RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.KHtmPi/RM_7442.SatJul272012242024 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: 1722136342 Database = /dev/shm/rModeler.KHtmPi/GCF_021184085.1_OgorEven_v1.0 - Sequences = 19028 - Bases = 2690283663 - N50 = 86172198 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 113159324-121242117 | [ 1 ] 105076532-113159324 | [ 3 ] 96993739-105076531 | [ 5 ] 88910947-96993739 | [ 1 ] 80828155-88910947 | [ 6 ] 72745362-80828154 | [ 2 ] 64662570-72745362 | [ 2 ] 56579777-64662569 | [ 2 ] 48496985-56579777 | [ 2 ] 40414193-48496985 | [ 2 ] 32331400-40414192 | [ ] 24248608-32331400 | [ ] 16165815-24248607 | [ ] 8083023-16165815 | [ ] 231-8083023 |************************************************** [ 19002 ] Storage Throughput = excellent ( 1039.48 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40039249 bp ( 40024638 non ambiguous ) - Num Contigs Represented = 396 - Sequence extraction : 00:01:31 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:23 (hh:mm:ss) Elapsed Time Round Time: 00:37:12 (hh:mm:ss) Elapsed Time : 747 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12722 repeats masked totaling 3553422 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10028466 bp Num Contigs Represented = 120 Non ambiguous bp: Initial: 10024366 bp After Masking: 3855303 bp Masked: 61.54 % -- Input Database Coverage: 10028466 bp out of 2690283663 bp ( 0.37 % ) Sampling Time: 00:10:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 45753 Comparison Time: 00:04:50 (hh:mm:ss) Elapsed Time, 3985 HSPs Collected Number of families returned by RECON: 1042 Round Time: 00:15:09 (hh:mm:ss) Elapsed Time : 7 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:26:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 37898 repeats masked totaling 10737505 bp(s). - TE Masking time 00:00:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30010782 bp Num Contigs Represented = 306 Non ambiguous bp: Initial: 30000271 bp After Masking: 11202418 bp Masked: 62.66 % -- Input Database Coverage: 40039248 bp out of 2690283663 bp ( 1.49 % ) Sampling Time: 00:27:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 400065 Comparison Time: 00:19:28 (hh:mm:ss) Elapsed Time, 34440 HSPs Collected Number of families returned by RECON: 3049 Round Time: 00:48:30 (hh:mm:ss) Elapsed Time : 108 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:18:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 117662 repeats masked totaling 32914976 bp(s). - TE Masking time 00:01:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90055614 bp Num Contigs Represented = 888 Non ambiguous bp: Initial: 90014684 bp After Masking: 32966164 bp Masked: 63.38 % -- Input Database Coverage: 130094862 bp out of 2690283663 bp ( 4.84 % ) Sampling Time: 01:24:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 3697840 Comparison Time: 01:52:23 (hh:mm:ss) Elapsed Time, 214334 HSPs Collected Number of families returned by RECON: 9220 Round Time: 03:26:06 (hh:mm:ss) Elapsed Time : 411 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:10:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 04:02:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 396472 repeats masked totaling 108525550 bp(s). - TE Masking time 00:08:56 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270149705 bp Num Contigs Represented = 2478 Non ambiguous bp: Initial: 270019817 bp After Masking: 86703422 bp Masked: 67.89 % -- Input Database Coverage: 400244567 bp out of 2690283663 bp ( 14.88 % ) Sampling Time: 04:21:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33003750 Comparison Time: 12:22:18 (hh:mm:ss) Elapsed Time, 488459 HSPs Collected Number of families returned by RECON: 30884 Round Time: 17:23:21 (hh:mm:ss) Elapsed Time : 851 families discovered. RepeatScout/RECON discovery complete: 2124 families found Classification Time: 01:26:02 (hh:mm:ss) Elapsed Time Program Time: 23:56:20 (hh:mm:ss) Elapsed Time