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tariks / peakachu

Genome-wide contact analysis using sklearn
MIT License
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IndexError: column index (15100) out of range #25

Open frwjo opened 7 months ago

frwjo commented 7 months ago

hello Tariks, I run the code : peakachu train -r 10000 -p maizeB73.allValidPairs_10000.hic.cool -O models -b maizeB73.10kb.bedpe ,
my maizeB73.allValidPairs_10000.hic.cool comes from hicpro'allvalidpairs and convert to .hic and .cool ,and my maizeB73.10kb.bedpe come from hicexplorer :hicConvertFormat -m maizeB73.allValidPairs_10000.hic.cool --inputFormat cool --outputFormat ginteractions -o maizeB73.allValidPairs.10kb.ginterections.tsv .But I met the problem : Traceback (most recent call last): File "/pub4/wujie/miniconda3/envs/peakachu/bin/peakachu", line 91, in run() File "/pub4/wujie/miniconda3/envs/peakachu/bin/peakachu", line 87, in run args.func(args) File "/pub4/wujie/miniconda3/envs/peakachu/lib/python3.10/site-packages/peakachu/train_models.py", line 64, in main if X[b1, b2] > maxv: File "/pub4/wujie/miniconda3/envs/peakachu/lib/python3.10/site-packages/scipy/sparse/_index.py", line 46, in getitem row, col = self._validate_indices(key) File "/pub4/wujie/miniconda3/envs/peakachu/lib/python3.10/site-packages/scipy/sparse/_index.py", line 163, in _validate_indices raise IndexError('column index (%d) out of range' % col) IndexError: column index (15100) out of range How to solve the problem?Many thanks. frwjo

frwjo commented 7 months ago

cut -f 1,2,3,4,5,6 maizeB73.allValidPairs.10kb.ginterections.tsv > maizeB73.10kb.bedpe