*********************************************************************
* 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 /projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/gwas/munged/ALS-vanRheenen_2016.sumstats.gz \
--ref-ld-chr /projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/1000G_ALL_Phase3_hg38_files/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.ALS-vanRheenen_2016.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/1000G_ALL_Phase3_hg38_files/weights/1000G.EUR.weights.hm3_noMHC. 

Beginning analysis at Mon Jun 24 14:15:48 2024
Reading summary statistics from /projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/gwas/munged/ALS-vanRheenen_2016.sumstats.gz ...
Read summary statistics for 1172035 SNPs.
Reading reference panel LD Score from /projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/1000G_ALL_Phase3_hg38_files/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 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 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 147, in ldscore
    first_fh = sub_chr(fh, chrs[0]) + suffix
IndexError: list index out of range

Analysis finished at Mon Jun 24 14:15:51 2024
Total time elapsed: 3.12s
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 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 147, in ldscore
    first_fh = sub_chr(fh, chrs[0]) + suffix
IndexError: list index out of range