chicViewpoint

[LeilyR]

chicViewpoint fails with the following error message:
miniconda3/envs/hicexplorer/lib/python3.6/site-packages/hicexplorer/lib/viewpoint.py", line 571, in computeSumOfDensities
background_nbinom[fixateRange] = nbinom(pBackgroundModel[fixateRange][0], pBackgroundModel[fixateRange][1])
KeyError: 500000

[joachimwolff]

Can you provide the full command for a) qc, b) background and c) the viewpoint itself?

[LeilyR]

The error comes from background model computation. The fixateRange in there is 500,000 and the resolution is 2,000 , so the last computed distance is 500,000 - 2,000 = 498,000 . The solution would be either adding the last distance to the bg model or calling fixateRange -1 here.

[LeilyR]

background model:
chicViewpointBackgroundModel -m mergedSamples_merged_bs2kb.corrected.h5
--referencePoints refPoint.bed -t 30
--outFileName bgModel.bed

viewPoint:

chicViewpoint -m mergedSamples_merged_bs2kb.corrected.h5
--referencePoints refPoint.bed -t 30
--backgroundModelFile bgModel.bed
--range 100000 100000 -o interactionFolder

[joachimwolff]

I changed so much in chic-modules in the last half year. Could be fixed by now the current release, or maybe this line of code is not even more there.

Please reopen in case it is still crashing.

Thanks,

Joachim