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