Oncotator Error -- Please help me

Haiying7Haiying7 Heidelberg, GermanyMember

I am running Oncotator 1.8.0.0 on MuTect2 output .vcf file. I did perform filtering for PASS before running Oncotator.

If I run this on command line:
oncotator -v --input_format=VCF --output_format=VCF ../PASS/B100327_T3398.vcf B100327_T3398.vcf hg19 --db-dir ${data_source}

The last part of log file is: (Some thing is wrong in the last line, and I cannot figure out how to fix it.)

2016-11-23 17:56:20,932 WARNING [oncotator.input.VcfInputMutationCreator:293] Tumor-Normal VCF detected. The Normal will assume GT= 0/0, unless GT field specified otherwise.
Traceback (most recent call last):
File "/home/kong/lib/miniconda2/envs/oncotator/bin/oncotator", line 9, in
load_entry_point('Oncotator==v1.8.0.0', 'console_scripts', 'oncotator')()
File "/home/kong/lib/miniconda2/envs/oncotator/lib/python2.7/site-packages/Oncotator-v1.8.0.0-py2.7.egg/oncotator/Oncotator.py", line 309, in main
annotator.annotate()
File "/home/kong/lib/miniconda2/envs/oncotator/lib/python2.7/site-packages/Oncotator-v1.8.0.0-py2.7.egg/oncotator/Annotator.py", line 437, in annotate
filename = self._outputRenderer.renderMutations(mutations, metadata=metadata, comments=comments)
File "/home/kong/lib/miniconda2/envs/oncotator/lib/python2.7/site-packages/Oncotator-v1.8.0.0-py2.7.egg/oncotator/output/VcfOutputRenderer.py", line 118, in renderMutations
dataManager = OutputDataManager(self.configTable, mutations, comments, metadata, path)
File "/home/kong/lib/miniconda2/envs/oncotator/lib/python2.7/site-packages/Oncotator-v1.8.0.0-py2.7.egg/oncotator/output/OutputDataManager.py", line 90, in init
self.mutation, self.mutations = self._fetchFirstMutation(muts)
File "/home/kong/lib/miniconda2/envs/oncotator/lib/python2.7/site-packages/Oncotator-v1.8.0.0-py2.7.egg/oncotator/output/OutputDataManager.py", line 105, in _fetchFirstMutation
for mutation in muts:
File "/home/kong/lib/miniconda2/envs/oncotator/lib/python2.7/site-packages/Oncotator-v1.8.0.0-py2.7.egg/oncotator/Annotator.py", line 448, in _applyManualAnnotations
for m in mutations:
File "/home/kong/lib/miniconda2/envs/oncotator/lib/python2.7/site-packages/Oncotator-v1.8.0.0-py2.7.egg/oncotator/Annotator.py", line 456, in _applyDefaultAnnotations
for m in mutations:
File "/home/kong/lib/miniconda2/envs/oncotator/lib/python2.7/site-packages/Oncotator-v1.8.0.0-py2.7.egg/oncotator/Annotator.py", line 519, in _annotate_mutations_using_datasources
m = self._annotate_func_ptr(m, datasource)
File "/home/kong/lib/miniconda2/envs/oncotator/lib/python2.7/site-packages/Oncotator-v1.8.0.0-py2.7.egg/oncotator/Annotator.py", line 88, in _annotate_mut
return ds.annotate_mutation(m)
File "/home/kong/lib/miniconda2/envs/oncotator/lib/python2.7/site-packages/Oncotator-v1.8.0.0-py2.7.egg/oncotator/datasources/TabixIndexedVcfDatasource.py", line 230, in annotate_mutation
vcf_records = self.vcf_reader.fetch(mutation.chr, mut_start - 1, mut_end) # query database for records
File "/home/kong/lib/miniconda2/envs/oncotator/lib/python2.7/site-packages/vcf/parser.py", line 626, in fetch
encoding=self.encoding)
File "ctabix.pyx", line 92, in pysam.ctabix.Tabixfile.cinit (pysam/ctabix.c:2234)
File "ctabix.pyx", line 98, in pysam.ctabix.Tabixfile._open (pysam/ctabix.c:2344)
TypeError: _open() got an unexpected keyword argument 'encoding'

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