cBioPortal validation report

Study directory:
test_data/study_es_0/

For details, please see the documentation on file formats supported by cBioPortal

cBioPortal version unknown -- offline instance

Validation status: Success
Line Number Column Number Message Value Encountered
Debug Reading portal information from test_data/api_json_system_tests/cancer-types.json
Debug Reading portal information from test_data/api_json_system_tests/genes.json
Debug Reading portal information from test_data/api_json_system_tests/genesets.json
Debug Reading portal information from test_data/api_json_system_tests/genesets_version.json
Debug Reading portal information from test_data/api_json_system_tests/gene-panels.json
Debug Reading portal information from test_data/api_json_system_tests/genesaliases.json
Debug Retrieving chromosome lengths from '/cbioportal/core/src/main/resources/scripts/importer/chromosome_sizes.json'
Debug Retrieving chromosome lengths from '/cbioportal/core/src/main/resources/scripts/importer/chromosome_sizes.json'
Debug Study Tag file found. It will be validated.
Debug Validating case lists
Info Validation of case list folder complete
Info Validation complete
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Line Number Column Number Message Value Encountered
Debug Starting validation of file
Info Validation of file complete
Info Read 1 lines. Lines with warning: 0. Lines with error: 0
Line Number Column Number Message Value Encountered
Debug Starting validation of file
Info Validation of file complete
Info Read 846 lines. Lines with warning: 0. Lines with error: 0
Line Number Column Number Message Value Encountered
Debug Starting validation of file
Info Validation of file complete
Info Read 850 lines. Lines with warning: 0. Lines with error: 0
Line Number Column Number Message Value Encountered
Debug Starting validation of file
Info 154, 155, 844… 6 Values contained in the column cbp_driver_tiers that will appear in the "Mutation Color" menu of the Oncoprint Class 2, Class 1 See all 4 values
Info Validation of file complete
Info Read 6305 lines. Lines with warning: 0. Lines with error: 0
Line Number Column Number Message Value Encountered
Debug Starting validation of file
Info Validation of file complete
Info Read 10 lines. Lines with warning: 0. Lines with error: 0
Line Number Column Number Message Value Encountered
Debug Starting validation of file
Info Validation of file complete
Info Read 8 lines. Lines with warning: 0. Lines with error: 0
Line Number Column Number Message Value Encountered
Debug Starting validation of file
Info Validation of file complete
Info Read 7 lines. Lines with warning: 0. Lines with error: 0
Line Number Column Number Message Value Encountered
Debug Starting validation of file
Info Validation of file complete
Info Read 6 lines. Lines with warning: 0. Lines with error: 0
Line Number Column Number Message Value Encountered
Debug Starting validation of file
Info 1 This column can be replaced by a 'gene_panel' property in the respective meta file gistic
Info Validation of file complete
Info Read 21 lines. Lines with warning: 0. Lines with error: 0
Line Number Column Number Message Value Encountered
Debug Starting validation of file
Info Validation of file complete
Info Read 3 lines. Lines with warning: 0. Lines with error: 0
Line Number Column Number Message Value Encountered
Debug Starting validation of file
Info Validation of file complete
Info Read 12 lines. Lines with warning: 0. Lines with error: 0
Line Number Column Number Message Value Encountered
Debug Starting validation of file
Info Validation of file complete
Info Read 8 lines. Lines with warning: 0. Lines with error: 0
Line Number Column Number Message Value Encountered
Debug Starting validation of file
Info Validation of file complete
Info Read 8 lines. Lines with warning: 0. Lines with error: 0
Line Number Column Number Message Value Encountered
Debug Starting validation of file
Info Validation of file complete
Info Read 9 lines. Lines with warning: 0. Lines with error: 0
Line Number Column Number Message Value Encountered
Debug Starting validation of file
Info Validation of file complete
Info Read 61 lines. Lines with warning: 0. Lines with error: 0
Line Number Column Number Message Value Encountered
Debug Starting validation of file
Info 4, 5, 6… 164 Values contained in the column cbp_driver_tiers that will appear in the "Mutation Color" menu of the Oncoprint Class 2, Class 1, Class 4… See all 11 values
Info 7, 9 Line will not be loaded due to the variant classification filter. Filtered types: [Silent, Intron, 3'UTR, 3'Flank, 5'UTR, 5'Flank, IGR, RNA] Silent
Info Validation of file complete
Info Read 38 lines. Lines with warning: 0. Lines with error: 0
Line Number Column Number Message Value Encountered
Debug Starting validation of file
Info Validation of file complete
Info Read 4 lines. Lines with warning: 0. Lines with error: 0
Line Number Column Number Message Value Encountered
Debug Starting validation of file
Info Validation of file complete
Info Read 4 lines. Lines with warning: 0. Lines with error: 0
Line Number Column Number Message Value Encountered
Debug Starting validation of file
Info Validation of file complete
Info Read 4 lines. Lines with warning: 0. Lines with error: 0
Line Number Column Number Message Value Encountered
Debug Starting validation of file
Info Validation of file complete
Info Read 2 lines. Lines with warning: 0. Lines with error: 0
Line Number Column Number Message Value Encountered
Debug Starting validation of file
Info 48 No Entrez gene id or gene symbol provided for site 2. Assuming either the intragenic, deletion, duplication, translocation or inversion variant
Info 49 No Entrez gene id or gene symbol provided for site 1. Assuming either the intragenic, deletion, duplication, translocation or inversion variant
Info Validation of file complete
Info Read 49 lines. Lines with warning: 0. Lines with error: 0
Line Number Column Number Message Value Encountered
Debug Starting validation of file
Info Validation of file complete
Info Read 11 lines. Lines with warning: 0. Lines with error: 0
Line Number Column Number Message Value Encountered
Debug Starting validation of file
Info Validation of file complete
Info Read 11 lines. Lines with warning: 0. Lines with error: 0
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Info Setting reference genome to human (GRCh37, hg19)
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Line Number Column Number Message Value Encountered
Debug Starting validation of study tags file
Info Validation of study tags file complete.

Legend

Click on a filename below to see a table of messages about the data in the file. The colors in the tables have the following meanings:

Error Error: cBioPortal will not know how to load this, please revise or remove
Warning Warning: possible cause of confusion, please check whether this is intended
Info Info: this looks good, no action required
Debug Verbose output: details on the progress of the validation script