RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.ev5YEV/RM_4052023.TueMay161802572023 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: 1684285376 Database = /dev/shm/rModeler.ev5YEV/GCF_027409825.1_fScoJap1.pri - Sequences = 360 - Bases = 828681152 - N50 = 36016775 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 41165659-44105842 | [ 2 ] 38225476-41165658 | [ 3 ] 35285293-38225475 | [ 5 ] 32345110-35285292 | [ 6 ] 29404927-32345109 | [ 4 ] 26464744-29404926 | [ 3 ] 23524561-26464743 | [ ] 20584379-23524561 | [ ] 17644196-20584378 | [ 1 ] 14704013-17644195 | [ ] 11763830-14704012 | [ ] 8823647-11763829 | [ ] 5883464-8823646 | [ ] 2943281-5883463 | [ ] 3099-2943281 |************************************************** [ 336 ] Storage Throughput = good ( 982.14 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40046483 bp ( 40013483 non ambiguous ) - Num Contigs Represented = 38 - Sequence extraction : 00:00:43 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:29 (hh:mm:ss) Elapsed Time Round Time: 00:25:22 (hh:mm:ss) Elapsed Time : 498 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6742 repeats masked totaling 1009543 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10045444 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 10034944 bp After Masking: 7899019 bp Masked: 21.28 % -- Input Database Coverage: 10045444 bp out of 828681152 bp ( 1.21 % ) Sampling Time: 00:04:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:07:25 (hh:mm:ss) Elapsed Time, 17661 HSPs Collected Number of families returned by RECON: 1665 Round Time: 00:12:42 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:22:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 23527 repeats masked totaling 3777493 bp(s). - TE Masking time 00:00:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30041039 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 30018539 bp After Masking: 23355715 bp Masked: 22.20 % -- Input Database Coverage: 40086483 bp out of 828681152 bp ( 4.84 % ) Sampling Time: 00:24:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 00:35:19 (hh:mm:ss) Elapsed Time, 59934 HSPs Collected Number of families returned by RECON: 6274 Round Time: 01:01:17 (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 : 00:01:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:31:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 77192 repeats masked totaling 11411987 bp(s). - TE Masking time 00:01:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90071423 bp Num Contigs Represented = 63 Non ambiguous bp: Initial: 90008998 bp After Masking: 69944570 bp Masked: 22.29 % -- Input Database Coverage: 130157906 bp out of 828681152 bp ( 15.71 % ) Sampling Time: 00:34:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2573046 Comparison Time: 03:40:45 (hh:mm:ss) Elapsed Time, 307549 HSPs Collected Number of families returned by RECON: 21114 Round Time: 04:33:25 (hh:mm:ss) Elapsed Time : 514 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:44:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 293943 repeats masked totaling 48205594 bp(s). - TE Masking time 00:10:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270241227 bp Num Contigs Represented = 148 Non ambiguous bp: Initial: 270028524 bp After Masking: 194871797 bp Masked: 27.83 % -- Input Database Coverage: 400399133 bp out of 828681152 bp ( 48.32 % ) Sampling Time: 02:00:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23191455 Comparison Time: 26:21:06 (hh:mm:ss) Elapsed Time, 1095678 HSPs Collected Number of families returned by RECON: 71807 Round Time: 30:11:26 (hh:mm:ss) Elapsed Time : 1426 families discovered. RepeatScout/RECON discovery complete: 2559 families found Classification Time: 01:50:17 (hh:mm:ss) Elapsed Time Program Time: 38:14:29 (hh:mm:ss) Elapsed Time