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Oncotator reports on error, could you please help?

mdevirmdevir IsraelMember
edited February 2017 in Oncotator

Hi,

I am trying to use Oncotator v1.9.0.0, and receiving the following error. Could you please help me to figure out what to do?
some details: I am running Oncotator v1.9.0.0 on a cluster, on anaconda env. pyhton 2.7. I installed the dependencies as described in http://gatkforums.broadinstitute.org/gatk/discussion/4153/what-are-the-platform-requirements-and-software-dependencies-for-running-oncotator. the error is: "TypeError: _open() got an unexpected keyword argument 'encoding'"
(Trace below).

Thanks,
Michal.

Traceback (most recent call last):
File "/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/env_oncotator19/b
in/oncotator", line 9, in
load_entry_point('Oncotator==v1.9.0.0', 'console_scripts', 'oncotator')()
File "/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/env_oncotator19/l
ib/python2.7/site-packages/Oncotator-v1.9.0.0-py2.7.egg/oncotator/Oncotator.py",
line 309, in main
annotator.annotate()
File "/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/env_oncotator19/l
ib/python2.7/site-packages/Oncotator-v1.9.0.0-py2.7.egg/oncotator/Annotator.py",
line 437, in annotate
filename = self._outputRenderer.renderMutations(mutations, metadata=metadata
, comments=comments)
File "/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/env_oncotator19/l
ib/python2.7/site-packages/Oncotator-v1.9.0.0-py2.7.egg/oncotator/output/TcgaMaf
OutputRenderer.py", line 268, in renderMutations
m = mutations.next()
File "/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/env_oncotator19/l
ib/python2.7/site-packages/Oncotator-v1.9.0.0-py2.7.egg/oncotator/Annotator.py",
line 448, in _applyManualAnnotations
for m in mutations:
File "/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/env_oncotator19/l
ib/python2.7/site-packages/Oncotator-v1.9.0.0-py2.7.egg/oncotator/Annotator.py",
line 456, in _applyDefaultAnnotations
for m in mutations:
File "/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/env_oncotator19/l
ib/python2.7/site-packages/Oncotator-v1.9.0.0-py2.7.egg/oncotator/Annotator.py",
line 519, in _annotate_mutations_using_datasources
m = self._annotate_func_ptr(m, datasource)
File "/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/env_oncotator19/l
ib/python2.7/site-packages/Oncotator-v1.9.0.0-py2.7.egg/oncotator/Annotator.py",
line 88, in _annotate_mut
return ds.annotate_mutation(m)
File "/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/env_oncotator19/l
ib/python2.7/site-packages/Oncotator-v1.9.0.0-py2.7.egg/oncotator/datasources/Ta
bixIndexedVcfDatasource.py", line 230, in annotate_mutation
vcf_records = self.vcf_reader.fetch(mutation.chr, mut_start - 1, mut_end) #
query database for records
File "/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/env_oncotator19/l
ib/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:23
44)
TypeError: _open() got an unexpected keyword argument 'encoding'

Post edited by mdevir on
Tagged:

Answers

  • shleeshlee CambridgeMember, Broadie, Moderator

    Hi @mdevir,

    I've let our developer know about your question. If you don't hear back in the next week, please ping us by posting to this thread.

    In the meanwhile, you might be interested in the web-based oncotator that we describe here.

  • LeeTL1220LeeTL1220 Arlington, MAMember, Broadie, Dev

    @mdevir Did you create the virtual environment via the oncotator script (create_oncotator_venv.sh)? It looks like you used python setup.py install only ... it's reasonable to expect that to work, but PyVCF has an issue. Can you do a pip freeze and make sure you have PyVCF 0.6.8?

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