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