Ashraf Shabaneh
Starting validation...
INFO: -: Running validation from cBioPortal version 1.11.1-SNAPSHOT
WARNING: -: Skipping validations relating to cancer types defined in the portal
WARNING: -: Skipping validations relating to gene identifiers and aliases defined in the portal
WARNING: -: Skipping validations relating to gene set identifiers
INFO: meta_clinical_sample.txt: Validation of meta file complete
INFO: meta_study.txt: Validation of meta file complete
INFO: meta_mutations_extended.txt: Validation of meta file complete
INFO: meta_clinical_patient.txt: Validation of meta file complete
INFO: data_clinical_sample.txt: Validation of file complete
INFO: data_clinical_sample.txt: Read 78 lines. Lines with warning: 0. Lines with error: 0
WARNING: data_clinical_patient.txt: Columns OS_MONTHS and/or OS_STATUS not found. Overall survival analysis feature will not be available for this study.
WARNING: data_clinical_patient.txt: Columns DFS_MONTHS and/or DFS_STATUS not found. Disease free analysis feature will not be available for this study.
INFO: data_clinical_patient.txt: Validation of file complete
INFO: data_clinical_patient.txt: Read 74 lines. Lines with warning: 0. Lines with error: 0
WARNING: data_mutations_extended.txt: line 1: Including the SWISSPROT column is recommended to make sure that the UniProt canonical isoform is used when drawing Pfam domains in the mutations view
INFO: data_mutations_extended.txt: lines [2, 6, 11, (278 more)]: 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]; values encountered: ['RNA', 'Silent', 'Intron', '(2 more)']
INFO: data_mutations_extended.txt: Validation of file complete
INFO: data_mutations_extended.txt: Read 1272 lines. Lines with warning: 1. Lines with error: 0
INFO: -: No directory named 'case_lists' found, so assuming no custom case lists.
INFO: -: Validation complete
#######################################################################
Overriding Warnings. Importing study now
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Data loading step using: /Users/shaba033/Documents/cbioportal-master/scripts/target/scripts-1.11.2-SNAPSHOT.jar
Checked DB schema version: (expected: 2.4.0) (found: 2.4.0)
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by org.apache.ibatis.reflection.Reflector (file:/Users/shaba033/Documents/cbioportal-master/scripts/target/scripts-1.11.2-SNAPSHOT.jar) to method java.lang.Class.checkPackageAccess(java.lang.SecurityManager,java.lang.ClassLoader,boolean)
WARNING: Please consider reporting this to the maintainers of org.apache.ibatis.reflection.Reflector
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
Checking if Cancer study with identifier all_stjude_2016 already exists before removing...
Recaching...
Finished recaching...
Cancer study with identifier all_stjude_2016 found in database, removing...
Recaching...
Finished recaching...
deleted study:
ID: 13
Done.
Total time: 8594 ms
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by org.apache.ibatis.reflection.Reflector (file:/Users/shaba033/Documents/cbioportal-master/scripts/target/scripts-1.11.2-SNAPSHOT.jar) to method java.lang.Class.checkPackageAccess(java.lang.SecurityManager,java.lang.ClassLoader,boolean)
WARNING: Please consider reporting this to the maintainers of org.apache.ibatis.reflection.Reflector
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
Recaching...
Finished recaching...
Recaching...
Finished recaching...
Loaded the following cancer study:
--> Study ID: 14
--> Name: Acute Lymphoblastic Leukemia (St Jude, Nat Genet 2016)
--> Description: Whole-genome and/or whole-exome sequencing was performed for ERG-altered B-ALL cases.
Done.
Total time: 4630 ms
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by org.apache.ibatis.reflection.Reflector (file:/Users/shaba033/Documents/cbioportal-master/scripts/target/scripts-1.11.2-SNAPSHOT.jar) to method java.lang.Class.checkPackageAccess(java.lang.SecurityManager,java.lang.ClassLoader,boolean)
WARNING: Please consider reporting this to the maintainers of org.apache.ibatis.reflection.Reflector
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
Recaching...
Finished recaching...
Reading data from: /Users/shaba033/Downloads/all_stjude_2016/data_clinical_sample.txt
--> total number of lines: 74
--> records inserted into `clinical_sample` table: 292
Total number of sample specific clinical attributes added: 292
Total number of samples processed: 73
Total number of attribute values skipped because of empty value: 0
Done.
Total time: 4741 ms
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by org.apache.ibatis.reflection.Reflector (file:/Users/shaba033/Documents/cbioportal-master/scripts/target/scripts-1.11.2-SNAPSHOT.jar) to method java.lang.Class.checkPackageAccess(java.lang.SecurityManager,java.lang.ClassLoader,boolean)
WARNING: Please consider reporting this to the maintainers of org.apache.ibatis.reflection.Reflector
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
Reading data from: /Users/shaba033/Downloads/all_stjude_2016/data_mutations_extended.txt
Recaching...
Finished recaching...
--> profile id: 33
--> profile name: Mutations
--> genetic alteration type: MUTATION_EXTENDED
--> records inserted into `sample_profile` table: 73
--> records inserted into `mutation_event` table: 973
--> records inserted into `mutation` table: 989
--> total number of data entries skipped (see table below): 282
--> total number of samples: 73
--> total number of genes for which one or more mutation events were stored: 812
Filtering table:
-----------------
Mutation filter decisions: 1215
Rejects: 226
Mutation Status 'None' Rejects: 0
LOH or Wild Type Rejects: 0
Empty Annotation Rejects: 0
Missense Germline Rejects: 0
5'Flank Rejects: 9
3'Flank Rejects: 30
Intron Rejects: 42
Silent Rejects: 145
Warnings / Errors:
-------------------
0. Ambiguous or missing gene: DKFZp566F0947 [] or ambiguous alias. Ignoring it and all mutation data associated with it!; 1x
1. Ambiguous or missing gene: LOC100499466 [] or ambiguous alias. Ignoring it and all mutation data associated with it!; 1x
2. Ambiguous or missing gene: LOC150381 [] or ambiguous alias. Ignoring it and all mutation data associated with it!; 1x
3. Ambiguous or missing gene: LOC154822 [] or ambiguous alias. Ignoring it and all mutation data associated with it!; 1x
4. Ambiguous or missing gene: LOC25845 [] or ambiguous alias. Ignoring it and all mutation data associated with it!; 1x
5. Ambiguous or missing gene: LOC284232 [] or ambiguous alias. Ignoring it and all mutation data associated with it!; 1x
6. Ambiguous or missing gene: LOC389043 [] or ambiguous alias. Ignoring it and all mutation data associated with it!; 1x
7. Ambiguous or missing gene: LOC400960 [] or ambiguous alias. Ignoring it and all mutation data associated with it!; 1x
8. Ambiguous or missing gene: LOC440905 [] or ambiguous alias. Ignoring it and all mutation data associated with it!; 1x
9. Ambiguous or missing gene: LOC729678 [] or ambiguous alias. Ignoring it and all mutation data associated with it!; 1x
10. CDKN2AP14ARF in the cbio cancer gene list config file [resources/cbio_cancer_genes.txt] is not a HUGO gene symbol. You should either update this file or update the `gene` and `gene_alias` tables to fix this.; 1x
11. CDKN2AP16INK4A in the cbio cancer gene list config file [resources/cbio_cancer_genes.txt] is not a HUGO gene symbol. You should either update this file or update the `gene` and `gene_alias` tables to fix this.; 1x
12. EGFRVIII in the cbio cancer gene list config file [resources/cbio_cancer_genes.txt] is not a HUGO gene symbol. You should either update this file or update the `gene` and `gene_alias` tables to fix this.; 1x
13. Skipping entry with mutation type: RNA; 46x
Done.
Total time: 6777 ms
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by org.apache.ibatis.reflection.Reflector (file:/Users/shaba033/Documents/cbioportal-master/scripts/target/scripts-1.11.2-SNAPSHOT.jar) to method java.lang.Class.checkPackageAccess(java.lang.SecurityManager,java.lang.ClassLoader,boolean)
WARNING: Please consider reporting this to the maintainers of org.apache.ibatis.reflection.Reflector
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
Recaching...
Finished recaching...
Reading data from: /Users/shaba033/Downloads/all_stjude_2016/data_clinical_patient.txt
--> total number of lines: 70
--> records inserted into `clinical_patient` table: 462
Total number of patient specific clinical attributes added: 462
Total number of attribute values skipped because of empty value: 21
Done.
Total time: 4624 ms
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by org.apache.ibatis.reflection.Reflector (file:/Users/shaba033/Documents/cbioportal-master/scripts/target/scripts-1.11.2-SNAPSHOT.jar) to method java.lang.Class.checkPackageAccess(java.lang.SecurityManager,java.lang.ClassLoader,boolean)
WARNING: Please consider reporting this to the maintainers of org.apache.ibatis.reflection.Reflector
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
Recaching...
Finished recaching...
Adding case list: all_stjude_2016_all...
--> stable ID: all_stjude_2016_all
--> case list name: All cases in study
--> number of cases: 73
Done.
Total time: 4621 ms
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by org.apache.ibatis.reflection.Reflector (file:/Users/shaba033/Documents/cbioportal-master/scripts/target/scripts-1.11.2-SNAPSHOT.jar) to method java.lang.Class.checkPackageAccess(java.lang.SecurityManager,java.lang.ClassLoader,boolean)
WARNING: Please consider reporting this to the maintainers of org.apache.ibatis.reflection.Reflector
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
Recaching...
Finished recaching...
Updating study status to : 'AVAILABLE' for study: all_stjude_2016
Done.
Total time: 4574 ms
Kelsey Zhu
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Kelsey Zhu
Thanks for the reply! Heres what I have,java -version
java version "9.0.4"
Java(TM) SE Runtime Environment (build 9.0.4+11)
Java HotSpot(TM) 64-Bit Server VM (build 9.0.4+11, mixed mode)