*********************************************************************
* 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 /projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/gwas/munged/Triglycerides-Willer_2013.sumstats.gz \
--ref-ld-chr /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Astro.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.D2H.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.Matrix.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.Striosome.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D2.Matrix.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D2.Striosome.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.INT.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Microglia.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Oligo.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.OPC.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.mergedReg2Map.EUR.,/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/conditional/Human_Striatum_snATAC.conditional.Triglycerides-Willer_2013.EUR \
--w-ld-chr /projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/1000G_ALL_Phase3_hg38_files/weights/1000G.EUR.weights.hm3_noMHC. \
--print-coefficients  

Beginning analysis at Mon Jun 24 14:15:53 2024
Reading summary statistics from /projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/gwas/munged/Triglycerides-Willer_2013.sumstats.gz ...
Read summary statistics for 1031428 SNPs.
Reading reference panel LD Score from /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Astro.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.D2H.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.Matrix.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.Striosome.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D2.Matrix.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D2.Striosome.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.INT.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Microglia.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Oligo.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.OPC.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.mergedReg2Map.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/1000G_ALL_Phase3_hg38_files/baseline_v1.1/baseline_v1.1.EUR.[1-22] ... (ldscore_fromlist)
Traceback (most recent call last):
  File "/home/bnphan/src/ldsc/ldsc.py", line 644, in <module>
    sumstats.estimate_h2(args, log)
  File "/home/bnphan/src/ldsc/ldscore/sumstats.py", line 326, in estimate_h2
    args, log, args.h2)
  File "/home/bnphan/src/ldsc/ldscore/sumstats.py", line 243, in _read_ld_sumstats
    ref_ld = _read_ref_ld(args, log)
  File "/home/bnphan/src/ldsc/ldscore/sumstats.py", line 82, in _read_ref_ld
    'reference panel LD Score', ps.ldscore_fromlist)
  File "/home/bnphan/src/ldsc/ldscore/sumstats.py", line 152, in _read_chr_split_files
    out = parsefunc(_splitp(chr_arg), _N_CHR, **kwargs)
  File "/home/bnphan/src/ldsc/ldscore/parse.py", line 103, in ldscore_fromlist
    y = ldscore(fh, num)
  File "/home/bnphan/src/ldsc/ldscore/parse.py", line 149, in ldscore
    chr_ld = [l2_parser(sub_chr(fh, i) + suffix + s, compression) for i in chrs]
  File "/home/bnphan/src/ldsc/ldscore/parse.py", line 119, in l2_parser
    x = read_csv(fh, header=0, 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: '/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.mergedReg2Map.EUR.14.l2.ldscore.gz'

Analysis finished at Mon Jun 24 14:17:02 2024
Total time elapsed: 1.0m:8.47s
Traceback (most recent call last):
  File "/home/bnphan/src/ldsc/ldsc.py", line 644, in <module>
    sumstats.estimate_h2(args, log)
  File "/home/bnphan/src/ldsc/ldscore/sumstats.py", line 326, in estimate_h2
    args, log, args.h2)
  File "/home/bnphan/src/ldsc/ldscore/sumstats.py", line 243, in _read_ld_sumstats
    ref_ld = _read_ref_ld(args, log)
  File "/home/bnphan/src/ldsc/ldscore/sumstats.py", line 82, in _read_ref_ld
    'reference panel LD Score', ps.ldscore_fromlist)
  File "/home/bnphan/src/ldsc/ldscore/sumstats.py", line 152, in _read_chr_split_files
    out = parsefunc(_splitp(chr_arg), _N_CHR, **kwargs)
  File "/home/bnphan/src/ldsc/ldscore/parse.py", line 103, in ldscore_fromlist
    y = ldscore(fh, num)
  File "/home/bnphan/src/ldsc/ldscore/parse.py", line 149, in ldscore
    chr_ld = [l2_parser(sub_chr(fh, i) + suffix + s, compression) for i in chrs]
  File "/home/bnphan/src/ldsc/ldscore/parse.py", line 119, in l2_parser
    x = read_csv(fh, header=0, 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: '/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.mergedReg2Map.EUR.14.l2.ldscore.gz'