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deeptools / HiCExplorer

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
https://hicexplorer.readthedocs.org
GNU General Public License v3.0
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Questions about hicMergeTADbins #461

Closed QianzhaoJ closed 4 years ago

QianzhaoJ commented 5 years ago

Hi: The scripts :hicMergeTADbins -m test.h5 --domains test.dm --outFile ./result.txt The errors:

ERROR:hicmatrix.HiCMatrix:Index error Traceback (most recent call last): File "/data1/liuzunpeng/04_Softwares/anaconda/envs/hicexplorer33/lib/python3.6/site-packages/hicmatrix/HiCMatrix.py", line 262, in getRegionBinRange endbin = sorted(self.interval_trees[chrname][endpos:endpos + 1])[0].data IndexError: list index out of range Traceback (most recent call last): File "/data2/liuzunpeng/04_Softwares/HiCExplorer-3.3.1/bin/hicMergeTADbins", line 7, in main() File "/data1/liuzunpeng/04_Softwares/anaconda/envs/hicexplorer33/lib/python3.6/site-packages/hicexplorer/hicMergeTADbins.py", line 143, in main boundary_id_list = get_boundary_bin_id(hic_ma, args.domains) File "/data1/liuzunpeng/04_Softwares/anaconda/envs/hicexplorer33/lib/python3.6/site-packages/hicexplorer/hicMergeTADbins.py", line 129, in get_boundary_bin_id start_bin, end_bin = hic.getRegionBinRange(chrom, start, end) TypeError: 'NoneType' object is not iterable

and the format of test.dm :

chr1 0 725000 ID1 . . 0 725000 . chr1 725000 1900000 ID2 . . 725000 1900000 . chr1 1900000 2000000 ID3 . . 1900000 2000000 . chr1 2000000 2600000 ID4 . . 2000000 2600000 .

Could you give me some suggestions about the format of domians ? Thanks in advance !

Qianzhao

QianzhaoJ commented 5 years ago

Hi : Now I have worked out the problem about the format of input files , hicMergeTADbins is running and no errors are reported . But I don't find the output files in ./result.txt . Qianzhao

LeilyR commented 5 years ago

hic.getRegionBinRange(chrom, start, end) TypeError: 'NoneType' object is not iterable could mean that the coordinates went out of range

LeilyR commented 4 years ago

@QianzhaoJ We assume that your problem is solved since we have not heard of you. I close this issue for now but feel free to reopen it if there is still any problem left.