Question: Unable to follow example SPADE usage - Cannot create iterator, invalid vertex id
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gravatar for duncanjamesmurray01
3.4 years ago by
United Kingdom
duncanjamesmurray010 wrote:

Hi There,

 

I am trying to get SPADE working in R 3.2.2 running on a 64-bit linux system (ubuntu-mate 14.04) in order to process some flowcytometry data.  I installed the package without any issues following this link: https://github.com/nolanlab/spade/wiki/GettingStarted from bioconductor.  This is my output from performing library(spade):

> library(spade)
Loading required package: igraph

Attaching package: ‘igraph’

The following objects are masked from ‘package:stats’:

    decompose, spectrum

The following object is masked from ‘package:base’:

    union

Loading required package: Rclusterpp
Loading required package: Rcpp
Loading required package: RcppEigen

I then downloaded the example data from https://github.com/nolanlab/spade/wiki/Example-Usage and followed the same instructions below:    

R> markers <- c("Cd(110,111,112,114)","Cell_length","Dy(163.929)-Dual","Er(165.930)-Dual","Er(166.932)-Dual","Er(167.932)-Dual","Er(169.935)-Dual","Eu(150.919)-Dual","Eu(152.921)-Dual","Gd(155.922)-Dual","Gd(157.924)-Dual","Gd(159.927)-Dual","Ho(164.930)-Dual","In(114.903)-Dual","Ir(190.960)-Dual","La(138.906)-Dual","Lu(174.940)-Dual","Nd(141.907)-Dual","Nd(143.910)-Dual","Nd(144.912)-Dual","Nd(145.913)-Dual","Nd(147.916)-Dual","Nd(149.920)-Dual","Pr(140.907)-Dual","Sm(146.914)-Dual","Sm(151.919)-Dual","Sm(153.922)-Dual","Tb(158.925)-Dual","Tm(168.934)-Dual","Yb(170.936)-Dual","Yb(171.936)-Dual","Yb(173.938)-Dual","Yb(175.942)-Dual")

R> PANELS <- list(list(panel_files=c("Bendall_et_al_Science_2011_Marrow_1_SurfacePanel_Live_CD44pos_Singlets.fcs"), median_cols=NULL,reference_files=c("Bendall_et_al_Science_2011_Marrow_1_SurfacePanel_Live_CD44pos_Singlets.fcs"),fold_cols=c()))

R> SPADE.driver("Bendall_et_al_Science_2011_Marrow_1_SurfacePanel_Live_CD44pos_Singlets.fcs", out_dir="output", cluster_cols=markers, panels=PANELS, transforms=flowCore::arcsinhTransform(a=0, b=0.2), layout=SPADE.layout.arch, downsampling_target_percent=0.1, downsampling_target_number=NULL, downsampling_target_pctile=NULL, downsampling_exclude_pctile=0.01, k=200, clustering_samples=50000)

It appears to work during this process, using all 4 threads of my processor, but then generates this error:

 

SPADE.driver("Bendall_et_al_Science_2011_Marrow_1_SurfacePanel_Live_CD44pos_Singlets.fcs", out_dir="output", cluster_cols=markers, panels=PANELS, transforms=flowCore::arcsinhTransform(a=0, b=0.2), layout=SPADE.layout.arch, downsampling_target_percent=0.1, downsampling_target_number=NULL, downsampling_target_pctile=NULL, downsampling_exclude_pctile=0.01, k=200, clustering_samples=50000)
Downsampling file: Bendall_et_al_Science_2011_Marrow_1_SurfacePanel_Live_CD44pos_Singlets.fcs
Estimated downsampling-I progress: 0% ...
Estimated downsampling-I progress: 100% ...
Targeting 9048 events for output/Bendall_et_al_Science_2011_Marrow_1_SurfacePanel_Live_CD44pos_Singlets.fcs.density.fcs
Clustering files...
Upsampling file: output/Bendall_et_al_Science_2011_Marrow_1_SurfacePanel_Live_CD44pos_Singlets.fcs.density.fcs
Error in .Call("R_igraph_get_shortest_paths", graph, as.igraph.vs(graph, :
At iterators.c:759 : Cannot create iterator, invalid vertex id, Invalid vertex id
In addition: Warning messages:
1: In write.FCS(out_frame, outfilename) :
'write.FCS' is not fully tested and should be considered as experimental.
2: In write.FCS(out_frame, outfilename) :
'write.FCS' is not fully tested and should be considered as experimental.
3: In write.FCS(ff, outfilename) :
'write.FCS' is not fully tested and should be considered as experimental.
4: In write.FCS(out_frame, outfilename) :
'write.FCS' is not fully tested and should be considered as experimental.

 

I would be hugely grateful for any help anyone can give regarding this.  I've tried browsing through the code of the SPADE.driver, and I think it's calling a C function, but I haven't gotten any further than that.

 

Many thanks,

Duncan Murray.

spade igraph • 787 views
ADD COMMENTlink modified 23 months ago by johnheath3460 • written 3.4 years ago by duncanjamesmurray010

How did you get through this error? I'm getting the same one on R 64 bit on WIndows 10 

 

Joey

ADD REPLYlink written 23 months ago by johnheath3460
Answer: Unable to follow example SPADE usage - Cannot create iterator, invalid vertex id
0
gravatar for johnheath346
23 months ago by
johnheath3460 wrote:

How did you get through this error? I'm getting the same one on R 64 bit on WIndows 10 

 

Joey

ADD COMMENTlink written 23 months ago by johnheath3460
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