RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.JhBWmn/RM_730441.MonApr141231452025 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: 1744659103 Database = /dev/shm/rModeler.JhBWmn/GCA_964205305.1_aBomVar4.maternal.1 - Sequences = 3497 - Bases = 9112230460 - N50 = 1134302525 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 1285409269-1377224146 | [ 1 ] 1193594393-1285409269 | [ 1 ] 1101779516-1193594392 | [ 1 ] 1009964640-1101779516 | [ 1 ] 918149764-1009964640 | [ 2 ] 826334887-918149763 | [ ] 734520011-826334887 | [ ] 642705134-734520010 | [ ] 550890258-642705134 | [ ] 459075382-550890258 | [ 1 ] 367260505-459075381 | [ ] 275445629-367260505 | [ 1 ] 183630752-275445628 | [ 2 ] 91815876-183630752 | [ 2 ] 1000-91815876 |************************************************** [ 3485 ] Storage Throughput = excellent ( 1627.17 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40036483 bp ( 40030683 non ambiguous ) - Num Contigs Represented = 93 - Sequence extraction : 00:09:23 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:09:58 (hh:mm:ss) Elapsed Time Round Time: 00:29:51 (hh:mm:ss) Elapsed Time : 695 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:02:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15442 repeats masked totaling 5522067 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10012246 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10010446 bp After Masking: 3475221 bp Masked: 65.28 % -- Input Database Coverage: 10012246 bp out of 9112230460 bp ( 0.11 % ) Sampling Time: 00:03:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:03:00 (hh:mm:ss) Elapsed Time, 8164 HSPs Collected Number of families returned by RECON: 1055 Round Time: 00:06:45 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:07:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 47270 repeats masked totaling 16725283 bp(s). - TE Masking time 00:00:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30024157 bp Num Contigs Represented = 78 Non ambiguous bp: Initial: 30020157 bp After Masking: 10458141 bp Masked: 65.16 % -- Input Database Coverage: 40036403 bp out of 9112230460 bp ( 0.44 % ) Sampling Time: 00:10:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 289180 Comparison Time: 00:11:28 (hh:mm:ss) Elapsed Time, 60623 HSPs Collected Number of families returned by RECON: 3552 Round Time: 00:22:35 (hh:mm:ss) Elapsed Time : 83 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:21:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 150431 repeats masked totaling 52634123 bp(s). - TE Masking time 00:01:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90030130 bp Num Contigs Represented = 176 Non ambiguous bp: Initial: 90015930 bp After Masking: 28796550 bp Masked: 68.01 % -- Input Database Coverage: 130066533 bp out of 9112230460 bp ( 1.43 % ) Sampling Time: 00:30:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2559453 Comparison Time: 00:47:42 (hh:mm:ss) Elapsed Time, 347546 HSPs Collected Number of families returned by RECON: 10575 Round Time: 01:21:47 (hh:mm:ss) Elapsed Time : 364 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 01:03:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:25:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 488665 repeats masked totaling 169895167 bp(s). - TE Masking time 00:05:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270069985 bp Num Contigs Represented = 475 Non ambiguous bp: Initial: 270036403 bp After Masking: 74155515 bp Masked: 72.54 % -- Input Database Coverage: 400136518 bp out of 9112230460 bp ( 4.39 % ) Sampling Time: 01:35:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23137003 Comparison Time: 04:19:27 (hh:mm:ss) Elapsed Time, 1275638 HSPs Collected Number of families returned by RECON: 27984 Round Time: 06:11:01 (hh:mm:ss) Elapsed Time : 908 families discovered. RepeatScout/RECON discovery complete: 2063 families found Classification Time: 00:47:31 (hh:mm:ss) Elapsed Time Program Time: 09:19:30 (hh:mm:ss) Elapsed Time