nesoni annotation error

[kwongj]

I've been trying to run nesoni make-reference (v0.122) using a .gbk file (mainly to preserve the annotations for nway), but keep getting an error:

jkwong@dna:~/Ecoli/analysis/nesoni/outbreak$ nesoni make-reference test-ref BPH0530.gbk

nesoni make-reference: \
    --ls ifavailable \
    --cs ifavailable \
    --bowtie ifavailable \
    --genome yes \
    --genome-select -source \
    --snpeff ifavailable \
    test-ref \
    BPH0530.gbk

Traceback:
  File "/bio/sw/python/env-pypy/site-packages/nesoni-0.122-py2.7.egg/nesoni/config.py", line 1069, in shell_run
    action.run()
  File "/bio/sw/python/env-pypy/site-packages/nesoni-0.122-py2.7.egg/nesoni/config.py", line 633, in inner
    return func(self,*args,**kwargs)
  File "/bio/sw/python/env-pypy/site-packages/nesoni-0.122-py2.7.egg/nesoni/config.py", line 633, in inner
    return func(self,*args,**kwargs)
  File "/bio/sw/python/env-pypy/site-packages/nesoni-0.122-py2.7.egg/nesoni/reference_directory.py", line 213, in run
    reference.set_sequences(sequences)
  File "/bio/sw/python/env-pypy/site-packages/nesoni-0.122-py2.7.egg/nesoni/reference_directory.py", line 34, in set_sequences
    for name, seq in io.read_sequences(filename, genbank_callback=genbank_callback):
  File "/bio/sw/python/env-pypy/site-packages/nesoni-0.122-py2.7.egg/nesoni/io.py", line 419, in read_genbank_sequence
    from Bio import SeqIO
  File "/bio/sw/python/env-pypy/site-packages/Bio/SeqIO/__init__.py", line 353, in <module>
    from Bio.File import as_handle
  File "/bio/sw/python/env-pypy/site-packages/Bio/File.py", line 35, in <module>
    from sqlite3 import dbapi2 as _sqlite
  File "/bio/sw/python/download/pypy/lib-python/2.7/sqlite3/__init__.py", line 24, in <module>
    from dbapi2 import *
  File "/bio/sw/python/download/pypy/lib-python/2.7/sqlite3/dbapi2.py", line 27, in <module>
    from _sqlite3 import *
  File "/bio/sw/python/download/pypy/lib_pypy/_sqlite3.py", line 52, in <module>
    _ffi = _FFI()
  File "/bio/sw/python/download/pypy/lib_pypy/cffi/api.py", line 59, in __init__
    backend.__version__ == __version__[:3])

AssertionError:

I've also tried using make-reference with a .gff file, but after then using nesoni bowtie to map reads, the resulting report.txt file is empty.

Using a reference file in FASTA format for nesoni make-reference is successful, but adding the annotation in nway (after running make-reference, bowtie, consensus, nway) by specifying the --gbk flag again comes up with an AssertionError with both .gbk and .gff files:

jkwong@dna:~/Ecoli/analysis/nesoni/outbreak$ nesoni nway --output outbreak.txt --as table --gbk BPH0530.gbk Ec_BPH*

nesoni nway: \
    --output outbreak.txt \
    --as table \
    --gbk BPH0530.gbk \
    --evidence yes \
    --consequences yes \
    --reference yes \
    --indels yes \
    --require-all no \
    --require-bisect no \
    --full no \
    Ec_BPH0532 Ec_BPH0657 Ec_BPH0658 Ec_BPH0659

Traceback:
  File "/bio/sw/python/env-pypy/site-packages/nesoni-0.122-py2.7.egg/nesoni/config.py", line 1069, in shell_run
    action.run()
  File "/bio/sw/python/env-pypy/site-packages/nesoni-0.122-py2.7.egg/nesoni/nway_diff.py", line 284, in run
    split_a=self.splitting, split_b=self.from_, f=f)
  File "/bio/sw/python/env-pypy/site-packages/nesoni-0.122-py2.7.egg/nesoni/nway_diff.py", line 344, in nway_main
    from Bio import SeqIO
  File "/bio/sw/python/env-pypy/site-packages/Bio/SeqIO/__init__.py", line 353, in <module>
    from Bio.File import as_handle
  File "/bio/sw/python/env-pypy/site-packages/Bio/File.py", line 35, in <module>
    from sqlite3 import dbapi2 as _sqlite
  File "/bio/sw/python/download/pypy/lib-python/2.7/sqlite3/__init__.py", line 24, in <module>
    from dbapi2 import *
  File "/bio/sw/python/download/pypy/lib-python/2.7/sqlite3/dbapi2.py", line 27, in <module>
    from _sqlite3 import *
  File "/bio/sw/python/download/pypy/lib_pypy/_sqlite3.py", line 52, in <module>
    _ffi = _FFI()
  File "/bio/sw/python/download/pypy/lib_pypy/cffi/api.py", line 59, in __init__
    backend.__version__ == __version__[:3])

AssertionError:

jkwong@dna:~/Ecoli/analysis/nesoni/outbreak$ 

The reference genome is a closed E.coli genome that was annotated with Prokka.

Any ideas? Thanks for the help.