math domain error

[smoothyly]

Hello！@JianjunJin，

I try to use hifiasm result to assembling the chloroplast genome.Here is my codes

get_organelle_config.py -a embplant_pt,embplant_mt --use-local ./GetOrganelleDB/0.0.1
get_organelle_from_assembly.py -g ./lh_green.hic.p_utg.gfa -o plastome_output  -F embplant_pt --max-depth 100

I get the error

2024-06-05 09:28:18,671 - INFO: Disentangling plastome_output/slimmed_assembly_graph.gfa as a circular genome ... 
2024-06-05 09:28:18,692 - ERROR: 
Traceback (most recent call last):
  File "/home/liuli/anaconda3/envs/py3.11/bin/get_organelle_from_assembly.py", line 815, in extract_organelle_genome
    disentangle_assembly(fastg_file=slim_out_fg, blast_db_base=blast_db, mode=organelle_type,
  File "/home/liuli/anaconda3/envs/py3.11/bin/get_organelle_from_assembly.py", line 798, in disentangle_assembly
    disentangle_inside(fastg_f=fastg_file, tab_f=tab_file, o_p=output, w_f=weight_factor, log_in=log_dis,
  File "/home/liuli/anaconda3/envs/py3.11/lib/python3.11/site-packages/GetOrganelleLib/pipe_control_func.py", line 139, in func_modified
    r = func(*args, **kwargs)
        ^^^^^^^^^^^^^^^^^^^^^
  File "/home/liuli/anaconda3/envs/py3.11/bin/get_organelle_from_assembly.py", line 619, in disentangle_inside
    target_results = input_graph.find_target_graph(tab_f,
                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/liuli/anaconda3/envs/py3.11/lib/python3.11/site-packages/GetOrganelleLib/assembly_parser.py", line 2478, in find_target_graph
    new_assembly.filter_by_coverage(database_n=database_name,
  File "/home/liuli/anaconda3/envs/py3.11/lib/python3.11/site-packages/GetOrganelleLib/assembly_parser.py", line 1749, in filter_by_coverage
    removing_low_cov = [candidate_v
                       ^^^^^^^^^^^^
  File "/home/liuli/anaconda3/envs/py3.11/lib/python3.11/site-packages/GetOrganelleLib/assembly_parser.py", line 1751, in <listcomp>
    if abs(log(self.vertex_info[candidate_v].cov / max_tagged_cov)) > log_hard_cov_threshold]
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: math domain error
2024-06-05 09:28:18,695 - ERROR: 
Traceback (most recent call last):
  File "/home/liuli/anaconda3/envs/py3.11/bin/get_organelle_from_assembly.py", line 1043, in main
    ext_res = extract_organelle_genome(out_base=options.output_base,
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/liuli/anaconda3/envs/py3.11/bin/get_organelle_from_assembly.py", line 845, in extract_organelle_genome
    raise e
  File "/home/liuli/anaconda3/envs/py3.11/bin/get_organelle_from_assembly.py", line 815, in extract_organelle_genome
    disentangle_assembly(fastg_file=slim_out_fg, blast_db_base=blast_db, mode=organelle_type,
  File "/home/liuli/anaconda3/envs/py3.11/bin/get_organelle_from_assembly.py", line 798, in disentangle_assembly
    disentangle_inside(fastg_f=fastg_file, tab_f=tab_file, o_p=output, w_f=weight_factor, log_in=log_dis,
  File "/home/liuli/anaconda3/envs/py3.11/lib/python3.11/site-packages/GetOrganelleLib/pipe_control_func.py", line 139, in func_modified
    r = func(*args, **kwargs)
        ^^^^^^^^^^^^^^^^^^^^^
  File "/home/liuli/anaconda3/envs/py3.11/bin/get_organelle_from_assembly.py", line 619, in disentangle_inside
    target_results = input_graph.find_target_graph(tab_f,
                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/liuli/anaconda3/envs/py3.11/lib/python3.11/site-packages/GetOrganelleLib/assembly_parser.py", line 2478, in find_target_graph
    new_assembly.filter_by_coverage(database_n=database_name,
  File "/home/liuli/anaconda3/envs/py3.11/lib/python3.11/site-packages/GetOrganelleLib/assembly_parser.py", line 1749, in filter_by_coverage
    removing_low_cov = [candidate_v
                       ^^^^^^^^^^^^
  File "/home/liuli/anaconda3/envs/py3.11/lib/python3.11/site-packages/GetOrganelleLib/assembly_parser.py", line 1751, in <listcomp>
    if abs(log(self.vertex_info[candidate_v].cov / max_tagged_cov)) > log_hard_cov_threshold]
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: math domain error

Here is my log file
get_org.log.txt

Any help would be appreciated！
Best，
Zhanwu