RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.YAF6rr/RM_5482.FriJul120829022024 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: 1720798140 Database = /dev/shm/rModeler.YAF6rr/GCF_002814215.2_Sedor1 - Sequences = 98345 - Bases = 731697021 - N50 = 1276847 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 7556818-8096577 | [ 2 ] 7017060-7556818 | [ ] 6477302-7017060 | [ 4 ] 5937543-6477301 | [ 1 ] 5397785-5937543 | [ 1 ] 4858027-5397785 | [ 2 ] 4318269-4858027 | [ 6 ] 3778510-4318268 | [ 4 ] 3238752-3778510 | [ 5 ] 2698994-3238752 | [ 12 ] 2159236-2698994 | [ 21 ] 1619477-2159235 | [ 46 ] 1079719-1619477 | [ 85 ] 539961-1079719 | [ 154 ] 203-539961 |************************************************** [ 98002 ] Storage Throughput = excellent ( 1120.79 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40982575 bp ( 40033818 non ambiguous ) - Num Contigs Represented = 6150 - Sequence extraction : 00:00:07 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:21:22 (hh:mm:ss) Elapsed Time Round Time: 00:29:44 (hh:mm:ss) Elapsed Time : 409 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6593 repeats masked totaling 736977 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10235563 bp Num Contigs Represented = 1662 Non ambiguous bp: Initial: 10010678 bp After Masking: 8832987 bp Masked: 11.76 % -- Input Database Coverage: 10235563 bp out of 731697021 bp ( 1.40 % ) Sampling Time: 00:00:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 1466328 Comparison Time: 00:13:20 (hh:mm:ss) Elapsed Time, 8193 HSPs Collected Number of families returned by RECON: 1826 Round Time: 00:14:27 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 20645 repeats masked totaling 2390128 bp(s). - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30746932 bp Num Contigs Represented = 4607 Non ambiguous bp: Initial: 30023060 bp After Masking: 26396236 bp Masked: 12.08 % -- Input Database Coverage: 40982495 bp out of 731697021 bp ( 5.60 % ) Sampling Time: 00:02:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 12105660 Comparison Time: 00:58:00 (hh:mm:ss) Elapsed Time, 51611 HSPs Collected Number of families returned by RECON: 6598 Round Time: 01:02:24 (hh:mm:ss) Elapsed Time : 132 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 77338 repeats masked totaling 9785885 bp(s). - TE Masking time 00:01:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 92035956 bp Num Contigs Represented = 13206 Non ambiguous bp: Initial: 90039367 bp After Masking: 76431607 bp Masked: 15.11 % -- Input Database Coverage: 133018451 bp out of 731697021 bp ( 18.18 % ) Sampling Time: 00:07:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 107670475 Comparison Time: 05:41:27 (hh:mm:ss) Elapsed Time, 243618 HSPs Collected Number of families returned by RECON: 23244 Round Time: 06:06:44 (hh:mm:ss) Elapsed Time : 442 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 298085 repeats masked totaling 40526173 bp(s). - TE Masking time 00:08:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 275977152 bp Num Contigs Represented = 37289 Non ambiguous bp: Initial: 270012727 bp After Masking: 218631064 bp Masked: 19.03 % -- Input Database Coverage: 408995603 bp out of 731697021 bp ( 55.90 % ) Sampling Time: 00:24:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 910257778 Comparison Time: 40:23:35 (hh:mm:ss) Elapsed Time, 870683 HSPs Collected Number of families returned by RECON: 91012 Round Time: 44:08:53 (hh:mm:ss) Elapsed Time : 1129 families discovered. RepeatScout/RECON discovery complete: 2124 families found Classification Time: 01:18:35 (hh:mm:ss) Elapsed Time Program Time: 53:20:47 (hh:mm:ss) Elapsed Time