I am trying to run the program genipe to do some genome-wide survival analysis. I have installed genipe and all the relevant directories. However, when I go to run the program I get the error:
"TypeError: _ init _() got an unexpected keyword argument 'normalize'"
I haven't edited any of the genipe scripts and I have run genipe with no issues on a different server so I am not sure what is going wrong! Any help would be greatly appreciated.
Many thanks,
Caragh
Edit: I am using python version 3.6.1
Traceback as follows:
Traceback (most recent call last):
File "/users/k1640238/miniconda/envs/genipe_pyvenv/lib/python3.6/multiprocessing/pool.py", line 119, in worker
result = (True, func(*args, **kwds))
File "/users/k1640238/miniconda/envs/genipe_pyvenv/lib/python3.6/multiprocessing/pool.py", line 44, in mapstar
return list(map(*args))
File "/users/k1640238/miniconda/envs/genipe_pyvenv/lib/python3.6/site-packages/genipe/tools/imputed_stats.py", line 965, in process_impute2_site
use_ml=site_info.use_ml,
File "/users/k1640238/miniconda/envs/genipe_pyvenv/lib/python3.6/site-packages/genipe/tools/imputed_stats.py", line 1048, in fit_cox
cf = CoxPHFitter(alpha=0.95, tie_method="Efron", normalize=False)
TypeError: __init__() got an unexpected keyword argument 'normalize'
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/users/k1640238/miniconda/envs/genipe_pyvenv/lib/python3.6/site-packages/genipe/tools/imputed_stats.py", line 811, in compute_statistics
for result in pool.map(process_impute2_site, sites_to_process):
File "/users/k1640238/miniconda/envs/genipe_pyvenv/lib/python3.6/multiprocessing/pool.py", line 260, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/users/k1640238/miniconda/envs/genipe_pyvenv/lib/python3.6/multiprocessing/pool.py", line 608, in get
raise self._value
TypeError: __init__() got an unexpected keyword argument 'normalize'
[2017-05-31 14:18:53 ERROR] __init__() got an unexpected keyword argument 'normalize'
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/users/k1640238/miniconda/envs/genipe_pyvenv/lib/python3.6/multiprocessing/pool.py", line 119, in worker
result = (True, func(*args, **kwds))
File "/users/k1640238/miniconda/envs/genipe_pyvenv/lib/python3.6/multiprocessing/pool.py", line 44, in mapstar
return list(map(*args))
File "/users/k1640238/miniconda/envs/genipe_pyvenv/lib/python3.6/site-packages/genipe/tools/imputed_stats.py", line 965, in process_impute2_site
use_ml=site_info.use_ml,
File "/users/k1640238/miniconda/envs/genipe_pyvenv/lib/python3.6/site-packages/genipe/tools/imputed_stats.py", line 1048, in fit_cox
cf = CoxPHFitter(alpha=0.95, tie_method="Efron", normalize=False)
TypeError: __init__() got an unexpected keyword argument 'normalize'
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/users/k1640238/miniconda/envs/genipe_pyvenv/bin/imputed-stats", line 11, in <module>
sys.exit(main())
File "/users/k1640238/miniconda/envs/genipe_pyvenv/lib/python3.6/site-packages/genipe/tools/imputed_stats.py", line 161, in main
options=args,
File "/users/k1640238/miniconda/envs/genipe_pyvenv/lib/python3.6/site-packages/genipe/tools/imputed_stats.py", line 811, in compute_statistics
for result in pool.map(process_impute2_site, sites_to_process):
File "/users/k1640238/miniconda/envs/genipe_pyvenv/lib/python3.6/multiprocessing/pool.py", line 260, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/users/k1640238/miniconda/envs/genipe_pyvenv/lib/python3.6/multiprocessing/pool.py", line 608, in get
raise self._value
TypeError: __init__() got an unexpected keyword argument 'normalize'
Judging by the lifeline changelog this keyword argument has been removed from this particular function. Lifeline is a package which contains this particular function and is used by genipe.
You can either install previous version of lifeline by yourself and see if that will help or wait for updates in genipe library.
Looking at further errors from your comments, it seems like this is problematic code. You are trying to use dmatrices but it seems like it is not defined. Probably because mentioned try/catch block couldn't find statsmodel installed and therefore patsy wasn't imported either.
Try to install few more packages manually, starting with
and see if you will get any errors then...