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[GATK 4.0.1.2] Oncotator fails in CNVSomaticPairWorkflow

Hello,

I would like to report an Oncotator failure. Oncotator was run as a part of CNVSomaticPairWorkflow on Google Cloud and oncotator_docker is configured as

"CNVSomaticPairWorkflow.oncotator_docker": "broadinstitute/oncotator:1.9.8.0"

Thanks!

2018-03-13 21:07:15,896 INFO [oncotator.Oncotator:241] Oncotator v1.9.8.0
2018-03-13 21:07:15,897 INFO [oncotator.Oncotator:242] Args: Namespace(allow_overwriting=False, cache_url='file:///root/onco_cache/', canonical_tx_file='/root/tx_exact_uniprot_matches.AKT1_CRLF2_FGFR1.txt', collapse_filter_cols=False, collapse_number_annotations=False, dbDir='/root/onco_dbdir/', default_cli=[], default_config=None, genome_build='hg19', infer_genotypes='false', infer_onps=False, input_file='AGRLBM.called.seg.seq_dict_removed.seg', input_format='SEG_FILE', log_name='oncotator.log', longer_other_tx=False, noMulticore=False, output_file='AGRLBM.called.seg.per_segment.oncotated.txt', output_format='SIMPLE_TSV', override_cli=[], override_config=None, prepend=False, prune_filter_cols=False, read_only_cache=True, reannotate_tcga_maf_cols=False, skip_no_alt=False, tx_mode='CANONICAL', verbose=6)
2018-03-13 21:07:15,898 INFO [oncotator.Oncotator:243] Log file: /cromwell_root/oncotator.log
2018-03-13 21:07:15,898 WARNING [oncotator.DatasourceFactory:260] %s does not exist, so there will be no datasources.
2018-03-13 21:07:15,898 INFO [oncotator.DatasourceFactory:325] No datasources to initialize
2018-03-13 21:07:15,899 INFO [oncotator.utils.RunSpecificationFactory:171] no prepend specified when output is not TCGAMAF.  Ignoring and proceeding.
2018-03-13 21:07:15,899 INFO [oncotator.utils.ConfigUtils:197] Could not find config file (seg_file_input.config).  Trying configs/ prepend.
2018-03-13 21:07:15,902 INFO [oncotator.input.MafliteInputMutationCreator:103] Initializing a maflite file with the following header: ['CONTIG', 'START', 'END', 'NUM_POINTS_COPY_RATIO', 'MEAN_LOG2_COPY_RATIO', 'CALL']
2018-03-13 21:07:15,902 INFO [oncotator.cache.DummyCache:57] No cache specified.  All cache attempts will be listed as cache misses.
2018-03-13 21:07:15,902 INFO [oncotator.Annotator:186] Generating db-dir key from datasources...
2018-03-13 21:07:15,903 INFO [oncotator.Annotator:192] Final db-dir md5: 74be16979710d4c4e7c6647856088456
2018-03-13 21:07:15,903 INFO [oncotator.cache.CacheFactory:73] Creating file-based cache: file:///root/onco_cache/
2018-03-13 21:07:15,903 INFO [oncotator.cache.CacheFactory:78] File cache being set up as faster, but NOT thread safe.
2018-03-13 21:07:15,903 INFO [oncotator.cache.CacheFactory:85] Creating shove cache: file:///root/onco_cache/, simple://
2018-03-13 21:07:15,912 INFO [oncotator.Annotator:426] Annotating with 0 datasources: Oncotator v1.9.8.0 |
2018-03-13 21:07:15,912 INFO [oncotator.output.SimpleOutputRenderer:110] Simple rendering output file: AGRLBM.called.seg.per_segment.oncotated.txt
2018-03-13 21:07:15,912 INFO [oncotator.output.SimpleOutputRenderer:111] Render starting...
2018-03-13 21:07:15,912 WARNING [oncotator.Annotator:500] THERE ARE NO DATASOURCES REGISTERED
2018-03-13 21:07:15,915 INFO [oncotator.output.SimpleOutputRenderer:144] Rendered 37 mutations into AGRLBM.called.seg.per_segment.oncotated.txt.
2018-03-13 21:07:15,916 INFO [oncotator.Annotator:440] Closing cache: (misses: 37  hits: 0)
2018-03-13 21:07:16,241 INFO [oncotator.Oncotator:241] Oncotator v1.9.8.0
2018-03-13 21:07:16,241 INFO [oncotator.Oncotator:242] Args: Namespace(allow_overwriting=False, cache_url='file:///root/onco_cache/', canonical_tx_file='/root/tx_exact_uniprot_matches.AKT1_CRLF2_FGFR1.txt', collapse_filter_cols=False, collapse_number_annotations=False, dbDir='/root/onco_dbdir/', default_cli=[], default_config=None, genome_build='hg19', infer_genotypes='false', infer_onps=False, input_file='AGRLBM.called.seg.seq_dict_removed.seg', input_format='SEG_FILE', log_name='oncotator.log', longer_other_tx=False, noMulticore=False, output_file='AGRLBM.called.seg.gene_list.txt', output_format='GENE_LIST', override_cli=[], override_config=None, prepend=False, prune_filter_cols=False, read_only_cache=True, reannotate_tcga_maf_cols=False, skip_no_alt=False, tx_mode='CANONICAL', verbose=6)
2018-03-13 21:07:16,241 INFO [oncotator.Oncotator:243] Log file: /cromwell_root/oncotator.log
2018-03-13 21:07:16,242 WARNING [oncotator.DatasourceFactory:260] %s does not exist, so there will be no datasources.
2018-03-13 21:07:16,242 INFO [oncotator.DatasourceFactory:325] No datasources to initialize
2018-03-13 21:07:16,242 INFO [oncotator.utils.RunSpecificationFactory:171] no prepend specified when output is not TCGAMAF.  Ignoring and proceeding.
2018-03-13 21:07:16,242 INFO [oncotator.utils.ConfigUtils:197] Could not find config file (seg_file_input.config).  Trying configs/ prepend.
2018-03-13 21:07:16,244 INFO [oncotator.input.MafliteInputMutationCreator:103] Initializing a maflite file with the following header: ['CONTIG', 'START', 'END', 'NUM_POINTS_COPY_RATIO', 'MEAN_LOG2_COPY_RATIO', 'CALL']
2018-03-13 21:07:16,244 INFO [oncotator.cache.DummyCache:57] No cache specified.  All cache attempts will be listed as cache misses.
2018-03-13 21:07:16,244 INFO [oncotator.Annotator:186] Generating db-dir key from datasources...
2018-03-13 21:07:16,245 INFO [oncotator.Annotator:192] Final db-dir md5: 74be16979710d4c4e7c6647856088456
2018-03-13 21:07:16,245 INFO [oncotator.cache.CacheFactory:73] Creating file-based cache: file:///root/onco_cache/
2018-03-13 21:07:16,245 INFO [oncotator.cache.CacheFactory:78] File cache being set up as faster, but NOT thread safe.
2018-03-13 21:07:16,245 INFO [oncotator.cache.CacheFactory:85] Creating shove cache: file:///root/onco_cache/, simple://
2018-03-13 21:07:16,249 INFO [oncotator.Annotator:426] Annotating with 0 datasources: Oncotator v1.9.8.0 |
2018-03-13 21:07:16,249 INFO [oncotator.utils.ConfigUtils:197] Could not find config file (gene_list_output.config).  Trying configs/ prepend.
2018-03-13 21:07:16,251 INFO [oncotator.output.GeneListOutputRenderer:54] Building alternative keys dictionary...
2018-03-13 21:07:16,252 WARNING [oncotator.Annotator:500] THERE ARE NO DATASOURCES REGISTERED
Traceback (most recent call last):
  File "/root/oncotator_venv/bin/oncotator", line 11, in <module>
    load_entry_point('Oncotator==1.9.8.0', 'console_scripts', 'oncotator')()
  File "build/bdist.linux-x86_64/egg/oncotator/Oncotator.py", line 311, in main
  File "build/bdist.linux-x86_64/egg/oncotator/Annotator.py", line 437, in annotate
  File "build/bdist.linux-x86_64/egg/oncotator/output/GeneListOutputRenderer.py", line 77, in renderMutations
  File "build/bdist.linux-x86_64/egg/oncotator/MutationData.py", line 219, in __getitem__
KeyError: 'genes'

Answers

  • dayzcooldayzcool Member

    I realized that some docker images are considerably larger in size (e.g. 1.9.5.0-eval-gatk-protected). I guess those are the ones which include datasources necessary for running Oncotator in CNVSomaticPairWorkflow?

  • shleeshlee CambridgeMember, Broadie ✭✭✭✭✭

    Hi @dayzcool,

    I think perhaps as you suggest the v4.0.1.2 script is meant to use the broadinstitute/oncotator:1.9.5.0-eval-gatk-protected image. Switching this to broadinstitute/oncotator:1.9.8.0 is likely the cause of your error. What happens when you specify the matched image version? Do you still get the error?

  • dayzcooldayzcool Member

    @shlee, unfortunately, it was run for a pilot project that I cannot easily experiment any longer. I'll test next time I have a chance.
    On a side note, I did get interesting somatic CNV calls, thanks to your help on running CNV workflow. Thanks again!

  • shleeshlee CambridgeMember, Broadie ✭✭✭✭✭

    Great to hear you are getting interesting results with somatic CNV. My pleasure to help you @dayzcool!

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