问题遇到的现象和发生背景
LDSC-SEG分析中,清洗数据已经完成,第二步,进行LDSC-SEG时报错
问题相关代码,请勿粘贴截图
python ~/zzzzzzz/ldsc/ldsc/ldsc.py --h2-cts test.sumstats.gz --ref-ld-chr 1000G_EUR_Phase3_baseline/baseline. --out TEST_${cts_name} --ref-ld-chr-cts $cts_name.ldcts --w-ld-chr weights_hm3_no_hla/weights
运行结果及报错内容
Reading reference panel LD Score from 1000G_EUR_Phase3_baseline/baseline.[1-22] ... (ldscore_fromlist)
Traceback (most recent call last):
File "/zzzzzzz/ldsc/ldsc/ldsc.py", line 646, in <module>
sumstats.cell_type_specific(args, log)
File "/zzzzzzz/ldsc/ldsc/ldscore/sumstats.py", line 263, in cell_type_specific
_read_ld_sumstats(args, log, args.h2_cts)
File "/zzzzzzz/ldsc/ldsc/ldscore/sumstats.py", line 243, in _read_ld_sumstats
ref_ld = _read_ref_ld(args, log)
File "/zzzzzzz/ldsc/ldsc/ldscore/sumstats.py", line 82, in _read_ref_ld
'reference panel LD Score', ps.ldscore_fromlist)
File "/zzzzzzz/ldsc/ldsc/ldscore/sumstats.py", line 152, in _read_chr_split_files
out = parsefunc(_splitp(chr_arg), _N_CHR, **kwargs)
File "/zzzzzzz/ldsc/ldsc/ldscore/parse.py", line 103, in ldscore_fromlist
y = ldscore(fh, num)
File "/zzzzzzz/ldsc/ldsc/ldscore/parse.py", line 155, in ldscore
x = x.sort_values(by=['CHR', 'BP']) # SEs will be wrong unless sorted
File "/miniconda3/envs/ldsc/lib/python2.7/site-packages/pandas/core/frame.py", line 4729, in sort_values
verify=False)
File "/miniconda3/envs/ldsc/lib/python2.7/site-packages/pandas/core/internals/managers.py", line 1350, in take
axis=axis, allow_dups=True)
File "/miniconda3/envs/ldsc/lib/python2.7/site-packages/pandas/core/internals/managers.py", line 1235, in reindex_indexer
for blk in self.blocks]
File "/miniconda3/envs/ldsc/lib/python2.7/site-packages/pandas/core/internals/blocks.py", line 1238, in take_nd
allow_fill=True, fill_value=fill_value)
File "/miniconda3/envs/ldsc/lib/python2.7/site-packages/pandas/core/algorithms.py", line 1651, in take_nd
out = np.empty(out_shape, dtype=dtype)
MemoryError
我的解答思路和尝试过的方法
不知道问题出在哪里,尝试搜索也没有找到,代码是GitHub上下载的,应该没有问题,怀疑问题出在配置或者指令上。
我想要达到的结果
成功执行该语句