Cooler Balance failed

[kimquililan]

Hi! I ran cooler balance with my cool file and it ran okay until it reached an error

Output exceeds the size limit. Open the full output data in a text editor INFO:cooler.cli.balance:Balancing "INO80_4_FA_FilteredbyDist_ShiftbyOrientation_80_bin20.cool" INFO:cooler.balance:variance is 340.4289927827929 INFO:cooler.balance:variance is 313.23710687493167 INFO:cooler.balance:variance is 185.8196031817053 INFO:cooler.balance:variance is 333.761573580506 INFO:cooler.balance:variance is 196.25432819720305 INFO:cooler.balance:variance is 358.0699084083024 INFO:cooler.balance:variance is 209.38936590752522 INFO:cooler.balance:variance is 376.30319720607156 INFO:cooler.balance:variance is 220.66785884443226 INFO:cooler.balance:variance is 390.03982936886524 INFO:cooler.balance:variance is 230.22842018905308 INFO:cooler.balance:variance is 401.1281708234125 INFO:cooler.balance:variance is 238.69538102448956 INFO:cooler.balance:variance is 410.96323399634514 INFO:cooler.balance:variance is 246.59651335609055 INFO:cooler.balance:variance is 420.5124418137992 INFO:cooler.balance:variance is 254.30424005915543 INFO:cooler.balance:variance is 430.42442586082234 INFO:cooler.balance:variance is 262.070027289631 INFO:cooler.balance:variance is 441.12642971726603 INFO:cooler.balance:variance is 270.0644332808771 INFO:cooler.balance:variance is 452.89700356277393 INFO:cooler.balance:variance is 278.4066275301745 INFO:cooler.balance:variance is 465.9168997527476 ... warnings.warn(

ERROR:cooler.cli.balance:Iteration limit reached without convergence ERROR:cooler.cli.balance:Storing final result. Check log to assess convergence.

When I do cooler dump, the balanced column is empty. Did I do something wrong?

[agalitsyna]

Hi, Kim! This usually means that the matrix is too sparse for balancing at this resolution, and rows/columns of Hi-C matrix have too little counts for balancing. Before confirming that, I would limit the number of iterations for balancing by --max-iters and set it to 10, just to see how the maps will look like!