ERROR:hicexplorer.hicDifferentialTAD:local variable 'right_boundary_index_target' referenced before assignmentTraceback

[antarikshtyagi]

Hello,

I am running hicDifferentialTAD using this command:

hicDifferentialTAD -tm cools/NlaIII_run01_UCSC_hg38.matrix.cool -cm cools/NlaIII_run03_UCSC_hg38.matrix.cool
-td run_01/TADs_run01_domains.bed -o differential -p 0.01 -t 32 -mr all

This was running for over an hour and then crashed with the error below. Could you please help me in getting this running

Thanks
Ant

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ERROR:hicexplorer.hicDifferentialTAD:local variable 'right_boundary_index_target' referenced before assignmentTraceback (most recent call last):
File "/home/antariksh.tyagi/miniconda3/envs/hicexplorer/lib/python3.8/site-packages/hicexplorer/hicDifferentialTAD.py", line 197, in computeDifferentialT$ intertad_left_target = matrix_target_inter_tad[outer_left_boundary_index_target:left_boundary_index_target, left_boundary_index_target:right_boundary_i$UnboundLocalError: local variable 'right_boundary_index_target' referenced before assignment

real 70m6.006s
user 184m27.765s
sys 71m52.225s

[joachimwolff]

Hi Ant,

The error message indicates a bug in the implementation. I need to check in detail why the variable right_boundary_index_target is not defined at this stage. I assume we have some '+1' aka 'the last element in the list' bug, meaning some boundary condition check is not correct.

What you can try to get some result in the meantime: run the command not with --mode all(that is the default case you used) but with --mode left-inter-TAD. Only the TAD and the left inter-TAD region are considered; the problematic the right inter-TAD boundaries are excluded, and it might run.

Best,

Joachim

[antarikshtyagi]

Thanks for responding. I tried with --mode left-inter-TAD but could not complete the run and resulted in the same error:

ERROR:hicexplorer.hicDifferentialTAD:local variable 'right_boundary_index_target' referenced before assignmentTraceback (most recent call last):
File "/home/antariksh.tyagi/miniconda3/envs/hicexplorer/lib/python3.8/site-packages/hicexplorer/hicDifferentialTAD.py", line 197, in computeDifferentialT$ intertad_left_target = matrix_target_inter_tad[outer_left_boundary_index_target:left_boundary_index_target, left_boundary_index_target:right_boundary_i$UnboundLocalError: local variable 'right_boundary_index_target' referenced before assignment

real 71m16.764s
user 186m38.889s
sys 75m51.119s

[nyuhic]

Hello, any update on this issue? I get the same error no matter what I set as the mode.

[nyuhic]

If someone is facing the same issue, I was able to get it working by not using multiple threads.

[joachimwolff]

Ok, thanks for the feedback. I will work on the parallelization for the next release.

[joachimwolff]

This bug could be fixed with the changes in the current develop branch. Can you check this @nyuhic @antarikshtyagi ? Thanks a lot!

[nyuhic]

Thanks, it works fine with multiple threads now.

I also have a related question. Once I get the differential tads, I want to know if interactions are increasing or decreasing in them. To check this I used deeptools multiBigwigSummary to extract the average score across the differential domains from the score.bedgraph files that are produced when calling tads. I then compare these scores between treatment and control condition. Does this make sense?