Traceback (most recent call last):


 "/bcbio/tools/bin/bcbio_nextgen.py", line 238, in <module>

main(**kwargs)


 "/bcbio/tools/bin/bcbio_nextgen.py", line 46, in main

run_main(**kwargs)


 "/bcbio/stable/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 45, in run_main

fc_dir, run_info_yaml)


 "/bcbio/stable/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 89, in _run_toplevel

for xs in pipeline(config, run_info_yaml, parallel, dirs, samples):


 "/bcbio/stable/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 328, in smallrnaseqpipeline

samples = run_parallel("srna_alignment", [samples])


 "/bcbio/stable/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 28, in run_parallel

return run_multicore(fn, items, config, parallel=parallel)


 "/bcbio/stable/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 86, in run_multicore

for data in joblib.Parallel(parallel["num_jobs"], batch_size=1, backend="multiprocessing")(joblib.delayed(fn)(x) for x in items):


 "/bcbio/stable/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 917, in __call__

if self.dispatch_one_batch(iterator):


 "/bcbio/stable/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 759, in dispatch_one_batch

self._dispatch(tasks)


 "/bcbio/stable/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 716, in _dispatch

job = self._backend.apply_async(batch, callback=cb)


 "/bcbio/stable/anaconda/lib/python2.7/site-packages/joblib/_parallel_backends.py", line 182, in apply_async

result = ImmediateResult(func)


 "/bcbio/stable/anaconda/lib/python2.7/site-packages/joblib/_parallel_backends.py", line 549, in __init__

self.results = batch()


 "/bcbio/stable/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 225, in __call__

for func, args, kwargs in self.items]


 "/bcbio/stable/anaconda/lib/python2.7/site-packages/bcbio/utils.py", line 52, in wrapper

return apply(f, *args, **kwargs)


 "/bcbio/stable/anaconda/lib/python2.7/site-packages/bcbio/distributed/multitasks.py", line 172, in srna_alignment

return seqcluster.run_align(*args)


 "/bcbio/stable/anaconda/lib/python2.7/site-packages/bcbio/srna/group.py", line 69, in run_align

sample = process_alignment(data[0][0], [seq_out, None])


 "/bcbio/stable/anaconda/lib/python2.7/site-packages/bcbio/pipeline/sample.py", line 128, in process_alignment

data = align_to_sort_bam(fastq1, fastq2, aligner, data)


 "/bcbio/stable/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.py", line 78, in align_to_sort_bam

names, align_dir, data)


 "/bcbio/stable/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.py", line 153, in _align_from_fastq

out = align_fn(fastq1, fastq2, align_ref, names, align_dir, data)


 "/bcbio/stable/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/star.py", line 100, in align

data = _update_data(star_dirs.final_out, star_dirs.out_dir, names, data)


 "/bcbio/stable/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/star.py", line 143, in _update_data

sjbed = junction2bed(sjfile)


 "/bcbio/stable/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/star.py", line 221, in junction2bed

base, _ = os.path.splitext(junction_file)


 "/bcbio/stable/anaconda/lib/python2.7/posixpath.py", line 98, in splitext

return genericpath._splitext(p, sep, altsep, extsep)


 "/bcbio/stable/anaconda/lib/python2.7/genericpath.py", line 99, in _splitext

sepIndex = p.rfind(sep)
AttributeError: 'NoneType' object has no attribute 'rfind'
Traceback (most recent call last):


 "./run_server.py", line 4, in <module>

from mead import app


 "/home/seth/Code/python/mead_dev/mead/mead/**init**.py", line 66, in <module>

import mead.core.views.content


 "/home/seth/Code/python/mead_dev/mead/mead/core/views/content.py", line 10, in <module>

from available import defaults


 "/home/seth/Code/python/mead_dev/mead/mead/core/views/available.py", line 22, in <module>

defaults.update(dict(pages = Page.query.all()))


 "/home/seth/Code/python/mead_dev/local/lib/python2.7/site-packages/Flask_SQLAlchemy-0.15-py2.7.egg/flaskext/sqlalchemy.py", line 386, in **get**

return type.query_class(mapper, session=self.sa.session())


 "/home/seth/Code/python/mead_dev/local/lib/python2.7/site-packages/SQLAlchemy-0.7.3-py2.7.egg/sqlalchemy/orm/scoping.py", line 53, in **call**

return self.registry()


 "/home/seth/Code/python/mead_dev/local/lib/python2.7/site-packages/SQLAlchemy-0.7.3-py2.7.egg/sqlalchemy/util/_collections.py", line 877, in __call__

val = self.registry.value = self.createfunc()


 "/home/seth/Code/python/mead_dev/local/lib/python2.7/site-packages/Flask_SQLAlchemy-0.15-py2.7.egg/flaskext/sqlalchemy.py", line 191, in **init**

bind=db.engine,


 "/home/seth/Code/python/mead_dev/local/lib/python2.7/site-packages/Flask_SQLAlchemy-0.15-py2.7.egg/flaskext/sqlalchemy.py", line 719, in engine

return self.get_engine(self.get_app())


 "/home/seth/Code/python/mead_dev/local/lib/python2.7/site-packages/Flask_SQLAlchemy-0.15-py2.7.egg/flaskext/sqlalchemy.py", line 736, in get_engine

return connector.get_engine()


 "/home/seth/Code/python/mead_dev/local/lib/python2.7/site-packages/Flask_SQLAlchemy-0.15-py2.7.egg/flaskext/sqlalchemy.py", line 428, in get_engine

self._sa.apply_driver_hacks(self._app, info, options)


 "/home/seth/Code/python/mead_dev/local/lib/python2.7/site-packages/Flask_SQLAlchemy-0.15-py2.7.egg/flaskext/sqlalchemy.py", line 679, in apply_driver_hacks

if info.drivername == 'mysql':
AttributeError: 'NoneType' object has no attribute 'drivername'
