1753 smcpp.commands.estimate WARNING The per-generation mutation rate is calculated to be 5.8e-13. Is this correct?
1753 smcpp.analysis INFO Loading data...
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/public/home/acsg9wshyg/anaconda3/envs/smcpp/lib/python3.5/multiprocessing/pool.py", line 119, in worker
result = (True, func(*args, **kwds))
File "/public/home/acsg9wshyg/anaconda3/envs/smcpp/lib/python3.5/multiprocessing/pool.py", line 44, in mapstar
return list(map(*args))
File "/public/home/acsg9wshyg/anaconda3/envs/smcpp/lib/python3.5/site-packages/smcpp/estimation_tools.py", line 182, in _load_data_helper
A = pd.read_csv(fn, sep=' ', comment="#", header=None).values
File "/public/home/acsg9wshyg/anaconda3/envs/smcpp/lib/python3.5/site-packages/pandas/io/parsers.py", line 655, in parser_f
return _read(filepath_or_buffer, kwds)
File "/public/home/acsg9wshyg/anaconda3/envs/smcpp/lib/python3.5/site-packages/pandas/io/parsers.py", line 405, in _read
parser = TextFileReader(filepath_or_buffer, **kwds)
File "/public/home/acsg9wshyg/anaconda3/envs/smcpp/lib/python3.5/site-packages/pandas/io/parsers.py", line 762, in __init__
self._make_engine(self.engine)
File "/public/home/acsg9wshyg/anaconda3/envs/smcpp/lib/python3.5/site-packages/pandas/io/parsers.py", line 966, in _make_engine
self._engine = CParserWrapper(self.f, **self.options)
File "/public/home/acsg9wshyg/anaconda3/envs/smcpp/lib/python3.5/site-packages/pandas/io/parsers.py", line 1582, in __init__
self._reader = parsers.TextReader(src, **kwds)
File "pandas/_libs/parsers.pyx", line 565, in pandas._libs.parsers.TextReader.__cinit__ (pandas/_libs/parsers.c:6260)
pandas.errors.EmptyDataError: No columns to parse from file
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/public/home/acsg9wshyg/anaconda3/envs/smcpp/bin/smc++", line 9, in <module>
load_entry_point('smcpp==1.3.21.dev0+ng54170d0.d20170114', 'console_scripts', 'smc++')()
File "/public/home/acsg9wshyg/anaconda3/envs/smcpp/lib/python3.5/site-packages/smcpp/frontend/console.py", line 23, in main
cmds[args.command].main(args)
File "/public/home/acsg9wshyg/anaconda3/envs/smcpp/lib/python3.5/site-packages/smcpp/commands/estimate.py", line 86, in main
analysis = Analysis(args.data, args)
File "/public/home/acsg9wshyg/anaconda3/envs/smcpp/lib/python3.5/site-packages/smcpp/analysis.py", line 255, in __init__
BaseAnalysis.__init__(self, files, args)
File "/public/home/acsg9wshyg/anaconda3/envs/smcpp/lib/python3.5/site-packages/smcpp/analysis.py", line 40, in __init__
self._load_data(files)
File "/public/home/acsg9wshyg/anaconda3/envs/smcpp/lib/python3.5/site-packages/smcpp/analysis.py", line 50, in _load_data
self._contigs = estimation_tools.load_data(files)
File "/public/home/acsg9wshyg/anaconda3/envs/smcpp/lib/python3.5/site-packages/smcpp/estimation_tools.py", line 216, in load_data
obs = list(p.map(_load_data_helper, files))
File "/public/home/acsg9wshyg/anaconda3/envs/smcpp/lib/python3.5/multiprocessing/pool.py", line 266, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/public/home/acsg9wshyg/anaconda3/envs/smcpp/lib/python3.5/multiprocessing/pool.py", line 644, in get
raise self._value
pandas.errors.EmptyDataError: No columns to parse from file
Is it something wrong with my inputted smc.gz files?
Or it is the problem of my python enviroment?
Hi @terhorst , I am using the conda installed smc++ I finished the vcf2smc without any error then i used this command
smc++ estimate -o All-1/ -t 1.16e-8 contig-A1/*.smc.gz
and received this error report
Is it something wrong with my inputted smc.gz files? Or it is the problem of my python enviroment?