Issue with HESS: pandas.errors.ParserError

[DaXuanGarden]

Subject: Issue with HESS: pandas.errors.ParserError

Email Body:

Dear HESS Development Team,

I hope this email finds you well.

I am currently experiencing an issue while using the HESS software and would appreciate your assistance. Below are the command I used and the error message I encountered:

Command:

python ./hess.py \
    --bfile 1kg_eur_1pct \
    --local-rhog RA_Fin.txt Depression_UKB.txt \
    --partition ldetect-data/EUR \
    --out step1 \
    --chrom 22

Full Error Message:

[INFO] @----------------------------------------------------------@
       |         HESS       |      v0.5      |    9/October/2017  |
       |----------------------------------------------------------|
       |  (C) 2017 Huwenbo Shi, GNU General Public License, v3    |
       |----------------------------------------------------------|
       |  For documentation, citation & bug-report instructions:  |
       |   http://bogdan.bioinformatics.ucla.edu/software/hess/   |
       @----------------------------------------------------------@
[INFO] Command started at: Wed, 24 Jul 2024 18:47:01
[INFO] Command issued:
    ./hess.py \
        --bfile 1kg_eur_1pct \
        --local-rhog RA_Fin.txt Depression_UKB.txt \
        --partition ldetect-data/EUR \
        --out step1 \
        --chrom 22
/mnt/data/home/daxuan03/fusion_twas-master/hess-0.5.3-beta/src/refpanel.py:13: FutureWarning: read_table is deprecated, use read_csv instead, passing sep='\t'.
  partition = pd.read_table(filename, delim_whitespace=True)
Traceback (most recent call last):
  File "./hess.py", line 217, in <module>
    main()
  File "./hess.py", line 45, in main
    argmap['out'])
  File "/mnt/data/home/daxuan03/fusion_twas-master/hess-0.5.3-beta/src/estimation.py", line 394, in local_rhog_step1
    partition = load_partition(partition_fnm, chrom)
  File "/mnt/data/home/daxuan03/fusion_twas-master/hess-0.5.3-beta/src/refpanel.py", line 13, in load_partition
    partition = pd.read_table(filename, delim_whitespace=True)
  File "/mnt/data/home/daxuan03/miniconda3/envs/hess_env/lib/python2.7/site-packages/pandas/io/parsers.py", line 702, in parser_f
    return _read(filepath_or_buffer, kwds)
  File "/mnt/data/home/daxuan03/miniconda3/envs/hess_env/lib/python2.7/site-packages/pandas/io/parsers.py", line 429, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
  File "/mnt/data/home/daxuan03/miniconda3/envs/hess_env/lib/python2.7/site-packages/pandas/io/parsers.py", line 895, in __init__
    self._make_engine(self.engine)
  File "/mnt/data/home/daxuan03/miniconda3/envs/hess_env/lib/python2.7/site-packages/pandas/io/parsers.py", line 1122, in _make_engine
    self._engine = CParserWrapper(self.f, **self.options)
  File "/mnt/data/home/daxuan03/miniconda3/envs/hess_env/lib/python2.7/site-packages/pandas/io/parsers.py", line 1853, in __init__
    self._reader = parsers.TextReader(src, **kwds)
  File "pandas/_libs/parsers.pyx", line 542, in pandas._libs.parsers.TextReader.__cinit__
  File "pandas/_libs/parsers.pyx", line 751, in pandas._libs.parsers.TextReader._get_header
  File "pandas/_libs/parsers.pyx", line 955, in pandas._libs.parsers.TextReader._tokenize_rows
  File "pandas/_libs/parsers.pyx", line 2172, in pandas._libs.parsers.raise_parser_error
pandas.errors.ParserError: Error tokenizing data. C error: Calling read(nbytes) on source failed. Try engine='python'.

Environment Information:

• Operating System: Ubuntu 20.04
• Python Version: 2.7
• Conda Environment: hess_env
• HESS Version: 0.5.3-beta
• Pandas Version: 0.24.2

Input Files:

• RA_Fin.txt and Depression_UKB.txt are two files containing local genetic correlation data.
• ldetect-data/EUR is a directory containing the partition information.

Problem Description:
When running the above command, I encountered a pandas.errors.ParserError with the message Error tokenizing data. C error: Calling read(nbytes) on source failed. Try engine='python'..

I have checked the format of the input files and tried different versions of Pandas, but the issue persists. Could you please provide some suggestions or a solution to this problem?

Thank you very much for your assistance!

Best regards,

Daxuan

[DaXuanGarden]

I've fixed this issue, thank you very much!