Traceback (most recent call last):

 "/data/run/Projects/project-123/cloudbiolinux/utils/prepare_tx_gff.py", line 821, in <module>
main(args.org_build, args.gtf, args.fasta, genome_dir, args.cores)

 "/data/run/Projects/project-123/cloudbiolinux/utils/prepare_tx_gff.py", line 286, in main
db = _get_gtf_db(gtf_file)

 "/data/run/Projects/project-123/cloudbiolinux/utils/prepare_tx_gff.py", line 757, in _get_gtf_db
disable_infer_transcripts, disable_infer_genes = guess_disable_infer_extent(gtf)

 "/data/run/Projects/project-123/cloudbiolinux/utils/prepare_tx_gff.py", line 729, in guess_disable_infer_extent
db = _create_tiny_gffutils_db(gtf_file)

 "/data/run/Projects/project-123/cloudbiolinux/utils/prepare_tx_gff.py", line 700, in _create_tiny_gffutils_db
disable_infer_transcripts=True)

 "/Tools/bcbio-0.9.9/anaconda/lib/python2.7/site-packages/gffutils/create.py", line 1273, in create_db
c.create()

 "/Tools/bcbio-0.9.9/anaconda/lib/python2.7/site-packages/gffutils/create.py", line 488, in create
self._populate_from_lines(self.iterator)

 "/Tools/bcbio-0.9.9/anaconda/lib/python2.7/site-packages/gffutils/create.py", line 609, in _populate_from_lines
raise ValueError("No lines parsed -- was an empty file provided?")ValueError: No lines parsed -- was an empty file provided?
Traceback (most recent call last):


 "<stdin>", line 1, in <module>


 "/Users/mmckerns/lib/python3.5/site-packages/dill-0.2.6.dev0-py3.5.egg/dill/dill.py", line 256, in dumps

dump(obj, file, protocol, byref, fmode, recurse)#, strictio)


 "/Users/mmckerns/lib/python3.5/site-packages/dill-0.2.6.dev0-py3.5.egg/dill/dill.py", line 249, in dump

pik.dump(obj)


 "/opt/local/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/pickle.py", line 408, in dump

self.save(obj)


 "/opt/local/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/pickle.py", line 520, in save

self.save_reduce(obj=obj, *rv)


 "/opt/local/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/pickle.py", line 623, in save_reduce

save(state)


 "/opt/local/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/pickle.py", line 475, in save

f(self, obj) # Call unbound method with explicit self


 "/Users/mmckerns/lib/python3.5/site-packages/dill-0.2.6.dev0-py3.5.egg/dill/dill.py", line 818, in save_module_dict

StockPickler.save_dict(pickler, obj)


 "/opt/local/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/pickle.py", line 810, in save_dict

self._batch_setitems(obj.items())


 "/opt/local/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/pickle.py", line 836, in _batch_setitems

save(v)


 "/opt/local/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/pickle.py", line 520, in save

self.save_reduce(obj=obj, *rv)


 "/opt/local/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/pickle.py", line 623, in save_reduce

save(state)


 "/opt/local/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/pickle.py", line 475, in save

f(self, obj) # Call unbound method with explicit self


 "/Users/mmckerns/lib/python3.5/site-packages/dill-0.2.6.dev0-py3.5.egg/dill/dill.py", line 818, in save_module_dict

StockPickler.save_dict(pickler, obj)


 "/opt/local/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/pickle.py", line 810, in save_dict

self._batch_setitems(obj.items())


 "/opt/local/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/pickle.py", line 836, in _batch_setitems

save(v)


 "/opt/local/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/pickle.py", line 475, in save

f(self, obj) # Call unbound method with explicit self


 "/Users/mmckerns/lib/python3.5/site-packages/dill-0.2.6.dev0-py3.5.egg/dill/dill.py", line 1236, in save_type

StockPickler.save_global(pickler, obj)


 "/opt/local/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/pickle.py", line 911, in save_global

(obj, module_name, name))
_pickle.PicklingError: Can't pickle <class 'sympy.polys.domains.mpelements.constant'>: it's not found as sympy.polys.domains.mpelements.constant
