RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.MYgvC5/RM_2455957.MonJul211616122025 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: 1753139770 Database = /dev/shm/rModeler.MYgvC5/GCA_965225695.1_fPagPag1.hap2.1 - Sequences = 249 - Bases = 786794581 - N50 = 34565770 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 35731042-38283188 |* [ 5 ] 33178896-35731041 |* [ 6 ] 30626750-33178895 | [ 4 ] 28074604-30626749 | [ 4 ] 25522458-28074603 | [ 2 ] 22970312-25522457 | [ 2 ] 20418166-22970311 | [ ] 17866021-20418166 | [ 1 ] 15313875-17866020 | [ ] 12761729-15313874 | [ ] 10209583-12761728 | [ ] 7657437-10209582 | [ ] 5105291-7657436 | [ ] 2553145-5105290 | [ ] 1000-2553145 |************************************************** [ 225 ] Storage Throughput = excellent ( 1125.47 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40014408 bp ( 40009008 non ambiguous ) - Num Contigs Represented = 63 - Sequence extraction : 00:00:41 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:52 (hh:mm:ss) Elapsed Time Round Time: 00:27:52 (hh:mm:ss) Elapsed Time : 553 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 00:00:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10316 repeats masked totaling 1300284 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10041556 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 10039756 bp After Masking: 8462858 bp Masked: 15.71 % -- Input Database Coverage: 10041556 bp out of 786794581 bp ( 1.28 % ) Sampling Time: 00:00:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:05:05 (hh:mm:ss) Elapsed Time, 10458 HSPs Collected Number of families returned by RECON: 2019 Round Time: 00:06:09 (hh:mm:ss) Elapsed Time : 20 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 32397 repeats masked totaling 4121828 bp(s). - TE Masking time 00:00:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30012775 bp Num Contigs Represented = 56 Non ambiguous bp: Initial: 30009175 bp After Masking: 24462686 bp Masked: 18.48 % -- Input Database Coverage: 40054331 bp out of 786794581 bp ( 5.09 % ) Sampling Time: 00:03:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:29:50 (hh:mm:ss) Elapsed Time, 76352 HSPs Collected Number of families returned by RECON: 6626 Round Time: 00:35:09 (hh:mm:ss) Elapsed Time : 160 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 112239 repeats masked totaling 14951847 bp(s). - TE Masking time 00:01:51 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90019033 bp Num Contigs Represented = 94 Non ambiguous bp: Initial: 90007433 bp After Masking: 71229876 bp Masked: 20.86 % -- Input Database Coverage: 130073364 bp out of 786794581 bp ( 16.53 % ) Sampling Time: 00:09:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2573046 Comparison Time: 03:40:16 (hh:mm:ss) Elapsed Time, 351892 HSPs Collected Number of families returned by RECON: 21299 Round Time: 04:37:32 (hh:mm:ss) Elapsed Time : 592 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:17:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 423669 repeats masked totaling 61389936 bp(s). - TE Masking time 00:12:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270049325 bp Num Contigs Represented = 156 Non ambiguous bp: Initial: 270011325 bp After Masking: 197507428 bp Masked: 26.85 % -- Input Database Coverage: 400122689 bp out of 786794581 bp ( 50.85 % ) Sampling Time: 00:35:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23082615 Comparison Time: 28:16:54 (hh:mm:ss) Elapsed Time, 938739 HSPs Collected Number of families returned by RECON: 70664 Round Time: 31:47:11 (hh:mm:ss) Elapsed Time : 1400 families discovered. RepeatScout/RECON discovery complete: 2725 families found Classification Time: 02:04:36 (hh:mm:ss) Elapsed Time Program Time: 39:38:29 (hh:mm:ss) Elapsed Time