RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.EJiaB1/RM_4017646.MonApr12219502024 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: 1712035189 Database = /dev/shm/rModeler.EJiaB1/GCF_028389875.1_bPtePen1.pri - Sequences = 180 - Bases = 1269016774 - N50 = 130205582 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 202474961-216936262 | [ 1 ] 188013660-202474960 | [ ] 173552359-188013659 | [ ] 159091058-173552358 | [ 1 ] 144629757-159091057 | [ ] 130168456-144629756 | [ 1 ] 115707155-130168455 | [ ] 101245855-115707155 | [ ] 86784554-101245854 | [ ] 72323253-86784553 | [ 2 ] 57861952-72323252 | [ 1 ] 43400651-57861951 | [ 1 ] 28939350-43400650 | [ 3 ] 14478049-28939349 |** [ 9 ] 16749-14478049 |************************************************** [ 161 ] Storage Throughput = excellent ( 1212.78 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40078731 bp ( 40037505 non ambiguous ) - Num Contigs Represented = 64 - Sequence extraction : 00:01:53 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:33 (hh:mm:ss) Elapsed Time Round Time: 00:22:37 (hh:mm:ss) Elapsed Time : 45 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 963 repeats masked totaling 492372 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10003070 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 10003057 bp After Masking: 9206042 bp Masked: 7.97 % -- Input Database Coverage: 10003070 bp out of 1269016774 bp ( 0.79 % ) Sampling Time: 00:00:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:07:24 (hh:mm:ss) Elapsed Time, 1737 HSPs Collected Number of families returned by RECON: 368 Round Time: 00:08:33 (hh:mm:ss) Elapsed Time : 5 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3498 repeats masked totaling 1474864 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30075659 bp Num Contigs Represented = 61 Non ambiguous bp: Initial: 30034446 bp After Masking: 26895622 bp Masked: 10.45 % -- Input Database Coverage: 40078729 bp out of 1269016774 bp ( 3.16 % ) Sampling Time: 00:03:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:37:44 (hh:mm:ss) Elapsed Time, 6284 HSPs Collected Number of families returned by RECON: 1626 Round Time: 00:41:44 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12156 repeats masked totaling 4623202 bp(s). - TE Masking time 00:00:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90149493 bp Num Contigs Represented = 86 Non ambiguous bp: Initial: 90023831 bp After Masking: 81624191 bp Masked: 9.33 % -- Input Database Coverage: 130228222 bp out of 1269016774 bp ( 10.26 % ) Sampling Time: 00:09:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2550411 Comparison Time: 04:16:20 (hh:mm:ss) Elapsed Time, 53466 HSPs Collected Number of families returned by RECON: 9752 Round Time: 04:32:15 (hh:mm:ss) Elapsed Time : 67 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:12:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 48984 repeats masked totaling 17661017 bp(s). - TE Masking time 00:03:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270281464 bp Num Contigs Represented = 119 Non ambiguous bp: Initial: 270010984 bp After Masking: 240260496 bp Masked: 11.02 % -- Input Database Coverage: 400509686 bp out of 1269016774 bp ( 31.56 % ) Sampling Time: 00:30:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22960476 Comparison Time: 33:15:18 (hh:mm:ss) Elapsed Time, 242830 HSPs Collected Number of families returned by RECON: 59318 Round Time: 34:43:25 (hh:mm:ss) Elapsed Time : 232 families discovered. RepeatScout/RECON discovery complete: 362 families found Classification Time: 00:38:41 (hh:mm:ss) Elapsed Time Program Time: 41:07:15 (hh:mm:ss) Elapsed Time