RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.mDMiCW/RM_409866.SunDec30755032023 Search Engine = rmblast 2.13.0+ Threads = 32 Dependencies: TRF 4.09, RECON , RepeatScout 1.0.6, RepeatMasker 4.1.4 LTR Structural Analysis: Disabled [use -LTRStruct to enable] Random Number Seed: 1701618903 Database = /dev/shm/rModeler.mDMiCW/GCF_023634155.1_bFalPer1.pri - Sequences = 125 - Bases = 1311598859 - N50 = 115608600 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 122060882-130779382 |* [ 4 ] 113342383-122060882 | [ 1 ] 104623883-113342382 | [ ] 95905384-104623883 | [ ] 87186884-95905383 | [ 2 ] 78468385-87186884 | [ 1 ] 69749885-78468384 | [ ] 61031386-69749885 | [ 1 ] 52312886-61031385 | [ ] 43594387-52312886 | [ ] 34875887-43594386 | [ 2 ] 26157388-34875887 |* [ 3 ] 17438888-26157387 | [ 2 ] 8720389-17438888 | [ 1 ] 1890-8720389 |************************************************** [ 108 ] Storage Throughput = excellent ( 1157.94 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40163430 bp ( 40004950 non ambiguous ) - Num Contigs Represented = 65 - Sequence extraction : 00:01:44 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:11 (hh:mm:ss) Elapsed Time Round Time: 00:22:34 (hh:mm:ss) Elapsed Time : 57 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1297 repeats masked totaling 411336 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10025494 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 10009952 bp After Masking: 8735443 bp Masked: 12.73 % -- Input Database Coverage: 10025494 bp out of 1311598859 bp ( 0.76 % ) Sampling Time: 00:03:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:06:45 (hh:mm:ss) Elapsed Time, 2806 HSPs Collected Number of families returned by RECON: 246 Round Time: 00:10:15 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3776 repeats masked totaling 1254443 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30177861 bp Num Contigs Represented = 59 Non ambiguous bp: Initial: 30034923 bp After Masking: 26169909 bp Masked: 12.87 % -- Input Database Coverage: 40203355 bp out of 1311598859 bp ( 3.07 % ) Sampling Time: 00:11:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:34:51 (hh:mm:ss) Elapsed Time, 4931 HSPs Collected Number of families returned by RECON: 1392 Round Time: 00:46:52 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:25:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13763 repeats masked totaling 4516694 bp(s). - TE Masking time 00:00:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90309813 bp Num Contigs Represented = 79 Non ambiguous bp: Initial: 90034826 bp After Masking: 78911407 bp Masked: 12.35 % -- Input Database Coverage: 130513168 bp out of 1311598859 bp ( 9.95 % ) Sampling Time: 00:30:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2559453 Comparison Time: 03:50:17 (hh:mm:ss) Elapsed Time, 54652 HSPs Collected Number of families returned by RECON: 8841 Round Time: 04:24:29 (hh:mm:ss) Elapsed Time : 81 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:11:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 52009 repeats masked totaling 16286500 bp(s). - TE Masking time 00:02:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271007306 bp Num Contigs Represented = 100 Non ambiguous bp: Initial: 270030155 bp After Masking: 233729038 bp Masked: 13.44 % -- Input Database Coverage: 401520474 bp out of 1311598859 bp ( 30.61 % ) Sampling Time: 01:25:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23028291 Comparison Time: 30:03:46 (hh:mm:ss) Elapsed Time, 191797 HSPs Collected Number of families returned by RECON: 56354 Round Time: 32:08:34 (hh:mm:ss) Elapsed Time : 206 families discovered. RepeatScout/RECON discovery complete: 354 families found Classification Time: 00:36:03 (hh:mm:ss) Elapsed Time Program Time: 38:28:47 (hh:mm:ss) Elapsed Time