnings() to see the first 50) Output saved to /scratch/2174604/RtmpVRaCmA/file93426388f8d3/ti/output.h5 Attempting to read in output with hdf5
Output with start_id and end_id:
Running singularity exec 'docker://dynverse/ti_slingshot:v1.0.3' echo hi Running /usr/bin/singularity exec --containall -B \ '/scratch/2174604/RtmpVRaCmA/file934232256d86/:/copy_mount,/scratch/2174604/RtmpVRaCmA/file93427cd0c49/tmp:/tmp2' \ 'docker://dynverse/ti_slingshot:v1.0.3' cp /code/definition.yml \ /copy_mount/ Executing 'slingshot' on '20200703_084151__data_wrapper__4DmAh8WqNR' With parameters: list(cluster_method = "pam", ndim = 20L, shrink = 1L, reweight = TRUE, reassign = TRUE, thresh = 0.001, maxit = 10L, stretch = 2L, smoother = "smooth.spline", shrink.method = "cosine", mc_cores = 8) inputs: expression priors : start_id, end_id Input saved to /scratch/2174604/RtmpVRaCmA/file93426c6aabaa/ti Running method using babelwhale Running /usr/bin/singularity run --containall --pwd /ti/workspace -B \ '/scratch/2174604/RtmpVRaCmA/file93426c6aabaa/ti:/ti,/scratch/2174604/RtmpVRaCmA/file9342b5eff24/tmp:/tmp2' \ 'docker://dynverse/ti_slingshot:v1.0.3' --dataset /ti/input.h5 --output \ /ti/output.h5 --use_priors all Warning messages: 1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display 2: 'rgl_init' failed, running with rgl.useNULL = TRUE Using full covariance matrix Error in sortIndex(X[, tree])[1, ] : incorrect number of dimensions Calls: <Anonymous> ... getLineages -> getLineages -> .local -> <Anonymous> Execution halted Warning messages: 1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display 2: 'rgl_init' failed, running with rgl.useNULL = TRUE Using full covariance matrix Error in sortIndex(X[, tree])[1, ] : incorrect number of dimensions Calls: <Anonymous> ... getLineages -> getLineages -> .local -> <Anonymous> Execution halted Error: Error during trajectory inference, see output above ↑↑↑ Traceback: 1. dynwrap::infer_trajectory(monocytes.pseudotime, dynmethods::ti_slingshot(shrink = 1L, . reweight = TRUE, reassign = TRUE, thresh = 0.001, maxit = 10L, . stretch = 2L, smoother = "smooth.spline", shrink.method = "cosine"), . verbose = TRUE, mc_cores = 8, give_priors = c("start_id", . "end_id")) 2. stop("Error during trajectory inference, see output above ↑↑↑", . call. = FALSE)
What would be the reason for this error?
Thanks in advance
Good day,
When using
ti_slingshot
, I can give start_id and it runs with no issue but once I add end_id, I get the next error:Output with start_id:
Output with start_id and end_id:
What would be the reason for this error?
Thanks in advance