INFO: [20/03/2023 19:58:43] -> Initializing Pipeline... INFO: [20/03/2023 19:58:43] -> Preprocessing Run #1 of 12... INFO: [20/03/2023 19:58:43] -> Searching DIA with Pulsar... INFO: [20/03/2023 19:58:43] -> Initialize Pipeline... INFO: [20/03/2023 19:58:43] -> Initialize Pipeline INFO: [20/03/2023 19:58:44] -> Initialize Pipeline... INFO: [20/03/2023 19:58:44] -> Creating Experiment Environment INFO: [20/03/2023 19:58:44] -> SuperRun 1/12: Initializing (APP_total_200ng_06.htrms) INFO: [20/03/2023 19:58:44] -> Run 1/12: Organizing Data from Run INFO: [20/03/2023 19:58:44] -> Run 1/12: Creating Calibration Search Space... INFO: [20/03/2023 19:58:45] -> Collecting Search Space Parameters... INFO: [20/03/2023 19:58:48] -> Creating the Search Space... INFO: [20/03/2023 19:58:50] -> Run 1/12: Creating Search Space... INFO: [20/03/2023 19:58:50] -> Collecting Search Space Parameters... INFO: [20/03/2023 19:59:07] -> Creating the Search Space... INFO: [20/03/2023 19:59:09] -> Size of search space [MB]: 0 INFO: [20/03/2023 19:59:09] -> Number of IMPGs in search space: 0 INFO: [20/03/2023 19:59:09] -> Run 1/12: MS2 Index Generation INFO: [20/03/2023 20:00:30] -> MS2 Index Generation Time: 1.34m INFO: [20/03/2023 20:00:30] -> Run 1/12: Method-Specific Pre-Processing... INFO: [20/03/2023 20:00:30] -> Initializing... INFO: [20/03/2023 20:00:37] -> Finalizing HTRMS File... INFO: [20/03/2023 20:01:23] -> Processed in 52.9s INFO: [20/03/2023 20:01:24] -> Done INFO: [20/03/2023 20:01:24] -> Run 1/12: Process Raw File... WARNING: [20/03/2023 20:01:24] -> Hard drive space is low (<100 GB)! Please free some space or set the temporary folder of SpectroMine to a different drive. INFO: [20/03/2023 20:01:38] -> Run 1/12: Preparing Partitions... INFO: [20/03/2023 20:01:38] -> Part 1/1 - Run 1/12: Preparing Calibration Searches... INFO: [20/03/2023 20:01:39] -> Part 1/1 - Run 1/12: First Pass Calibration Search... INFO: [20/03/2023 20:01:45] -> Part 1/1 - Run 1/12: Calibration Search... INFO: [20/03/2023 20:01:50] -> The number of PSMs identified during calibration with FDR <= 0.01 is 7319 [5.2s] INFO: [20/03/2023 20:01:55] -> Part 1/1 - Run 1/12: Preparing Main Search... INFO: [20/03/2023 20:01:56] -> Part 1/1 - Run 1/12: Main Search... INFO: [20/03/2023 20:03:49] -> Extracting 178604 MS1 XICs INFO: [20/03/2023 20:04:38] -> Run 1/12: Cleaning Up Run.. INFO: [20/03/2023 20:04:38] -> SuperRun 2/12: Initializing (APP_total_200ng_08.htrms) INFO: [20/03/2023 20:04:38] -> Run 2/12: Organizing Data from Run INFO: [20/03/2023 20:04:38] -> Run 2/12: Creating Calibration Search Space... INFO: [20/03/2023 20:04:38] -> Run 2/12: Creating Search Space... INFO: [20/03/2023 20:04:38] -> Size of search space [MB]: 0 INFO: [20/03/2023 20:04:38] -> Number of IMPGs in search space: 0 INFO: [20/03/2023 20:04:38] -> Run 2/12: MS2 Index Generation INFO: [20/03/2023 20:04:39] -> MS2 Index Generation Time: 1.51s INFO: [20/03/2023 20:04:39] -> Run 2/12: Method-Specific Pre-Processing... INFO: [20/03/2023 20:04:39] -> Initializing... INFO: [20/03/2023 20:04:46] -> Finalizing HTRMS File... INFO: [20/03/2023 20:05:31] -> Processed in 52.2s INFO: [20/03/2023 20:05:33] -> Done INFO: [20/03/2023 20:05:33] -> Run 2/12: Process Raw File... INFO: [20/03/2023 20:05:46] -> Run 2/12: Preparing Partitions... INFO: [20/03/2023 20:05:46] -> Part 1/1 - Run 2/12: Preparing Calibration Searches... INFO: [20/03/2023 20:05:48] -> Part 1/1 - Run 2/12: First Pass Calibration Search... INFO: [20/03/2023 20:05:53] -> Part 1/1 - Run 2/12: Calibration Search... INFO: [20/03/2023 20:05:59] -> The number of PSMs identified during calibration with FDR <= 0.01 is 7507 [5.8s] INFO: [20/03/2023 20:06:03] -> Part 1/1 - Run 2/12: Preparing Main Search... INFO: [20/03/2023 20:06:04] -> Part 1/1 - Run 2/12: Main Search... INFO: [20/03/2023 20:08:00] -> Extracting 186118 MS1 XICs INFO: [20/03/2023 20:08:47] -> Run 2/12: Cleaning Up Run.. INFO: [20/03/2023 20:08:47] -> SuperRun 3/12: Initializing (APP_total_200ng_09.htrms) INFO: [20/03/2023 20:08:47] -> Run 3/12: Organizing Data from Run INFO: [20/03/2023 20:08:47] -> Run 3/12: Creating Calibration Search Space... INFO: [20/03/2023 20:08:47] -> Run 3/12: Creating Search Space... INFO: [20/03/2023 20:08:47] -> Size of search space [MB]: 0 INFO: [20/03/2023 20:08:47] -> Number of IMPGs in search space: 0 INFO: [20/03/2023 20:08:47] -> Run 3/12: MS2 Index Generation INFO: [20/03/2023 20:08:49] -> MS2 Index Generation Time: 1.19s INFO: [20/03/2023 20:08:49] -> Run 3/12: Method-Specific Pre-Processing... INFO: [20/03/2023 20:08:49] -> Initializing... INFO: [20/03/2023 20:08:56] -> Finalizing HTRMS File... INFO: [20/03/2023 20:09:35] -> Processed in 46.6s INFO: [20/03/2023 20:09:37] -> Done INFO: [20/03/2023 20:09:37] -> Run 3/12: Process Raw File... INFO: [20/03/2023 20:09:51] -> Run 3/12: Preparing Partitions... INFO: [20/03/2023 20:09:51] -> Part 1/1 - Run 3/12: Preparing Calibration Searches... INFO: [20/03/2023 20:09:52] -> Part 1/1 - Run 3/12: First Pass Calibration Search... INFO: [20/03/2023 20:09:58] -> Part 1/1 - Run 3/12: Calibration Search... INFO: [20/03/2023 20:10:03] -> The number of PSMs identified during calibration with FDR <= 0.01 is 7238 [5.3s] INFO: [20/03/2023 20:10:07] -> Part 1/1 - Run 3/12: Preparing Main Search... INFO: [20/03/2023 20:10:08] -> Part 1/1 - Run 3/12: Main Search... INFO: [20/03/2023 20:12:22] -> Extracting 207639 MS1 XICs INFO: [20/03/2023 20:13:16] -> Run 3/12: Cleaning Up Run.. INFO: [20/03/2023 20:13:16] -> SuperRun 4/12: Initializing (APP_total_200ng_12.htrms) INFO: [20/03/2023 20:13:16] -> Run 4/12: Organizing Data from Run INFO: [20/03/2023 20:13:16] -> Run 4/12: Creating Calibration Search Space... INFO: [20/03/2023 20:13:16] -> Run 4/12: Creating Search Space... INFO: [20/03/2023 20:13:16] -> Size of search space [MB]: 0 INFO: [20/03/2023 20:13:16] -> Number of IMPGs in search space: 0 INFO: [20/03/2023 20:13:16] -> Run 4/12: MS2 Index Generation INFO: [20/03/2023 20:13:17] -> MS2 Index Generation Time: 1.28s INFO: [20/03/2023 20:13:17] -> Run 4/12: Method-Specific Pre-Processing... INFO: [20/03/2023 20:13:17] -> Initializing... INFO: [20/03/2023 20:13:24] -> Finalizing HTRMS File... INFO: [20/03/2023 20:14:07] -> Processed in 50s INFO: [20/03/2023 20:14:09] -> Done INFO: [20/03/2023 20:14:09] -> Run 4/12: Process Raw File... INFO: [20/03/2023 20:14:21] -> Run 4/12: Preparing Partitions... INFO: [20/03/2023 20:14:21] -> Part 1/1 - Run 4/12: Preparing Calibration Searches... INFO: [20/03/2023 20:14:23] -> Part 1/1 - Run 4/12: First Pass Calibration Search... INFO: [20/03/2023 20:14:28] -> Part 1/1 - Run 4/12: Calibration Search... INFO: [20/03/2023 20:14:34] -> The number of PSMs identified during calibration with FDR <= 0.01 is 7372 [5.7s] INFO: [20/03/2023 20:14:38] -> Part 1/1 - Run 4/12: Preparing Main Search... INFO: [20/03/2023 20:14:39] -> Part 1/1 - Run 4/12: Main Search... INFO: [20/03/2023 20:16:45] -> Extracting 203243 MS1 XICs INFO: [20/03/2023 20:17:39] -> Run 4/12: Cleaning Up Run.. INFO: [20/03/2023 20:17:39] -> SuperRun 5/12: Initializing (APP_total_200ng_13.htrms) INFO: [20/03/2023 20:17:39] -> Run 5/12: Organizing Data from Run INFO: [20/03/2023 20:17:39] -> Run 5/12: Creating Calibration Search Space... INFO: [20/03/2023 20:17:39] -> Run 5/12: Creating Search Space... INFO: [20/03/2023 20:17:39] -> Size of search space [MB]: 0 INFO: [20/03/2023 20:17:39] -> Number of IMPGs in search space: 0 INFO: [20/03/2023 20:17:39] -> Run 5/12: MS2 Index Generation INFO: [20/03/2023 20:17:40] -> MS2 Index Generation Time: 1.37s INFO: [20/03/2023 20:17:40] -> Run 5/12: Method-Specific Pre-Processing... INFO: [20/03/2023 20:17:40] -> Initializing... INFO: [20/03/2023 20:17:47] -> Finalizing HTRMS File... INFO: [20/03/2023 20:18:25] -> Processed in 44.9s INFO: [20/03/2023 20:18:26] -> Done INFO: [20/03/2023 20:18:26] -> Run 5/12: Process Raw File... INFO: [20/03/2023 20:18:42] -> Run 5/12: Preparing Partitions... INFO: [20/03/2023 20:18:42] -> Part 1/1 - Run 5/12: Preparing Calibration Searches... INFO: [20/03/2023 20:18:43] -> Part 1/1 - Run 5/12: First Pass Calibration Search... INFO: [20/03/2023 20:18:49] -> Part 1/1 - Run 5/12: Calibration Search... INFO: [20/03/2023 20:18:57] -> The number of PSMs identified during calibration with FDR <= 0.01 is 5666 [7.8s] INFO: [20/03/2023 20:19:00] -> Part 1/1 - Run 5/12: Preparing Main Search... INFO: [20/03/2023 20:19:02] -> Part 1/1 - Run 5/12: Main Search... INFO: [20/03/2023 20:21:17] -> Extracting 183004 MS1 XICs INFO: [20/03/2023 20:22:07] -> Run 5/12: Cleaning Up Run.. INFO: [20/03/2023 20:22:07] -> SuperRun 6/12: Initializing (APP_total_200ng_14.htrms) INFO: [20/03/2023 20:22:07] -> Run 6/12: Organizing Data from Run INFO: [20/03/2023 20:22:07] -> Run 6/12: Creating Calibration Search Space... INFO: [20/03/2023 20:22:07] -> Run 6/12: Creating Search Space... INFO: [20/03/2023 20:22:07] -> Size of search space [MB]: 0 INFO: [20/03/2023 20:22:07] -> Number of IMPGs in search space: 0 INFO: [20/03/2023 20:22:07] -> Run 6/12: MS2 Index Generation INFO: [20/03/2023 20:22:09] -> MS2 Index Generation Time: 1.51s INFO: [20/03/2023 20:22:09] -> Run 6/12: Method-Specific Pre-Processing... INFO: [20/03/2023 20:22:09] -> Initializing... INFO: [20/03/2023 20:22:16] -> Finalizing HTRMS File... INFO: [20/03/2023 20:22:55] -> Processed in 45.9s INFO: [20/03/2023 20:22:56] -> Done INFO: [20/03/2023 20:22:56] -> Run 6/12: Process Raw File... INFO: [20/03/2023 20:23:10] -> Run 6/12: Preparing Partitions... INFO: [20/03/2023 20:23:10] -> Part 1/1 - Run 6/12: Preparing Calibration Searches... INFO: [20/03/2023 20:23:11] -> Part 1/1 - Run 6/12: First Pass Calibration Search... INFO: [20/03/2023 20:23:16] -> Part 1/1 - Run 6/12: Calibration Search... INFO: [20/03/2023 20:23:22] -> The number of PSMs identified during calibration with FDR <= 0.01 is 6900 [5.9s] INFO: [20/03/2023 20:23:26] -> Part 1/1 - Run 6/12: Preparing Main Search... INFO: [20/03/2023 20:23:27] -> Part 1/1 - Run 6/12: Main Search... INFO: [20/03/2023 20:25:47] -> Extracting 206494 MS1 XICs INFO: [20/03/2023 20:26:43] -> Run 6/12: Cleaning Up Run.. INFO: [20/03/2023 20:26:43] -> SuperRun 7/12: Initializing (WT_total_200ng_01.htrms) INFO: [20/03/2023 20:26:43] -> Run 7/12: Organizing Data from Run INFO: [20/03/2023 20:26:43] -> Run 7/12: Creating Calibration Search Space... INFO: [20/03/2023 20:26:43] -> Run 7/12: Creating Search Space... INFO: [20/03/2023 20:26:43] -> Size of search space [MB]: 0 INFO: [20/03/2023 20:26:43] -> Number of IMPGs in search space: 0 INFO: [20/03/2023 20:26:43] -> Run 7/12: MS2 Index Generation INFO: [20/03/2023 20:26:44] -> MS2 Index Generation Time: 1.29s INFO: [20/03/2023 20:26:44] -> Run 7/12: Method-Specific Pre-Processing... INFO: [20/03/2023 20:26:44] -> Initializing... INFO: [20/03/2023 20:26:51] -> Finalizing HTRMS File... INFO: [20/03/2023 20:27:37] -> Processed in 52.1s INFO: [20/03/2023 20:27:38] -> Done INFO: [20/03/2023 20:27:38] -> Run 7/12: Process Raw File... INFO: [20/03/2023 20:27:51] -> Run 7/12: Preparing Partitions... INFO: [20/03/2023 20:27:51] -> Part 1/1 - Run 7/12: Preparing Calibration Searches... INFO: [20/03/2023 20:27:52] -> Part 1/1 - Run 7/12: First Pass Calibration Search... INFO: [20/03/2023 20:27:57] -> Part 1/1 - Run 7/12: Calibration Search... INFO: [20/03/2023 20:28:03] -> The number of PSMs identified during calibration with FDR <= 0.01 is 6767 [5.7s] INFO: [20/03/2023 20:28:07] -> Part 1/1 - Run 7/12: Preparing Main Search... INFO: [20/03/2023 20:28:08] -> Part 1/1 - Run 7/12: Main Search... INFO: [20/03/2023 20:30:13] -> Extracting 197008 MS1 XICs INFO: [20/03/2023 20:31:04] -> Run 7/12: Cleaning Up Run.. INFO: [20/03/2023 20:31:04] -> SuperRun 8/12: Initializing (WT_total_200ng_02.htrms) INFO: [20/03/2023 20:31:04] -> Run 8/12: Organizing Data from Run INFO: [20/03/2023 20:31:04] -> Run 8/12: Creating Calibration Search Space... INFO: [20/03/2023 20:31:04] -> Run 8/12: Creating Search Space... INFO: [20/03/2023 20:31:04] -> Size of search space [MB]: 0 INFO: [20/03/2023 20:31:04] -> Number of IMPGs in search space: 0 INFO: [20/03/2023 20:31:04] -> Run 8/12: MS2 Index Generation INFO: [20/03/2023 20:31:06] -> MS2 Index Generation Time: 1.31s INFO: [20/03/2023 20:31:06] -> Run 8/12: Method-Specific Pre-Processing... INFO: [20/03/2023 20:31:06] -> Initializing... INFO: [20/03/2023 20:31:12] -> Finalizing HTRMS File... INFO: [20/03/2023 20:31:54] -> Processed in 48.2s INFO: [20/03/2023 20:31:55] -> Done INFO: [20/03/2023 20:31:55] -> Run 8/12: Process Raw File... INFO: [20/03/2023 20:32:09] -> Run 8/12: Preparing Partitions... INFO: [20/03/2023 20:32:09] -> Part 1/1 - Run 8/12: Preparing Calibration Searches... INFO: [20/03/2023 20:32:10] -> Part 1/1 - Run 8/12: First Pass Calibration Search... INFO: [20/03/2023 20:32:15] -> Part 1/1 - Run 8/12: Calibration Search... INFO: [20/03/2023 20:32:20] -> The number of PSMs identified during calibration with FDR <= 0.01 is 6948 [5s] INFO: [20/03/2023 20:32:24] -> Part 1/1 - Run 8/12: Preparing Main Search... INFO: [20/03/2023 20:32:26] -> Part 1/1 - Run 8/12: Main Search... INFO: [20/03/2023 20:34:07] -> Extracting 167281 MS1 XICs INFO: [20/03/2023 20:34:50] -> Run 8/12: Cleaning Up Run.. INFO: [20/03/2023 20:34:50] -> SuperRun 9/12: Initializing (WT_total_200ng_03.htrms) INFO: [20/03/2023 20:34:50] -> Run 9/12: Organizing Data from Run INFO: [20/03/2023 20:34:50] -> Run 9/12: Creating Calibration Search Space... INFO: [20/03/2023 20:34:51] -> Run 9/12: Creating Search Space... INFO: [20/03/2023 20:34:51] -> Size of search space [MB]: 0 INFO: [20/03/2023 20:34:51] -> Number of IMPGs in search space: 0 INFO: [20/03/2023 20:34:51] -> Run 9/12: MS2 Index Generation INFO: [20/03/2023 20:34:52] -> MS2 Index Generation Time: 1.24s INFO: [20/03/2023 20:34:52] -> Run 9/12: Method-Specific Pre-Processing... INFO: [20/03/2023 20:34:52] -> Initializing... INFO: [20/03/2023 20:34:59] -> Finalizing HTRMS File... INFO: [20/03/2023 20:35:45] -> Processed in 52.8s INFO: [20/03/2023 20:35:46] -> Done INFO: [20/03/2023 20:35:46] -> Run 9/12: Process Raw File... INFO: [20/03/2023 20:35:59] -> Run 9/12: Preparing Partitions... INFO: [20/03/2023 20:35:59] -> Part 1/1 - Run 9/12: Preparing Calibration Searches... INFO: [20/03/2023 20:36:01] -> Part 1/1 - Run 9/12: First Pass Calibration Search... INFO: [20/03/2023 20:36:06] -> Part 1/1 - Run 9/12: Calibration Search... INFO: [20/03/2023 20:36:11] -> The number of PSMs identified during calibration with FDR <= 0.01 is 6850 [5.6s] INFO: [20/03/2023 20:36:15] -> Part 1/1 - Run 9/12: Preparing Main Search... INFO: [20/03/2023 20:36:16] -> Part 1/1 - Run 9/12: Main Search... INFO: [20/03/2023 20:38:26] -> Extracting 203468 MS1 XICs INFO: [20/03/2023 20:39:19] -> Run 9/12: Cleaning Up Run.. INFO: [20/03/2023 20:39:19] -> SuperRun 10/12: Initializing (WT_total_200ng_04.htrms) INFO: [20/03/2023 20:39:19] -> Run 10/12: Organizing Data from Run INFO: [20/03/2023 20:39:19] -> Run 10/12: Creating Calibration Search Space... INFO: [20/03/2023 20:39:19] -> Run 10/12: Creating Search Space... INFO: [20/03/2023 20:39:19] -> Size of search space [MB]: 0 INFO: [20/03/2023 20:39:19] -> Number of IMPGs in search space: 0 INFO: [20/03/2023 20:39:19] -> Run 10/12: MS2 Index Generation INFO: [20/03/2023 20:39:20] -> MS2 Index Generation Time: 1.2s INFO: [20/03/2023 20:39:20] -> Run 10/12: Method-Specific Pre-Processing... INFO: [20/03/2023 20:39:20] -> Initializing... INFO: [20/03/2023 20:39:27] -> Finalizing HTRMS File... INFO: [20/03/2023 20:40:09] -> Processed in 48.5s INFO: [20/03/2023 20:40:10] -> Done INFO: [20/03/2023 20:40:10] -> Run 10/12: Process Raw File... INFO: [20/03/2023 20:40:23] -> Run 10/12: Preparing Partitions... INFO: [20/03/2023 20:40:23] -> Part 1/1 - Run 10/12: Preparing Calibration Searches... INFO: [20/03/2023 20:40:24] -> Part 1/1 - Run 10/12: First Pass Calibration Search... INFO: [20/03/2023 20:40:29] -> Part 1/1 - Run 10/12: Calibration Search... INFO: [20/03/2023 20:40:35] -> The number of PSMs identified during calibration with FDR <= 0.01 is 7601 [5.8s] INFO: [20/03/2023 20:40:39] -> Part 1/1 - Run 10/12: Preparing Main Search... INFO: [20/03/2023 20:40:40] -> Part 1/1 - Run 10/12: Main Search... INFO: [20/03/2023 20:42:30] -> Extracting 183041 MS1 XICs INFO: [20/03/2023 20:43:18] -> Run 10/12: Cleaning Up Run.. INFO: [20/03/2023 20:43:18] -> SuperRun 11/12: Initializing (WT_total_200ng_05.htrms) INFO: [20/03/2023 20:43:18] -> Run 11/12: Organizing Data from Run INFO: [20/03/2023 20:43:18] -> Run 11/12: Creating Calibration Search Space... INFO: [20/03/2023 20:43:18] -> Run 11/12: Creating Search Space... INFO: [20/03/2023 20:43:18] -> Size of search space [MB]: 0 INFO: [20/03/2023 20:43:18] -> Number of IMPGs in search space: 0 INFO: [20/03/2023 20:43:18] -> Run 11/12: MS2 Index Generation INFO: [20/03/2023 20:43:19] -> MS2 Index Generation Time: 1.22s INFO: [20/03/2023 20:43:19] -> Run 11/12: Method-Specific Pre-Processing... INFO: [20/03/2023 20:43:19] -> Initializing... INFO: [20/03/2023 20:43:25] -> Finalizing HTRMS File... INFO: [20/03/2023 20:44:09] -> Processed in 50s INFO: [20/03/2023 20:44:10] -> Done INFO: [20/03/2023 20:44:10] -> Run 11/12: Process Raw File... INFO: [20/03/2023 20:44:24] -> Run 11/12: Preparing Partitions... INFO: [20/03/2023 20:44:24] -> Part 1/1 - Run 11/12: Preparing Calibration Searches... INFO: [20/03/2023 20:44:25] -> Part 1/1 - Run 11/12: First Pass Calibration Search... INFO: [20/03/2023 20:44:30] -> Part 1/1 - Run 11/12: Calibration Search... INFO: [20/03/2023 20:44:36] -> The number of PSMs identified during calibration with FDR <= 0.01 is 7123 [5.7s] INFO: [20/03/2023 20:44:40] -> Part 1/1 - Run 11/12: Preparing Main Search... INFO: [20/03/2023 20:44:41] -> Part 1/1 - Run 11/12: Main Search... INFO: [20/03/2023 20:46:49] -> Extracting 190368 MS1 XICs INFO: [20/03/2023 20:47:38] -> Run 11/12: Cleaning Up Run.. INFO: [20/03/2023 20:47:38] -> SuperRun 12/12: Initializing (WT_total_200ng_07.htrms) INFO: [20/03/2023 20:47:38] -> Run 12/12: Organizing Data from Run INFO: [20/03/2023 20:47:38] -> Run 12/12: Creating Calibration Search Space... INFO: [20/03/2023 20:47:38] -> Run 12/12: Creating Search Space... INFO: [20/03/2023 20:47:38] -> Size of search space [MB]: 0 INFO: [20/03/2023 20:47:38] -> Number of IMPGs in search space: 0 INFO: [20/03/2023 20:47:38] -> Run 12/12: MS2 Index Generation INFO: [20/03/2023 20:47:40] -> MS2 Index Generation Time: 1.41s INFO: [20/03/2023 20:47:40] -> Run 12/12: Method-Specific Pre-Processing... INFO: [20/03/2023 20:47:40] -> Initializing... INFO: [20/03/2023 20:47:46] -> Finalizing HTRMS File... INFO: [20/03/2023 20:48:31] -> Processed in 50.8s INFO: [20/03/2023 20:48:32] -> Done INFO: [20/03/2023 20:48:32] -> Run 12/12: Process Raw File... INFO: [20/03/2023 20:48:46] -> Run 12/12: Preparing Partitions... INFO: [20/03/2023 20:48:46] -> Part 1/1 - Run 12/12: Preparing Calibration Searches... INFO: [20/03/2023 20:48:47] -> Part 1/1 - Run 12/12: First Pass Calibration Search... INFO: [20/03/2023 20:48:52] -> Part 1/1 - Run 12/12: Calibration Search... INFO: [20/03/2023 20:48:58] -> The number of PSMs identified during calibration with FDR <= 0.01 is 5763 [5.5s] INFO: [20/03/2023 20:49:01] -> Part 1/1 - Run 12/12: Preparing Main Search... INFO: [20/03/2023 20:49:02] -> Part 1/1 - Run 12/12: Main Search... INFO: [20/03/2023 20:50:52] -> Extracting 164329 MS1 XICs INFO: [20/03/2023 20:51:34] -> Run 12/12: Cleaning Up Run.. INFO: [20/03/2023 20:51:38] -> Remove Aborted Runs (if any) from the Experiment... INFO: [20/03/2023 20:51:38] -> Score Post-Processing INFO: [20/03/2023 20:53:19] -> Score Post-Processing: 1.69m INFO: [20/03/2023 20:53:19] -> PSM FDR... INFO: [20/03/2023 20:54:15] -> PSM FDR: 55.87s INFO: [20/03/2023 20:54:15] -> Converting to non-redundant data structure... INFO: [20/03/2023 20:54:40] -> Performing Peptide FDR... INFO: [20/03/2023 20:54:48] -> Performing Protein Inference... INFO: [20/03/2023 20:54:49] -> Performing Protein FDR... INFO: [20/03/2023 20:54:51] -> Calculating Result Values at Run and Experiment Level... INFO: [20/03/2023 20:55:11] -> Pulsar identified 763398 PSMs, 35359 stripped sequences, 44535 peptide precursors, 3802 protein groups. INFO: [20/03/2023 20:55:11] -> Writing experiment store.. INFO: [20/03/2023 20:55:14] -> Selecting Data For Quantification... INFO: [20/03/2023 20:55:14] -> Calculating Quantities... INFO: [20/03/2023 20:55:31] -> Calculating Protein Group Quantities using MaxLFQ Algorithm... INFO: [20/03/2023 20:55:31] -> Collapsing PTM-Locations... INFO: [20/03/2023 20:55:31] -> Summarizing Fractions... INFO: [20/03/2023 20:55:33] -> Gathering Protein Information of all Matching Proteins INFO: [20/03/2023 20:55:33] -> Running Post Analysis Processes... INFO: [20/03/2023 20:55:33] -> Identifying Calibration Peptides... INFO: [20/03/2023 20:55:34] -> iRT Calibration... INFO: [20/03/2023 20:55:39] -> Assigning iRT Source... INFO: [20/03/2023 20:55:39] -> Calculating iRT... INFO: [20/03/2023 20:55:40] -> Summarizing Identifications INFO: [20/03/2023 20:56:36] -> Generating directDIA+ search space INFO: [20/03/2023 21:00:39] -> directDIA+ search: APP_total_200ng_06.htrms INFO: [20/03/2023 21:03:57] -> directDIA+ search: APP_total_200ng_08.htrms INFO: [20/03/2023 21:07:10] -> directDIA+ search: APP_total_200ng_09.htrms INFO: [20/03/2023 21:10:25] -> directDIA+ search: APP_total_200ng_12.htrms INFO: [20/03/2023 21:13:34] -> directDIA+ search: APP_total_200ng_13.htrms INFO: [20/03/2023 21:16:40] -> directDIA+ search: APP_total_200ng_14.htrms INFO: [20/03/2023 21:19:58] -> directDIA+ search: WT_total_200ng_01.htrms INFO: [20/03/2023 21:23:17] -> directDIA+ search: WT_total_200ng_02.htrms INFO: [20/03/2023 21:26:36] -> directDIA+ search: WT_total_200ng_03.htrms INFO: [20/03/2023 21:29:55] -> directDIA+ search: WT_total_200ng_04.htrms INFO: [20/03/2023 21:33:19] -> directDIA+ search: WT_total_200ng_05.htrms INFO: [20/03/2023 21:36:29] -> directDIA+ search: WT_total_200ng_07.htrms INFO: [20/03/2023 21:41:17] -> Identifiying Significant Precurors... INFO: [20/03/2023 21:41:35] -> Predicting Ion Mobility INFO: [20/03/2023 21:41:37] -> Calculating Median iRT INFO: [20/03/2023 21:41:38] -> Building BGS Protein Grouping... INFO: [20/03/2023 21:41:39] -> Digesting Fasta... INFO: [20/03/2023 21:41:39] -> Annotating Proteins... INFO: [20/03/2023 21:41:39] -> Grouping Proteins... INFO: [20/03/2023 21:41:40] -> Calculating Run Summary Statistics... INFO: [20/03/2023 21:42:08] -> Building Consensus Fragment Spectra... INFO: [20/03/2023 21:43:20] -> Selecting best fragment ions INFO: [20/03/2023 21:45:25] -> Cleaning Up Experiment... INFO: [20/03/2023 21:45:26] -> Initializing Experiment... INFO: [20/03/2023 21:45:26] -> Loading Spectral Libraries... INFO: [20/03/2023 21:45:39] -> Initialize Scoring... INFO: [20/03/2023 21:45:39] -> Generating Scan Map... INFO: [20/03/2023 21:45:39] -> Initializing Workpackages... INFO: [20/03/2023 21:45:39] -> Performing Basic Calibration... INFO: [20/03/2023 21:45:40] -> Identifying Calibration Peptides... INFO: [20/03/2023 21:45:40] -> Correcting Gradient Fine Structure... INFO: [20/03/2023 21:45:42] -> Initializing Pipeline... INFO: [20/03/2023 21:45:42] -> Preprocessing Run #1 of 12... INFO: [20/03/2023 21:45:42] -> Initialize Scoring... INFO: [20/03/2023 21:45:42] -> Extracting Ion Currents... INFO: [20/03/2023 21:46:00] -> Machine Learning... INFO: [20/03/2023 21:46:01] -> Pipeline executed in 18.44s INFO: [20/03/2023 21:46:04] -> Initializing Pipeline... INFO: [20/03/2023 21:46:04] -> Preprocessing Run #1 of 12... INFO: [20/03/2023 21:46:04] -> Initialize Scoring... INFO: [20/03/2023 21:46:04] -> Extracting Ion Currents... INFO: [20/03/2023 21:46:18] -> Machine Learning... INFO: [20/03/2023 21:46:20] -> Pipeline executed in 16.09s INFO: [20/03/2023 21:46:26] -> Initialize Scoring... INFO: [20/03/2023 21:46:26] -> Preprocessing Run #2 of 12... INFO: [20/03/2023 21:46:26] -> Searching DIA with Pulsar... INFO: [20/03/2023 21:46:26] -> Initializing Experiment... INFO: [20/03/2023 21:46:26] -> Loading Spectral Libraries... INFO: [20/03/2023 21:46:26] -> Initialize Scoring... INFO: [20/03/2023 21:46:26] -> Generating Scan Map... INFO: [20/03/2023 21:46:26] -> Initializing Workpackages... INFO: [20/03/2023 21:46:26] -> Performing Basic Calibration... INFO: [20/03/2023 21:46:27] -> Identifying Calibration Peptides... INFO: [20/03/2023 21:46:27] -> Correcting Gradient Fine Structure... INFO: [20/03/2023 21:46:29] -> Initializing Pipeline... INFO: [20/03/2023 21:46:29] -> Preprocessing Run #2 of 12... INFO: [20/03/2023 21:46:29] -> Initialize Scoring... INFO: [20/03/2023 21:46:29] -> Extracting Ion Currents... INFO: [20/03/2023 21:46:47] -> Machine Learning... INFO: [20/03/2023 21:46:48] -> Pipeline executed in 19.23s INFO: [20/03/2023 21:46:52] -> Initializing Pipeline... INFO: [20/03/2023 21:46:52] -> Preprocessing Run #2 of 12... INFO: [20/03/2023 21:46:52] -> Initialize Scoring... INFO: [20/03/2023 21:46:52] -> Extracting Ion Currents... INFO: [20/03/2023 21:47:06] -> Machine Learning... INFO: [20/03/2023 21:47:08] -> Pipeline executed in 16.39s INFO: [20/03/2023 21:47:13] -> Initialize Scoring... INFO: [20/03/2023 21:47:13] -> Preprocessing Run #3 of 12... INFO: [20/03/2023 21:47:13] -> Searching DIA with Pulsar... INFO: [20/03/2023 21:47:13] -> Initializing Experiment... INFO: [20/03/2023 21:47:13] -> Loading Spectral Libraries... INFO: [20/03/2023 21:47:13] -> Initialize Scoring... INFO: [20/03/2023 21:47:13] -> Generating Scan Map... INFO: [20/03/2023 21:47:13] -> Initializing Workpackages... INFO: [20/03/2023 21:47:13] -> Performing Basic Calibration... INFO: [20/03/2023 21:47:14] -> Identifying Calibration Peptides... INFO: [20/03/2023 21:47:14] -> Correcting Gradient Fine Structure... INFO: [20/03/2023 21:47:16] -> Initializing Pipeline... INFO: [20/03/2023 21:47:16] -> Preprocessing Run #3 of 12... INFO: [20/03/2023 21:47:16] -> Initialize Scoring... INFO: [20/03/2023 21:47:16] -> Extracting Ion Currents... INFO: [20/03/2023 21:47:35] -> Machine Learning... INFO: [20/03/2023 21:47:36] -> Pipeline executed in 19.31s INFO: [20/03/2023 21:47:39] -> Initializing Pipeline... INFO: [20/03/2023 21:47:39] -> Preprocessing Run #3 of 12... INFO: [20/03/2023 21:47:39] -> Initialize Scoring... INFO: [20/03/2023 21:47:39] -> Extracting Ion Currents... INFO: [20/03/2023 21:47:53] -> Machine Learning... INFO: [20/03/2023 21:47:55] -> Pipeline executed in 16.09s INFO: [20/03/2023 21:48:00] -> Initialize Scoring... INFO: [20/03/2023 21:48:00] -> Preprocessing Run #4 of 12... INFO: [20/03/2023 21:48:00] -> Searching DIA with Pulsar... INFO: [20/03/2023 21:48:00] -> Initializing Experiment... INFO: [20/03/2023 21:48:00] -> Loading Spectral Libraries... INFO: [20/03/2023 21:48:00] -> Initialize Scoring... INFO: [20/03/2023 21:48:00] -> Generating Scan Map... INFO: [20/03/2023 21:48:00] -> Initializing Workpackages... INFO: [20/03/2023 21:48:00] -> Performing Basic Calibration... INFO: [20/03/2023 21:48:01] -> Identifying Calibration Peptides... INFO: [20/03/2023 21:48:01] -> Correcting Gradient Fine Structure... INFO: [20/03/2023 21:48:03] -> Initializing Pipeline... INFO: [20/03/2023 21:48:03] -> Preprocessing Run #4 of 12... INFO: [20/03/2023 21:48:03] -> Initialize Scoring... INFO: [20/03/2023 21:48:03] -> Extracting Ion Currents... INFO: [20/03/2023 21:48:21] -> Machine Learning... INFO: [20/03/2023 21:48:22] -> Pipeline executed in 18.69s INFO: [20/03/2023 21:48:25] -> Initializing Pipeline... INFO: [20/03/2023 21:48:25] -> Preprocessing Run #4 of 12... INFO: [20/03/2023 21:48:25] -> Initialize Scoring... INFO: [20/03/2023 21:48:25] -> Extracting Ion Currents... INFO: [20/03/2023 21:48:39] -> Machine Learning... INFO: [20/03/2023 21:48:42] -> Pipeline executed in 16.22s INFO: [20/03/2023 21:48:47] -> Initialize Scoring... INFO: [20/03/2023 21:48:47] -> Preprocessing Run #5 of 12... INFO: [20/03/2023 21:48:47] -> Searching DIA with Pulsar... INFO: [20/03/2023 21:48:47] -> Initializing Experiment... INFO: [20/03/2023 21:48:47] -> Loading Spectral Libraries... INFO: [20/03/2023 21:48:47] -> Initialize Scoring... INFO: [20/03/2023 21:48:47] -> Generating Scan Map... INFO: [20/03/2023 21:48:47] -> Initializing Workpackages... INFO: [20/03/2023 21:48:47] -> Performing Basic Calibration... INFO: [20/03/2023 21:48:48] -> Identifying Calibration Peptides... INFO: [20/03/2023 21:48:48] -> Correcting Gradient Fine Structure... INFO: [20/03/2023 21:48:50] -> Initializing Pipeline... INFO: [20/03/2023 21:48:50] -> Preprocessing Run #5 of 12... INFO: [20/03/2023 21:48:50] -> Initialize Scoring... INFO: [20/03/2023 21:48:50] -> Extracting Ion Currents... INFO: [20/03/2023 21:49:07] -> Machine Learning... INFO: [20/03/2023 21:49:08] -> Pipeline executed in 18.59s INFO: [20/03/2023 21:49:12] -> Initializing Pipeline... INFO: [20/03/2023 21:49:12] -> Preprocessing Run #5 of 12... INFO: [20/03/2023 21:49:12] -> Initialize Scoring... INFO: [20/03/2023 21:49:12] -> Extracting Ion Currents... INFO: [20/03/2023 21:49:25] -> Machine Learning... INFO: [20/03/2023 21:49:28] -> Pipeline executed in 15.94s INFO: [20/03/2023 21:49:33] -> Initialize Scoring... INFO: [20/03/2023 21:49:33] -> Preprocessing Run #6 of 12... INFO: [20/03/2023 21:49:33] -> Searching DIA with Pulsar... INFO: [20/03/2023 21:49:33] -> Initializing Experiment... INFO: [20/03/2023 21:49:33] -> Loading Spectral Libraries... INFO: [20/03/2023 21:49:33] -> Initialize Scoring... INFO: [20/03/2023 21:49:33] -> Generating Scan Map... INFO: [20/03/2023 21:49:33] -> Initializing Workpackages... INFO: [20/03/2023 21:49:33] -> Performing Basic Calibration... INFO: [20/03/2023 21:49:34] -> Identifying Calibration Peptides... INFO: [20/03/2023 21:49:34] -> Correcting Gradient Fine Structure... INFO: [20/03/2023 21:49:36] -> Initializing Pipeline... INFO: [20/03/2023 21:49:36] -> Preprocessing Run #6 of 12... INFO: [20/03/2023 21:49:36] -> Initialize Scoring... INFO: [20/03/2023 21:49:36] -> Extracting Ion Currents... INFO: [20/03/2023 21:49:54] -> Machine Learning... INFO: [20/03/2023 21:49:55] -> Pipeline executed in 18.95s INFO: [20/03/2023 21:49:59] -> Initializing Pipeline... INFO: [20/03/2023 21:49:59] -> Preprocessing Run #6 of 12... INFO: [20/03/2023 21:49:59] -> Initialize Scoring... INFO: [20/03/2023 21:49:59] -> Extracting Ion Currents... INFO: [20/03/2023 21:50:14] -> Machine Learning... INFO: [20/03/2023 21:50:16] -> Pipeline executed in 16.76s INFO: [20/03/2023 21:50:21] -> Initialize Scoring... INFO: [20/03/2023 21:50:21] -> Preprocessing Run #7 of 12... INFO: [20/03/2023 21:50:21] -> Searching DIA with Pulsar... INFO: [20/03/2023 21:50:21] -> Initializing Experiment... INFO: [20/03/2023 21:50:21] -> Loading Spectral Libraries... INFO: [20/03/2023 21:50:21] -> Initialize Scoring... INFO: [20/03/2023 21:50:21] -> Generating Scan Map... INFO: [20/03/2023 21:50:21] -> Initializing Workpackages... INFO: [20/03/2023 21:50:21] -> Performing Basic Calibration... INFO: [20/03/2023 21:50:22] -> Identifying Calibration Peptides... INFO: [20/03/2023 21:50:22] -> Correcting Gradient Fine Structure... INFO: [20/03/2023 21:50:24] -> Initializing Pipeline... INFO: [20/03/2023 21:50:24] -> Preprocessing Run #7 of 12... INFO: [20/03/2023 21:50:24] -> Initialize Scoring... INFO: [20/03/2023 21:50:24] -> Extracting Ion Currents... INFO: [20/03/2023 21:50:42] -> Machine Learning... INFO: [20/03/2023 21:50:43] -> Pipeline executed in 18.27s INFO: [20/03/2023 21:50:46] -> Initializing Pipeline... INFO: [20/03/2023 21:50:46] -> Preprocessing Run #7 of 12... INFO: [20/03/2023 21:50:46] -> Initialize Scoring... INFO: [20/03/2023 21:50:46] -> Extracting Ion Currents... INFO: [20/03/2023 21:51:01] -> Machine Learning... INFO: [20/03/2023 21:51:03] -> Pipeline executed in 16.94s INFO: [20/03/2023 21:51:08] -> Initialize Scoring... INFO: [20/03/2023 21:51:08] -> Preprocessing Run #8 of 12... INFO: [20/03/2023 21:51:08] -> Searching DIA with Pulsar... INFO: [20/03/2023 21:51:08] -> Initializing Experiment... INFO: [20/03/2023 21:51:08] -> Loading Spectral Libraries... INFO: [20/03/2023 21:51:08] -> Initialize Scoring... INFO: [20/03/2023 21:51:08] -> Generating Scan Map... INFO: [20/03/2023 21:51:08] -> Initializing Workpackages... INFO: [20/03/2023 21:51:08] -> Performing Basic Calibration... INFO: [20/03/2023 21:51:09] -> Identifying Calibration Peptides... INFO: [20/03/2023 21:51:09] -> Correcting Gradient Fine Structure... INFO: [20/03/2023 21:51:11] -> Initializing Pipeline... INFO: [20/03/2023 21:51:11] -> Preprocessing Run #8 of 12... INFO: [20/03/2023 21:51:11] -> Initialize Scoring... INFO: [20/03/2023 21:51:11] -> Extracting Ion Currents... INFO: [20/03/2023 21:51:29] -> Machine Learning... INFO: [20/03/2023 21:51:30] -> Pipeline executed in 18.65s INFO: [20/03/2023 21:51:33] -> Initializing Pipeline... INFO: [20/03/2023 21:51:33] -> Preprocessing Run #8 of 12... INFO: [20/03/2023 21:51:33] -> Initialize Scoring... INFO: [20/03/2023 21:51:33] -> Extracting Ion Currents... INFO: [20/03/2023 21:51:47] -> Machine Learning... INFO: [20/03/2023 21:51:50] -> Pipeline executed in 16.32s INFO: [20/03/2023 21:51:55] -> Initialize Scoring... INFO: [20/03/2023 21:51:55] -> Preprocessing Run #9 of 12... INFO: [20/03/2023 21:51:55] -> Searching DIA with Pulsar... INFO: [20/03/2023 21:51:55] -> Initializing Experiment... INFO: [20/03/2023 21:51:55] -> Loading Spectral Libraries... INFO: [20/03/2023 21:51:55] -> Initialize Scoring... INFO: [20/03/2023 21:51:55] -> Generating Scan Map... INFO: [20/03/2023 21:51:55] -> Initializing Workpackages... INFO: [20/03/2023 21:51:55] -> Performing Basic Calibration... INFO: [20/03/2023 21:51:55] -> Identifying Calibration Peptides... INFO: [20/03/2023 21:51:56] -> Correcting Gradient Fine Structure... INFO: [20/03/2023 21:51:58] -> Initializing Pipeline... INFO: [20/03/2023 21:51:58] -> Preprocessing Run #9 of 12... INFO: [20/03/2023 21:51:58] -> Initialize Scoring... INFO: [20/03/2023 21:51:58] -> Extracting Ion Currents... INFO: [20/03/2023 21:52:15] -> Machine Learning... INFO: [20/03/2023 21:52:16] -> Pipeline executed in 18.57s INFO: [20/03/2023 21:52:20] -> Initializing Pipeline... INFO: [20/03/2023 21:52:20] -> Preprocessing Run #9 of 12... INFO: [20/03/2023 21:52:20] -> Initialize Scoring... INFO: [20/03/2023 21:52:20] -> Extracting Ion Currents... INFO: [20/03/2023 21:52:33] -> Machine Learning... INFO: [20/03/2023 21:52:36] -> Pipeline executed in 16.29s INFO: [20/03/2023 21:52:42] -> Initialize Scoring... INFO: [20/03/2023 21:52:42] -> Preprocessing Run #10 of 12... INFO: [20/03/2023 21:52:42] -> Searching DIA with Pulsar... INFO: [20/03/2023 21:52:42] -> Initializing Experiment... INFO: [20/03/2023 21:52:42] -> Loading Spectral Libraries... INFO: [20/03/2023 21:52:42] -> Initialize Scoring... INFO: [20/03/2023 21:52:42] -> Generating Scan Map... INFO: [20/03/2023 21:52:42] -> Initializing Workpackages... INFO: [20/03/2023 21:52:42] -> Performing Basic Calibration... INFO: [20/03/2023 21:52:42] -> Identifying Calibration Peptides... INFO: [20/03/2023 21:52:42] -> Correcting Gradient Fine Structure... INFO: [20/03/2023 21:52:45] -> Initializing Pipeline... INFO: [20/03/2023 21:52:45] -> Preprocessing Run #10 of 12... INFO: [20/03/2023 21:52:45] -> Initialize Scoring... INFO: [20/03/2023 21:52:45] -> Extracting Ion Currents... INFO: [20/03/2023 21:53:02] -> Machine Learning... INFO: [20/03/2023 21:53:03] -> Pipeline executed in 18.81s INFO: [20/03/2023 21:53:07] -> Initializing Pipeline... INFO: [20/03/2023 21:53:07] -> Preprocessing Run #10 of 12... INFO: [20/03/2023 21:53:07] -> Initialize Scoring... INFO: [20/03/2023 21:53:07] -> Extracting Ion Currents... INFO: [20/03/2023 21:53:21] -> Machine Learning... INFO: [20/03/2023 21:53:23] -> Pipeline executed in 16.4s INFO: [20/03/2023 21:53:28] -> Initialize Scoring... INFO: [20/03/2023 21:53:28] -> Preprocessing Run #11 of 12... INFO: [20/03/2023 21:53:28] -> Searching DIA with Pulsar... INFO: [20/03/2023 21:53:28] -> Initializing Experiment... INFO: [20/03/2023 21:53:28] -> Loading Spectral Libraries... INFO: [20/03/2023 21:53:28] -> Initialize Scoring... INFO: [20/03/2023 21:53:28] -> Generating Scan Map... INFO: [20/03/2023 21:53:28] -> Initializing Workpackages... INFO: [20/03/2023 21:53:28] -> Performing Basic Calibration... INFO: [20/03/2023 21:53:29] -> Identifying Calibration Peptides... INFO: [20/03/2023 21:53:29] -> Correcting Gradient Fine Structure... INFO: [20/03/2023 21:53:31] -> Initializing Pipeline... INFO: [20/03/2023 21:53:31] -> Preprocessing Run #11 of 12... INFO: [20/03/2023 21:53:31] -> Initialize Scoring... INFO: [20/03/2023 21:53:31] -> Extracting Ion Currents... INFO: [20/03/2023 21:53:49] -> Machine Learning... INFO: [20/03/2023 21:53:49] -> Pipeline executed in 18.34s INFO: [20/03/2023 21:53:53] -> Initializing Pipeline... INFO: [20/03/2023 21:53:53] -> Preprocessing Run #11 of 12... INFO: [20/03/2023 21:53:53] -> Initialize Scoring... INFO: [20/03/2023 21:53:53] -> Extracting Ion Currents... INFO: [20/03/2023 21:54:07] -> Machine Learning... INFO: [20/03/2023 21:54:09] -> Pipeline executed in 16.18s INFO: [20/03/2023 21:54:14] -> Initialize Scoring... INFO: [20/03/2023 21:54:14] -> Preprocessing Run #12 of 12... INFO: [20/03/2023 21:54:14] -> Searching DIA with Pulsar... INFO: [20/03/2023 21:54:14] -> Initializing Experiment... INFO: [20/03/2023 21:54:14] -> Loading Spectral Libraries... INFO: [20/03/2023 21:54:14] -> Initialize Scoring... INFO: [20/03/2023 21:54:14] -> Generating Scan Map... INFO: [20/03/2023 21:54:14] -> Initializing Workpackages... INFO: [20/03/2023 21:54:14] -> Performing Basic Calibration... INFO: [20/03/2023 21:54:15] -> Identifying Calibration Peptides... INFO: [20/03/2023 21:54:15] -> Correcting Gradient Fine Structure... INFO: [20/03/2023 21:54:17] -> Initializing Pipeline... INFO: [20/03/2023 21:54:17] -> Preprocessing Run #12 of 12... INFO: [20/03/2023 21:54:17] -> Initialize Scoring... INFO: [20/03/2023 21:54:17] -> Extracting Ion Currents... INFO: [20/03/2023 21:54:34] -> Machine Learning... INFO: [20/03/2023 21:54:35] -> Pipeline executed in 18.22s INFO: [20/03/2023 21:54:38] -> Initializing Pipeline... INFO: [20/03/2023 21:54:38] -> Preprocessing Run #12 of 12... INFO: [20/03/2023 21:54:38] -> Initialize Scoring... INFO: [20/03/2023 21:54:38] -> Extracting Ion Currents... INFO: [20/03/2023 21:54:52] -> Machine Learning... INFO: [20/03/2023 21:54:55] -> Pipeline executed in 16.28s INFO: [20/03/2023 21:55:00] -> Initialize Scoring... INFO: [20/03/2023 21:55:00] -> Initializing QC... INFO: [20/03/2023 21:55:00] -> Determining Calibration Parameter... INFO: [20/03/2023 21:55:00] -> Assigning ML Features... INFO: [20/03/2023 21:55:01] -> Generating Decoys... INFO: [20/03/2023 21:55:05] -> Extracting Ion Currents... INFO: [20/03/2023 21:55:33] -> Releasing Raw Files... INFO: [20/03/2023 21:55:33] -> Machine Learning... INFO: [20/03/2023 21:55:52] -> Initializing HTRMS... INFO: [20/03/2023 21:55:52] -> Releasing Run Resources... INFO: [20/03/2023 21:55:54] -> Calculating Qvalues... INFO: [20/03/2023 21:55:54] -> Unique precursors: 60,213 of 61,631 | modified peptides: 53,134 of 54,279 | peptides: 47,108 of 48,047 | protein groups: 4,714 (Qvalue <= 0.01) [APP_total_200ng_06.htrms] INFO: [20/03/2023 21:55:55] -> Collapsing Search Tree... INFO: [20/03/2023 21:55:55] -> Processed in 54.23s INFO: [20/03/2023 21:55:55] -> Initializing QC... INFO: [20/03/2023 21:55:55] -> Determining Calibration Parameter... INFO: [20/03/2023 21:55:55] -> Assigning ML Features... INFO: [20/03/2023 21:55:55] -> Generating Decoys... INFO: [20/03/2023 21:55:55] -> Extracting Ion Currents... INFO: [20/03/2023 21:56:23] -> Releasing Raw Files... INFO: [20/03/2023 21:56:23] -> Machine Learning... INFO: [20/03/2023 21:56:43] -> Initializing HTRMS... INFO: [20/03/2023 21:56:43] -> Releasing Run Resources... INFO: [20/03/2023 21:56:45] -> Calculating Qvalues... INFO: [20/03/2023 21:56:46] -> Unique precursors: 59,715 of 61,631 | modified peptides: 52,746 of 54,279 | peptides: 46,764 of 48,047 | protein groups: 4,705 (Qvalue <= 0.01) [APP_total_200ng_08.htrms] INFO: [20/03/2023 21:56:46] -> Collapsing Search Tree... INFO: [20/03/2023 21:56:46] -> Processed in 51.07s INFO: [20/03/2023 21:56:46] -> Initializing QC... INFO: [20/03/2023 21:56:46] -> Determining Calibration Parameter... INFO: [20/03/2023 21:56:46] -> Assigning ML Features... INFO: [20/03/2023 21:56:46] -> Generating Decoys... INFO: [20/03/2023 21:56:46] -> Extracting Ion Currents... INFO: [20/03/2023 21:57:15] -> Releasing Raw Files... INFO: [20/03/2023 21:57:15] -> Machine Learning... INFO: [20/03/2023 21:57:33] -> Initializing HTRMS... INFO: [20/03/2023 21:57:33] -> Releasing Run Resources... INFO: [20/03/2023 21:57:35] -> Calculating Qvalues... INFO: [20/03/2023 21:57:36] -> Unique precursors: 60,374 of 61,631 | modified peptides: 53,215 of 54,279 | peptides: 47,127 of 48,047 | protein groups: 4,708 (Qvalue <= 0.01) [APP_total_200ng_09.htrms] INFO: [20/03/2023 21:57:36] -> Collapsing Search Tree... INFO: [20/03/2023 21:57:36] -> Processed in 50.2s INFO: [20/03/2023 21:57:36] -> Initializing QC... INFO: [20/03/2023 21:57:36] -> Determining Calibration Parameter... INFO: [20/03/2023 21:57:36] -> Assigning ML Features... INFO: [20/03/2023 21:57:36] -> Generating Decoys... INFO: [20/03/2023 21:57:36] -> Extracting Ion Currents... INFO: [20/03/2023 21:58:04] -> Releasing Raw Files... INFO: [20/03/2023 21:58:04] -> Machine Learning... INFO: [20/03/2023 21:58:22] -> Initializing HTRMS... INFO: [20/03/2023 21:58:22] -> Releasing Run Resources... INFO: [20/03/2023 21:58:24] -> Calculating Qvalues... INFO: [20/03/2023 21:58:25] -> Unique precursors: 59,207 of 61,631 | modified peptides: 52,344 of 54,279 | peptides: 46,453 of 48,047 | protein groups: 4,710 (Qvalue <= 0.01) [APP_total_200ng_12.htrms] INFO: [20/03/2023 21:58:25] -> Collapsing Search Tree... INFO: [20/03/2023 21:58:25] -> Processed in 49.1s INFO: [20/03/2023 21:58:25] -> Initializing QC... INFO: [20/03/2023 21:58:25] -> Determining Calibration Parameter... INFO: [20/03/2023 21:58:25] -> Assigning ML Features... INFO: [20/03/2023 21:58:25] -> Generating Decoys... INFO: [20/03/2023 21:58:25] -> Extracting Ion Currents... INFO: [20/03/2023 21:58:54] -> Releasing Raw Files... INFO: [20/03/2023 21:58:54] -> Machine Learning... INFO: [20/03/2023 21:59:15] -> Initializing HTRMS... INFO: [20/03/2023 21:59:15] -> Releasing Run Resources... INFO: [20/03/2023 21:59:16] -> Calculating Qvalues... INFO: [20/03/2023 21:59:17] -> Unique precursors: 59,762 of 61,631 | modified peptides: 52,743 of 54,279 | peptides: 46,713 of 48,047 | protein groups: 4,698 (Qvalue <= 0.01) [APP_total_200ng_13.htrms] INFO: [20/03/2023 21:59:17] -> Collapsing Search Tree... INFO: [20/03/2023 21:59:17] -> Processed in 51.97s INFO: [20/03/2023 21:59:17] -> Initializing QC... INFO: [20/03/2023 21:59:17] -> Determining Calibration Parameter... INFO: [20/03/2023 21:59:17] -> Assigning ML Features... INFO: [20/03/2023 21:59:17] -> Generating Decoys... INFO: [20/03/2023 21:59:17] -> Extracting Ion Currents... INFO: [20/03/2023 21:59:45] -> Releasing Raw Files... INFO: [20/03/2023 21:59:45] -> Machine Learning... INFO: [20/03/2023 22:00:05] -> Initializing HTRMS... INFO: [20/03/2023 22:00:05] -> Releasing Run Resources... INFO: [20/03/2023 22:00:07] -> Calculating Qvalues... INFO: [20/03/2023 22:00:08] -> Unique precursors: 60,141 of 61,631 | modified peptides: 53,048 of 54,279 | peptides: 46,982 of 48,047 | protein groups: 4,703 (Qvalue <= 0.01) [APP_total_200ng_14.htrms] INFO: [20/03/2023 22:00:08] -> Collapsing Search Tree... INFO: [20/03/2023 22:00:08] -> Processed in 50.65s INFO: [20/03/2023 22:00:08] -> Initializing QC... INFO: [20/03/2023 22:00:08] -> Determining Calibration Parameter... INFO: [20/03/2023 22:00:08] -> Assigning ML Features... INFO: [20/03/2023 22:00:08] -> Generating Decoys... INFO: [20/03/2023 22:00:08] -> Extracting Ion Currents... INFO: [20/03/2023 22:00:36] -> Releasing Raw Files... INFO: [20/03/2023 22:00:36] -> Machine Learning... INFO: [20/03/2023 22:00:54] -> Initializing HTRMS... INFO: [20/03/2023 22:00:54] -> Releasing Run Resources... INFO: [20/03/2023 22:00:56] -> Calculating Qvalues... INFO: [20/03/2023 22:00:57] -> Unique precursors: 59,818 of 61,631 | modified peptides: 52,770 of 54,279 | peptides: 46,769 of 48,047 | protein groups: 4,696 (Qvalue <= 0.01) [WT_total_200ng_01.htrms] INFO: [20/03/2023 22:00:57] -> Collapsing Search Tree... INFO: [20/03/2023 22:00:57] -> Processed in 49.13s INFO: [20/03/2023 22:00:57] -> Initializing QC... INFO: [20/03/2023 22:00:57] -> Determining Calibration Parameter... INFO: [20/03/2023 22:00:57] -> Assigning ML Features... INFO: [20/03/2023 22:00:57] -> Generating Decoys... INFO: [20/03/2023 22:00:57] -> Extracting Ion Currents... INFO: [20/03/2023 22:01:26] -> Releasing Raw Files... INFO: [20/03/2023 22:01:26] -> Machine Learning... INFO: [20/03/2023 22:01:47] -> Initializing HTRMS... INFO: [20/03/2023 22:01:47] -> Releasing Run Resources... INFO: [20/03/2023 22:01:49] -> Calculating Qvalues... INFO: [20/03/2023 22:01:50] -> Unique precursors: 59,053 of 61,631 | modified peptides: 52,283 of 54,279 | peptides: 46,335 of 48,047 | protein groups: 4,712 (Qvalue <= 0.01) [WT_total_200ng_02.htrms] INFO: [20/03/2023 22:01:50] -> Collapsing Search Tree... INFO: [20/03/2023 22:01:50] -> Processed in 52.94s INFO: [20/03/2023 22:01:50] -> Initializing QC... INFO: [20/03/2023 22:01:50] -> Determining Calibration Parameter... INFO: [20/03/2023 22:01:50] -> Assigning ML Features... INFO: [20/03/2023 22:01:50] -> Generating Decoys... INFO: [20/03/2023 22:01:50] -> Extracting Ion Currents... INFO: [20/03/2023 22:02:18] -> Releasing Raw Files... INFO: [20/03/2023 22:02:18] -> Machine Learning... INFO: [20/03/2023 22:02:36] -> Initializing HTRMS... INFO: [20/03/2023 22:02:36] -> Releasing Run Resources... INFO: [20/03/2023 22:02:38] -> Calculating Qvalues... INFO: [20/03/2023 22:02:38] -> Unique precursors: 60,118 of 61,631 | modified peptides: 53,009 of 54,279 | peptides: 46,975 of 48,047 | protein groups: 4,714 (Qvalue <= 0.01) [WT_total_200ng_03.htrms] INFO: [20/03/2023 22:02:38] -> Collapsing Search Tree... INFO: [20/03/2023 22:02:38] -> Processed in 48.84s INFO: [20/03/2023 22:02:38] -> Initializing QC... INFO: [20/03/2023 22:02:39] -> Determining Calibration Parameter... INFO: [20/03/2023 22:02:39] -> Assigning ML Features... INFO: [20/03/2023 22:02:39] -> Generating Decoys... INFO: [20/03/2023 22:02:39] -> Extracting Ion Currents... INFO: [20/03/2023 22:03:07] -> Releasing Raw Files... INFO: [20/03/2023 22:03:07] -> Machine Learning... INFO: [20/03/2023 22:03:27] -> Initializing HTRMS... INFO: [20/03/2023 22:03:27] -> Releasing Run Resources... INFO: [20/03/2023 22:03:29] -> Calculating Qvalues... INFO: [20/03/2023 22:03:30] -> Unique precursors: 59,679 of 61,631 | modified peptides: 52,679 of 54,279 | peptides: 46,720 of 48,047 | protein groups: 4,710 (Qvalue <= 0.01) [WT_total_200ng_04.htrms] INFO: [20/03/2023 22:03:30] -> Collapsing Search Tree... INFO: [20/03/2023 22:03:30] -> Processed in 51.16s INFO: [20/03/2023 22:03:30] -> Initializing QC... INFO: [20/03/2023 22:03:30] -> Determining Calibration Parameter... INFO: [20/03/2023 22:03:30] -> Assigning ML Features... INFO: [20/03/2023 22:03:30] -> Generating Decoys... INFO: [20/03/2023 22:03:30] -> Extracting Ion Currents... INFO: [20/03/2023 22:03:59] -> Releasing Raw Files... INFO: [20/03/2023 22:03:59] -> Machine Learning... INFO: [20/03/2023 22:04:17] -> Initializing HTRMS... INFO: [20/03/2023 22:04:17] -> Releasing Run Resources... INFO: [20/03/2023 22:04:20] -> Calculating Qvalues... INFO: [20/03/2023 22:04:20] -> Unique precursors: 60,404 of 61,631 | modified peptides: 53,254 of 54,279 | peptides: 47,193 of 48,047 | protein groups: 4,723 (Qvalue <= 0.01) [WT_total_200ng_05.htrms] INFO: [20/03/2023 22:04:20] -> Collapsing Search Tree... INFO: [20/03/2023 22:04:20] -> Processed in 50.3s INFO: [20/03/2023 22:04:20] -> Initializing QC... INFO: [20/03/2023 22:04:20] -> Determining Calibration Parameter... INFO: [20/03/2023 22:04:20] -> Assigning ML Features... INFO: [20/03/2023 22:04:20] -> Generating Decoys... INFO: [20/03/2023 22:04:20] -> Extracting Ion Currents... INFO: [20/03/2023 22:04:48] -> Releasing Raw Files... INFO: [20/03/2023 22:04:48] -> Machine Learning... INFO: [20/03/2023 22:05:09] -> Initializing HTRMS... INFO: [20/03/2023 22:05:09] -> Releasing Run Resources... INFO: [20/03/2023 22:05:11] -> Calculating Qvalues... INFO: [20/03/2023 22:05:11] -> Unique precursors: 57,906 of 61,631 | modified peptides: 51,273 of 54,279 | peptides: 45,565 of 48,047 | protein groups: 4,674 (Qvalue <= 0.01) [WT_total_200ng_07.htrms] INFO: [20/03/2023 22:05:11] -> Collapsing Search Tree... INFO: [20/03/2023 22:05:11] -> Processed in 51.09s INFO: [20/03/2023 22:05:11] -> Normalizing Cscores... INFO: [20/03/2023 22:05:12] -> Initializing Protein Groups... INFO: [20/03/2023 22:05:27] -> Correcting Interferences... INFO: [20/03/2023 22:06:02] -> Calculating Global CVs INFO: [20/03/2023 22:06:03] -> Calculating Precursor Quantities... INFO: [20/03/2023 22:06:03] -> Normalizing Quantification... INFO: [20/03/2023 22:06:03] -> Cross-run normalization disabled! INFO: [20/03/2023 22:06:03] -> Calculating Global CVs INFO: [20/03/2023 22:06:04] -> Calculating Condition CVs INFO: [20/03/2023 22:06:06] -> Excluding Library Duplicates... INFO: [20/03/2023 22:06:06] -> Calculating Global CVs INFO: [20/03/2023 22:06:07] -> Building Protein Groups... INFO: [20/03/2023 22:06:20] -> Calculating Run-Wise Protein Group FDR... INFO: [20/03/2023 22:06:23] -> Annotating Protein Single Hits... INFO: [20/03/2023 22:06:24] -> Calculating Global CVs INFO: [20/03/2023 22:06:25] -> Updating Identification Counts... INFO: [20/03/2023 22:06:27] -> Resetting existing imputation... INFO: [20/03/2023 22:06:27] -> Calculating Protein Quantities... INFO: [20/03/2023 22:06:28] -> Calculating Protein Quantities... INFO: [20/03/2023 22:06:28] -> Calculating MaxLFQ Protein Quantities... INFO: [20/03/2023 22:06:38] -> Collapsing PTM-Locations... INFO: [20/03/2023 22:06:38] -> Creating Protein Map... INFO: [20/03/2023 22:06:38] -> Compiling Run Summary Information... INFO: [20/03/2023 22:06:38] -> Running Post Analysis Processes... INFO: [20/03/2023 22:21:56] -> Saving Qc Data... INFO: [20/03/2023 22:22:02] -> Writing Summary Information... INFO: [20/03/2023 22:22:02] -> Unique precursors: 60,051 of 61,631 | modified peptides: 52,972 of 54,279 | peptides: 46,952 of 48,047 | protein groups: 4,565 (Qvalue <= 0.01) for run #1 "APP_total_200ng_06.htrms" INFO: [20/03/2023 22:22:02] -> Unique precursors: 59,537 of 61,631 | modified peptides: 52,568 of 54,279 | peptides: 46,592 of 48,047 | protein groups: 4,545 (Qvalue <= 0.01) for run #2 "APP_total_200ng_08.htrms" INFO: [20/03/2023 22:22:02] -> Unique precursors: 60,203 of 61,631 | modified peptides: 53,044 of 54,279 | peptides: 46,963 of 48,047 | protein groups: 4,552 (Qvalue <= 0.01) for run #3 "APP_total_200ng_09.htrms" INFO: [20/03/2023 22:22:02] -> Unique precursors: 59,063 of 61,631 | modified peptides: 52,200 of 54,279 | peptides: 46,315 of 48,047 | protein groups: 4,577 (Qvalue <= 0.01) for run #4 "APP_total_200ng_12.htrms" INFO: [20/03/2023 22:22:02] -> Unique precursors: 59,610 of 61,631 | modified peptides: 52,591 of 54,279 | peptides: 46,565 of 48,047 | protein groups: 4,557 (Qvalue <= 0.01) for run #5 "APP_total_200ng_13.htrms" INFO: [20/03/2023 22:22:02] -> Unique precursors: 59,987 of 61,631 | modified peptides: 52,894 of 54,279 | peptides: 46,834 of 48,047 | protein groups: 4,564 (Qvalue <= 0.01) for run #6 "APP_total_200ng_14.htrms" INFO: [20/03/2023 22:22:02] -> Unique precursors: 59,670 of 61,631 | modified peptides: 52,622 of 54,279 | peptides: 46,627 of 48,047 | protein groups: 4,559 (Qvalue <= 0.01) for run #7 "WT_total_200ng_01.htrms" INFO: [20/03/2023 22:22:02] -> Unique precursors: 58,863 of 61,631 | modified peptides: 52,094 of 54,279 | peptides: 46,154 of 48,047 | protein groups: 4,541 (Qvalue <= 0.01) for run #8 "WT_total_200ng_02.htrms" INFO: [20/03/2023 22:22:02] -> Unique precursors: 59,974 of 61,631 | modified peptides: 52,865 of 54,279 | peptides: 46,837 of 48,047 | protein groups: 4,580 (Qvalue <= 0.01) for run #9 "WT_total_200ng_03.htrms" INFO: [20/03/2023 22:22:02] -> Unique precursors: 59,509 of 61,631 | modified peptides: 52,509 of 54,279 | peptides: 46,556 of 48,047 | protein groups: 4,553 (Qvalue <= 0.01) for run #10 "WT_total_200ng_04.htrms" INFO: [20/03/2023 22:22:02] -> Unique precursors: 60,254 of 61,631 | modified peptides: 53,104 of 54,279 | peptides: 47,049 of 48,047 | protein groups: 4,586 (Qvalue <= 0.01) for run #11 "WT_total_200ng_05.htrms" INFO: [20/03/2023 22:22:02] -> Unique precursors: 57,744 of 61,631 | modified peptides: 51,111 of 54,279 | peptides: 45,408 of 48,047 | protein groups: 4,522 (Qvalue <= 0.01) for run #12 "WT_total_200ng_07.htrms" INFO: [20/03/2023 22:22:02] -> Unique precursors: 61,457 of 61,631 | modified peptides: 54,118 of 54,279 | peptides: 47,892 of 48,047 | protein groups: 4,612 (Qvalue <= 0.01) for whole experiment "277-Pol_Total" INFO: [20/03/2023 22:22:02] -> Saving SNE File... INFO: [20/03/2023 22:22:02] -> Storing SNE File: D:\Proyectos\20230320_222202_277-Pol_Total.sne INFO: [20/03/2023 22:22:02] -> Initializing Pipeline... INFO: [20/03/2023 22:22:02] -> Calculating Qvalues... INFO: [20/03/2023 22:22:03] -> Saving... INFO: [20/03/2023 22:22:25] -> Pipeline executed in 23s INFO: [20/03/2023 22:22:27] -> Pipeline executed in 2.4h