Errors occurred while running example data

Dear author, Hello，when I run python3 ../Construct_pan_and_Call_sv.py genome_gff_dir_example genome_list -fqd fq_dir_example -o step1, I am experiencing the following error：

`Input delta file: pan_dir_result/ref2_R498_0-2M/ref2_R498_0-2M.delta
Output prefix: pan_dir_result/ref2_R498_0-2M/ref2_R498_0-2M.bed
Unique anchor length: 1000
Minimum variant size to call: 50
Maximum variant size to call: 10000000
Logging progress updates in pan_dir_result/ref2_R498_0-2M/progress.log
1. Filter delta file
2. Finding variants between alignments
Loaded 141 alignments
3. Finding variants within alignments
4. Combine variants between and within alignments
Warning messages:
1: Removed 12 rows containing missing values (`geom_bar()`). 
2: Removed 10 rows containing missing values (`geom_bar()`). 
3: The dot-dot notation (`..count..`) was deprecated in ggplot2 3.4.0.
ℹ Please use `after_stat(count)` instead. 
4: Removed 12 rows containing missing values (`geom_bar()`). 
5: Removed 12 rows containing missing values (`geom_bar()`). 
6: Removed 10 rows containing missing values (`geom_bar()`). 
7: Removed 12 rows containing missing values (`geom_bar()`). 
Warning messages:
1: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead. 
2: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead. 
Warning message:
Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead. 
index file pan_dir_result/ref2.fa.fai not found, generating...
Traceback (most recent call last):
  File "/gss1/home/gaozhh01/biosoft/psvcp_v1.01/example7/../construct_pan_script/11gene_in_pv_screen.py", line 7, in <module>
    df = pd.read_csv(sys.argv[1],sep='\t',header=None)
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/gss1/home/gaozhh01/miniconda3/envs/pan/lib/python3.11/site-packages/pandas/util/_decorators.py", line 211, in wrapper
    return func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/gss1/home/gaozhh01/miniconda3/envs/pan/lib/python3.11/site-packages/pandas/util/_decorators.py", line 331, in wrapper
    return func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/gss1/home/gaozhh01/miniconda3/envs/pan/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 950, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/gss1/home/gaozhh01/miniconda3/envs/pan/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 605, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/gss1/home/gaozhh01/miniconda3/envs/pan/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1442, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/gss1/home/gaozhh01/miniconda3/envs/pan/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1735, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/gss1/home/gaozhh01/miniconda3/envs/pan/lib/python3.11/site-packages/pandas/io/common.py", line 856, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'pan_dir_result/R498_0-2M.gff.in_pv'
Error in file(file, "rt") : cannot open the connection
Calls: read.table -> file
In addition: Warning message:
In file(file, "rt") :
  cannot open file 'pan_dir_result/R498_0-2M.gff_gene_absolutly.in_pv': No such file or directory
Execution halted
cat: pan_dir_result/R498_0-2M.gene_absolutly_in_pv.gff: No such file or directory`

This is the resulting file.

R version：R-4.0.3 and Python version: python3.9.4.env I would appreciate it if you could answer my questions！ tanwei 2023.03.15

wjian8 / psvcp_v1.01

Errors occurred while running example data #5