search

Roth-Lab / pyclone

Probabilistic model for inferring clonal population structure from deep NGS sequencing.
https://bitbucket.org/aroth85/pyclone/wiki/Home
Other
98 stars 36 forks source link

ValueError: gammavariate: alpha and beta must be > 0.0 #1

Open 1988liszt opened 7 years ago

1988liszt commented 7 years ago

Hi,

I am running pyclone and meet the follwing error. I don't know where the problem is. Could you help me? Thanks!

Here is my code:

[list@mu01 SB160306-1]$ PyClone run_analysis_pipeline --in_files XJX2_vs_XJX_1.tsv XJX3_vs_XJX_1.tsv --working_dir pyclone_analysis3 --prior total_copy_number 0 0 1.0 1000 Traceback (most recent call last): File "/data3/list/soft/miniconda2/bin/PyClone", line 337, in main() File "/data3/list/soft/miniconda2/bin/PyClone", line 78, in main args.func(args) File "/data3/list/soft/miniconda2/lib/python2.7/site-packages/pyclone/run.py", line 38, in run_analysis_pipeline _run_analysis(config_file, args.seed) File "/data3/list/soft/miniconda2/lib/python2.7/site-packages/pyclone/run.py", line 173, in _run_analysis alpha_priors File "/data3/list/soft/miniconda2/lib/python2.7/site-packages/pyclone/pyclone_beta_binomial.py", line 68, in run_pyclone_beta_binomial_analysis sampler.sample(data.values(), trace, num_iters) File "/data3/list/soft/miniconda2/lib/python2.7/site-packages/pydp/samplers/dp.py", line 105, in sample self.interactive_sample(data) File "/data3/list/soft/miniconda2/lib/python2.7/site-packages/pydp/samplers/dp.py", line 115, in interactive_sample self.partition.number_of_items) File "/data3/list/soft/miniconda2/lib/python2.7/site-packages/pydp/samplers/concentration.py", line 56, in sample eta = beta_rvs(old_value + 1, n) File "/data3/list/soft/miniconda2/lib/python2.7/random.py", line 629, in betavariate return y / (y + self.gammavariate(beta, 1.)) File "/data3/list/soft/miniconda2/lib/python2.7/random.py", line 508, in gammavariate raise ValueError, 'gammavariate: alpha and beta must be > 0.0' ValueError: gammavariate: alpha and beta must be > 0.0

choosehappy commented 6 years ago

I have the same issue using a fresh install and the provided example files:

PyClone run_analysis_pipeline --in_files SRR385938.tsv SRR385939.tsv SRR385940.tsv SRR385941.tsv --working_dir pyclone_analysis

Did anyone else come across this? Find a fix?

desnar commented 6 years ago

You need pydp 0.2.4, https://github.com/aroth85/pydp/tree/0.2.4

logan-leak commented 4 years ago

How do you update the existing pydp to the newer version 0.2.4?

qindan2008 commented 3 years ago

You need pydp 0.2.4, https://github.com/aroth85/pydp/tree/0.2.4

I have tried this, but also failed.