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computational-chemical-biology / ChemWalker

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Error in Perform propagation inside a given connected component #2

Closed anani-a-missinou closed 1 year ago

anani-a-missinou commented 1 year ago

Hi dear developper,

I try to use your pipeline to propagate metabolic networks. By at the step of "Perform propagation inside a given connected component" I get an error.

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Please, can you help me to solve the error

ridasilva commented 1 year ago

@tiagocabralborelli, please help the user.

tiagocabralborelli commented 1 year ago

Hi, @anani-a-missinou. Thanks for using Chemwalker. I gonna try to reproduce this error to solve it. Did you use your own GNPS job id or just trayed with ours? Can you provide it to me?

Here is a possible explanation: based on the returned message "component with 0 nodes" I think you forgot to pass the component index of the cluster that you want to propagate. Check the table called net to see what component index (cluster of nodes) your node (CLUSTERID1 or CLUSTERID2 ) belongs to. Then pass it to the parameter __comp_index in the function walk_comp_index__

To propagate information, chemwalker needs at least a known node.

Please update me when your try again.

anani-a-missinou commented 1 year ago

Hi Tiago,

Sorry for too late response.

I try with my own id=0da29a762fa74751a9e0afc6f2b8efeb. Thank you for this useful explanation.

Also, I use the code basic_use_colab.ipynb. Now I try to reproduce this error, but I can't.

So I retry to use exactly our code and our id, but it doesn't work

Thank you for your help.

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