RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Xey4ut/RM_3653.TueJul90629522024 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: 1720531791 Database = /dev/shm/rModeler.Xey4ut/GCF_001649575.2_ASM164957v2 - Sequences = 300 - Bases = 680655669 - N50 = 29747159 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 35487058-38021566 | [ 2 ] 32952551-35487058 | [ 2 ] 30418043-32952550 | [ 3 ] 27883536-30418043 | [ 4 ] 25349028-27883535 |* [ 6 ] 22814521-25349028 | [ 5 ] 20280013-22814520 | [ 1 ] 17745506-20280013 | [ ] 15210998-17745505 | [ 1 ] 12676491-15210998 | [ ] 10141983-12676490 | [ ] 7607476-10141983 | [ ] 5072968-7607475 | [ ] 2538461-5072968 | [ ] 3954-2538461 |************************************************** [ 276 ] Storage Throughput = good ( 952.64 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 42476581 bp ( 40034179 non ambiguous ) - Num Contigs Represented = 47 - Sequence extraction : 00:00:44 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:49 (hh:mm:ss) Elapsed Time Round Time: 00:24:48 (hh:mm:ss) Elapsed Time : 552 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 00:00:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13542 repeats masked totaling 1776271 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10623372 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 10027766 bp After Masking: 8165201 bp Masked: 18.57 % -- Input Database Coverage: 10623372 bp out of 680655669 bp ( 1.56 % ) Sampling Time: 00:00:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 35245 Comparison Time: 00:06:21 (hh:mm:ss) Elapsed Time, 12782 HSPs Collected Number of families returned by RECON: 1418 Round Time: 00:07:52 (hh:mm:ss) Elapsed Time : 19 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:33 (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... 41029 repeats masked totaling 5541096 bp(s). - TE Masking time 00:00:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 31853129 bp Num Contigs Represented = 45 Non ambiguous bp: Initial: 30006333 bp After Masking: 24170784 bp Masked: 19.45 % -- Input Database Coverage: 42476501 bp out of 680655669 bp ( 6.24 % ) Sampling Time: 00:02:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 324415 Comparison Time: 00:37:29 (hh:mm:ss) Elapsed Time, 51017 HSPs Collected Number of families returned by RECON: 4687 Round Time: 00:41:07 (hh:mm:ss) Elapsed Time : 109 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 136975 repeats masked totaling 19927042 bp(s). - TE Masking time 00:01:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 95754121 bp Num Contigs Represented = 74 Non ambiguous bp: Initial: 90023911 bp After Masking: 69308815 bp Masked: 23.01 % -- Input Database Coverage: 138230622 bp out of 680655669 bp ( 20.31 % ) Sampling Time: 00:06:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2939100 Comparison Time: 04:33:14 (hh:mm:ss) Elapsed Time, 244754 HSPs Collected Number of families returned by RECON: 16156 Round Time: 04:52:02 (hh:mm:ss) Elapsed Time : 436 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 467163 repeats masked totaling 71329113 bp(s). - TE Masking time 00:10:58 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 286421059 bp Num Contigs Represented = 164 Non ambiguous bp: Initial: 270011606 bp After Masking: 196347823 bp Masked: 27.28 % -- Input Database Coverage: 424651681 bp out of 680655669 bp ( 62.39 % ) Sampling Time: 00:24:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 26335653 Comparison Time: 36:06:17 (hh:mm:ss) Elapsed Time, 516989 HSPs Collected Number of families returned by RECON: 61762 Round Time: 38:06:15 (hh:mm:ss) Elapsed Time : 862 families discovered. RepeatScout/RECON discovery complete: 1978 families found Classification Time: 01:20:00 (hh:mm:ss) Elapsed Time Program Time: 45:32:04 (hh:mm:ss) Elapsed Time