To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at https://software.broadinstitute.org/firecloud/documentation/freecredits

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'

Answers

Sign In or Register to comment.