INFO @ Tue, 18 Oct 2016 17:31:35: Parameters: /Users/bibaswan/anaconda/bin/mageck mle --norm-method median --output-prefix results/test/myexperiment1 --sgrna-eff-name-column 3 --sgrna-eff-score-column 4 --sgrna-efficiency annotation/sgrnas.bed --genes-var 0 --count-table results/count/all.count.txt --design-matrix /Users/bibaswan/Downloads/esc/esc-testdata/designmatrix.txt INFO @ Tue, 18 Oct 2016 17:31:36: Cannot parse design matrix as a string; try to parse it as a file name ... INFO @ Tue, 18 Oct 2016 17:31:36: Design matrix: INFO @ Tue, 18 Oct 2016 17:31:36: [[ 1. 0.] INFO @ Tue, 18 Oct 2016 17:31:36: [ 1. 1.] INFO @ Tue, 18 Oct 2016 17:31:36: [ 1. 1.]] INFO @ Tue, 18 Oct 2016 17:31:36: Beta labels:baseline,esc INFO @ Tue, 18 Oct 2016 17:31:36: Included samples:plasmid,esc1,esc2 INFO @ Tue, 18 Oct 2016 17:31:36: 87434 lines processed in sgRNA efficiency prediction file annotation/sgrnas.bed. INFO @ Tue, 18 Oct 2016 17:31:36: Loaded samples:plasmid;esc1;esc2 INFO @ Tue, 18 Oct 2016 17:31:36: Sample index: 0;1;2 INFO @ Tue, 18 Oct 2016 17:31:37: Loaded 19149 genes. INFO @ Tue, 18 Oct 2016 17:31:37: Converting sgRNA efficiency prediction to the initial guess of pi... DEBUG @ Tue, 18 Oct 2016 17:31:37: Initial (total) size factor: 1.0 1.0 1.0 DEBUG @ Tue, 18 Oct 2016 17:31:38: Median factor: 2.0 2.0 2.0 INFO @ Tue, 18 Oct 2016 17:31:38: Final size factor: 2.0 2.0 2.0 INFO @ Tue, 18 Oct 2016 17:31:38: size factor: 0.5,0.5,0.5 INFO @ Tue, 18 Oct 2016 17:31:38: Thread 0 started. INFO @ Tue, 18 Oct 2016 17:31:38: Thread 0: total 1 instances. INFO @ Tue, 18 Oct 2016 17:31:38: Thread 0 completed. INFO @ Tue, 18 Oct 2016 17:31:38: All threads completed. INFO @ Tue, 18 Oct 2016 17:31:38: Modeling the mean and variance ... INFO @ Tue, 18 Oct 2016 17:31:38: Run the algorithm for the second time ... INFO @ Tue, 18 Oct 2016 17:31:38: Calculating HSF2BP (1) ... INFO @ Tue, 18 Oct 2016 17:31:45: Calculating NFKB1 (1001) ... INFO @ Tue, 18 Oct 2016 17:31:52: Calculating STK38L (2001) ... INFO @ Tue, 18 Oct 2016 17:31:59: Calculating CENPJ (3001) ... INFO @ Tue, 18 Oct 2016 17:32:06: Calculating LILRB4 (4001) ... INFO @ Tue, 18 Oct 2016 17:32:13: Calculating GNPTG (5001) ... INFO @ Tue, 18 Oct 2016 17:32:20: Calculating OLFR1264 (6001) ... INFO @ Tue, 18 Oct 2016 17:32:28: Calculating OLFR1030 (7001) ... INFO @ Tue, 18 Oct 2016 17:32:35: Calculating JMJD7 (8001) ... INFO @ Tue, 18 Oct 2016 17:32:42: Calculating RNASE12 (9001) ... INFO @ Tue, 18 Oct 2016 17:32:49: Calculating MBTPS1 (10001) ... INFO @ Tue, 18 Oct 2016 17:32:56: Calculating TAAR8B (11001) ... INFO @ Tue, 18 Oct 2016 17:33:03: Calculating TM4SF19 (12001) ... INFO @ Tue, 18 Oct 2016 17:33:10: Calculating MARCKSL1 (13001) ... INFO @ Tue, 18 Oct 2016 17:33:17: Calculating FBXW7 (14001) ... INFO @ Tue, 18 Oct 2016 17:33:24: Calculating DUSP14 (15001) ... INFO @ Tue, 18 Oct 2016 17:33:31: Calculating KLHL12 (16001) ... INFO @ Tue, 18 Oct 2016 17:33:38: Calculating RNF183 (17001) ... INFO @ Tue, 18 Oct 2016 17:33:45: Calculating DBX1 (18001) ... INFO @ Tue, 18 Oct 2016 17:33:52: Calculating PCP2 (19001) ... INFO @ Tue, 18 Oct 2016 17:33:53: Start permuting 10 rounds ... INFO @ Tue, 18 Oct 2016 17:33:54: Collecting 87437 sgRNAs from 19149 genes. INFO @ Tue, 18 Oct 2016 17:33:56: Permuting round 0 ... INFO @ Tue, 18 Oct 2016 17:33:56: Thread 0 started. INFO @ Tue, 18 Oct 2016 17:33:56: Thread 0: total 19149 instances. INFO @ Tue, 18 Oct 2016 17:33:56: Thread 0: Calculating HSF2BP (1) ... INFO @ Tue, 18 Oct 2016 17:34:04: Thread 0: Calculating ADAMTS7 (1001) ... INFO @ Tue, 18 Oct 2016 17:34:12: Thread 0: Calculating MCM3AP (2001) ... INFO @ Tue, 18 Oct 2016 17:34:19: Thread 0: Calculating HPSE2 (3001) ... INFO @ Tue, 18 Oct 2016 17:34:27: Thread 0: Calculating UTP23 (4001) ... INFO @ Tue, 18 Oct 2016 17:34:35: Thread 0: Calculating SEC24B (5001) ... INFO @ Tue, 18 Oct 2016 17:34:42: Thread 0: Calculating WDR45L (6001) ... INFO @ Tue, 18 Oct 2016 17:34:50: Thread 0: Calculating POFUT2 (7001) ... INFO @ Tue, 18 Oct 2016 17:34:57: Thread 0: Calculating SYDE1 (8001) ... INFO @ Tue, 18 Oct 2016 17:35:05: Thread 0: Calculating MR1 (9001) ... INFO @ Tue, 18 Oct 2016 17:35:13: Thread 0: Calculating NPRL2 (10001) ... INFO @ Tue, 18 Oct 2016 17:35:21: Thread 0: Calculating DNAJC7 (11001) ... INFO @ Tue, 18 Oct 2016 17:35:28: Thread 0: Calculating MYT1 (12001) ... INFO @ Tue, 18 Oct 2016 17:35:36: Thread 0: Calculating FAM83A (13001) ... INFO @ Tue, 18 Oct 2016 17:35:44: Thread 0: Calculating APOA1 (14001) ... INFO @ Tue, 18 Oct 2016 17:35:51: Thread 0: Calculating TIRAP (15001) ... INFO @ Tue, 18 Oct 2016 17:35:59: Thread 0: Calculating PLSCR5 (16001) ... INFO @ Tue, 18 Oct 2016 17:36:06: Thread 0: Calculating APBA1 (17001) ... INFO @ Tue, 18 Oct 2016 17:36:14: Thread 0: Calculating SH3BGR (18001) ... INFO @ Tue, 18 Oct 2016 17:36:22: Thread 0: Calculating OLAH (19001) ... INFO @ Tue, 18 Oct 2016 17:36:23: Thread 0 completed. INFO @ Tue, 18 Oct 2016 17:36:23: All threads completed. INFO @ Tue, 18 Oct 2016 17:36:29: Permuting round 1 ... INFO @ Tue, 18 Oct 2016 17:36:30: Thread 0 started. INFO @ Tue, 18 Oct 2016 17:36:30: Thread 0: total 19149 instances. INFO @ Tue, 18 Oct 2016 17:36:30: Thread 0: Calculating HSF2BP (1) ... INFO @ Tue, 18 Oct 2016 17:36:38: Thread 0: Calculating ADAMTS7 (1001) ... INFO @ Tue, 18 Oct 2016 17:36:45: Thread 0: Calculating MCM3AP (2001) ... INFO @ Tue, 18 Oct 2016 17:36:53: Thread 0: Calculating HPSE2 (3001) ... INFO @ Tue, 18 Oct 2016 17:37:00: Thread 0: Calculating UTP23 (4001) ... INFO @ Tue, 18 Oct 2016 17:37:08: Thread 0: Calculating SEC24B (5001) ... INFO @ Tue, 18 Oct 2016 17:37:16: Thread 0: Calculating WDR45L (6001) ... INFO @ Tue, 18 Oct 2016 17:37:24: Thread 0: Calculating POFUT2 (7001) ... INFO @ Tue, 18 Oct 2016 17:37:31: Thread 0: Calculating SYDE1 (8001) ... INFO @ Tue, 18 Oct 2016 17:37:39: Thread 0: Calculating MR1 (9001) ... INFO @ Tue, 18 Oct 2016 17:37:46: Thread 0: Calculating NPRL2 (10001) ... INFO @ Tue, 18 Oct 2016 17:37:54: Thread 0: Calculating DNAJC7 (11001) ... INFO @ Tue, 18 Oct 2016 17:38:01: Thread 0: Calculating MYT1 (12001) ... INFO @ Tue, 18 Oct 2016 17:38:09: Thread 0: Calculating FAM83A (13001) ... INFO @ Tue, 18 Oct 2016 17:38:17: Thread 0: Calculating APOA1 (14001) ... INFO @ Tue, 18 Oct 2016 17:38:24: Thread 0: Calculating TIRAP (15001) ... INFO @ Tue, 18 Oct 2016 17:38:32: Thread 0: Calculating PLSCR5 (16001) ... INFO @ Tue, 18 Oct 2016 17:38:40: Thread 0: Calculating APBA1 (17001) ... INFO @ Tue, 18 Oct 2016 17:38:47: Thread 0: Calculating SH3BGR (18001) ... INFO @ Tue, 18 Oct 2016 17:38:55: Thread 0: Calculating OLAH (19001) ... INFO @ Tue, 18 Oct 2016 17:38:56: Thread 0 completed. INFO @ Tue, 18 Oct 2016 17:38:56: All threads completed. INFO @ Tue, 18 Oct 2016 17:39:02: Permuting round 2 ... INFO @ Tue, 18 Oct 2016 17:39:03: Thread 0 started. INFO @ Tue, 18 Oct 2016 17:39:03: Thread 0: total 19149 instances. INFO @ Tue, 18 Oct 2016 17:39:03: Thread 0: Calculating HSF2BP (1) ... INFO @ Tue, 18 Oct 2016 17:39:11: Thread 0: Calculating ADAMTS7 (1001) ... INFO @ Tue, 18 Oct 2016 17:39:19: Thread 0: Calculating MCM3AP (2001) ... INFO @ Tue, 18 Oct 2016 17:39:26: Thread 0: Calculating HPSE2 (3001) ... INFO @ Tue, 18 Oct 2016 17:39:34: Thread 0: Calculating UTP23 (4001) ... INFO @ Tue, 18 Oct 2016 17:39:41: Thread 0: Calculating SEC24B (5001) ... INFO @ Tue, 18 Oct 2016 17:39:49: Thread 0: Calculating WDR45L (6001) ... INFO @ Tue, 18 Oct 2016 17:39:57: Thread 0: Calculating POFUT2 (7001) ... INFO @ Tue, 18 Oct 2016 17:40:04: Thread 0: Calculating SYDE1 (8001) ... INFO @ Tue, 18 Oct 2016 17:40:12: Thread 0: Calculating MR1 (9001) ... INFO @ Tue, 18 Oct 2016 17:40:19: Thread 0: Calculating NPRL2 (10001) ... INFO @ Tue, 18 Oct 2016 17:40:27: Thread 0: Calculating DNAJC7 (11001) ... INFO @ Tue, 18 Oct 2016 17:40:35: Thread 0: Calculating MYT1 (12001) ... INFO @ Tue, 18 Oct 2016 17:40:42: Thread 0: Calculating FAM83A (13001) ... INFO @ Tue, 18 Oct 2016 17:40:50: Thread 0: Calculating APOA1 (14001) ... INFO @ Tue, 18 Oct 2016 17:40:57: Thread 0: Calculating TIRAP (15001) ... INFO @ Tue, 18 Oct 2016 17:41:05: Thread 0: Calculating PLSCR5 (16001) ... INFO @ Tue, 18 Oct 2016 17:41:13: Thread 0: Calculating APBA1 (17001) ... INFO @ Tue, 18 Oct 2016 17:41:20: Thread 0: Calculating SH3BGR (18001) ... INFO @ Tue, 18 Oct 2016 17:41:28: Thread 0: Calculating OLAH (19001) ... INFO @ Tue, 18 Oct 2016 17:41:29: Thread 0 completed. INFO @ Tue, 18 Oct 2016 17:41:29: All threads completed. INFO @ Tue, 18 Oct 2016 17:41:36: Permuting round 3 ... INFO @ Tue, 18 Oct 2016 17:41:36: Thread 0 started. INFO @ Tue, 18 Oct 2016 17:41:36: Thread 0: total 19149 instances. INFO @ Tue, 18 Oct 2016 17:41:36: Thread 0: Calculating HSF2BP (1) ... INFO @ Tue, 18 Oct 2016 17:41:44: Thread 0: Calculating ADAMTS7 (1001) ... INFO @ Tue, 18 Oct 2016 17:41:52: Thread 0: Calculating MCM3AP (2001) ... INFO @ Tue, 18 Oct 2016 17:42:00: Thread 0: Calculating HPSE2 (3001) ... INFO @ Tue, 18 Oct 2016 17:42:08: Thread 0: Calculating UTP23 (4001) ... INFO @ Tue, 18 Oct 2016 17:42:16: Thread 0: Calculating SEC24B (5001) ... INFO @ Tue, 18 Oct 2016 17:42:23: Thread 0: Calculating WDR45L (6001) ... INFO @ Tue, 18 Oct 2016 17:42:31: Thread 0: Calculating POFUT2 (7001) ... INFO @ Tue, 18 Oct 2016 17:42:39: Thread 0: Calculating SYDE1 (8001) ... INFO @ Tue, 18 Oct 2016 17:42:46: Thread 0: Calculating MR1 (9001) ... INFO @ Tue, 18 Oct 2016 17:42:54: Thread 0: Calculating NPRL2 (10001) ... INFO @ Tue, 18 Oct 2016 17:43:01: Thread 0: Calculating DNAJC7 (11001) ... INFO @ Tue, 18 Oct 2016 17:43:09: Thread 0: Calculating MYT1 (12001) ... INFO @ Tue, 18 Oct 2016 17:43:16: Thread 0: Calculating FAM83A (13001) ... INFO @ Tue, 18 Oct 2016 17:43:24: Thread 0: Calculating APOA1 (14001) ... INFO @ Tue, 18 Oct 2016 17:43:32: Thread 0: Calculating TIRAP (15001) ... INFO @ Tue, 18 Oct 2016 17:43:39: Thread 0: Calculating PLSCR5 (16001) ... INFO @ Tue, 18 Oct 2016 17:43:47: Thread 0: Calculating APBA1 (17001) ... INFO @ Tue, 18 Oct 2016 17:43:55: Thread 0: Calculating SH3BGR (18001) ... INFO @ Tue, 18 Oct 2016 17:44:02: Thread 0: Calculating OLAH (19001) ... INFO @ Tue, 18 Oct 2016 17:44:04: Thread 0 completed. INFO @ Tue, 18 Oct 2016 17:44:04: All threads completed. INFO @ Tue, 18 Oct 2016 17:44:10: Permuting round 4 ... INFO @ Tue, 18 Oct 2016 17:44:11: Thread 0 started. INFO @ Tue, 18 Oct 2016 17:44:11: Thread 0: total 19149 instances. INFO @ Tue, 18 Oct 2016 17:44:11: Thread 0: Calculating HSF2BP (1) ... INFO @ Tue, 18 Oct 2016 17:44:19: Thread 0: Calculating ADAMTS7 (1001) ... INFO @ Tue, 18 Oct 2016 17:44:27: Thread 0: Calculating MCM3AP (2001) ... INFO @ Tue, 18 Oct 2016 17:44:35: Thread 0: Calculating HPSE2 (3001) ... INFO @ Tue, 18 Oct 2016 17:44:42: Thread 0: Calculating UTP23 (4001) ... INFO @ Tue, 18 Oct 2016 17:44:50: Thread 0: Calculating SEC24B (5001) ... INFO @ Tue, 18 Oct 2016 17:44:58: Thread 0: Calculating WDR45L (6001) ... INFO @ Tue, 18 Oct 2016 17:45:05: Thread 0: Calculating POFUT2 (7001) ... INFO @ Tue, 18 Oct 2016 17:45:13: Thread 0: Calculating SYDE1 (8001) ... INFO @ Tue, 18 Oct 2016 17:45:20: Thread 0: Calculating MR1 (9001) ... INFO @ Tue, 18 Oct 2016 17:45:28: Thread 0: Calculating NPRL2 (10001) ... INFO @ Tue, 18 Oct 2016 17:45:36: Thread 0: Calculating DNAJC7 (11001) ... INFO @ Tue, 18 Oct 2016 17:45:43: Thread 0: Calculating MYT1 (12001) ... INFO @ Tue, 18 Oct 2016 17:45:51: Thread 0: Calculating FAM83A (13001) ... INFO @ Tue, 18 Oct 2016 17:45:59: Thread 0: Calculating APOA1 (14001) ... INFO @ Tue, 18 Oct 2016 17:46:06: Thread 0: Calculating TIRAP (15001) ... INFO @ Tue, 18 Oct 2016 17:46:14: Thread 0: Calculating PLSCR5 (16001) ... INFO @ Tue, 18 Oct 2016 17:46:21: Thread 0: Calculating APBA1 (17001) ... INFO @ Tue, 18 Oct 2016 17:46:29: Thread 0: Calculating SH3BGR (18001) ... INFO @ Tue, 18 Oct 2016 17:46:37: Thread 0: Calculating OLAH (19001) ... INFO @ Tue, 18 Oct 2016 17:46:38: Thread 0 completed. INFO @ Tue, 18 Oct 2016 17:46:38: All threads completed. INFO @ Tue, 18 Oct 2016 17:46:45: Permuting round 5 ... INFO @ Tue, 18 Oct 2016 17:46:46: Thread 0 started. INFO @ Tue, 18 Oct 2016 17:46:46: Thread 0: total 19149 instances. INFO @ Tue, 18 Oct 2016 17:46:46: Thread 0: Calculating HSF2BP (1) ... INFO @ Tue, 18 Oct 2016 17:46:53: Thread 0: Calculating ADAMTS7 (1001) ... INFO @ Tue, 18 Oct 2016 17:47:01: Thread 0: Calculating MCM3AP (2001) ... INFO @ Tue, 18 Oct 2016 17:47:08: Thread 0: Calculating HPSE2 (3001) ... INFO @ Tue, 18 Oct 2016 17:47:16: Thread 0: Calculating UTP23 (4001) ... INFO @ Tue, 18 Oct 2016 17:47:24: Thread 0: Calculating SEC24B (5001) ... INFO @ Tue, 18 Oct 2016 17:47:31: Thread 0: Calculating WDR45L (6001) ... INFO @ Tue, 18 Oct 2016 17:47:39: Thread 0: Calculating POFUT2 (7001) ... INFO @ Tue, 18 Oct 2016 17:47:46: Thread 0: Calculating SYDE1 (8001) ... INFO @ Tue, 18 Oct 2016 17:47:54: Thread 0: Calculating MR1 (9001) ... INFO @ Tue, 18 Oct 2016 17:48:02: Thread 0: Calculating NPRL2 (10001) ... INFO @ Tue, 18 Oct 2016 17:48:09: Thread 0: Calculating DNAJC7 (11001) ... INFO @ Tue, 18 Oct 2016 17:48:17: Thread 0: Calculating MYT1 (12001) ... INFO @ Tue, 18 Oct 2016 17:48:24: Thread 0: Calculating FAM83A (13001) ... INFO @ Tue, 18 Oct 2016 17:48:32: Thread 0: Calculating APOA1 (14001) ... INFO @ Tue, 18 Oct 2016 17:48:40: Thread 0: Calculating TIRAP (15001) ... INFO @ Tue, 18 Oct 2016 17:48:48: Thread 0: Calculating PLSCR5 (16001) ... INFO @ Tue, 18 Oct 2016 17:48:55: Thread 0: Calculating APBA1 (17001) ... INFO @ Tue, 18 Oct 2016 17:49:03: Thread 0: Calculating SH3BGR (18001) ... INFO @ Tue, 18 Oct 2016 17:49:10: Thread 0: Calculating OLAH (19001) ... INFO @ Tue, 18 Oct 2016 17:49:11: Thread 0 completed. INFO @ Tue, 18 Oct 2016 17:49:11: All threads completed. INFO @ Tue, 18 Oct 2016 17:49:18: Permuting round 6 ... INFO @ Tue, 18 Oct 2016 17:49:19: Thread 0 started. INFO @ Tue, 18 Oct 2016 17:49:19: Thread 0: total 19149 instances. INFO @ Tue, 18 Oct 2016 17:49:19: Thread 0: Calculating HSF2BP (1) ... INFO @ Tue, 18 Oct 2016 17:49:26: Thread 0: Calculating ADAMTS7 (1001) ... INFO @ Tue, 18 Oct 2016 17:49:34: Thread 0: Calculating MCM3AP (2001) ... INFO @ Tue, 18 Oct 2016 17:49:42: Thread 0: Calculating HPSE2 (3001) ... INFO @ Tue, 18 Oct 2016 17:49:50: Thread 0: Calculating UTP23 (4001) ... INFO @ Tue, 18 Oct 2016 17:49:57: Thread 0: Calculating SEC24B (5001) ... INFO @ Tue, 18 Oct 2016 17:50:05: Thread 0: Calculating WDR45L (6001) ... INFO @ Tue, 18 Oct 2016 17:50:13: Thread 0: Calculating POFUT2 (7001) ... INFO @ Tue, 18 Oct 2016 17:50:20: Thread 0: Calculating SYDE1 (8001) ... INFO @ Tue, 18 Oct 2016 17:50:28: Thread 0: Calculating MR1 (9001) ... INFO @ Tue, 18 Oct 2016 17:50:35: Thread 0: Calculating NPRL2 (10001) ... INFO @ Tue, 18 Oct 2016 17:50:43: Thread 0: Calculating DNAJC7 (11001) ... INFO @ Tue, 18 Oct 2016 17:50:50: Thread 0: Calculating MYT1 (12001) ... INFO @ Tue, 18 Oct 2016 17:50:58: Thread 0: Calculating FAM83A (13001) ... INFO @ Tue, 18 Oct 2016 17:51:06: Thread 0: Calculating APOA1 (14001) ... INFO @ Tue, 18 Oct 2016 17:51:13: Thread 0: Calculating TIRAP (15001) ... INFO @ Tue, 18 Oct 2016 17:51:21: Thread 0: Calculating PLSCR5 (16001) ... INFO @ Tue, 18 Oct 2016 17:51:28: Thread 0: Calculating APBA1 (17001) ... INFO @ Tue, 18 Oct 2016 17:51:36: Thread 0: Calculating SH3BGR (18001) ... INFO @ Tue, 18 Oct 2016 17:51:44: Thread 0: Calculating OLAH (19001) ... INFO @ Tue, 18 Oct 2016 17:51:45: Thread 0 completed. INFO @ Tue, 18 Oct 2016 17:51:45: All threads completed. INFO @ Tue, 18 Oct 2016 17:51:51: Permuting round 7 ... INFO @ Tue, 18 Oct 2016 17:51:52: Thread 0 started. INFO @ Tue, 18 Oct 2016 17:51:52: Thread 0: total 19149 instances. INFO @ Tue, 18 Oct 2016 17:51:52: Thread 0: Calculating HSF2BP (1) ... INFO @ Tue, 18 Oct 2016 17:52:00: Thread 0: Calculating ADAMTS7 (1001) ... INFO @ Tue, 18 Oct 2016 17:52:08: Thread 0: Calculating MCM3AP (2001) ... INFO @ Tue, 18 Oct 2016 17:52:15: Thread 0: Calculating HPSE2 (3001) ... INFO @ Tue, 18 Oct 2016 17:52:23: Thread 0: Calculating UTP23 (4001) ... INFO @ Tue, 18 Oct 2016 17:52:31: Thread 0: Calculating SEC24B (5001) ... INFO @ Tue, 18 Oct 2016 17:52:38: Thread 0: Calculating WDR45L (6001) ... INFO @ Tue, 18 Oct 2016 17:52:46: Thread 0: Calculating POFUT2 (7001) ... INFO @ Tue, 18 Oct 2016 17:52:54: Thread 0: Calculating SYDE1 (8001) ... INFO @ Tue, 18 Oct 2016 17:53:02: Thread 0: Calculating MR1 (9001) ... INFO @ Tue, 18 Oct 2016 17:53:10: Thread 0: Calculating NPRL2 (10001) ... INFO @ Tue, 18 Oct 2016 17:53:18: Thread 0: Calculating DNAJC7 (11001) ... INFO @ Tue, 18 Oct 2016 17:53:26: Thread 0: Calculating MYT1 (12001) ... INFO @ Tue, 18 Oct 2016 17:53:34: Thread 0: Calculating FAM83A (13001) ... INFO @ Tue, 18 Oct 2016 17:53:41: Thread 0: Calculating APOA1 (14001) ... INFO @ Tue, 18 Oct 2016 17:53:49: Thread 0: Calculating TIRAP (15001) ... INFO @ Tue, 18 Oct 2016 17:53:57: Thread 0: Calculating PLSCR5 (16001) ... INFO @ Tue, 18 Oct 2016 17:54:05: Thread 0: Calculating APBA1 (17001) ... INFO @ Tue, 18 Oct 2016 17:54:13: Thread 0: Calculating SH3BGR (18001) ... INFO @ Tue, 18 Oct 2016 17:54:20: Thread 0: Calculating OLAH (19001) ... INFO @ Tue, 18 Oct 2016 17:54:22: Thread 0 completed. INFO @ Tue, 18 Oct 2016 17:54:22: All threads completed. INFO @ Tue, 18 Oct 2016 17:54:28: Permuting round 8 ... INFO @ Tue, 18 Oct 2016 17:54:29: Thread 0 started. INFO @ Tue, 18 Oct 2016 17:54:29: Thread 0: total 19149 instances. INFO @ Tue, 18 Oct 2016 17:54:29: Thread 0: Calculating HSF2BP (1) ... INFO @ Tue, 18 Oct 2016 17:54:37: Thread 0: Calculating ADAMTS7 (1001) ... INFO @ Tue, 18 Oct 2016 17:54:44: Thread 0: Calculating MCM3AP (2001) ... INFO @ Tue, 18 Oct 2016 17:54:52: Thread 0: Calculating HPSE2 (3001) ... INFO @ Tue, 18 Oct 2016 17:55:00: Thread 0: Calculating UTP23 (4001) ... INFO @ Tue, 18 Oct 2016 17:55:08: Thread 0: Calculating SEC24B (5001) ... INFO @ Tue, 18 Oct 2016 17:55:15: Thread 0: Calculating WDR45L (6001) ... INFO @ Tue, 18 Oct 2016 17:55:23: Thread 0: Calculating POFUT2 (7001) ... INFO @ Tue, 18 Oct 2016 17:55:30: Thread 0: Calculating SYDE1 (8001) ... INFO @ Tue, 18 Oct 2016 17:55:38: Thread 0: Calculating MR1 (9001) ... INFO @ Tue, 18 Oct 2016 17:55:46: Thread 0: Calculating NPRL2 (10001) ... INFO @ Tue, 18 Oct 2016 17:55:54: Thread 0: Calculating DNAJC7 (11001) ... INFO @ Tue, 18 Oct 2016 17:56:01: Thread 0: Calculating MYT1 (12001) ... INFO @ Tue, 18 Oct 2016 17:56:09: Thread 0: Calculating FAM83A (13001) ... INFO @ Tue, 18 Oct 2016 17:56:18: Thread 0: Calculating APOA1 (14001) ... INFO @ Tue, 18 Oct 2016 17:56:27: Thread 0: Calculating TIRAP (15001) ... INFO @ Tue, 18 Oct 2016 17:56:35: Thread 0: Calculating PLSCR5 (16001) ... INFO @ Tue, 18 Oct 2016 17:56:44: Thread 0: Calculating APBA1 (17001) ... INFO @ Tue, 18 Oct 2016 17:56:53: Thread 0: Calculating SH3BGR (18001) ... INFO @ Tue, 18 Oct 2016 17:57:02: Thread 0: Calculating OLAH (19001) ... INFO @ Tue, 18 Oct 2016 17:57:03: Thread 0 completed. INFO @ Tue, 18 Oct 2016 17:57:03: All threads completed. INFO @ Tue, 18 Oct 2016 17:57:11: Permuting round 9 ... INFO @ Tue, 18 Oct 2016 17:57:12: Thread 0 started. INFO @ Tue, 18 Oct 2016 17:57:12: Thread 0: total 19149 instances. INFO @ Tue, 18 Oct 2016 17:57:12: Thread 0: Calculating HSF2BP (1) ... INFO @ Tue, 18 Oct 2016 17:57:21: Thread 0: Calculating ADAMTS7 (1001) ... INFO @ Tue, 18 Oct 2016 17:57:30: Thread 0: Calculating MCM3AP (2001) ... INFO @ Tue, 18 Oct 2016 17:57:38: Thread 0: Calculating HPSE2 (3001) ... INFO @ Tue, 18 Oct 2016 17:57:46: Thread 0: Calculating UTP23 (4001) ... INFO @ Tue, 18 Oct 2016 17:57:53: Thread 0: Calculating SEC24B (5001) ... INFO @ Tue, 18 Oct 2016 17:58:01: Thread 0: Calculating WDR45L (6001) ... INFO @ Tue, 18 Oct 2016 17:58:09: Thread 0: Calculating POFUT2 (7001) ... INFO @ Tue, 18 Oct 2016 17:58:17: Thread 0: Calculating SYDE1 (8001) ... INFO @ Tue, 18 Oct 2016 17:58:24: Thread 0: Calculating MR1 (9001) ... INFO @ Tue, 18 Oct 2016 17:58:32: Thread 0: Calculating NPRL2 (10001) ... INFO @ Tue, 18 Oct 2016 17:58:40: Thread 0: Calculating DNAJC7 (11001) ... INFO @ Tue, 18 Oct 2016 17:58:48: Thread 0: Calculating MYT1 (12001) ... INFO @ Tue, 18 Oct 2016 17:58:55: Thread 0: Calculating FAM83A (13001) ... INFO @ Tue, 18 Oct 2016 17:59:03: Thread 0: Calculating APOA1 (14001) ... INFO @ Tue, 18 Oct 2016 17:59:11: Thread 0: Calculating TIRAP (15001) ... INFO @ Tue, 18 Oct 2016 17:59:19: Thread 0: Calculating PLSCR5 (16001) ... INFO @ Tue, 18 Oct 2016 17:59:26: Thread 0: Calculating APBA1 (17001) ... INFO @ Tue, 18 Oct 2016 17:59:34: Thread 0: Calculating SH3BGR (18001) ... INFO @ Tue, 18 Oct 2016 17:59:42: Thread 0: Calculating OLAH (19001) ... INFO @ Tue, 18 Oct 2016 17:59:43: Thread 0 completed. INFO @ Tue, 18 Oct 2016 17:59:43: All threads completed. INFO @ Tue, 18 Oct 2016 17:59:49: Assigning p values... INFO @ Tue, 18 Oct 2016 18:00:04: Writing gene results to results/test/myexperiment1.gene_summary.txt INFO @ Tue, 18 Oct 2016 18:00:04: Writing sgRNA results to results/test/myexperiment1.sgrna_summary.txt