XiaoTaoWang
commented
4 months ago Hi, you may need to run cooler balance before you run correct-cnv. Please also refer to this similar issue #8 for more explanation.
Open biosciences opened 4 months ago
XiaoTaoWang
commented
4 months ago Hi, you may need to run cooler balance before you run correct-cnv. Please also refer to this similar issue #8 for more explanation.
When I try to run this command: correct-cnv -H patient_hg38_contact_map.mcool::resolutions/100000 \ --cnv-file patient_hg38_contact_map_100kb.CNV-seg.bedGraph --nproc 4 -f
It return such error: Traceback (most recent call last): File "/home/user1/var/opt/mambaforge/envs/neoloop/lib/python3.10/site-packages/pandas/core/indexes/base.py", line 3791, in get_loc return self._engine.get_loc(casted_key) File "index.pyx", line 152, in pandas._libs.index.IndexEngine.get_loc File "index.pyx", line 181, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/hashtable_class_helper.pxi", line 7080, in pandas._libs.hashtable.PyObjectHashTable.get_item File "pandas/_libs/hashtable_class_helper.pxi", line 7088, in pandas._libs.hashtable.PyObjectHashTable.get_item KeyError: 'weight'
It seems to find certain metadata, including normalization vectors. If these vectors are absent or not recognized, it could result in a KeyError: 'weight' because the tool cannot find the expected data.
I used JuiceBox Tools to generate HiC data by following the instructions: https://protect-au.mimecast.com/s/0EM_CjZ1N7iYvJw2BhWhDsz?domain=dovetail-capture.readthedocs.io, and use below command to convert the hic file: hic2cool patient_hg38_contact_map.hic patient_170052_18_hg38_contact_map.mcool