_pickle.PicklingError

[PengfeiInTuebingen]

Hi,
I want to use chess-hic on my Hi-C data, I successfully installed chess-hic on my own mac following your manual. I generated a pair input file, but I failed to run the search with chess sim with my cool format Hi-C data, could you please give me some comments about the error I met? the commands I used are below:
(chess) a5-phd-mbp :: Ectocarpus_hic/HiC_Matrix/chess-hic » chess sim 561_2k.cool 560_2k.cool v5_win_200kb_step_2000.bed test.tsv
2022-08-09 22:23:47,257 INFO Running '/Users/pliu/miniconda3/envs/chess/bin/chess sim 561_2k.cool 560_2k.cool v5_win_200kb_step_2000.bed test.tsv'
2022-08-09 22:23:48,347 INFO CHESS version: 0.3.7
2022-08-09 22:23:48,347 INFO FAN-C version: 0.9.24
2022-08-09 22:23:48,348 INFO Loading reference contact data
Expected 100% (81203859 of 81203859) |#################################################################################| Elapsed Time: 0:08:54 Time: 0:08:54
2022-08-09 22:46:19,544 INFO Loading query contact data
Expected 100% (60447784 of 60447784) |#################################################################################| Elapsed Time: 0:06:47 Time: 0:06:47
2022-08-09 23:03:07,090 INFO Loading region pairs
2022-08-09 23:03:07,919 INFO Launching workers
Traceback (most recent call last):
File "/Users/pliu/miniconda3/envs/chess/bin/chess", line 585, in
Chess()
File "/Users/pliu/miniconda3/envs/chess/bin/chess", line 75, in init
getattr(self, args.command)([sys.argv[0]] + sys.argv[option_ix:])
File "/Users/pliu/miniconda3/envs/chess/bin/chess", line 196, in sim
pool = mp.Pool(threads,
File "/Users/pliu/miniconda3/envs/chess/lib/python3.10/multiprocessing/context.py", line 119, in Pool
return Pool(processes, initializer, initargs, maxtasksperchild,
File "/Users/pliu/miniconda3/envs/chess/lib/python3.10/multiprocessing/pool.py", line 212, in init
self._repopulate_pool()
File "/Users/pliu/miniconda3/envs/chess/lib/python3.10/multiprocessing/pool.py", line 303, in _repopulate_pool
return self._repopulate_pool_static(self._ctx, self.Process,
File "/Users/pliu/miniconda3/envs/chess/lib/python3.10/multiprocessing/pool.py", line 326, in _repopulate_pool_static
w.start()
File "/Users/pliu/miniconda3/envs/chess/lib/python3.10/multiprocessing/process.py", line 121, in start
self._popen = self._Popen(self)
File "/Users/pliu/miniconda3/envs/chess/lib/python3.10/multiprocessing/context.py", line 284, in _Popen
return Popen(process_obj)
File "/Users/pliu/miniconda3/envs/chess/lib/python3.10/multiprocessing/popen_spawn_posix.py", line 32, in init
super().init(process_obj)
File "/Users/pliu/miniconda3/envs/chess/lib/python3.10/multiprocessing/popen_fork.py", line 19, in init
self._launch(process_obj)
File "/Users/pliu/miniconda3/envs/chess/lib/python3.10/multiprocessing/popen_spawn_posix.py", line 47, in _launch
reduction.dump(process_obj, fp)
File "/Users/pliu/miniconda3/envs/chess/lib/python3.10/multiprocessing/reduction.py", line 60, in dump
ForkingPickler(file, protocol).dump(obj)
_pickle.PicklingError: Can't pickle <class 'pandas.core.frame.Pandas'>: attribute lookup Pandas on pandas.core.frame failed

[PengfeiInTuebingen]

another info, I can run the sample data with chess

[liz-is]

If you can run CHESS successfully on the sample data, then I think this is likely an issue with your input data and not with CHESS itself. You could try converting the data to FAN-C .hic format using fanc hic data.cool data.hic? Processing of cooler files can be very slow, as they don't store expected values, so this may also be quicker for you in the end.