Traceback (most recent call last):


 "/tmp/Bazel.runfiles_yOE450/runfiles/com_google_deepvariant/deepvariant/make_examples.py", line 1235, in <module>

tf.app.run()


 "/home/nyakovenko/.local/lib/python2.7/site-packages/tensorflow/python/platform/app.py", line 125, in run

_sys.exit(main(argv))


 "/tmp/Bazel.runfiles_yOE450/runfiles/com_google_deepvariant/deepvariant/make_examples.py", line 1225, in main

make_examples_runner(options)


 "/tmp/Bazel.runfiles_yOE450/runfiles/com_google_deepvariant/deepvariant/make_examples.py", line 1127, in make_examples_runner

candidates, examples, gvcfs = region_processor.process(region)


 "/tmp/Bazel.runfiles_yOE450/runfiles/com_google_deepvariant/deepvariant/make_examples.py", line 849, in process

self.in_memory_sam_reader.replace_reads(self.region_reads(region))


 "/tmp/Bazel.runfiles_yOE450/runfiles/com_google_deepvariant/deepvariant/make_examples.py", line 889, in region_reads

_, reads = self.realigner.realign_reads(reads, region)


 "/tmp/Bazel.runfiles_yOE450/runfiles/com_google_deepvariant/deepvariant/realigner/realigner.py", line 606, in realign_reads

self.config.ws_config, self.ref_reader, reads, region)


 "/tmp/Bazel.runfiles_yOE450/runfiles/com_google_deepvariant/deepvariant/realigner/window_selector.py", line 232, in select_windows

candidates = _candidates_from_reads(config, ref_reader, reads, region)


 "/tmp/Bazel.runfiles_yOE450/runfiles/com_google_deepvariant/deepvariant/realigner/window_selector.py", line 84, in _candidates_from_reads

region, expanded_region)


 "/tmp/Bazel.runfiles_yOE450/runfiles/com_google_deepvariant/deepvariant/realigner/window_selector.py", line 152, in _allele_count_linear_selector

allele_counter, model_conf))
TypeError: allele_count_linear_candidates_from_allele_counter() argument counter is not valid for ::learning::genomics::deepvariant::AlleleCounter (deepvariant.python.allelecounter.AlleleCounter instance given): expecting deepvariant.python.allelecounter.AlleleCounter instance, got deepvariant.python.allelecounter.AlleleCounter instance

Traceback (most recent call last):


 "/home/centos/software/anaconda2/lib/python2.7/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run

node.run(updatehash=updatehash)


 "/home/centos/software/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 476, in run

savepkl(op.join(outdir, '_node.pklz'), self)


 "/home/centos/software/anaconda2/lib/python2.7/site-packages/nipype/utils/filemanip.py", line 731, in savepkl

pickle.dump(record, pkl_file)


 "/home/centos/software/anaconda2/lib/python2.7/pickle.py", line 1376, in dump

Pickler(file, protocol).dump(obj)


 "/home/centos/software/anaconda2/lib/python2.7/pickle.py", line 224, in dump

self.save(obj)


 "/home/centos/software/anaconda2/lib/python2.7/pickle.py", line 331, in save

self.save_reduce(obj=obj, *rv)


 "/home/centos/software/anaconda2/lib/python2.7/pickle.py", line 425, in save_reduce

save(state)


 "/home/centos/software/anaconda2/lib/python2.7/pickle.py", line 286, in save

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


 "/home/centos/software/anaconda2/lib/python2.7/pickle.py", line 655, in save_dict

self._batch_setitems(obj.iteritems())


 "/home/centos/software/anaconda2/lib/python2.7/pickle.py", line 669, in _batch_setitems

save(v)


 "/home/centos/software/anaconda2/lib/python2.7/pickle.py", line 331, in save

self.save_reduce(obj=obj, *rv)


 "/home/centos/software/anaconda2/lib/python2.7/pickle.py", line 425, in save_reduce

save(state)


 "/home/centos/software/anaconda2/lib/python2.7/pickle.py", line 286, in save

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


 "/home/centos/software/anaconda2/lib/python2.7/pickle.py", line 655, in save_dict

self._batch_setitems(obj.iteritems())


 "/home/centos/software/anaconda2/lib/python2.7/pickle.py", line 669, in _batch_setitems

save(v)


 "/home/centos/software/anaconda2/lib/python2.7/pickle.py", line 286, in save

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


 "/home/centos/software/anaconda2/lib/python2.7/pickle.py", line 655, in save_dict

self._batch_setitems(obj.iteritems())


 "/home/centos/software/anaconda2/lib/python2.7/pickle.py", line 669, in _batch_setitems

save(v)


 "/home/centos/software/anaconda2/lib/python2.7/pickle.py", line 331, in save

self.save_reduce(obj=obj, *rv)


 "/home/centos/software/anaconda2/lib/python2.7/pickle.py", line 425, in save_reduce

save(state)


 "/home/centos/software/anaconda2/lib/python2.7/pickle.py", line 286, in save

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


 "/home/centos/software/anaconda2/lib/python2.7/pickle.py", line 568, in save_tuple

save(element)


 "/home/centos/software/anaconda2/lib/python2.7/pickle.py", line 331, in save

self.save_reduce(obj=obj, *rv)


 "/home/centos/software/anaconda2/lib/python2.7/pickle.py", line 425, in save_reduce

save(state)


 "/home/centos/software/anaconda2/lib/python2.7/pickle.py", line 286, in save

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


 "/home/centos/software/anaconda2/lib/python2.7/pickle.py", line 655, in save_dict

self._batch_setitems(obj.iteritems())


 "/home/centos/software/anaconda2/lib/python2.7/pickle.py", line 669, in _batch_setitems

save(v)


 "/home/centos/software/anaconda2/lib/python2.7/pickle.py", line 286, in save

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


 "/home/centos/software/anaconda2/lib/python2.7/pickle.py", line 655, in save_dict

self._batch_setitems(obj.iteritems())


 "/home/centos/software/anaconda2/lib/python2.7/pickle.py", line 669, in _batch_setitems

save(v)


 "/home/centos/software/anaconda2/lib/python2.7/pickle.py", line 331, in save

self.save_reduce(obj=obj, *rv)


 "/home/centos/software/anaconda2/lib/python2.7/pickle.py", line 425, in save_reduce

save(state)


 "/home/centos/software/anaconda2/lib/python2.7/pickle.py", line 286, in save

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


 "/home/centos/software/anaconda2/lib/python2.7/pickle.py", line 655, in save_dict

self._batch_setitems(obj.iteritems())


 "/home/centos/software/anaconda2/lib/python2.7/pickle.py", line 669, in _batch_setitems

save(v)


 "/home/centos/software/anaconda2/lib/python2.7/pickle.py", line 331, in save

self.save_reduce(obj=obj, *rv)


 "/home/centos/software/anaconda2/lib/python2.7/pickle.py", line 425, in save_reduce

save(state)


 "/home/centos/software/anaconda2/lib/python2.7/pickle.py", line 286, in save

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


 "/home/centos/software/anaconda2/lib/python2.7/pickle.py", line 568, in save_tuple

save(element)


 "/home/centos/software/anaconda2/lib/python2.7/pickle.py", line 331, in save

self.save_reduce(obj=obj, *rv)


 "/home/centos/software/anaconda2/lib/python2.7/pickle.py", line 425, in save_reduce

save(state)


 "/home/centos/software/anaconda2/lib/python2.7/pickle.py", line 286, in save

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


 "/home/centos/software/anaconda2/lib/python2.7/pickle.py", line 655, in save_dict

self._batch_setitems(obj.iteritems())


 "/home/centos/software/anaconda2/lib/python2.7/pickle.py", line 669, in _batch_setitems

save(v)


 "/home/centos/software/anaconda2/lib/python2.7/pickle.py", line 286, in save

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


 "/home/centos/software/anaconda2/lib/python2.7/pickle.py", line 606, in save_list

self._batch_appends(iter(obj))


 "/home/centos/software/anaconda2/lib/python2.7/pickle.py", line 621, in _batch_appends

save(x)


 "/home/centos/software/anaconda2/lib/python2.7/pickle.py", line 306, in save

rv = reduce(self.proto)


 "/home/centos/software/anaconda2/lib/python2.7/copy_reg.py", line 70, in _reduce_ex

raise TypeError, "can't pickle %s objects" % base.__name__
TypeError: can't pickle instancemethod objects
