Potentially something wrong with the current DB pack?

[JohnMCMa]

I just installed Oncotator v1.9.9.0 on Python 2.7.15, and using it with the current annotation DB (oncotator_v1_ds_April052016). I got an error associated with the COSMIC annotation; what could be happening here?

oncotator -v --no-multicore -i VCF --db-dir ~/oncotator_v1_ds_April052016 -o TCGAMAF "/rsrch3/scratch/lym_myl_rsch/mma/Green/WGS/Biovest/output/PM1008/FLC03/FLC03.SNV.final.vcf" "/rsrch3/scratch/lym_myl_rsch/mma/Green/WGS/Biovest/output/PM1008/FLC03/FLC03.SNV.final.maf" hg19
Verbose mode on
Path:
['/rsrch3/home/lym_myl_rsch/mma/.local/bin', '/risapps/rhel7/python/2.7.15/lib/python27.zip', '/risapps/rhel7/python/2.7.15/lib/python2.7', '/risapps/rhel7/python/2.7.15/lib/python2.7/plat-linux2', '/risapps/rhel7/python/2.7.15/lib/python2.7/lib-tk', '/risapps/rhel7/python/2.7.15/lib/python2.7/lib-old', '/risapps/rhel7/python/2.7.15/lib/python2.7/lib-dynload', '/rsrch3/home/lym_myl_rsch/mma/.local/lib/python2.7/site-packages', '/rsrch3/home/lym_myl_rsch/mma/.local/lib/python2.7/site-packages/misopy-0.5.4-py2.7-linux-x86_64.egg', '/risapps/rhel7/python/2.7.15/lib/python2.7/site-packages', '/risapps/rhel7/python/2.7.15/lib/python2.7/site-packages/colorbrewer-0.2.0-py2.7.egg', '/risapps/rhel7/python/2.7.15/lib/python2.7/site-packages/gdc_client-1.3.0-py2.7.egg', '/risapps/build7/CellProfiler-Analyst', '/risapps/rhel7/python/2.7.15/lib/python2.7/site-packages/sequenza_utils-3.0.0-py2.7-linux-x86_64.egg', '/risapps/rhel7/python/2.7.15/lib/python2.7/site-packages/trust-3.0.3-py2.7-linux-x86_64.egg', '/risapps/rhel7/python/2.7.15/lib/python2.7/site-packages/regex-2019.6.8-py2.7-linux-x86_64.egg', '/risapps/rhel7/python/2.7.15/lib/python2.7/site-packages/parasail-1.1.17-py2.7.egg', '/risapps/rhel7/python/2.7.15/lib/python2.7/site-packages/multiprocessing-2.6.2.1-py2.7-linux-x86_64.egg', '/risapps/rhel7/python/2.7.15/lib/python2.7/site-packages/genomedata-1.3.6-py2.7.egg', '/risapps/rhel7/python/2.7.15/lib/python2.7/site-packages/hgtools-8.1.1-py2.7.egg', '/risapps/rhel7/python/2.7.15/lib/python2.7/site-packages/optbuild-0.2.1-py2.7.egg', '/risapps/rhel7/python/2.7.15/lib/python2.7/site-packages/optplus-0.2-py2.7.egg', '/risapps/rhel7/python/2.7.15/lib/python2.7/site-packages', '/risapps/rhel7/python/2.7.15/lib/python2.7/site-packages/textinput-0.2.0-py2.7.egg']

2019-07-17 11:22:36,725 INFO [oncotator.Oncotator:241] Oncotator v1.9.9.0
2019-07-17 11:22:36,726 INFO [oncotator.Oncotator:242] Args: Namespace(allow_overwriting=False, cache_url=None, canonical_tx_file=None, collapse_filter_cols=False, collapse_number_annotations=False, dbDir='/rsrch3/home/lym_myl_rsch/mma/oncotator_v1_ds_April052016', default_cli=[], default_config=None, genome_build='hg19', infer_genotypes='false', infer_onps=False, input_file='/rsrch3/scratch/lym_myl_rsch/mma/Green/WGS/Biovest/output/PM1008/FLC03/FLC03.SNV.final.vcf', input_format='VCF', log_name='oncotator.log', longer_other_tx=False, noMulticore=True, output_file='/rsrch3/scratch/lym_myl_rsch/mma/Green/WGS/Biovest/output/PM1008/FLC03/FLC03.SNV.final.maf', output_format='TCGAMAF', override_cli=[], override_config=None, prepend=False, prune_filter_cols=False, read_only_cache=False, reannotate_tcga_maf_cols=False, skip_no_alt=False, tx_mode='CANONICAL', verbose=6)
2019-07-17 11:22:36,726 INFO [oncotator.Oncotator:243] Log file: /rsrch3/scratch/lym_myl_rsch/mma/Green/ATAC-seq/BCL7/fastq/QD-ATAC_PM1044/oncotator.log
2019-07-17 11:22:36,726 WARNING [oncotator.Oncotator:249] ngslib module not installed.  Will be unable to annotate with BigWig datasources.
2019-07-17 11:22:36,744 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /rsrch3/home/lym_myl_rsch/mma/oncotator_v1_ds_April052016/ccle_by_gp/hg19/ccle_by_gp.config
2019-07-17 11:22:36,745 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /rsrch3/home/lym_myl_rsch/mma/oncotator_v1_ds_April052016/uniprot_aa_xform/hg19/uniprot_aa_xform.config
2019-07-17 11:22:36,746 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /rsrch3/home/lym_myl_rsch/mma/oncotator_v1_ds_April052016/exac/hg19/exac.config
2019-07-17 11:22:36,746 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /rsrch3/home/lym_myl_rsch/mma/oncotator_v1_ds_April052016/gencode_xrefseq/hg19/gencode_xrefseq.config
2019-07-17 11:22:36,747 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /rsrch3/home/lym_myl_rsch/mma/oncotator_v1_ds_April052016/simple_uniprot/hg19/simple_uniprot.config
2019-07-17 11:22:36,748 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /rsrch3/home/lym_myl_rsch/mma/oncotator_v1_ds_April052016/ccle_by_gene/hg19/ccle_by_gene.config
2019-07-17 11:22:36,749 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /rsrch3/home/lym_myl_rsch/mma/oncotator_v1_ds_April052016/gencode_out2/hg19/gencode_out2.config
2019-07-17 11:22:36,749 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /rsrch3/home/lym_myl_rsch/mma/oncotator_v1_ds_April052016/cosmic/hg19/cosmic.config
2019-07-17 11:22:36,750 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /rsrch3/home/lym_myl_rsch/mma/oncotator_v1_ds_April052016/cosmic_fusion/hg19/cosmic_fusion.config
2019-07-17 11:22:36,750 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /rsrch3/home/lym_myl_rsch/mma/oncotator_v1_ds_April052016/clinvar/hg19/clinvar.config
2019-07-17 11:22:36,750 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /rsrch3/home/lym_myl_rsch/mma/oncotator_v1_ds_April052016/cancer_gene_census/hg19/cancer_gene_census.config
2019-07-17 11:22:36,752 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /rsrch3/home/lym_myl_rsch/mma/oncotator_v1_ds_April052016/ref_hg/hg19/ref_hg.config
2019-07-17 11:22:36,752 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /rsrch3/home/lym_myl_rsch/mma/oncotator_v1_ds_April052016/familial/hg19/familial.config
2019-07-17 11:22:36,753 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /rsrch3/home/lym_myl_rsch/mma/oncotator_v1_ds_April052016/cosmic_tissue/hg19/cosmic_tissue.config
2019-07-17 11:22:36,754 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /rsrch3/home/lym_myl_rsch/mma/oncotator_v1_ds_April052016/oreganno/hg19/oreganno.config
2019-07-17 11:22:36,755 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /rsrch3/home/lym_myl_rsch/mma/oncotator_v1_ds_April052016/tumorscape/hg19/tumorscape.config
2019-07-17 11:22:36,755 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /rsrch3/home/lym_myl_rsch/mma/oncotator_v1_ds_April052016/dbNSFP_ds/hg19/dbNSFP_ds.config
2019-07-17 11:22:36,756 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /rsrch3/home/lym_myl_rsch/mma/oncotator_v1_ds_April052016/achilles/hg19/achilles.config
2019-07-17 11:22:36,757 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /rsrch3/home/lym_myl_rsch/mma/oncotator_v1_ds_April052016/hgnc/hg19/hgnc.config
2019-07-17 11:22:36,757 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /rsrch3/home/lym_myl_rsch/mma/oncotator_v1_ds_April052016/dna_repair_genes/hg19/dna_repair_genes.config
2019-07-17 11:22:36,758 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /rsrch3/home/lym_myl_rsch/mma/oncotator_v1_ds_April052016/uniprot_aa_annotation/hg19/uniprot_aa_annotation.config
2019-07-17 11:22:36,758 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /rsrch3/home/lym_myl_rsch/mma/oncotator_v1_ds_April052016/tcgascape/hg19/tcgascape.config
2019-07-17 11:22:36,759 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /rsrch3/home/lym_myl_rsch/mma/oncotator_v1_ds_April052016/mutsig/hg19/mutsig.config
2019-07-17 11:22:36,760 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /rsrch3/home/lym_myl_rsch/mma/oncotator_v1_ds_April052016/1000genome_db/hg19/1000genome_db.config
2019-07-17 11:22:36,761 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /rsrch3/home/lym_myl_rsch/mma/oncotator_v1_ds_April052016/dbsnp/hg19/dbsnp.config
2019-07-17 11:22:36,762 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /rsrch3/home/lym_myl_rsch/mma/oncotator_v1_ds_April052016/so_terms/hg19/so_terms.config
2019-07-17 11:22:36,768 INFO [root:73] Loading /rsrch3/home/lym_myl_rsch/mma/oncotator_v1_ds_April052016/ccle_by_gp/hg19//ccle_results_by_pos.hg19.import.bin...
2019-07-17 11:22:37,014 INFO [root:73] Loading /rsrch3/home/lym_myl_rsch/mma/oncotator_v1_ds_April052016/gencode_xrefseq/hg19//gencode_xrefseq_v19.bin...
2019-07-17 11:22:37,264 INFO [root:73] Loading /rsrch3/home/lym_myl_rsch/mma/oncotator_v1_ds_April052016/simple_uniprot/hg19//simple_uniprot_Dec012014.bin...
2019-07-17 11:22:37,800 INFO [root:73] Loading /rsrch3/home/lym_myl_rsch/mma/oncotator_v1_ds_April052016/ccle_by_gene/hg19//ccle_results_by_gene.import.bin...
2019-07-17 11:22:37,806 INFO [oncotator.datasources.EnsemblTranscriptDatasource:97] GENCODE v19 is being set up in faster, NOT thread-safe mode (for annotation).
2019-07-17 11:22:37,855 INFO [oncotator.datasources.EnsemblTranscriptDatasource:108] GENCODE v19 is being set up with default tx-mode: CANONICAL.
2019-07-17 11:22:37,855 WARNING [oncotator.datasources.EnsemblTranscriptDatasource:127] Attempting to set transcript mode of CANONICAL for ensembl.  This operation is only supported for GENCODE.  Otherwise, will be the same as EFFECT.
2019-07-17 11:22:37,855 INFO [oncotator.datasources.EnsemblTranscriptDatasource:111] GENCODE v19 is being set up with basic filtering.
Traceback (most recent call last):
  File "/rsrch3/home/lym_myl_rsch/mma/.local/bin/oncotator", line 10, in <module>
    sys.exit(main())
  File "/rsrch3/home/lym_myl_rsch/mma/.local/lib/python2.7/site-packages/oncotator/Oncotator.py", line 307, in main
    other_opts=other_opts, annotating_type=annotating_type)
  File "/rsrch3/home/lym_myl_rsch/mma/.local/lib/python2.7/site-packages/oncotator/utils/RunSpecificationFactory.py", line 113, in create_run_spec
    datasource_list = DatasourceFactory.createDatasources(datasource_dir, genomeBuild, isMulticore=is_multicore, numCores=num_cores, tx_mode=tx_mode)
  File "/rsrch3/home/lym_myl_rsch/mma/.local/lib/python2.7/site-packages/oncotator/DatasourceFactory.py", line 292, in createDatasources
    result.append(DatasourceFactory.createDatasourceGivenTuple(dsTuple))
  File "/rsrch3/home/lym_myl_rsch/mma/.local/lib/python2.7/site-packages/oncotator/DatasourceFactory.py", line 106, in createDatasourceGivenTuple
    return DatasourceFactory.createDatasource(configTuple[0], configTuple[1])
  File "/rsrch3/home/lym_myl_rsch/mma/.local/lib/python2.7/site-packages/oncotator/DatasourceFactory.py", line 100, in createDatasource
    return DatasourceFactory.createDatasourceFromConfigParser(configParser, leafDir)
  File "/rsrch3/home/lym_myl_rsch/mma/.local/lib/python2.7/site-packages/oncotator/DatasourceFactory.py", line 152, in createDatasourceFromConfigParser
    result = Cosmic(src_file=filePrefix + configParser.get('general', 'src_file'), version=configParser.get('general', 'version'), gpp_tabix_file=filePrefix + configParser.get('general', 'gpp_src_file'))
  File "/rsrch3/home/lym_myl_rsch/mma/.local/lib/python2.7/site-packages/oncotator/datasources/Cosmic.py", line 96, in __init__
    header = self.db_genomePos.header.next()
AttributeError: 'list' object has no attribute 'next'

[chunmei1991]

I have the same problem.Do you have fixed?

[DaringSky]

Have anyone fixed it? I also have the same error. I installed oncotator v1.9.9.0 on python2.7.11 by anaconda2 and use oncotator_v1_ds_April052016.

[DaringSky]

I have fixed the 【Cosmic.py】 and now it can run!

[JohnMCMa]

Hi @DaringSky , Can you provide the fix as a pull request?

[bdanubius]

Hi all, has anyone figured this out? Getting the same issues with this python and oncotator version! I didn't see the solution posted as a pull request.

[lbergelson]

Oncotator is essentially no longer maintained, development has moved to Funcotator, a GATK tool which provides the same style of annotation but has many bug fixes and improvements. See this tutorial for information on how to run funcotator.

It does the same thing, but it's less of pain to install, it's faster, and it has 3 years of bugfixes.

[bdanubius]

Unfortunately oncotator seems to be the one used in the broad internal pipelines (RNA Mutect), which require MAF input/output. So a fix for this Oncotator bug is needed...

[lbergelson]

@bdanubius. That pipeline is using the original Mutect which has been superseded by the much more powerful Mutect 2. Is there a more recent pipeline using Mutect2 which produces vcf?

[DaringSky]

@JohnMCMa Sorry, I forgot to set a reminder.

I fixed Cosmic.py, I can provide it for you.

Cosmic.py.txt

You can compare the raw file, and know where I fixed.