RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.bz3a8m/RM_3580638.TueDec31827512024 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: 1733279269 Database = /data/tmp/rModeler.bz3a8m/GCA_964273795.1_rNatHel1.hap2.1 - Sequences = 502 - Bases = 1513526581 - N50 = 293621049 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 349064343-373997439 | [ 1 ] 324131247-349064342 | [ ] 299198151-324131246 | [ ] 274265055-299198150 | [ 1 ] 249331959-274265054 | [ ] 224398863-249331958 | [ ] 199465767-224398862 | [ ] 174532671-199465766 | [ 1 ] 149599575-174532670 | [ 1 ] 124666479-149599574 | [ 1 ] 99733383-124666478 | [ ] 74800287-99733382 | [ 2 ] 49867191-74800286 | [ ] 24934095-49867190 | [ 2 ] 1000-24934095 |************************************************** [ 493 ] Storage Throughput = excellent ( 1221.36 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40026430 bp ( 40019630 non ambiguous ) - Num Contigs Represented = 38 - Sequence extraction : 00:04:19 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:11 (hh:mm:ss) Elapsed Time Round Time: 00:24:57 (hh:mm:ss) Elapsed Time : 631 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16820 repeats masked totaling 3803441 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10030068 bp Num Contigs Represented = 22 Non ambiguous bp: Initial: 10027868 bp After Masking: 5759355 bp Masked: 42.57 % -- Input Database Coverage: 10030068 bp out of 1513526581 bp ( 0.66 % ) Sampling Time: 00:02:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:08 (hh:mm:ss) Elapsed Time, 19128 HSPs Collected Number of families returned by RECON: 861 Round Time: 00:09:20 (hh:mm:ss) Elapsed Time : 17 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:03:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 51290 repeats masked totaling 11651034 bp(s). - TE Masking time 00:00:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30036282 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 30031682 bp After Masking: 17230997 bp Masked: 42.62 % -- Input Database Coverage: 40066350 bp out of 1513526581 bp ( 2.65 % ) Sampling Time: 00:06:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:24:06 (hh:mm:ss) Elapsed Time, 38497 HSPs Collected Number of families returned by RECON: 3094 Round Time: 00:34:57 (hh:mm:ss) Elapsed Time : 83 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:09:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 162472 repeats masked totaling 36362786 bp(s). - TE Masking time 00:02:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90046758 bp Num Contigs Represented = 51 Non ambiguous bp: Initial: 90027853 bp After Masking: 50007898 bp Masked: 44.45 % -- Input Database Coverage: 130113108 bp out of 1513526581 bp ( 8.60 % ) Sampling Time: 00:19:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2577585 Comparison Time: 02:34:20 (hh:mm:ss) Elapsed Time, 189216 HSPs Collected Number of families returned by RECON: 9660 Round Time: 03:16:18 (hh:mm:ss) Elapsed Time : 326 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:26:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:20:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 549119 repeats masked totaling 119062239 bp(s). - TE Masking time 00:08:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270057566 bp Num Contigs Represented = 147 Non ambiguous bp: Initial: 270002932 bp After Masking: 139875580 bp Masked: 48.19 % -- Input Database Coverage: 400170674 bp out of 1513526581 bp ( 26.44 % ) Sampling Time: 00:55:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23171028 Comparison Time: 17:17:43 (hh:mm:ss) Elapsed Time, 663208 HSPs Collected Number of families returned by RECON: 31651 Round Time: 19:59:27 (hh:mm:ss) Elapsed Time : 833 families discovered. RepeatScout/RECON discovery complete: 1890 families found Classification Time: 01:02:33 (hh:mm:ss) Elapsed Time Program Time: 25:27:32 (hh:mm:ss) Elapsed Time