Phenograph fails in windows with index out of bounds error in windows

[ramgridhc]

Greetings, My phenograph analysis is failing on a Windows server as I try to scale my analysis on AWS EC2 instance. The analysis works on my Mac which has limited memory but is very slow due to limited memory. Looking at installed doc, I have installed visual studio on Windows server as a pre-requisite. Am I missing any configuration on the windows Server? Let me know. I have enclosed the error log below:

Log Error on cmd line Attempted to access hierarchy_output(:,2); index out of bounds because size(hierarchy_output)=[0,0]. Error in LouvainfromBin_Windows (line 63) Error in phenograph (line 73) Error in Run_Phenograph_Callback (line 37) Error in analyze_button_Callback (line 80) Error in gui_mainfcn (line 95) Error in histoCAT (line 42) Error in @(hObject,eventdata)histoCAT('analyze_button_Callback',hObject,eventdata,guidata(hObject)) Error while evaluating UIControl Callback

[DenisSch]

It looks like the output file is empty.

I would check:

• whether you have rights to read and write in the folders
• that no "spaces" or special characters are in the folder names
• what error messages are thrown by the system outside of MATLAB

Maybe we should also post this issue here: https://github.com/jacoblevine/PhenoGraph/issues

What Windows version are you using on AWS?

[DenisSch]

Is this solved?

[ramgridhc]

Windows version for histoCAT did not work. So, we went back for a bigger MAC workstation 32G memory. 8G macbook had loading challenges. AWS windows instance was 96G but we still got OOM errors. Naming and folders config were valid.

Ram Bhandarkar 703620034

On Thu, Aug 13, 2020 at 12:05 AM DenisSch notifications@github.com wrote:

Is this solved?

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[JC19C]

Hi, I have the exact same issue of "empty" output, with admin rights, no spaces in names:

Normalizing according to the 99th percentile...Warning: Default string does not match any button string name. Finding 30 nearest neighbors... Building Jaccard Graph... 10 percent complete: 0.17 s 20 percent complete: 0.34 s 30 percent complete: 0.51 s 40 percent complete: 0.66 s 50 percent complete: 0.83 s 60 percent complete: 1.00 s 70 percent complete: 1.16 s 80 percent complete: 1.34 s 90 percent complete: 1.51 s Finished Jaccard graph in 1.65 s Edge number pruned from 176343 to 117226 Sparsity: 0.0033917 Writing graph to .bin file Percent done: 10 20 30 40 50 60 70 80 90 Finished writing .bin file in 1.06 s In windows.. MATLAB: calling convert: C:\Users\JC\AppData\Local\Temp\JC\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\convert.exe -i C:\hll\custom_gates_0\G.bin -o C:\hll\custom_gates_0\G_graph.bin -w C:\hll\custom_gates_0\G_graph.weights MATLAB: running community detection, ITERATION 1 C:\Users\JC\AppData\Local\Temp\JC\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\community.exe C:\hll\custom_gates_0\G_graph.bin -l -1 -v -w C:\hll\custom_gates_0\G_graph.weights > C:\hll\custom_gates_0\G.tree

MATLAB: modularity scores: C:\Users\JC\AppData\Local\Temp\JC\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\hll\custom_gates_0\G.tree

MATLAB: max level is NaN MATLAB: importing level NaN C:\Users\JC\AppData\Local\Temp\JC\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\hll\custom_gates_0\G.tree -l NaN > C:\hll\custom_gates_0\G.tmp Attempted to access hierarchy_output(:,2); index out of bounds because size(hierarchy_output)=[0,0].

Error in LouvainfromBin_Windows (line 63)

Error in phenograph (line 73)

Error in Run_Phenograph_Callback (line 37)

Error in analyze_button_Callback (line 80)

Error in gui_mainfcn (line 95)

Error in histoCAT (line 42)

Error in @(hObject,eventdata)histoCAT('analyze_button_Callback',hObject,eventdata,guidata(hObject))

Error while evaluating UIControl Callback

Did you end up finding a solution in the end? Thanks for your help, JC