RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Dnfw1p/RM_3518658.WedJul100505572024 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: 1720613157 Database = /dev/shm/rModeler.Dnfw1p/GCF_029890125.1_OSU_Roscu_1.1 - Sequences = 930 - Bases = 1065491053 - N50 = 2967639 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 20586855-22056461 | [ 1 ] 19117249-20586854 | [ ] 17647643-19117248 | [ ] 16178037-17647642 | [ 1 ] 14708432-16178037 | [ 1 ] 13238826-14708431 | [ ] 11769220-13238825 | [ ] 10299614-11769219 | [ 4 ] 8830008-10299613 | [ 4 ] 7360403-8830008 | [ 5 ] 5890797-7360402 | [ 12 ] 4421191-5890796 |* [ 22 ] 2951585-4421190 |*** [ 46 ] 1481979-2951584 |******* [ 113 ] 12374-1481979 |************************************************** [ 721 ] Storage Throughput = excellent ( 1273.14 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40014664 bp ( 40014664 non ambiguous ) - Num Contigs Represented = 396 - Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:33 (hh:mm:ss) Elapsed Time Round Time: 00:37:32 (hh:mm:ss) Elapsed Time : 1284 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 00:01:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15460 repeats masked totaling 3858603 bp(s). - TE Masking time 00:00:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10036359 bp Num Contigs Represented = 188 Non ambiguous bp: Initial: 10036359 bp After Masking: 5513545 bp Masked: 45.06 % -- Input Database Coverage: 10036359 bp out of 1065491053 bp ( 0.94 % ) Sampling Time: 00:02:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33153 Comparison Time: 00:05:13 (hh:mm:ss) Elapsed Time, 7951 HSPs Collected Number of families returned by RECON: 1620 Round Time: 00:07:50 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 48082 repeats masked totaling 11214032 bp(s). - TE Masking time 00:01:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30018152 bp Num Contigs Represented = 330 Non ambiguous bp: Initial: 30018152 bp After Masking: 16818613 bp Masked: 43.97 % -- Input Database Coverage: 40054511 bp out of 1065491053 bp ( 3.76 % ) Sampling Time: 00:05:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:26:03 (hh:mm:ss) Elapsed Time, 57196 HSPs Collected Number of families returned by RECON: 5557 Round Time: 00:33:37 (hh:mm:ss) Elapsed Time : 119 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 150542 repeats masked totaling 34774698 bp(s). - TE Masking time 00:03:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90030241 bp Num Contigs Represented = 573 Non ambiguous bp: Initial: 90030241 bp After Masking: 49739822 bp Masked: 44.75 % -- Input Database Coverage: 130084752 bp out of 1065491053 bp ( 12.21 % ) Sampling Time: 00:17:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2614041 Comparison Time: 02:32:21 (hh:mm:ss) Elapsed Time, 414556 HSPs Collected Number of families returned by RECON: 15086 Round Time: 03:03:31 (hh:mm:ss) Elapsed Time : 724 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:37:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 542903 repeats masked totaling 127289716 bp(s). - TE Masking time 00:18:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270028083 bp Num Contigs Represented = 750 Non ambiguous bp: Initial: 270028083 bp After Masking: 126899286 bp Masked: 53.01 % -- Input Database Coverage: 400112835 bp out of 1065491053 bp ( 37.55 % ) Sampling Time: 00:57:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23444128 Comparison Time: 16:15:58 (hh:mm:ss) Elapsed Time, 1091086 HSPs Collected Number of families returned by RECON: 40081 Round Time: 18:12:47 (hh:mm:ss) Elapsed Time : 1677 families discovered. RepeatScout/RECON discovery complete: 3815 families found Classification Time: 02:28:38 (hh:mm:ss) Elapsed Time Program Time: 25:03:55 (hh:mm:ss) Elapsed Time