Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Attention:
We will be out of the office on November 11th and 13th 2019, due to the U.S. holiday(Veteran's day) and due to a team event(Nov 13th). We will return to monitoring the GATK forum on November 12th and 14th respectively. Thank you for your patience.

Oncotator run error: Could not find config file (maflite_input.config)

I have installed oncotator 1.2.6 in Ubuntu 14.04. It installed successfully but when I am running it throws following error:

Command: oncotator -i MAFLITE --db-dir /home/oncotator_1.2.6.0/oncotator_v1_ds_June112014/ -o TCGAMAF input.maflite output.maf hg19

Verbose mode on
Path:
['/usr/local/bin', '/usr/local/lib/python2.7/dist-packages/SQLAlchemy-0.9.4-py2.7.egg', '/usr/local/lib/python2.7/dist-packages/shove-0.5.6-py2.7.egg', '/usr/local/lib/python2.7/dist-packages/Cython-0.20.2-py2.7-linux-x86_64.egg', '/usr/local/lib/python2.7/dist-packages/PyVCF-0.6.7-py2.7-linux-x86_64.egg', '/usr/local/lib/python2.7/dist-packages/biopython-1.64-py2.7-linux-x86_64.egg', '/usr/local/lib/python2.7/dist-packages/pandas-0.14.0-py2.7-linux-x86_64.egg', '/usr/local/lib/python2.7/dist-packages/stuf-0.9.4-py2.7.egg', '/usr/local/lib/python2.7/dist-packages/futures-2.1.6-py2.7.egg', '/usr/local/lib/python2.7/dist-packages/pytz-2014.4-py2.7.egg', '/usr/local/lib/python2.7/dist-packages/python_dateutil-2.2-py2.7.egg', '/usr/local/lib/python2.7/dist-packages/parse-1.4.1-py2.7.egg', '/usr/local/lib/python2.7/dist-packages/Oncotator-v1.2.6.0-py2.7.egg', '/usr/local/lib/python2.7/dist-packages/leveldb-0.193-py2.7-linux-x86_64.egg', '/usr/local/lib/python2.7/dist-packages/natsort-3.3.0-py2.7.egg', '/usr/local/lib/python2.7/dist-packages/python_memcached-1.53-py2.7.egg', '/usr/local/lib/python2.7/dist-packages/nose-1.3.3-py2.7.egg', '/usr/local/lib/python2.7/dist-packages/pysam-0.7.5-py2.7-linux-x86_64.egg', '/usr/local/lib/python2.7/dist-packages/bcbio_gff-0.4-py2.7.egg', '/usr/local/lib/python2.7/dist-packages', '/usr/lib/python2.7', '/usr/lib/python2.7/plat-x86_64-linux-gnu', '/usr/lib/python2.7/lib-tk', '/usr/lib/python2.7/lib-old', '/usr/lib/python2.7/lib-dynload', '/usr/lib/python2.7/dist-packages', '/usr/lib/python2.7/dist-packages/PILcompat', '/usr/lib/python2.7/dist-packages/gtk-2.0', '/usr/lib/python2.7/dist-packages/ubuntu-sso-client']

2014-07-01 17:14:15,384 INFO [oncotator.Oncotator:236] Oncotator v1.2.6.0
2014-07-01 17:14:15,385 INFO [oncotator.Oncotator:237] Args: Namespace(cache_url=None, dbDir='/home/adlab/ngs_soft/oncotator_1.2.6.0/oncotator_v1_ds_June112014/', default_cli=[], default_config=None, genome_build='hg19', infer_genotypes='false', input_file='0748.maflite', input_format='MAFLITE', log_name='oncotator.log', noMulticore=False, output_file='0748.maf', output_format='TCGAMAF', override_cli=[], override_config=None, prepend=False, read_only_cache=False, skip_no_alt=False, tx_mode='CANONICAL', verbose=5)
2014-07-01 17:14:15,385 INFO [oncotator.Oncotator:238] Log file: /media/adlab/Data/cervical_final/cervical_Reshma/SNP/T-N_VCF/corrected_SNP/coverage_3x_filter_VCF/oncotator_input_GATK/oncotator.log
2014-07-01 17:14:15,385 WARNING [oncotator.utils.ConfigUtils:197] Could not find config file (maflite_input.config). Trying configs/ prepend.
Traceback (most recent call last):
File "/usr/local/bin/oncotator", line 9, in
load_entry_point('Oncotator==v1.2.6.0', 'console_scripts', 'oncotator')()
File "/usr/local/lib/python2.7/dist-packages/Oncotator-v1.2.6.0-py2.7.egg/oncotator/Oncotator.py", line 293, in main
other_opts=determineOtherOptions(args, logger))
File "/usr/local/lib/python2.7/dist-packages/Oncotator-v1.2.6.0-py2.7.egg/oncotator/utils/OncotatorCLIUtils.py", line 342, in create_run_spec
inputCreator = OncotatorCLIUtils.create_input_creator(inputFilename, inputFormat, genomeBuild, other_opts)
File "/usr/local/lib/python2.7/dist-packages/Oncotator-v1.2.6.0-py2.7.egg/oncotator/utils/OncotatorCLIUtils.py", line 302, in create_input_creator
inputCreator = inputCreatorDict[inputFormat][0](inputFilename, inputConfig, genome_build, input_creator_options)
File "/usr/local/lib/python2.7/dist-packages/Oncotator-v1.2.6.0-py2.7.egg/oncotator/input/MafliteInputMutationCreator.py", line 104, in init
for alt in self._alternativeDict[col]:
KeyError: 'build'

Please suggest what is going wrong..!! Python packages were installed correctly using easy_install-2.7.
Thanks in advance.

Best Answer

Answers

Sign In or Register to comment.