*********************************************************************
* LD Score Regression (LDSC)
* Version 1.0.1
* (C) 2014-2019 Brendan Bulik-Sullivan and Hilary Finucane
* Broad Institute of MIT and Harvard / MIT Department of Mathematics
* GNU General Public License v3
*********************************************************************
Call: 
./ldsc.py \
--h2-cts I/projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/gwas/munged/nsomnia_E-Watanabe_2022.sumstats.gz \
--ref-ld-chr /projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/1000G_ALL_Phase3_hg38_files/baseline_v1.1/baseline_v1.1.EUR. \
--out /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/enrichments/Human_Striatum_snATAC.Insomnia_E-Watanabe_2022.EUR \
--ref-ld-chr-cts /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/Human_Striatum_snATAC.EUR_hg38.ldcts \
--w-ld-chr /projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/1000G_ALL_Phase3_hg38_files/weights/1000G.EUR.weights.hm3_noMHC. 

Beginning analysis at Fri Jun 28 15:43:04 2024
Reading summary statistics from I/projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/gwas/munged/nsomnia_E-Watanabe_2022.sumstats.gz ...
Traceback (most recent call last):
  File "/home/bnphan/src/ldsc/ldsc.py", line 646, in <module>
    sumstats.cell_type_specific(args, log)
  File "/home/bnphan/src/ldsc/ldscore/sumstats.py", line 263, in cell_type_specific
    _read_ld_sumstats(args, log, args.h2_cts)
  File "/home/bnphan/src/ldsc/ldscore/sumstats.py", line 242, in _read_ld_sumstats
    sumstats = _read_sumstats(args, log, fh, alleles=alleles, dropna=dropna)
  File "/home/bnphan/src/ldsc/ldscore/sumstats.py", line 163, in _read_sumstats
    sumstats = ps.sumstats(fh, alleles=alleles, dropna=dropna)
  File "/home/bnphan/src/ldsc/ldscore/parse.py", line 89, in sumstats
    x = read_csv(fh, usecols=usecols, dtype=dtype_dict, compression=compression)
  File "/home/bnphan/src/ldsc/ldscore/parse.py", line 21, in read_csv
    return pd.read_csv(fh, delim_whitespace=True, na_values='.', **kwargs)
  File "/home/bnphan/miniforge3/envs/ldsc/lib/python2.7/site-packages/pandas/io/parsers.py", line 655, in parser_f
    return _read(filepath_or_buffer, kwds)
  File "/home/bnphan/miniforge3/envs/ldsc/lib/python2.7/site-packages/pandas/io/parsers.py", line 405, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
  File "/home/bnphan/miniforge3/envs/ldsc/lib/python2.7/site-packages/pandas/io/parsers.py", line 762, in __init__
    self._make_engine(self.engine)
  File "/home/bnphan/miniforge3/envs/ldsc/lib/python2.7/site-packages/pandas/io/parsers.py", line 966, in _make_engine
    self._engine = CParserWrapper(self.f, **self.options)
  File "/home/bnphan/miniforge3/envs/ldsc/lib/python2.7/site-packages/pandas/io/parsers.py", line 1582, in __init__
    self._reader = parsers.TextReader(src, **kwds)
  File "pandas/_libs/parsers.pyx", line 394, in pandas._libs.parsers.TextReader.__cinit__ (pandas/_libs/parsers.c:4209)
  File "pandas/_libs/parsers.pyx", line 651, in pandas._libs.parsers.TextReader._setup_parser_source (pandas/_libs/parsers.c:7620)
  File "/home/bnphan/miniforge3/envs/ldsc/lib/python2.7/gzip.py", line 94, in __init__
    fileobj = self.myfileobj = __builtin__.open(filename, mode or 'rb')
IOError: [Errno 2] No such file or directory: 'I/projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/gwas/munged/nsomnia_E-Watanabe_2022.sumstats.gz'

Analysis finished at Fri Jun 28 15:43:04 2024
Total time elapsed: 0.01s
Traceback (most recent call last):
  File "/home/bnphan/src/ldsc/ldsc.py", line 646, in <module>
    sumstats.cell_type_specific(args, log)
  File "/home/bnphan/src/ldsc/ldscore/sumstats.py", line 263, in cell_type_specific
    _read_ld_sumstats(args, log, args.h2_cts)
  File "/home/bnphan/src/ldsc/ldscore/sumstats.py", line 242, in _read_ld_sumstats
    sumstats = _read_sumstats(args, log, fh, alleles=alleles, dropna=dropna)
  File "/home/bnphan/src/ldsc/ldscore/sumstats.py", line 163, in _read_sumstats
    sumstats = ps.sumstats(fh, alleles=alleles, dropna=dropna)
  File "/home/bnphan/src/ldsc/ldscore/parse.py", line 89, in sumstats
    x = read_csv(fh, usecols=usecols, dtype=dtype_dict, compression=compression)
  File "/home/bnphan/src/ldsc/ldscore/parse.py", line 21, in read_csv
    return pd.read_csv(fh, delim_whitespace=True, na_values='.', **kwargs)
  File "/home/bnphan/miniforge3/envs/ldsc/lib/python2.7/site-packages/pandas/io/parsers.py", line 655, in parser_f
    return _read(filepath_or_buffer, kwds)
  File "/home/bnphan/miniforge3/envs/ldsc/lib/python2.7/site-packages/pandas/io/parsers.py", line 405, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
  File "/home/bnphan/miniforge3/envs/ldsc/lib/python2.7/site-packages/pandas/io/parsers.py", line 762, in __init__
    self._make_engine(self.engine)
  File "/home/bnphan/miniforge3/envs/ldsc/lib/python2.7/site-packages/pandas/io/parsers.py", line 966, in _make_engine
    self._engine = CParserWrapper(self.f, **self.options)
  File "/home/bnphan/miniforge3/envs/ldsc/lib/python2.7/site-packages/pandas/io/parsers.py", line 1582, in __init__
    self._reader = parsers.TextReader(src, **kwds)
  File "pandas/_libs/parsers.pyx", line 394, in pandas._libs.parsers.TextReader.__cinit__ (pandas/_libs/parsers.c:4209)
  File "pandas/_libs/parsers.pyx", line 651, in pandas._libs.parsers.TextReader._setup_parser_source (pandas/_libs/parsers.c:7620)
  File "/home/bnphan/miniforge3/envs/ldsc/lib/python2.7/gzip.py", line 94, in __init__
    fileobj = self.myfileobj = __builtin__.open(filename, mode or 'rb')
IOError: [Errno 2] No such file or directory: 'I/projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/gwas/munged/nsomnia_E-Watanabe_2022.sumstats.gz'