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Victorian-Bioinformatics-Consortium / nesoni

High throughput sequencing analysis tools
GNU General Public License v2.0
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Issue with nesoni import? #9

Open ewilbanks opened 10 years ago

ewilbanks commented 10 years ago

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....]]

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