RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.IYacXE/RM_1230608.ThuApr101813442025 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: 1744334022 Database = /data/tmp/rModeler.IYacXE/GCA_049190665.1_fLepSal2.hap1 - Sequences = 2987 - Bases = 735065728 - N50 = 28524080 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 57832889-61963674 | [ 1 ] 53702105-57832889 | [ ] 49571320-53702104 | [ ] 45440536-49571320 | [ 1 ] 41309751-45440535 | [ ] 37178967-41309751 | [ 1 ] 33048182-37178966 | [ 2 ] 28917398-33048182 | [ 3 ] 24786613-28917397 | [ 6 ] 20655829-24786613 | [ 3 ] 16525044-20655828 | [ 2 ] 12394260-16525044 | [ 1 ] 8263475-12394259 | [ ] 4132691-8263475 | [ ] 1907-4132691 |************************************************** [ 2967 ] Storage Throughput = excellent ( 1247.57 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40016648 bp ( 40001259 non ambiguous ) - Num Contigs Represented = 263 - Sequence extraction : 00:00:37 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:48 (hh:mm:ss) Elapsed Time Round Time: 00:33:27 (hh:mm:ss) Elapsed Time : 820 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10116 repeats masked totaling 2094765 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10011760 bp Num Contigs Represented = 88 Non ambiguous bp: Initial: 10006560 bp After Masking: 6665334 bp Masked: 33.39 % -- Input Database Coverage: 10011760 bp out of 735065728 bp ( 1.36 % ) Sampling Time: 00:02:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 36046 Comparison Time: 00:05:57 (hh:mm:ss) Elapsed Time, 11079 HSPs Collected Number of families returned by RECON: 1400 Round Time: 00:09:30 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 31223 repeats masked totaling 5940264 bp(s). - TE Masking time 00:00:57 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30044831 bp Num Contigs Represented = 205 Non ambiguous bp: Initial: 30034642 bp After Masking: 20050866 bp Masked: 33.24 % -- Input Database Coverage: 40056591 bp out of 735065728 bp ( 5.45 % ) Sampling Time: 00:08:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 335790 Comparison Time: 00:31:05 (hh:mm:ss) Elapsed Time, 53164 HSPs Collected Number of families returned by RECON: 5449 Round Time: 00:45:58 (hh:mm:ss) Elapsed Time : 115 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:19:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 97788 repeats masked totaling 18845178 bp(s). - TE Masking time 00:03:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90044132 bp Num Contigs Represented = 576 Non ambiguous bp: Initial: 90011609 bp After Masking: 58815924 bp Masked: 34.66 % -- Input Database Coverage: 130100723 bp out of 735065728 bp ( 17.70 % ) Sampling Time: 00:24:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 3123750 Comparison Time: 02:47:10 (hh:mm:ss) Elapsed Time, 345652 HSPs Collected Number of families returned by RECON: 18543 Round Time: 03:52:57 (hh:mm:ss) Elapsed Time : 491 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:59:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 362270 repeats masked totaling 74313309 bp(s). - TE Masking time 00:14:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270128847 bp Num Contigs Represented = 1342 Non ambiguous bp: Initial: 270031363 bp After Masking: 159678364 bp Masked: 40.87 % -- Input Database Coverage: 400229570 bp out of 735065728 bp ( 54.45 % ) Sampling Time: 01:17:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 27324528 Comparison Time: 21:53:50 (hh:mm:ss) Elapsed Time, 1220370 HSPs Collected Number of families returned by RECON: 60845 Round Time: 27:45:53 (hh:mm:ss) Elapsed Time : 1307 families discovered. RepeatScout/RECON discovery complete: 2742 families found Classification Time: 02:34:48 (hh:mm:ss) Elapsed Time Program Time: 35:42:33 (hh:mm:ss) Elapsed Time