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Roth-Lab / pyclone

Probabilistic model for inferring clonal population structure from deep NGS sequencing.
https://bitbucket.org/aroth85/pyclone/wiki/Home
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run testfile meet error #4

Open WRui opened 5 years ago

WRui commented 5 years ago

PyClone run_analysis_pipeline --in_files SRR385938.tsv SRR385939.tsv --working_dir /datb1/wangrui/test

Traceback (most recent call last): File "/datb1/wangrui/software/anaconda/bin/PyClone", line 11, in load_entry_point('PyClone==0.13.1', 'console_scripts', 'PyClone')() File "/datb1/wangrui/software/anaconda/lib/python2.7/site-packages/pyclone/cli.py", line 78, in main args.func(args) File "/datb1/wangrui/software/anaconda/lib/python2.7/site-packages/pyclone/run.py", line 47, in run_analysis_pipeline _run_analysis(config_file, args.seed) File "/datb1/wangrui/software/anaconda/lib/python2.7/site-packages/pyclone/run.py", line 199, in _run_analysis alpha_priors File "/datb1/wangrui/software/anaconda/lib/python2.7/site-packages/pyclone/pyclone_beta_binomial.py", line 103, in run_pyclone_beta_binomial_analysis sampler.interactive_sample(data.values()) File "/datb1/wangrui/software/anaconda/lib/python2.7/site-packages/pydp/samplers/dp.py", line 118, in interactive_sample self.partition_sampler.sample(data, self.partition, self.alpha) File "/datb1/wangrui/software/anaconda/lib/python2.7/site-packages/pydp/samplers/partition.py", line 85, in sample cluster_log_p = self.cluster_density.log_p(data_point, cell.value) File "/datb1/wangrui/software/anaconda/lib/python2.7/site-packages/pyclone/multi_sample.py", line 111, in log_p log_p += density.log_p(data[sample_id], params[sample_id]) File "/datb1/wangrui/software/anaconda/lib/python2.7/site-packages/pyclone/pyclone_beta_binomial.py", line 113, in log_p return self._log_p(data, params) File "/datb1/wangrui/software/anaconda/lib/python2.7/site-packages/pyclone/pyclone_beta_binomial.py", line 121, in _log_p params.x, data.tumour_content, self.params.x File "/datb1/wangrui/software/anaconda/lib/python2.7/site-packages/numba/dispatcher.py", line 157, in _compile_for_args return self.compile(sig) File "/datb1/wangrui/software/anaconda/lib/python2.7/site-packages/numba/dispatcher.py", line 272, in compile self.targetdescr.options.parse_as_flags(flags, self.targetoptions) File "/datb1/wangrui/software/anaconda/lib/python2.7/site-packages/numba/targets/options.py", line 26, in parse_as_flags opt.from_dict(options) File "/datb1/wangrui/software/anaconda/lib/python2.7/site-packages/numba/targets/options.py", line 19, in from_dict raise KeyError(fmt % k) KeyError: "Does not support option: 'cache'"