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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

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @Haiying7
    Hi,

    I have moved your question to the Oncotator category where Lee @LeeTL1220 will help you.

    -Sheila

  • LeeTL1220LeeTL1220 Arlington, MAMember, Broadie, Dev

    Hello @Haiying7 ... Can you upgrade Oncotator? I think that is all you need to get around this. Post here if you get the same error or a new one.

  • YanjaneYanjane BeijingMember
    edited June 6

    Hello @LeeTL1220 , I am using oncotator 1.9.1.0. When I run it on my Ubuntu,It can't work correctly.
    ....
    2017-06-06 03:15:06,964 WARNING [root:97] Index field (gene) not found. Remember that datasources must be ordered. Please put a datasource that provides the 'gene' annotation in front of this datasource, such as any TranscriptProvider.
    2017-06-06 03:15:06,964 WARNING [root:97] Index field (gene) not found. Remember that datasources must be ordered. Please put a datasource that provides the 'gene' annotation in front of this datasource, such as any TranscriptProvider.
    ...
    Can you help me to fix it. Thanks!

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @Yanjane
    Hi,

    Can you please post the exact command you ran?

    -Sheila

  • YanjaneYanjane BeijingMember
    edited July 12

    @Sheila

    Thank you for answering, the problem has been solved already.

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