Closed ZQY19960810 closed 2 years ago
kaukrise
commented
2 years ago Hey, this is a FAN-C error - are the Hi-C files you are using publicly available? If so, could you point me to a download link? I would really like to use them for testing. Thanks in advance!
ZQY19960810
commented
2 years ago Thank you ! But I am already solved this problem. I checked my .hic file,I produced it from juicerbox pre command,but I didn't give it enough memeory ,so some .hic file have confusing file formats . I now rerun these programs,then it works again
Hi, I was using two hic matrices (generated from juicer in resolution 50000, chromosome was all, when I trying to use chess sim but shows the following error. Do you know the possible reason? Thank you! _2022-05-25 09:52:23,118 INFO Running '/home/zhaoqianyi/miniconda3/envs/hicex3.6/bin/chess sim -p 1 SAMN09691012.hic@50kb SAMEA7629254.hic@50kb susScr11_chr1_5mb_win_200kb_step.bed SAMN09691012_vs_SAMEA7629254_chess_results.tsv' 2022-05-25 09:52:37,504 INFO CHESS version: 0.3.7 2022-05-25 09:52:37,505 INFO FAN-C version: 0.9.23 2022-05-25 09:52:37,510 INFO Loading reference contact data Traceback (most recent call last): File "/home/zhaoqianyi/miniconda3/envs/hicex3.6/bin/chess", line 585, in
Chess()
File "/home/zhaoqianyi/miniconda3/envs/hicex3.6/bin/chess", line 75, in init
getattr(self, args.command)([sys.argv[0]] + sys.argv[option_ix:])
File "/home/zhaoqianyi/miniconda3/envs/hicex3.6/bin/chess", line 118, in sim
reference_matrix_file, reference_regions_file)
File "/home/zhaoqianyi/miniconda3/envs/hicex3.6/lib/python3.7/site-packages/chess/helpers.py", line 554, in load_contacts
edges = oe_edges_dict_from_fanc(reference_loaded)
File "/home/zhaoqianyi/miniconda3/envs/hicex3.6/lib/python3.7/site-packages/chess/helpers.py", line 389, in oe_edges_dict_from_fanc
for e in hic.edges(oe=True, lazy=True):
File "/home/zhaoqianyi/miniconda3/envs/hicex3.6/lib/python3.7/site-packages/fanc/matrix.py", line 696, in call
bias = self._regions_pairs.bias_vector()
File "/home/zhaoqianyi/miniconda3/envs/hicex3.6/lib/python3.7/site-packages/fanc/compatibility/juicer.py", line 1198, in bias_vector
x = np.array([r.bias for r in self.regions(lazy=True)])
File "/home/zhaoqianyi/miniconda3/envs/hicex3.6/lib/python3.7/site-packages/fanc/compatibility/juicer.py", line 1198, in
x = np.array([r.bias for r in self.regions(lazy=True)])
File "/home/zhaoqianyi/miniconda3/envs/hicex3.6/lib/python3.7/site-packages/fanc/compatibility/juicer.py", line 856,
in _region_iter
norm = self.normalisation_vector(chromosome)
File "/home/zhaoqianyi/miniconda3/envs/hicex3.6/lib/python3.7/site-packages/fanc/compatibility/juicer.py", line 745,
in normalisation_vector
JuicerHic._skip_to_normalisation_vectors(req)
File "/home/zhaoqianyi/miniconda3/envs/hicex3.6/lib/python3.7/site-packages/fanc/compatibility/juicer.py", line 569,
in _skip_to_normalisation_vectors
nvectors = struct.unpack('<i', req.read(4))[0]
struct.error: unpack requires a buffer of 4 bytes