MEGAHIT v1.0.3-7-g663eb28 --- [Mon Nov 30 11:29:50 2015] Start assembly. Number of CPU threads 8 --- --- [Mon Nov 30 11:29:50 2015] k list: 25,29,33,37,41,45,49,53,57,61,65,69,73,77,81,85,89,93,97,99 --- --- [Mon Nov 30 11:29:50 2015] Converting reads to binaries --- [read_lib_functions-inl.h : 209] Lib 0 (/output/Preprocessing/MT.R1.preprocessed.fq,/output/Preprocessing/MT.R2.preprocessed.fq): pe, 18239880 reads, 101 max length [read_lib_functions-inl.h : 209] Lib 1 (/output/Preprocessing/MT.SE.preprocessed.fq): se, 1951440 reads, 101 max length [utils.h : 124] Real: 18.8231 user: 17.2680 sys: 1.5640 maxrss: 156252 --- [Mon Nov 30 11:30:09 2015] Extracting solid (k+1)-mers for k = 25 --- --- [Mon Nov 30 11:32:13 2015] Building graph for k = 25 --- --- [Mon Nov 30 11:34:18 2015] Assembling contigs from SdBG for k = 25 --- --- [Mon Nov 30 11:41:44 2015] Local assembling k = 25 --- --- [Mon Nov 30 11:42:59 2015] Extracting iterative edges from k = 25 to 29 --- --- [Mon Nov 30 11:45:02 2015] Building graph for k = 29 --- --- [Mon Nov 30 11:46:15 2015] Assembling contigs from SdBG for k = 29 --- --- [Mon Nov 30 11:56:37 2015] Local assembling k = 29 --- --- [Mon Nov 30 11:57:43 2015] Extracting iterative edges from k = 29 to 33 --- --- [Mon Nov 30 11:59:54 2015] Building graph for k = 33 --- --- [Mon Nov 30 12:00:45 2015] Assembling contigs from SdBG for k = 33 --- --- [Mon Nov 30 12:08:32 2015] Local assembling k = 33 --- --- [Mon Nov 30 12:10:00 2015] Extracting iterative edges from k = 33 to 37 --- --- [Mon Nov 30 12:11:55 2015] Building graph for k = 37 --- --- [Mon Nov 30 12:12:41 2015] Assembling contigs from SdBG for k = 37 --- --- [Mon Nov 30 12:19:53 2015] Local assembling k = 37 --- --- [Mon Nov 30 12:21:54 2015] Extracting iterative edges from k = 37 to 41 --- --- [Mon Nov 30 12:24:47 2015] Building graph for k = 41 --- --- [Mon Nov 30 12:25:27 2015] Assembling contigs from SdBG for k = 41 --- --- [Mon Nov 30 12:30:11 2015] Local assembling k = 41 --- --- [Mon Nov 30 12:31:31 2015] Extracting iterative edges from k = 41 to 45 --- --- [Mon Nov 30 12:32:47 2015] Building graph for k = 45 --- --- [Mon Nov 30 12:33:19 2015] Assembling contigs from SdBG for k = 45 --- --- [Mon Nov 30 12:37:09 2015] Local assembling k = 45 --- --- [Mon Nov 30 12:39:23 2015] Extracting iterative edges from k = 45 to 49 --- --- [Mon Nov 30 12:42:04 2015] Building graph for k = 49 --- --- [Mon Nov 30 12:42:34 2015] Assembling contigs from SdBG for k = 49 --- --- [Mon Nov 30 12:45:35 2015] Local assembling k = 49 --- --- [Mon Nov 30 12:47:02 2015] Extracting iterative edges from k = 49 to 53 --- --- [Mon Nov 30 12:48:01 2015] Building graph for k = 53 --- --- [Mon Nov 30 12:48:24 2015] Assembling contigs from SdBG for k = 53 --- --- [Mon Nov 30 12:50:39 2015] Local assembling k = 53 --- --- [Mon Nov 30 12:52:49 2015] Extracting iterative edges from k = 53 to 57 --- --- [Mon Nov 30 12:54:35 2015] Building graph for k = 57 --- --- [Mon Nov 30 12:54:56 2015] Assembling contigs from SdBG for k = 57 --- --- [Mon Nov 30 12:56:44 2015] Local assembling k = 57 --- --- [Mon Nov 30 12:59:02 2015] Extracting iterative edges from k = 57 to 61 --- --- [Mon Nov 30 13:00:53 2015] Building graph for k = 61 --- --- [Mon Nov 30 13:01:10 2015] Assembling contigs from SdBG for k = 61 --- --- [Mon Nov 30 13:02:06 2015] Local assembling k = 61 --- --- [Mon Nov 30 13:03:23 2015] Extracting iterative edges from k = 61 to 65 --- --- [Mon Nov 30 13:04:21 2015] Building graph for k = 65 --- --- [Mon Nov 30 13:04:36 2015] Assembling contigs from SdBG for k = 65 --- --- [Mon Nov 30 13:06:05 2015] Local assembling k = 65 --- --- [Mon Nov 30 13:08:15 2015] Extracting iterative edges from k = 65 to 69 --- --- [Mon Nov 30 13:08:42 2015] Building graph for k = 69 --- --- [Mon Nov 30 13:08:54 2015] Assembling contigs from SdBG for k = 69 --- --- [Mon Nov 30 13:09:35 2015] Local assembling k = 69 --- --- [Mon Nov 30 13:11:25 2015] Extracting iterative edges from k = 69 to 73 --- --- [Mon Nov 30 13:11:54 2015] Building graph for k = 73 --- --- [Mon Nov 30 13:12:03 2015] Assembling contigs from SdBG for k = 73 --- --- [Mon Nov 30 13:12:41 2015] Local assembling k = 73 --- --- [Mon Nov 30 13:14:00 2015] Extracting iterative edges from k = 73 to 77 --- --- [Mon Nov 30 13:14:19 2015] Building graph for k = 77 --- --- [Mon Nov 30 13:14:27 2015] Assembling contigs from SdBG for k = 77 --- --- [Mon Nov 30 13:15:22 2015] Local assembling k = 77 --- --- [Mon Nov 30 13:17:06 2015] Extracting iterative edges from k = 77 to 81 --- --- [Mon Nov 30 13:17:29 2015] Building graph for k = 81 --- --- [Mon Nov 30 13:17:36 2015] Assembling contigs from SdBG for k = 81 --- --- [Mon Nov 30 13:18:07 2015] Local assembling k = 81 --- --- [Mon Nov 30 13:19:13 2015] Extracting iterative edges from k = 81 to 85 --- --- [Mon Nov 30 13:19:30 2015] Building graph for k = 85 --- --- [Mon Nov 30 13:19:37 2015] Assembling contigs from SdBG for k = 85 --- --- [Mon Nov 30 13:20:05 2015] Local assembling k = 85 --- --- [Mon Nov 30 13:21:40 2015] Extracting iterative edges from k = 85 to 89 --- --- [Mon Nov 30 13:21:55 2015] Building graph for k = 89 --- --- [Mon Nov 30 13:22:02 2015] Assembling contigs from SdBG for k = 89 --- --- [Mon Nov 30 13:22:37 2015] Local assembling k = 89 --- --- [Mon Nov 30 13:23:49 2015] Extracting iterative edges from k = 89 to 93 --- --- [Mon Nov 30 13:24:00 2015] Building graph for k = 93 --- --- [Mon Nov 30 13:24:06 2015] Assembling contigs from SdBG for k = 93 --- --- [Mon Nov 30 13:24:32 2015] Local assembling k = 93 --- --- [Mon Nov 30 13:25:43 2015] Extracting iterative edges from k = 93 to 97 --- --- [Mon Nov 30 13:25:53 2015] Building graph for k = 97 --- --- [Mon Nov 30 13:25:57 2015] Assembling contigs from SdBG for k = 97 --- --- [Mon Nov 30 13:26:20 2015] Local assembling k = 97 --- --- [Mon Nov 30 13:27:21 2015] Extracting iterative edges from k = 97 to 99 --- --- [Mon Nov 30 13:27:30 2015] Building graph for k = 99 --- --- [Mon Nov 30 13:27:34 2015] Assembling contigs from SdBG for k = 99 --- --- [Mon Nov 30 13:28:02 2015] Merging to output final contigs --- --- [STAT] 45514 contigs, total 22673854 bp, min 200 bp, max 9397 bp, avg 498 bp, N50 482 bp --- [Mon Nov 30 13:28:02 2015] ALL DONE. Time elapsed: 7091.661336 seconds --- MEGAHIT v1.0.3-7-g663eb28 --- [Mon Nov 30 13:42:11 2015] Start assembly. Number of CPU threads 8 --- --- [Mon Nov 30 13:42:11 2015] k list: 25,29,33,37,41,45,49,53,57,61,65,69,73,77,81,85,89,93,97,99 --- --- [Mon Nov 30 13:42:11 2015] Converting reads to binaries --- [read_lib_functions-inl.h : 209] Lib 0 (/output/Assembly/MT.R1.unmapped.fq,/output/Assembly/MT.R2.unmapped.fq): pe, 10604182 reads, 101 max length [read_lib_functions-inl.h : 209] Lib 1 (/output/Assembly/MT.SE.unmapped.fq): se, 1152175 reads, 101 max length [utils.h : 124] Real: 10.9741 user: 10.0880 sys: 0.8880 maxrss: 156584 --- [Mon Nov 30 13:42:22 2015] Extracting solid (k+1)-mers for k = 25 --- --- [Mon Nov 30 13:43:57 2015] Building graph for k = 25 --- --- [Mon Nov 30 13:45:46 2015] Assembling contigs from SdBG for k = 25 --- --- [Mon Nov 30 13:54:27 2015] Local assembling k = 25 --- --- [Mon Nov 30 13:55:13 2015] Extracting iterative edges from k = 25 to 29 --- --- [Mon Nov 30 13:56:25 2015] Building graph for k = 29 --- --- [Mon Nov 30 13:57:14 2015] Assembling contigs from SdBG for k = 29 --- --- [Mon Nov 30 14:04:08 2015] Local assembling k = 29 --- --- [Mon Nov 30 14:05:20 2015] Extracting iterative edges from k = 29 to 33 --- --- [Mon Nov 30 14:07:10 2015] Building graph for k = 33 --- --- [Mon Nov 30 14:07:55 2015] Assembling contigs from SdBG for k = 33 --- --- [Mon Nov 30 14:16:05 2015] Local assembling k = 33 --- --- [Mon Nov 30 14:16:46 2015] Extracting iterative edges from k = 33 to 37 --- --- [Mon Nov 30 14:17:25 2015] Building graph for k = 37 --- --- [Mon Nov 30 14:17:58 2015] Assembling contigs from SdBG for k = 37 --- --- [Mon Nov 30 14:22:35 2015] Local assembling k = 37 --- --- [Mon Nov 30 14:24:08 2015] Extracting iterative edges from k = 37 to 41 --- --- [Mon Nov 30 14:25:46 2015] Building graph for k = 41 --- --- [Mon Nov 30 14:26:04 2015] Assembling contigs from SdBG for k = 41 --- --- [Mon Nov 30 14:27:49 2015] Local assembling k = 41 --- --- [Mon Nov 30 14:28:30 2015] Extracting iterative edges from k = 41 to 45 --- --- [Mon Nov 30 14:30:03 2015] Building graph for k = 45 --- --- [Mon Nov 30 14:30:20 2015] Assembling contigs from SdBG for k = 45 --- --- [Mon Nov 30 14:32:31 2015] Local assembling k = 45 --- --- [Mon Nov 30 14:33:49 2015] Extracting iterative edges from k = 45 to 49 --- --- [Mon Nov 30 14:34:48 2015] Building graph for k = 49 --- --- [Mon Nov 30 14:35:01 2015] Assembling contigs from SdBG for k = 49 --- --- [Mon Nov 30 14:36:03 2015] Local assembling k = 49 --- --- [Mon Nov 30 14:36:37 2015] Extracting iterative edges from k = 49 to 53 --- --- [Mon Nov 30 14:36:59 2015] Building graph for k = 53 --- --- [Mon Nov 30 14:37:07 2015] Assembling contigs from SdBG for k = 53 --- --- [Mon Nov 30 14:38:14 2015] Local assembling k = 53 --- --- [Mon Nov 30 14:39:47 2015] Extracting iterative edges from k = 53 to 57 --- --- [Mon Nov 30 14:40:37 2015] Building graph for k = 57 --- --- [Mon Nov 30 14:40:44 2015] Assembling contigs from SdBG for k = 57 --- --- [Mon Nov 30 14:41:45 2015] Local assembling k = 57 --- --- [Mon Nov 30 14:42:26 2015] Extracting iterative edges from k = 57 to 61 --- --- [Mon Nov 30 14:42:44 2015] Building graph for k = 61 --- --- [Mon Nov 30 14:42:48 2015] Assembling contigs from SdBG for k = 61 --- --- [Mon Nov 30 14:43:34 2015] Local assembling k = 61 --- --- [Mon Nov 30 14:44:52 2015] Extracting iterative edges from k = 61 to 65 --- --- [Mon Nov 30 14:45:22 2015] Building graph for k = 65 --- --- [Mon Nov 30 14:45:26 2015] Assembling contigs from SdBG for k = 65 --- --- [Mon Nov 30 14:45:57 2015] Local assembling k = 65 --- --- [Mon Nov 30 14:47:17 2015] Extracting iterative edges from k = 65 to 69 --- --- [Mon Nov 30 14:47:48 2015] Building graph for k = 69 --- --- [Mon Nov 30 14:47:51 2015] Assembling contigs from SdBG for k = 69 --- --- [Mon Nov 30 14:48:18 2015] Local assembling k = 69 --- --- [Mon Nov 30 14:49:35 2015] Extracting iterative edges from k = 69 to 73 --- --- [Mon Nov 30 14:49:57 2015] Building graph for k = 73 --- --- [Mon Nov 30 14:50:00 2015] Assembling contigs from SdBG for k = 73 --- --- [Mon Nov 30 14:50:20 2015] Local assembling k = 73 --- --- [Mon Nov 30 14:51:59 2015] Extracting iterative edges from k = 73 to 77 --- --- [Mon Nov 30 14:52:13 2015] Building graph for k = 77 --- --- [Mon Nov 30 14:52:15 2015] Assembling contigs from SdBG for k = 77 --- --- [Mon Nov 30 14:52:27 2015] Local assembling k = 77 --- --- [Mon Nov 30 14:53:39 2015] Extracting iterative edges from k = 77 to 81 --- --- [Mon Nov 30 14:53:56 2015] Building graph for k = 81 --- --- [Mon Nov 30 14:53:58 2015] Assembling contigs from SdBG for k = 81 --- --- [Mon Nov 30 14:54:08 2015] Local assembling k = 81 --- --- [Mon Nov 30 14:55:25 2015] Extracting iterative edges from k = 81 to 85 --- --- [Mon Nov 30 14:55:40 2015] Building graph for k = 85 --- --- [Mon Nov 30 14:55:42 2015] Assembling contigs from SdBG for k = 85 --- --- [Mon Nov 30 14:55:51 2015] Local assembling k = 85 --- --- [Mon Nov 30 14:56:18 2015] Extracting iterative edges from k = 85 to 89 --- --- [Mon Nov 30 14:56:25 2015] Building graph for k = 89 --- --- [Mon Nov 30 14:56:26 2015] Assembling contigs from SdBG for k = 89 --- --- [Mon Nov 30 14:56:32 2015] Local assembling k = 89 --- --- [Mon Nov 30 14:57:35 2015] Extracting iterative edges from k = 89 to 93 --- --- [Mon Nov 30 14:57:45 2015] Building graph for k = 93 --- --- [Mon Nov 30 14:57:46 2015] Assembling contigs from SdBG for k = 93 --- --- [Mon Nov 30 14:57:52 2015] Local assembling k = 93 --- --- [Mon Nov 30 14:59:10 2015] Extracting iterative edges from k = 93 to 97 --- --- [Mon Nov 30 14:59:16 2015] Building graph for k = 97 --- --- [Mon Nov 30 14:59:17 2015] Assembling contigs from SdBG for k = 97 --- --- [Mon Nov 30 14:59:21 2015] Local assembling k = 97 --- --- [Mon Nov 30 14:59:57 2015] Extracting iterative edges from k = 97 to 99 --- --- [Mon Nov 30 15:00:01 2015] Building graph for k = 99 --- --- [Mon Nov 30 15:00:01 2015] Assembling contigs from SdBG for k = 99 --- --- [Mon Nov 30 15:00:04 2015] Merging to output final contigs --- --- [STAT] 2285 contigs, total 777767 bp, min 207 bp, max 710 bp, avg 340 bp, N50 329 bp --- [Mon Nov 30 15:00:04 2015] ALL DONE. Time elapsed: 4672.840854 seconds ---