Traceback (most recent call last):


 "C:\Users\thomasonc\AppData\Local\Continuum\anaconda3\lib\site-packages\spyder\widgets\variableexplorer\dataframeeditor.py", line 295, in data

value = self.get_value(row, column-1)


 "C:\Users\thomasonc\AppData\Local\Continuum\anaconda3\lib\site-packages\spyder\widgets\variableexplorer\dataframeeditor.py", line 270, in get_value

value = self.df.iloc[row, column]


 "C:\Users\thomasonc\AppData\Local\Continuum\anaconda3\lib\site-packages\pandas\core\indexing.py", line 1491, in __getitem__

return self._getitem_scalar(key)


 "C:\Users\thomasonc\AppData\Local\Continuum\anaconda3\lib\site-packages\pandas\core\indexing.py", line 2113, in _getitem_scalar

values = self.obj._get_value(*key, takeable=True)


 "C:\Users\thomasonc\AppData\Local\Continuum\anaconda3\lib\site-packages\pandas\core\frame.py", line 2765, in _get_value

return com.maybe_box_datetimelike(series._values[index])


 "C:\Users\thomasonc\AppData\Local\Continuum\anaconda3\lib\site-packages\pandas\core\arrays\sparse.py", line 1010, in __getitem__

return self._get_val_at(key)


 "C:\Users\thomasonc\AppData\Local\Continuum\anaconda3\lib\site-packages\pandas\core\arrays\sparse.py", line 1053, in _get_val_at

return libindex.get_value_at(self.sp_values, sp_loc)
TypeError: Argument 'arr' has incorrect type (expected numpy.ndarray, got IntegerArray)

Traceback (most recent call last):

 "/home/pastore/usr/local/bcbio/anaconda/bin/bcbio_nextgen.py", line 226, in <module>
main(**kwargs)

 "/home/pastore/usr/local/bcbio/anaconda/bin/bcbio_nextgen.py", line 43, in main
run_main(**kwargs)

 "/home/pastore/usr/local/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 37, in run_main
fc_dir, run_info_yaml)

 "/home/pastore/usr/local/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 80, in _run_toplevel
for xs in pipeline.run(config, run_info_yaml, parallel, dirs, samples):

 "/home/pastore/usr/local/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 174, in run
samples = run_parallel("postprocess_variants", samples)

 "/home/pastore/usr/local/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 28, in run_parallel
return run_multicore(fn, items, config, parallel=parallel)

 "/home/pastore/usr/local/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 86, in run_multicore
for data in joblib.Parallel(parallel["num_jobs"])(joblib.delayed(fn)(x) for x in items):

 "/home/pastore/usr/local/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 657, in __call__
self.dispatch(function, args, kwargs)

 "/home/pastore/usr/local/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 404, in dispatch
job = ImmediateApply(func, args, kwargs)

 "/home/pastore/usr/local/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 142, in **init**
self.results = func(_args, *_kwargs)

 "/home/pastore/usr/local/bcbio/anaconda/lib/python2.7/site-packages/bcbio/utils.py", line 49, in wrapper
return apply(f, _args, *_kwargs)

 "/home/pastore/usr/local/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multitasks.py", line 90, in postprocess_variants
return variation.postprocess_variants(*args)

 "/home/pastore/usr/local/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/variation.py", line 28, in postprocess_variants
data["vrn_file"] = prioritize.handle_vcf_calls(data["vrn_file"], data)

 "/home/pastore/usr/local/bcbio/anaconda/lib/python2.7/site-packages/bcbio/variation/prioritize.py", line 33, in handle_vcf_calls
gemini_db = population.create_gemini_db(vcf_file, data)

 "/home/pastore/usr/local/bcbio/anaconda/lib/python2.7/site-packages/bcbio/variation/population.py", line 79, in create_gemini_db
do.run(cmd, "Create gemini database for %s" % gemini_vcf, data)

 "/home/pastore/usr/local/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run
_do_run(cmd, checks, log_stdout)

 "/home/pastore/usr/local/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run
raise subprocess.CalledProcessError(exitcode, error_msg)subprocess.CalledProcessError: Command 'set -o pipefail; /home/pastore/usr/local/bcbio/anaconda/bin/gemini
load
--passonly --skip-cadd --skip-gerp-bp
-v /ifs/e63data/sander-lab/pastore/project/HZL/hzl_noaln/work/freebayes/60T-vepeffects-ploidyfix-filter.vcf.gz -t VEP --cores 6 --tempdir /ifs/e63data/sander-lab/pastore/project/HZL/hzl_noaln/work/freebayes/tx/tmpXM0Pbp --no-bcolz /ifs/e63data/sander-lab/pastore/project/HZL/hzl_noaln/work/freebayes/tx/tmpXM0Pbp/60T-vepeffects-ploidyfix-filter.db