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Inferring, interpreting and visualising trajectories using a streamlined set of packages 🦕
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Error when adding end_id to ti_slingshot #87

Open ccruizm opened 4 years ago

ccruizm commented 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:

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