RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.0oQ7Ot/RM_31679.FriJan122346532024 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: 1705132010 Database = /dev/shm/rModeler.0oQ7Ot/GCA_031878675.1_mThoBot2.hap1 - Sequences = 630 - Bases = 2025650949 - N50 = 66969139 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 99136827-106217240 | [ 2 ] 92056415-99136827 | [ 1 ] 84976003-92056415 | [ 3 ] 77895591-84976003 | [ 2 ] 70815179-77895591 | [ 1 ] 63734767-70815179 | [ 3 ] 56654355-63734767 | [ 5 ] 49573942-56654354 | [ 1 ] 42493530-49573942 | [ 3 ] 35413118-42493530 | [ 2 ] 28332706-35413118 | [ 2 ] 21252294-28332706 | [ 3 ] 14171882-21252294 | [ 3 ] 7091470-14171882 | [ 9 ] 11058-7091470 |************************************************** [ 590 ] Storage Throughput = excellent ( 1085.90 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40024810 bp ( 40021610 non ambiguous ) - Num Contigs Represented = 112 - Sequence extraction : 00:01:16 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:48 (hh:mm:ss) Elapsed Time Round Time: 00:39:59 (hh:mm:ss) Elapsed Time : 175 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18962 repeats masked totaling 3262314 bp(s). - TE Masking time 00:00:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10039271 bp Num Contigs Represented = 53 Non ambiguous bp: Initial: 10038871 bp After Masking: 6314537 bp Masked: 37.10 % -- Input Database Coverage: 10039271 bp out of 2025650949 bp ( 0.50 % ) Sampling Time: 00:04:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:14:10 (hh:mm:ss) Elapsed Time, 2707 HSPs Collected Number of families returned by RECON: 433 Round Time: 00:19:17 (hh:mm:ss) Elapsed Time : 7 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 53042 repeats masked totaling 9759710 bp(s). - TE Masking time 00:01:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30025464 bp Num Contigs Represented = 99 Non ambiguous bp: Initial: 30022664 bp After Masking: 18788942 bp Masked: 37.42 % -- Input Database Coverage: 40064735 bp out of 2025650949 bp ( 1.98 % ) Sampling Time: 00:13:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 289180 Comparison Time: 00:31:12 (hh:mm:ss) Elapsed Time, 27674 HSPs Collected Number of families returned by RECON: 1475 Round Time: 00:45:40 (hh:mm:ss) Elapsed Time : 28 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:29:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 171455 repeats masked totaling 30338113 bp(s). - TE Masking time 00:02:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90037649 bp Num Contigs Represented = 165 Non ambiguous bp: Initial: 90032449 bp After Masking: 55668341 bp Masked: 38.17 % -- Input Database Coverage: 130102384 bp out of 2025650949 bp ( 6.42 % ) Sampling Time: 00:35:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2552670 Comparison Time: 03:47:10 (hh:mm:ss) Elapsed Time, 52226 HSPs Collected Number of families returned by RECON: 6943 Round Time: 04:28:43 (hh:mm:ss) Elapsed Time : 108 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:08:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:37:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 533309 repeats masked totaling 95471318 bp(s). - TE Masking time 00:09:57 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270030153 bp Num Contigs Represented = 319 Non ambiguous bp: Initial: 270007953 bp After Masking: 161805048 bp Masked: 40.07 % -- Input Database Coverage: 400132537 bp out of 2025650949 bp ( 19.75 % ) Sampling Time: 01:56:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23075821 Comparison Time: 26:28:24 (hh:mm:ss) Elapsed Time, 224334 HSPs Collected Number of families returned by RECON: 28711 Round Time: 28:55:55 (hh:mm:ss) Elapsed Time : 301 families discovered. RepeatScout/RECON discovery complete: 619 families found Classification Time: 00:39:33 (hh:mm:ss) Elapsed Time Program Time: 35:49:07 (hh:mm:ss) Elapsed Time