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edroaldo / cellrouter

Reconstruction of complex single-cell trajectories using CellRouter
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Java error in "findPaths" #33

Open AndreaRP opened 2 years ago

AndreaRP commented 2 years ago

Hi,

I'm having an issue when I try to run the findPaths function. I'm following the tutorial with my own data, and up to that point everything works fine. When I get to 

##Identify trajectories
cellrouter <- findPaths(cellrouter, column='seurat_clusters', libdir, paste(getwd()
, 'reports/CellRanger/files/paths', sep='/'), method="graph")

I get the following error for each trajectory (I copy here only 3 to 6 as an example):

-------------------Transition: 3.6  -----------------------
1) Computing flow network
Creating flow network...
Uncaught exception - null
java.lang.NullPointerException
    at cellrouter.InputOutput.getNetworkData(InputOutput.java:54)
    at cellrouter.CellRouter.createFlowNetwork(CellRouter.java:83)
    at cellrouter.CellRouter.runAnalysis(CellRouter.java:63)
    at cellrouter.CellRouter.main(CellRouter.java:244)

Can you give me any clue as to what could be causing the problem?