Issue with nesoni import?

[ewilbanks]

Hi there,

I'm trying to use nesoni to polish a genome assembled from pacbio reads using some moleculo reads aligned with pbalign.py/blasr. To import these I'm trying to use nesoni import, by running:

nesoni import:
--snp-cost 2.000
n2
/Users/ewilbanks/Dropbox/_personal/BERRIES/Metagenomics/pacbio/PSB_binMod_asm/reads_and_annot/pbalign1/mol_otuA_pbalign1.sorted.bam
PROKKA_07022014.sizeSorted.fna

Everything seems to go OK, until I get the error shown below. It doesn't seem to have created the appropriate files for importing the bam alignements since later filter / variant detection fails. Any thoughts on what I can do to troubleshoot it?

Thanks!!
Lizzy

---

[[other normal seeming output then....]]

• Processing contig unitig_59
• Processing contig unitig_110
  Loaded Genome
  Saving genome map to n2/reference/reference-cs

Traceback:
File "/Users/ewilbanks/anaconda/lib/python2.7/site-packages/nesoni/config.py", line 1069, in shell_run
action.run()
File "/Users/ewilbanks/anaconda/lib/python2.7/site-packages/nesoni/config.py", line 633, in inner
return func(self,_args,__kwargs)
File "/Users/ewilbanks/anaconda/lib/python2.7/site-packages/nesoni/config.py", line 633, in inner
return func(self,_args,**kwargs)
File "/Users/ewilbanks/anaconda/lib/python2.7/site-packages/nesoni/samimport.py", line 21, in run
workspace.setup_reference(self.reference)
File "/Users/ewilbanks/anaconda/lib/python2.7/site-packages/nesoni/working_directory.py", line 16, in setup_reference
reference_directory.Make_reference(path, filenames=filenames, bowtie=bowtie).run()
File "/Users/ewilbanks/anaconda/lib/python2.7/site-packages/nesoni/config.py", line 633, in inner
return func(self,*args,**kwargs)
File "/Users/ewilbanks/anaconda/lib/python2.7/site-packages/nesoni/config.py", line 633, in inner
return func(self,args,*kwargs)
File "/Users/ewilbanks/anaconda/lib/python2.7/site-packages/nesoni/reference_directory.py", line 225, in run
if config.apply_ifavailable_jar(self.snpeff, 'snpEff.jar'):
File "/Users/ewilbanks/anaconda/lib/python2.7/site-packages/nesoni/config.py", line 269, in apply_ifavailable_jar
try: io.find_jar(jar)
File "/Users/ewilbanks/anaconda/lib/python2.7/site-packages/nesoni/io.py", line 28, in find_jar
raise Error('Couldn't find "%s". Directories listed in JARPATH and PATH were searched. %s' % (jarname, extra_help))

NameError:
global name 'Error' is not defined