RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.Hm1CLL/RM_3715.SatDec72322072024 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: 1733642516 Database = /scratch/tmp/rModeler.Hm1CLL/GCA_038048865.1_aMixFle1.hap2 - Sequences = 914 - Bases = 2876209288 - N50 = 347890010 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 438958389-470311846 | [ 1 ] 407604932-438958388 | [ ] 376251475-407604931 | [ 1 ] 344898018-376251474 | [ 1 ] 313544562-344898018 | [ 1 ] 282191105-313544561 | [ ] 250837648-282191104 | [ 1 ] 219484191-250837647 | [ 1 ] 188130734-219484190 | [ ] 156777278-188130734 | [ ] 125423821-156777277 | [ 3 ] 94070364-125423820 | [ 2 ] 62716907-94070363 | [ 1 ] 31363450-62716906 | [ ] 9994-31363450 |************************************************** [ 902 ] Storage Throughput = fair ( 587.56 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40082535 bp ( 40037361 non ambiguous ) - Num Contigs Represented = 38 - Sequence extraction : 00:06:03 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:42 (hh:mm:ss) Elapsed Time Round Time: 00:46:48 (hh:mm:ss) Elapsed Time : 823 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15008 repeats masked totaling 3871707 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10022593 bp Num Contigs Represented = 18 Non ambiguous bp: Initial: 10021993 bp After Masking: 5491914 bp Masked: 45.20 % -- Input Database Coverage: 10022593 bp out of 2876209288 bp ( 0.35 % ) Sampling Time: 00:02:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:01 (hh:mm:ss) Elapsed Time, 13299 HSPs Collected Number of families returned by RECON: 1576 Round Time: 00:08:38 (hh:mm:ss) Elapsed Time : 31 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:04:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 47987 repeats masked totaling 12215854 bp(s). - TE Masking time 00:00:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30059862 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 30015288 bp After Masking: 15560421 bp Masked: 48.16 % -- Input Database Coverage: 40082455 bp out of 2876209288 bp ( 1.39 % ) Sampling Time: 00:13:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:23:38 (hh:mm:ss) Elapsed Time, 48591 HSPs Collected Number of families returned by RECON: 5003 Round Time: 00:42:15 (hh:mm:ss) Elapsed Time : 116 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:13:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:23:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 153709 repeats masked totaling 38369724 bp(s). - TE Masking time 00:02:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90220262 bp Num Contigs Represented = 89 Non ambiguous bp: Initial: 90008087 bp After Masking: 44811130 bp Masked: 50.21 % -- Input Database Coverage: 130302717 bp out of 2876209288 bp ( 4.53 % ) Sampling Time: 00:40:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2584401 Comparison Time: 02:32:08 (hh:mm:ss) Elapsed Time, 290565 HSPs Collected Number of families returned by RECON: 14934 Round Time: 03:48:31 (hh:mm:ss) Elapsed Time : 563 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:40:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:07:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 539086 repeats masked totaling 133841474 bp(s). - TE Masking time 00:14:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270316756 bp Num Contigs Represented = 214 Non ambiguous bp: Initial: 270030921 bp After Masking: 115242071 bp Masked: 57.32 % -- Input Database Coverage: 400619473 bp out of 2876209288 bp ( 13.93 % ) Sampling Time: 02:03:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23171028 Comparison Time: 17:14:51 (hh:mm:ss) Elapsed Time, 822565 HSPs Collected Number of families returned by RECON: 39813 Round Time: 22:08:00 (hh:mm:ss) Elapsed Time : 1329 families discovered. RepeatScout/RECON discovery complete: 2862 families found Classification Time: 02:01:25 (hh:mm:ss) Elapsed Time Program Time: 29:35:37 (hh:mm:ss) Elapsed Time