Question about unknown in oncotator results

suimyesuimye TokyoMember

Dear Oncotator developers,
I am trying to use Oncotator to annotate MAF or VCF files. According to instruction in this forum, I tried to run with test data "Patient0.snp.maf.txt", then Oncotator provides only "UNKNOWN" information from Oncotator results.
Here is my command line,

oncotator -v --db-dir /path/to/oncotator_v1_ds_Jan262015 /home/suimye/tool/oncotator-1.8.0.0/test/testdata/maflite/Patient0.snp.maf.txt exampleOutput.tsv hg19

In this result, all variants were not annotated. To evaluate this result, I put this data on Oncotator web. Then, the variants are annotated successfully.
From searching by google, I found out similar oncotator results as

.

Is this correct output? I suspect several warning messages observed in above logs may influence this problem such as " THERE ARE NO DATASOURCES REGISTERED" and "%s does not exist, so there will be no datasources".
If you have any suggestion, please reply me.

Thanks for development of great tools!!
Masaki

Best Answer

  • LeeTL1220LeeTL1220 Arlington, MA ✭✭✭
    Accepted Answer

    @suimye A couple of things...

    First: Please upgrade to Oncotator 1.9.0.0 and the new datasources. I doubt this will be an issue.

    Second: Did you create a virtualenv and run oncotator from there? It looks like your version of pysam is not compatible with Oncotator 1.8.0.0 (what you are running in your example).

Answers

  • suimyesuimye TokyoMember
    edited July 2016

    Dear everyone,

    I have never successfully annotated to the test file.

    I got following messages at the running.

    -bash-4.1$ Oncotator -v --db-dir /home/suimye/tool/oncotator_v1_ds_Jan262014/ /home/suimye/tool/oncotator-1.8.0.0/testdata/maflite/Patient0.snp.maf.txt exampleOutput.tsv hg19
    Verbose mode on
    Path:
    ['/home/suimye/bin/bin', '/home/suimye/bin/lib/python2.7/site-packages/setuptools-3.4.1-py2.7.egg', '/home/suimye/bin/lib/python2.7/site-packages/Oncotator-v1.8.0.0-py2.7.egg', '/home/suimye/bin/lib/python2.7/site-packages/enum34-1.1.6-py2.7.egg', '/home/suimye/bin/lib/python2.7/site-packages/more_itertools-2.2-py2.7.egg', '/home/suimye/bin/lib/python2.7/site-packages/natsort-5.0.1-py2.7.egg', '/home/suimye/bin/lib/python2.7/site-packages/python_memcached-1.58-py2.7.egg', '/home/suimye/bin/lib/python2.7/site-packages/nose-1.3.7-py2.7.egg', '/home/suimye/bin/lib/python2.7/site-packages/SQLAlchemy-1.1.0b2-py2.7-linux-x86_64.egg', '/home/suimye/bin/lib/python2.7/site-packages/shove-0.6.6-py2.7.egg', '/home/suimye/bin/lib/python2.7/site-packages/Cython-0.24-py2.7-linux-x86_64.egg', '/home/suimye/bin/lib/python2.7/site-packages/pandas-0.18.1-py2.7-linux-x86_64.egg', '/home/suimye/bin/lib/python2.7/site-packages/bcbio_gff-0.6.2-py2.7.egg', '/home/suimye/bin/lib/python2.7/site-packages/six-1.10.0-py2.7.egg', '/home/suimye/bin/lib/python2.7/site-packages/stuf-0.9.16-py2.7.egg', '/home/suimye/bin/lib/python2.7/site-packages/futures-3.0.5-py2.7.egg', '/home/suimye/bin/lib/python2.7/site-packages/pytz-2016.4-py2.7.egg', '/home/suimye/bin/lib/python2.7/site-packages/python_dateutil-2.5.3-py2.7.egg', '/home/suimye/bin/lib/python2.7/site-packages/parse-1.6.6-py2.7.egg', '/home/suimye/bin/lib/python2.7/site-packages/pysam-0.7.5-py2.7-linux-x86_64.egg', '/home/suimye/bin/lib/python2.7/site-packages/distribute-0.6.15-py2.7.egg', '/home/suimye/bin/lib/python27.zip', '/home/suimye/bin/lib/python2.7', '/home/suimye/bin/lib/python2.7/plat-linux2', '/home/suimye/bin/lib/python2.7/lib-tk', '/home/suimye/bin/lib/python2.7/lib-old', '/home/suimye/bin/lib/python2.7/lib-dynload', '/home/suimye/bin/lib/python2.7/site-packages']
    
    2016-07-25 16:35:22,182 INFO [oncotator.Oncotator:239] Oncotator v1.8.0.0
    2016-07-25 16:35:22,182 INFO [oncotator.Oncotator:240] Args: Namespace(allow_overwriting=False, cache_url=None, canonical_tx_file=None, collapse_filter_cols=False, collapse_number_annotations=False, dbDir='/home/suimye/tool/oncotator_v1_ds_Jan262014/', default_cli=[], default_config=None, genome_build='hg19', infer_genotypes='false', infer_onps=False, input_file='/home/suimye/tool/oncotator-1.8.0.0/testdata/maflite/Patient0.snp.maf.txt', input_format='MAFLITE', log_name='oncotator.log', noMulticore=False, output_file='exampleOutput.tsv', output_format='TCGAMAF', override_cli=[], override_config=None, prepend=False, read_only_cache=False, reannotate_tcga_maf_cols=False, skip_no_alt=False, tx_mode='CANONICAL', verbose=6)
    2016-07-25 16:35:22,182 INFO [oncotator.Oncotator:241] Log file: /home/suimye/onco_test/oncotator.log
    2016-07-25 16:35:22,183 WARNING [oncotator.DatasourceFactory:266] Potential datasource directory is missing a genome build subdirectory and will be ignored: /home/suimye/tool/oncotator_v1_ds_Jan262014/oncotator.log
    2016-07-25 16:35:22,183 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /home/suimye/tool/oncotator_v1_ds_Jan262014/cosmic_fusion/hg19/cosmic_fusion.config
    2016-07-25 16:35:22,183 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /home/suimye/tool/oncotator_v1_ds_Jan262014/gencode_xrefseq/hg19/gencode_xrefseq.config
    2016-07-25 16:35:22,183 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /home/suimye/tool/oncotator_v1_ds_Jan262014/clinvar/hg19/clinvar.config
    2016-07-25 16:35:22,183 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /home/suimye/tool/oncotator_v1_ds_Jan262014/esp6500SI_v2/hg19/esp6500SI_v2.config
    2016-07-25 16:35:22,184 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /home/suimye/tool/oncotator_v1_ds_Jan262014/ccle_by_gene/hg19/ccle_by_gene.config
    2016-07-25 16:35:22,184 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /home/suimye/tool/oncotator_v1_ds_Jan262014/oreganno/hg19/oreganno.config
    2016-07-25 16:35:22,184 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /home/suimye/tool/oncotator_v1_ds_Jan262014/achilles/hg19/achilles.config
    2016-07-25 16:35:22,184 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /home/suimye/tool/oncotator_v1_ds_Jan262014/cancer_gene_census/hg19/cancer_gene_census.config
    2016-07-25 16:35:22,184 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /home/suimye/tool/oncotator_v1_ds_Jan262014/simple_uniprot/hg19/simple_uniprot.config
    2016-07-25 16:35:22,184 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /home/suimye/tool/oncotator_v1_ds_Jan262014/dna_repair_genes/hg19/dna_repair_genes.config
    2016-07-25 16:35:22,184 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /home/suimye/tool/oncotator_v1_ds_Jan262014/dbsnp/hg19/dbsnp.config
    2016-07-25 16:35:22,184 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /home/suimye/tool/oncotator_v1_ds_Jan262014/ref_hg/hg19/ref_hg.config
    2016-07-25 16:35:22,184 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /home/suimye/tool/oncotator_v1_ds_Jan262014/uniprot_aa_xform/hg19/uniprot_aa_xform.config
    2016-07-25 16:35:22,184 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /home/suimye/tool/oncotator_v1_ds_Jan262014/gencode_out2/hg19/gencode_out2.config
    2016-07-25 16:35:22,185 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /home/suimye/tool/oncotator_v1_ds_Jan262014/hgnc/hg19/hgnc.config
    2016-07-25 16:35:22,185 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /home/suimye/tool/oncotator_v1_ds_Jan262014/ccle_by_gp/hg19/ccle_by_gp.config
    2016-07-25 16:35:22,185 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /home/suimye/tool/oncotator_v1_ds_Jan262014/cosmic_tissue/hg19/cosmic_tissue.config
    2016-07-25 16:35:22,185 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /home/suimye/tool/oncotator_v1_ds_Jan262014/familial/hg19/familial.config
    2016-07-25 16:35:22,185 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /home/suimye/tool/oncotator_v1_ds_Jan262014/tumorscape/hg19/tumorscape.config
    2016-07-25 16:35:22,185 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /home/suimye/tool/oncotator_v1_ds_Jan262014/cosmic/hg19/cosmic.config
    2016-07-25 16:35:22,185 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /home/suimye/tool/oncotator_v1_ds_Jan262014/1000genome_db/hg19/1000genome_db.config
    2016-07-25 16:35:22,185 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /home/suimye/tool/oncotator_v1_ds_Jan262014/uniprot_aa_annotation/hg19/uniprot_aa_annotation.config
    2016-07-25 16:35:22,185 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /home/suimye/tool/oncotator_v1_ds_Jan262014/dbNSFP_ds/hg19/dbNSFP_ds.config
    2016-07-25 16:35:22,186 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /home/suimye/tool/oncotator_v1_ds_Jan262014/esp6500SI_v2_coverage/hg19/esp6500SI_v2_coverage.config
    2016-07-25 16:35:22,186 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /home/suimye/tool/oncotator_v1_ds_Jan262014/so_terms/hg19/so_terms.config
    2016-07-25 16:35:22,186 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /home/suimye/tool/oncotator_v1_ds_Jan262014/tcgascape/hg19/tcgascape.config
    2016-07-25 16:35:22,186 INFO [oncotator.DatasourceFactory:286] Queuing datasource creation for /home/suimye/tool/oncotator_v1_ds_Jan262014/mutsig/hg19/mutsig.config
    2016-07-25 16:35:22,186 INFO [oncotator.DatasourceFactory:304] Creating pool
    2016-07-25 16:35:22,192 INFO [oncotator.DatasourceFactory:307] Pool created
    2016-07-25 16:35:22,214 INFO [oncotator.datasources.EnsemblTranscriptDatasource:95] GENCODE v19 is being set up in faster, NOT thread-safe mode (for annotation).  
    2016-07-25 16:35:22,254 INFO [oncotator.datasources.EnsemblTranscriptDatasource:106] GENCODE v19 is being set up with default tx-mode: CANONICAL.  
    2016-07-25 16:35:22,255 WARNING [oncotator.datasources.EnsemblTranscriptDatasource:123] Attempting to set transcript mode of CANONICAL for ensembl.  This operation is only supported for GENCODE.  Otherwise, will be the same as EFFECT.
    2016-07-25 16:35:22,255 INFO [oncotator.datasources.EnsemblTranscriptDatasource:109] GENCODE v19 is being set up with basic filtering.  
    2016-07-25 16:35:22,265 INFO [root:73] Loading /home/suimye/tool/oncotator_v1_ds_Jan262014/so_terms/hg19//SO_Ensembl_consequence_terms.bin...
    2016-07-25 16:35:22,268 INFO [root:73] Loading /home/suimye/tool/oncotator_v1_ds_Jan262014/cosmic_fusion/hg19//CosmicMutantExportIncFus_v62_291112_fusion.bin...
    2016-07-25 16:35:22,268 INFO [root:73] Loading /home/suimye/tool/oncotator_v1_ds_Jan262014/clinvar/hg19//clinvar_hgmd.12-03-20.bin...
    2016-07-25 16:35:22,268 INFO [root:73] Loading /home/suimye/tool/oncotator_v1_ds_Jan262014/cancer_gene_census/hg19//CancerGeneCensus_Table_1_full_2012-03-15.bin...
    2016-07-25 16:35:22,268 INFO [root:73] Loading /home/suimye/tool/oncotator_v1_ds_Jan262014/oreganno/hg19//oreganno_results_by_pos.hg19.import.bin...
    2016-07-25 16:35:22,270 INFO [root:73] Loading /home/suimye/tool/oncotator_v1_ds_Jan262014/gencode_xrefseq/hg19//gencode_xrefseq_v19.bin...
    2016-07-25 16:35:22,278 INFO [root:73] Loading /home/suimye/tool/oncotator_v1_ds_Jan262014/simple_uniprot/hg19//simple_uniprot_Dec012014.bin...
    2016-07-25 16:35:22,601 INFO [root:73] Loading /home/suimye/tool/oncotator_v1_ds_Jan262014/dna_repair_genes/hg19//Wood_DNARepairGenes.no_dupes.bin...
    2016-07-25 16:35:22,603 INFO [root:73] Loading /home/suimye/tool/oncotator_v1_ds_Jan262014/hgnc/hg19//hgnc_download_Sept172014.bin...
    2016-07-25 16:35:22,819 INFO [root:73] Loading /home/suimye/tool/oncotator_v1_ds_Jan262014/achilles/hg19//achilles_lineage_results.import.bin...
    2016-07-25 16:35:22,907 INFO [root:73] Loading /home/suimye/tool/oncotator_v1_ds_Jan262014/ccle_by_gp/hg19//ccle_results_by_pos.hg19.import.bin...
    2016-07-25 16:35:22,915 INFO [root:73] Loading /home/suimye/tool/oncotator_v1_ds_Jan262014/cosmic_tissue/hg19//CosmicMutantExportIncFus_v62_291112.geneHistology.bin...
    2016-07-25 16:35:22,984 INFO [root:73] Loading /home/suimye/tool/oncotator_v1_ds_Jan262014/familial/hg19//Familial Cancer Genes.no_dupes.bin...
    2016-07-25 16:35:22,988 INFO [root:73] Loading /home/suimye/tool/oncotator_v1_ds_Jan262014/tumorscape/hg19//tumorscape_20100104_generated.bin...
    2016-07-25 16:35:23,118 INFO [root:73] Loading /home/suimye/tool/oncotator_v1_ds_Jan262014/uniprot_aa_annotation/hg19//uniprot_aa_annotations.bin...
    2016-07-25 16:35:23,151 INFO [root:73] Loading /home/suimye/tool/oncotator_v1_ds_Jan262014/mutsig/hg19//mutsig_results.import.20110905.bin...
    2016-07-25 16:35:23,787 INFO [root:73] Loading /home/suimye/tool/oncotator_v1_ds_Jan262014/ccle_by_gene/hg19//ccle_results_by_gene.import.bin...
    2016-07-25 16:35:26,054 INFO [root:73] Loading /home/suimye/tool/oncotator_v1_ds_Jan262014/tcgascape/hg19//tcgascape_110405_generated.bin...
    2016-07-25 16:35:27,820 INFO [oncotator.DatasourceFactory:321] Mapping complete: 17 datasources created in multiprocess
    2016-07-25 16:35:28,037 INFO [oncotator.utils.RunSpecificationFactory:124] Setting GENCODE v19 to tx-mode of CANONICAL...
    2016-07-25 16:35:28,037 WARNING [oncotator.datasources.EnsemblTranscriptDatasource:123] Attempting to set transcript mode of CANONICAL for ensembl.  This operation is only supported for GENCODE.  Otherwise, will be the same as EFFECT.
    2016-07-25 16:35:28,037 INFO [oncotator.utils.RunSpecificationFactory:135] No custom canonical transcripts specified.
    2016-07-25 16:35:28,038 INFO [oncotator.input.MafliteInputMutationCreator:103] Initializing a maflite file with the following header: ['build', 'chr', 'start', 'end', 'ref_allele', 'tum_allele1', 'tum_allele2', 'tumor_barcode', 'normal_barcode', 'tumor_f', 'init_t_lod', 't_lod_fstar', 't_alt_count', 't_ref_count', 'judgement']
    2016-07-25 16:35:28,039 INFO [oncotator.output.TcgaMafOutputRenderer:93] Building alternative keys dictionary...
    2016-07-25 16:35:28,040 INFO [oncotator.cache.DummyCache:57] No cache specified.  All cache attempts will be listed as cache misses.
    2016-07-25 16:35:28,040 INFO [oncotator.Annotator:426] Annotating with 27 datasources: Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 CANONICAL | UniProt_AAxform 2014_12 | ESP 6500SI-V2 | dbSNP build 142 | COSMIC v62_291112 | 1000gp3 20130502 | dbNSFP v2.4 | ESP 6500SI-V2 | ClinVar 12.03.20 | ORegAnno UCSC Track | CCLE_By_GP 09292010 | UniProt_AA 2014_12 | Ensembl ICGC MUCOPA | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | TCGAScape 110405 | MutSig Published Results 20110905 
    2016-07-25 16:35:28,040 INFO [oncotator.output.TcgaMafOutputRenderer:256] TCGA MAF output file: exampleOutput.tsv
    2016-07-25 16:35:28,041 INFO [oncotator.output.TcgaMafOutputRenderer:257] Render starting...
    Traceback (most recent call last):
      File "/home/suimye/bin/bin/Oncotator", line 9, in <module>
        load_entry_point('Oncotator==v1.8.0.0', 'console_scripts', 'Oncotator')()
      File "/home/suimye/bin/lib/python2.7/site-packages/Oncotator-v1.8.0.0-py2.7.egg/oncotator/Oncotator.py", line 309, in main
        annotator.annotate()
      File "/home/suimye/bin/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/suimye/bin/lib/python2.7/site-packages/Oncotator-v1.8.0.0-py2.7.egg/oncotator/output/TcgaMafOutputRenderer.py", line 268, in renderMutations
        m = mutations.next()
      File "/home/suimye/bin/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/suimye/bin/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/suimye/bin/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/suimye/bin/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/suimye/bin/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/suimye/bin/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'
    
    

    Here, this is output file

    -bash-4.1$ head exampleOutput.maf.tsv 
    #version 2.4
    ## 
    ## Oncotator v1.8.0.0 |
    Hugo_Symbol Entrez_Gene_Id  Center  NCBI_Build  Chromosome  Start_position  End_position    Strand  Variant_Classification  Variant_Type    Reference_Allele    Tumor_Seq_Allele1   Tumor_Seq_Allele2   dbSNP_RS    dbSNP_Val_Status    Tumor_Sample_Barcode    Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1  Match_Norm_Seq_Allele2  Tumor_Validation_Allele1    Tumor_Validation_Allele2    Match_Norm_Validation_Allele1   Match_Norm_Validation_Allele2   Verification_Status Validation_Status   Mutation_Status Sequencing_Phase    Sequence_Source Validation_Method   Score   BAM_file    Sequencer   Tumor_Sample_UUID   Matched_Norm_Sample_UUID    Genome_Change   Annotation_Transcript   Transcript_Strand   Transcript_Exon Transcript_Position cDNA_Change Codon_Change    Protein_Change  Other_Transcripts   Refseq_mRNA_Id  Refseq_prot_Id  SwissProt_acc_Id    SwissProt_entry_Id  Description UniProt_AApos   UniProt_Region  UniProt_Site    UniProt_Natural_Variations  UniProt_Experimental_Info   GO_Biological_Process   GO_Cellular_Component   GO_Molecular_Function   COSMIC_overlapping_mutations    COSMIC_fusion_geneCOSMIC_tissue_types_affected  COSMIC_total_alterations_in_gene    Tumorscape_Amplification_Peaks  Tumorscape_Deletion_Peaks   TCGAscape_Amplification_Peaks   TCGAscape_Deletion_Peaks    DrugBank    ref_context gc_content  CCLE_ONCOMAP_overlapping_mutations  CCLE_ONCOMAP_total_mutations_in_gene    CGC_Mutation_Type   CGC_Translocation_Partner   CGC_Tumor_Types_Somatic CGC_Tumor_Types_Germline    CGC_Other_Diseases  DNARepairGenes_Role FamilialCancerDatabase_Syndromes    MUTSIG_Published_Results    OREGANNO_ID OREGANNO_Values build
    __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ 20  14370   14370   __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ G   G   G   __UNKNOWN__ __UNKNOWN__ __UNKNOWN___UNKNOWN__   __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN___UNKNOWN__   __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN___UNKNOWN__   __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN___UNKNOWN__   __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN___UNKNOWN__   __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ hg19
    __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ 20  14370   14370   __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ G   G   G   __UNKNOWN__ __UNKNOWN__ __UNKNOWN___UNKNOWN__   __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN___UNKNOWN__   __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN___UNKNOWN__   __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN___UNKNOWN__   __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN___UNKNOWN__   __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ hg19
    __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ 21  123090  123090  __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ T   T   T   __UNKNOWN__ __UNKNOWN__ __UNKNOWN___UNKNOWN__   __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN___UNKNOWN__   __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN___UNKNOWN__   __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN___UNKNOWN__   __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN___UNKNOWN__   __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ hg19
    __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ 22  3239880 3239881 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ G   G   G   __UNKNOWN__ __UNKNOWN__ __UNKNOWN___UNKNOWN__   __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__
    ......
    
    

    Can you please help with this issue?
    Thanks in advance,

    Suimye

  • LeeTL1220LeeTL1220 Arlington, MAMember, Broadie, Dev ✭✭✭
    Accepted Answer

    @suimye A couple of things...

    First: Please upgrade to Oncotator 1.9.0.0 and the new datasources. I doubt this will be an issue.

    Second: Did you create a virtualenv and run oncotator from there? It looks like your version of pysam is not compatible with Oncotator 1.8.0.0 (what you are running in your example).

  • suimyesuimye TokyoMember

    Im sorry for too late replying. I not use Oncotator now... Thanks for your replying!

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