ashbymorrison

Hi, I am having the same problem but I am not using _--proteinFile_. I am just using _--domainFiles_ produced by the _hicMergeTADS_ function. __domain.bed_ files that use 1MB, 100KB, 50KB...

Thanks for the advice. I did check the chromosome names and all were normal 'chrN' and matching in each 'domainFiles'. I added some extra debugging output and it looks like...

In my case, the error seemed to be resolved when listing the bins in order of small bins to large bins in the —hicMergeTADS function. When I listed large bins...