2018-09-13 09:07:27::INFO Checking for broad-firecloud-gdac/awg_TCGA-UVM ... 2018-09-13 09:07:40::INFO Creating workspace broad-firecloud-gdac/awg_TCGA-UVM 2018-09-13 09:07:43::INFO Initializing stddata run. 2018-09-13 09:07:43::INFO Adding GROUP_broadgdac@firecloud.org as workspace owner(s) 2018-09-13 09:07:44::INFO Adding Getz_Lab@firecloud.org as workspace reader(s) 2018-09-13 09:07:45::INFO Setting package to "true" 2018-09-13 09:07:45::INFO Loading Participants 2018-09-13 09:07:45::INFO Loading Samples 2018-09-13 09:07:47::INFO Loading Sample Sets 2018-09-13 09:07:47::INFO Copying method configs from broad-firecloud-gdac/Production to broad-firecloud-gdac/awg_TCGA-UVM 2018-09-13 09:07:53::INFO Initiating run. Recovery file is at: awg_TCGA-UVM.json If run fails due to FireCloud issues, it can be continued by running: fissfc supervise_recover awg_TCGA-UVM.json 2018-09-13 09:07:53::INFO Initiating dashboard generation cron job 2018-09-13 09:07:55::INFO Following command(s) added to queue /xchip/gdac_data/runs/current_awg_runs.tsv: gdac_dashboard -D /xchip/gdac_data/runs/tmp/SOP/awg_TCGA-UVM awg_TCGA-UVM 2018-09-13 09:07:55::INFO Initializing FireCloud Supervisor... 2018-09-13 09:07:55::INFO Saving recovery checkpoints to awg_TCGA-UVM.json 2018-09-13 09:07:55::INFO Validating supervisor data... 2018-09-13 09:07:57::INFO Starting workflow Merge_miR__geneExp on TCGA-UVM 2018-09-13 09:07:57::INFO Starting workflow Merge_miR__geneExp on TCGA-UVM-NB 2018-09-13 09:07:58::INFO Starting workflow Merge_miR__geneExp on TCGA-UVM-TP 2018-09-13 09:07:58::INFO Starting workflow Merge_CNV__unfiltered__snp6 on TCGA-UVM 2018-09-13 09:07:59::INFO Starting workflow Merge_CNV__unfiltered__snp6 on TCGA-UVM-NB 2018-09-13 09:07:59::INFO Starting workflow Merge_CNV__unfiltered__snp6 on TCGA-UVM-TP 2018-09-13 09:08:00::INFO Starting workflow Merge_clinical on TCGA-UVM 2018-09-13 09:08:00::INFO Starting workflow Merge_clinical on TCGA-UVM-NB 2018-09-13 09:08:01::INFO Starting workflow Merge_clinical on TCGA-UVM-TP 2018-09-13 09:08:01::INFO Starting workflow Merge_mRNA__geneExp__FPKM on TCGA-UVM 2018-09-13 09:08:02::INFO Starting workflow Merge_mRNA__geneExp__FPKM on TCGA-UVM-NB 2018-09-13 09:08:02::INFO Starting workflow Merge_mRNA__geneExp__FPKM on TCGA-UVM-TP 2018-09-13 09:08:03::INFO Starting workflow Merge_miR__isoformExp on TCGA-UVM 2018-09-13 09:08:03::INFO Starting workflow Merge_miR__isoformExp on TCGA-UVM-NB 2018-09-13 09:08:04::INFO Starting workflow Merge_miR__isoformExp on TCGA-UVM-TP 2018-09-13 09:08:04::INFO Starting workflow Merge_SNV__mutect on TCGA-UVM 2018-09-13 09:08:05::INFO Starting workflow Merge_SNV__mutect on TCGA-UVM-NB 2018-09-13 09:08:05::INFO Starting workflow Merge_SNV__mutect on TCGA-UVM-TP 2018-09-13 09:08:06::INFO Starting workflow Merge_methylation__HM450 on TCGA-UVM 2018-09-13 09:08:06::INFO Starting workflow Merge_methylation__HM450 on TCGA-UVM-NB 2018-09-13 09:08:07::INFO Starting workflow Merge_methylation__HM450 on TCGA-UVM-TP 2018-09-13 09:08:07::INFO Starting workflow Merge_mRNA__geneExpNormed__FPKM on TCGA-UVM 2018-09-13 09:08:08::INFO Starting workflow Merge_mRNA__geneExpNormed__FPKM on TCGA-UVM-NB 2018-09-13 09:08:08::INFO Starting workflow Merge_mRNA__geneExpNormed__FPKM on TCGA-UVM-TP 2018-09-13 09:08:09::INFO Starting workflow Merge_methylation__HM27 on TCGA-UVM 2018-09-13 09:08:09::INFO Starting workflow Merge_methylation__HM27 on TCGA-UVM-NB 2018-09-13 09:08:10::INFO Starting workflow Merge_methylation__HM27 on TCGA-UVM-TP 2018-09-13 09:08:10::INFO Starting workflow Merge_CNV__snp6 on TCGA-UVM 2018-09-13 09:08:11::INFO Starting workflow Merge_CNV__snp6 on TCGA-UVM-NB 2018-09-13 09:08:11::INFO Starting workflow Merge_CNV__snp6 on TCGA-UVM-TP 2018-09-13 09:08:12::INFO 6 Waiting, 30 Running, 0 Completed 2018-09-13 09:08:42::INFO Workflow Merge_CNV__unfiltered__snp6 completed for TCGA-UVM-NB 2018-09-13 09:08:42::INFO 6 Waiting, 29 Running, 1 Completed 2018-09-13 09:09:12::INFO Workflow Merge_miR__geneExp completed for TCGA-UVM-TP 2018-09-13 09:09:13::INFO Workflow Merge_methylation__HM450 completed for TCGA-UVM-TP 2018-09-13 09:09:13::INFO 6 Waiting, 27 Running, 3 Completed 2018-09-13 09:09:43::INFO Workflow Merge_CNV__unfiltered__snp6 completed for TCGA-UVM-TP 2018-09-13 09:09:43::INFO Workflow Merge_mRNA__geneExp__FPKM completed for TCGA-UVM-TP 2018-09-13 09:09:43::INFO Workflow Merge_SNV__mutect completed for TCGA-UVM-TP 2018-09-13 09:09:43::INFO Workflow Merge_CNV__snp6 completed for TCGA-UVM-NB 2018-09-13 09:09:43::INFO 6 Waiting, 23 Running, 7 Completed 2018-09-13 09:10:14::INFO Workflow Merge_CNV__snp6 completed for TCGA-UVM-TP 2018-09-13 09:10:14::INFO 6 Waiting, 22 Running, 8 Completed 2018-09-13 09:10:44::INFO 6 Waiting, 22 Running, 8 Completed 2018-09-13 09:11:14::INFO Workflow Merge_mRNA__geneExpNormed__FPKM completed for TCGA-UVM 2018-09-13 09:11:14::INFO Starting workflow mRNA_Preprocess on TCGA-UVM 2018-09-13 09:11:15::INFO 5 Waiting, 22 Running, 9 Completed 2018-09-13 09:11:45::INFO Workflow Merge_miR__geneExp completed for TCGA-UVM-NB 2018-09-13 09:11:45::INFO Workflow Merge_mRNA__geneExp__FPKM completed for TCGA-UVM 2018-09-13 09:11:45::INFO 5 Waiting, 20 Running, 11 Completed 2018-09-13 09:12:16::INFO Workflow Merge_mRNA__geneExpNormed__FPKM completed for TCGA-UVM-NB 2018-09-13 09:12:16::INFO 4 Waiting, 19 Running, 13 Completed 2018-09-13 09:12:47::INFO Workflow Merge_mRNA__geneExp__FPKM completed for TCGA-UVM-NB 2018-09-13 09:12:47::INFO Workflow Merge_miR__isoformExp completed for TCGA-UVM-NB 2018-09-13 09:12:47::INFO Workflow Merge_methylation__HM27 completed for TCGA-UVM-NB 2018-09-13 09:12:47::INFO Workflow Merge_methylation__HM27 completed for TCGA-UVM-TP 2018-09-13 09:12:47::INFO 4 Waiting, 15 Running, 17 Completed 2018-09-13 09:13:17::INFO Workflow Merge_SNV__mutect completed for TCGA-UVM-NB 2018-09-13 09:13:17::INFO 4 Waiting, 14 Running, 18 Completed 2018-09-13 09:13:48::INFO Workflow mRNA_Preprocess completed for TCGA-UVM 2018-09-13 09:13:48::INFO 4 Waiting, 13 Running, 19 Completed 2018-09-13 09:14:18::INFO Workflow Merge_methylation__HM27 completed for TCGA-UVM 2018-09-13 09:14:18::INFO 4 Waiting, 12 Running, 20 Completed 2018-09-13 09:14:48::INFO Workflow Merge_methylation__HM450 completed for TCGA-UVM-NB 2018-09-13 09:14:48::INFO 4 Waiting, 11 Running, 21 Completed 2018-09-13 09:15:19::INFO 4 Waiting, 11 Running, 21 Completed 2018-09-13 09:15:49::INFO 4 Waiting, 11 Running, 21 Completed 2018-09-13 09:16:20::INFO 4 Waiting, 11 Running, 21 Completed 2018-09-13 09:16:50::INFO 4 Waiting, 11 Running, 21 Completed 2018-09-13 09:17:21::INFO 4 Waiting, 11 Running, 21 Completed 2018-09-13 09:17:51::INFO 4 Waiting, 11 Running, 21 Completed 2018-09-13 09:18:21::INFO 4 Waiting, 11 Running, 21 Completed 2018-09-13 09:18:52::INFO 4 Waiting, 11 Running, 21 Completed 2018-09-13 09:19:22::INFO 4 Waiting, 11 Running, 21 Completed 2018-09-13 09:19:53::INFO 4 Waiting, 11 Running, 21 Completed 2018-09-13 09:20:24::INFO 4 Waiting, 11 Running, 21 Completed 2018-09-13 09:20:54::INFO 4 Waiting, 11 Running, 21 Completed 2018-09-13 09:21:24::INFO 4 Waiting, 11 Running, 21 Completed 2018-09-13 09:21:55::INFO 4 Waiting, 11 Running, 21 Completed 2018-09-13 09:22:25::INFO 4 Waiting, 11 Running, 21 Completed 2018-09-13 09:22:56::INFO 4 Waiting, 11 Running, 21 Completed 2018-09-13 09:23:26::INFO 4 Waiting, 11 Running, 21 Completed 2018-09-13 09:23:57::INFO Workflow Merge_miR__isoformExp completed for TCGA-UVM 2018-09-13 09:23:57::INFO 4 Waiting, 10 Running, 22 Completed 2018-09-13 09:24:27::INFO Workflow Merge_methylation__HM450 completed for TCGA-UVM 2018-09-13 09:24:27::INFO 4 Waiting, 9 Running, 23 Completed 2018-09-13 09:24:58::INFO Workflow Merge_miR__geneExp completed for TCGA-UVM 2018-09-13 09:24:58::INFO 4 Waiting, 8 Running, 24 Completed 2018-09-13 09:25:28::INFO Workflow Merge_CNV__unfiltered__snp6 completed for TCGA-UVM 2018-09-13 09:25:28::INFO Workflow Merge_clinical completed for TCGA-UVM-TP 2018-09-13 09:25:28::INFO Workflow Merge_mRNA__geneExpNormed__FPKM completed for TCGA-UVM-TP 2018-09-13 09:25:28::INFO Starting workflow mRNA_Preprocess on TCGA-UVM-TP 2018-09-13 09:25:29::INFO Workflow Merge_CNV__snp6 completed for TCGA-UVM 2018-09-13 09:25:29::INFO 3 Waiting, 5 Running, 28 Completed 2018-09-13 09:25:59::INFO Starting workflow Clinical_Pick_Tier1 on TCGA-UVM-TP 2018-09-13 09:26:00::INFO Workflow Merge_miR__isoformExp completed for TCGA-UVM-TP 2018-09-13 09:26:00::INFO Workflow Merge_SNV__mutect completed for TCGA-UVM 2018-09-13 09:26:00::INFO 2 Waiting, 4 Running, 30 Completed 2018-09-13 09:26:31::INFO 2 Waiting, 4 Running, 30 Completed 2018-09-13 09:27:01::INFO Workflow Clinical_Pick_Tier1 completed for TCGA-UVM-TP 2018-09-13 09:27:01::INFO 2 Waiting, 3 Running, 31 Completed 2018-09-13 09:27:31::INFO 2 Waiting, 3 Running, 31 Completed 2018-09-13 09:28:02::INFO 2 Waiting, 3 Running, 31 Completed 2018-09-13 09:28:32::INFO 2 Waiting, 3 Running, 31 Completed 2018-09-13 09:29:03::INFO 2 Waiting, 3 Running, 31 Completed 2018-09-13 09:29:33::INFO 2 Waiting, 3 Running, 31 Completed 2018-09-13 09:30:04::INFO 2 Waiting, 3 Running, 31 Completed 2018-09-13 09:30:34::INFO 2 Waiting, 3 Running, 31 Completed 2018-09-13 09:31:04::INFO 2 Waiting, 3 Running, 31 Completed 2018-09-13 09:31:35::INFO 2 Waiting, 3 Running, 31 Completed 2018-09-13 09:32:05::INFO 2 Waiting, 3 Running, 31 Completed 2018-09-13 09:32:36::INFO 2 Waiting, 3 Running, 31 Completed 2018-09-13 09:33:06::INFO 2 Waiting, 3 Running, 31 Completed 2018-09-13 09:33:37::INFO 2 Waiting, 3 Running, 31 Completed 2018-09-13 09:34:07::INFO 2 Waiting, 3 Running, 31 Completed 2018-09-13 09:34:38::INFO 2 Waiting, 3 Running, 31 Completed 2018-09-13 09:35:08::INFO 2 Waiting, 3 Running, 31 Completed 2018-09-13 09:35:39::INFO 2 Waiting, 3 Running, 31 Completed 2018-09-13 09:36:10::INFO 2 Waiting, 3 Running, 31 Completed 2018-09-13 09:36:40::INFO 2 Waiting, 3 Running, 31 Completed 2018-09-13 09:37:11::INFO 2 Waiting, 3 Running, 31 Completed 2018-09-13 09:37:41::INFO 2 Waiting, 3 Running, 31 Completed 2018-09-13 09:38:12::INFO 2 Waiting, 3 Running, 31 Completed 2018-09-13 09:38:42::INFO 2 Waiting, 3 Running, 31 Completed 2018-09-13 09:39:13::INFO Workflow mRNA_Preprocess completed for TCGA-UVM-TP 2018-09-13 09:39:13::INFO 2 Waiting, 2 Running, 32 Completed 2018-09-13 09:39:43::INFO Workflow Merge_clinical completed for TCGA-UVM-NB 2018-09-13 09:39:43::INFO 2 Waiting, 1 Running, 33 Completed 2018-09-13 09:40:13::INFO Starting workflow Clinical_Pick_Tier1 on TCGA-UVM-NB 2018-09-13 09:40:14::INFO 1 Waiting, 2 Running, 33 Completed 2018-09-13 09:40:45::INFO 1 Waiting, 2 Running, 33 Completed 2018-09-13 09:41:15::INFO 1 Waiting, 2 Running, 33 Completed 2018-09-13 09:41:46::INFO 1 Waiting, 2 Running, 33 Completed 2018-09-13 09:42:16::INFO Workflow Clinical_Pick_Tier1 completed for TCGA-UVM-NB 2018-09-13 09:42:16::INFO 1 Waiting, 1 Running, 34 Completed 2018-09-13 09:42:47::INFO 1 Waiting, 1 Running, 34 Completed 2018-09-13 09:43:17::INFO 1 Waiting, 1 Running, 34 Completed 2018-09-13 09:43:48::INFO 1 Waiting, 1 Running, 34 Completed 2018-09-13 09:44:18::INFO 1 Waiting, 1 Running, 34 Completed 2018-09-13 09:44:48::INFO 1 Waiting, 1 Running, 34 Completed 2018-09-13 09:45:19::INFO 1 Waiting, 1 Running, 34 Completed 2018-09-13 09:45:50::INFO 1 Waiting, 1 Running, 34 Completed 2018-09-13 09:46:20::INFO 1 Waiting, 1 Running, 34 Completed 2018-09-13 09:46:51::INFO 1 Waiting, 1 Running, 34 Completed 2018-09-13 09:47:21::INFO 1 Waiting, 1 Running, 34 Completed 2018-09-13 09:47:52::INFO 1 Waiting, 1 Running, 34 Completed 2018-09-13 09:48:22::INFO 1 Waiting, 1 Running, 34 Completed 2018-09-13 09:48:53::INFO 1 Waiting, 1 Running, 34 Completed 2018-09-13 09:49:23::INFO 1 Waiting, 1 Running, 34 Completed 2018-09-13 09:49:53::INFO 1 Waiting, 1 Running, 34 Completed 2018-09-13 09:50:24::INFO 1 Waiting, 1 Running, 34 Completed 2018-09-13 09:50:54::INFO Workflow Merge_clinical completed for TCGA-UVM 2018-09-13 09:50:54::INFO 1 Waiting, 0 Running, 35 Completed 2018-09-13 09:51:25::INFO Starting workflow Clinical_Pick_Tier1 on TCGA-UVM 2018-09-13 09:51:26::INFO 0 Waiting, 1 Running, 35 Completed 2018-09-13 09:51:57::INFO 0 Waiting, 1 Running, 35 Completed 2018-09-13 09:52:27::INFO 0 Waiting, 1 Running, 35 Completed 2018-09-13 09:52:57::INFO 0 Waiting, 1 Running, 35 Completed 2018-09-13 09:53:28::INFO Workflow Clinical_Pick_Tier1 completed for TCGA-UVM 2018-09-13 09:53:28::INFO 0 Waiting, 0 Running, 36 Completed 2018-09-13 09:53:28::INFO DONE. 2018-09-13 09:53:28::INFO Successfully completed stddata run. To begin analyses, re-run by populating the --entities option with any of the following Sample Sets: TCGA-UVM TCGA-UVM-NB TCGA-UVM-TP