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maxplanck-ie / HiCAssembler

Software to assemble contigs/scaffolds into chromosomes using Hi-C data
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ValueError: The first argument of bincount must be non-negative #15

Open zhanyinx opened 4 years ago

zhanyinx commented 4 years ago

Hi Fidel,

I am trying to use HiCAssemble to build a genome from Hi-C data. I have analysed the data using HiC-Pro and converted the output to h5 format using HiCExplorer 3.0

Then I used HiCAssemble to build the new genome as follow:

assemble -m goat_2019_july_120000_abs.h5 -o assembled_genome_goat --min_scaffold_length 100000 --bin_size 120000 --misassembly_zscore_threshold -1.0 --num_iterations 3 --num_processors 10 -f goat_v1_scaffolds.fa

This gave me the following error:

/work2/ggiorget/zhan/bin/Python-2.7.12/lib/python2.7/site-packages/hicexplorer/HiCMatrix.py:819: RuntimeWarning: divide by zero encountered in true_divide dist_list = (np.array(dist_list).astype(float) / binsize).astype(int) + 1 /work2/ggiorget/zhan/bin/Python-2.7.12/lib/python2.7/site-packages/hicexplorer/HiCMatrix.py:819: RuntimeWarning: invalid value encountered in true_divide dist_list = (np.array(dist_list).astype(float) / binsize).astype(int) + 1 Traceback (most recent call last): File "/work2/ggiorget/zhan/bin/Python-2.7.12/bin/assemble", line 312, in main(args) File "/work2/ggiorget/zhan/bin/Python-2.7.12/bin/assemble", line 304, in main scaffolds_to_ignore=args.scaffolds_to_ignore) File "/work2/ggiorget/zhan/bin/Python-2.7.12/lib/python2.7/site-packages/hicassembler/HiCAssembler.py", line 88, in init self.load_hic_matrix(hic_file_name, split_misassemblies, split_positions_file, matrix_bin_size) File "/work2/ggiorget/zhan/bin/Python-2.7.12/lib/python2.7/site-packages/hicassembler/HiCAssembler.py", line 141, in load_hic_matrix self.split_misassemblies(hic_file_name, split_positions_file) File "/work2/ggiorget/zhan/bin/Python-2.7.12/lib/python2.7/site-packages/hicassembler/HiCAssembler.py", line 848, in split_misassemblies ft.hic_ma.matrix = ft.hic_ma.convert_to_obs_exp_matrix(perchr=True) File "/work2/ggiorget/zhan/bin/Python-2.7.12/lib/python2.7/site-packages/hicexplorer/HiCMatrix.py", line 822, in convert_to_obs_exp_matrix sum_counts = np.bincount(dist_list, weights=submatrix.data) ValueError: The first argument of bincount must be non-negative

HiCExplorer version on server: 2.1.1 HiCAssembler on server: last version python version 2.7.12

Do you have any idea why this happend?

Thanks for your help best Zhan

fidelram commented 4 years ago

Converting the data from HiC pro to HiC explorer may not work properly because of the structure of the data. Can you try producing the data directly with HiCExplorer?