Configuring R environment ... gdac_reports: running for analyses__2012_03_21 [1] "analyses__2012_03_21__ucec_00/Individual_Set/UCEC" UCEC/00 reports: 13 Path: copynumber/gistic2/report.RData Path: correlate/copyNumber_vs_mRNA/report.RData Path: mutation/significance/report.RData Path: pathway/paradigm_expression/report.RData Path: correlate/methylation_vs_mRNA/nozzle.RData Path: mRNA/clustering_CNMF/nozzle.RData Path: mRNA/clustering_Consensus/nozzle.RData Path: mRNAseq/clustering_CNMF/nozzle.RData Path: mRNAseq/clustering_Consensus/nozzle.RData Path: methylation/clustering_CNMF/nozzle.RData Path: miRseq/clustering_CNMF/nozzle.RData Path: miRseq/clustering_Consensus/nozzle.RData Path: pathway/findEnrichedGenes/nozzle.RData Writing UCEC report Copy number analysis (GISTIC2) ... WARNING: No archive for UCEC: CopyNumber_Gistic2 Copying /xchip/cga1/tcga_gdac_firehose_output/analyses__2012_03_21__ucec_00/Individual_Set/UCEC/copynumber/gistic2/amp_genes.conf_99.txt ... 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