vertesy / seurat.cbe.issues Goto Github PK

> if (TRUE) source('~/GitHub/Packages/Seurat.pipeline/elements/Differential.gene.expression.Loop.R'); create_set_Original_OutDir()
[1] "All files will be saved under the original OutDir:  ~/Dropbox/Abel.IMBA/AnalysisD/Abel/SEO2/2021.04.12.rPCA.premRNA.dSample.Organoids/"
[1] "Differential.Gene.expression"
[1] "All files will be saved under 'NewOutDir':  ~/Dropbox/Abel.IMBA/AnalysisD/Abel/SEO2/2021.04.12.rPCA.premRNA.dSample.Organoids/Differential.Gene.expression/"
[1] "ParentDir was defined as: ~/Dropbox/Abel.IMBA/AnalysisD/Abel/SEO2/2021.04.12.rPCA.premRNA.dSample.Organoids/"
[1] "ParentDir will be: ~/Dropbox/Abel.IMBA/AnalysisD/Abel/SEO2/2021.04.12.rPCA.premRNA.dSample.Organoids/"
[1] "Call *create_set_Original_OutDir()* when chaning back to the main dir."
[1] "Resolutions analyzed:  0.2 0.5"
[1] "All files will be saved under 'OutDir':  ~/Dropbox/Abel.IMBA/AnalysisD/Abel/SEO2/2021.04.12.rPCA.premRNA.dSample.Organoids/Differential.Gene.expression/res.0.2/"
Calculating cluster 0
Calculating cluster 1
Calculating cluster 10
Calculating cluster 11
Calculating cluster 2
Calculating cluster 3
Calculating cluster 4
Calculating cluster 5
Calculating cluster 6
Calculating cluster 7
Calculating cluster 8
Calculating cluster 9
4987.281 sec elapsed
Error in `$<-.data.frame`(`*tmp*`, "combined.score", value = numeric(0)) :
  replacement has 0 rows, data has 7937

combined.obj <- Calcq90Expression(obj = combined.obj)
Error in asMethod(object) :
  Cholmod error 'problem too large' at file ../Core/cholmod_dense.c, line 105

> workers
[1] 30
> tic(); combined.obj <- IntegrateData(anchorset = anchors, dims = 1:p$'n.CC'); toc(); say()
Finding integration vector weights
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Integrating data
Merging dataset 17 into 22 33
Extracting anchors for merged samples
Finding integration vectors
Finding integration vector weights
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

...

Integrating data
Merging dataset 22 33 17 36 37 35 38 39 40 1 into 6 15 18 19 14 20 7 8 10 11 9
Extracting anchors for merged samples
Finding integration vectors
Finding integration vector weights
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Integrating data
Merging dataset 24 41 23 31 29 30 28 3 21 32 25 26 27 12 13 16 into 6 15 18 19 14 20 7 8 10 11 9 22 33 17 36 37 35 38 39 40 1
Extracting anchors for merged samples
Finding integration vectors
Error in validityMethod(as(object, superClass)) :
  long vectors not supported yet: ../../src/include/Rinlinedfuns.h:535
In addition: There were 50 or more warnings (use warnings() to see the first 50)

Error in file(filename, "r", encoding = encoding) :
  cannot open the connection to 'https://raw.githubusercontent.com/vertesy/SEO/master/GO-scoring/Seurat.gene.sets.and.GO.terms.R?token=XXXXXXXXXXXXXXXXXXXXXXXXXXXX'
In addition: Warning messages:
1: no DISPLAY variable so Tk is not available
2: In file(filename, "r", encoding = encoding) :
  cannot open URL 'https://raw.githubusercontent.com/vertesy/SEO/master/GO-scoring/Seurat.gene.sets.and.GO.terms.R?token=XXXXXXXXXXXXXXXXXXXXXXXXXXXX': HTTP status was '404 Not Found'
Using V8 engine 6.8.275.32-node.12

 tic(); anchors <- FindIntegrationAnchors(object.list = ls.Seurat, dims = 1:p$'n.CC', reduction = "rpca"); toc(); say();

Computing 2000 integration features
Scaling features for provided objects
Error: Failed to retrieve the result of MulticoreFuture (future_lapply-21) from the forked worker (on localhost; PID 85677). Post-mortem diagnostic: No process exists with this PID, i.e. the forked localhost worker is no longer alive.
In addition: There were 19 warnings (use warnings() to see them)