RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.kC3Eca/RM_29725.FriDec10041512023 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: 1701420108 Database = /dev/shm/rModeler.kC3Eca/GCA_030020295.1_rGavGan2.hap2 - Sequences = 160 - Bases = 2328538659 - N50 = 299944300 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 441734988-473287416 | [ 1 ] 410182560-441734987 | [ ] 378630132-410182559 | [ ] 347077705-378630132 | [ ] 315525277-347077704 | [ ] 283972849-315525276 | [ 2 ] 252420421-283972848 | [ 1 ] 220867994-252420421 | [ ] 189315566-220867993 | [ 1 ] 157763138-189315565 | [ ] 126210710-157763137 | [ ] 94658283-126210710 | [ 2 ] 63105855-94658282 |* [ 5 ] 31553427-63105854 | [ 2 ] 1000-31553427 |************************************************** [ 146 ] Storage Throughput = excellent ( 1151.69 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40026430 bp ( 40026417 non ambiguous ) - Num Contigs Represented = 22 - Sequence extraction : 00:05:14 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:45 (hh:mm:ss) Elapsed Time Round Time: 00:33:54 (hh:mm:ss) Elapsed Time : 550 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12490 repeats masked totaling 2768675 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10034846 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 10034846 bp After Masking: 7172015 bp Masked: 28.53 % -- Input Database Coverage: 10034846 bp out of 2328538659 bp ( 0.43 % ) Sampling Time: 00:02:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:10:57 (hh:mm:ss) Elapsed Time, 11635 HSPs Collected Number of families returned by RECON: 1386 Round Time: 00:13:36 (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 : 00:03:52 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 37307 repeats masked totaling 8655863 bp(s). - TE Masking time 00:00:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30031425 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 30031412 bp After Masking: 20815602 bp Masked: 30.69 % -- Input Database Coverage: 40066271 bp out of 2328538659 bp ( 1.72 % ) Sampling Time: 00:07:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:31:25 (hh:mm:ss) Elapsed Time, 76350 HSPs Collected Number of families returned by RECON: 4349 Round Time: 00:41:10 (hh:mm:ss) Elapsed Time : 131 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:11:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 132550 repeats masked totaling 30591759 bp(s). - TE Masking time 00:02:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90015372 bp Num Contigs Represented = 21 Non ambiguous bp: Initial: 90011714 bp After Masking: 58510721 bp Masked: 35.00 % -- Input Database Coverage: 130081643 bp out of 2328538659 bp ( 5.59 % ) Sampling Time: 00:19:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2530125 Comparison Time: 03:07:08 (hh:mm:ss) Elapsed Time, 280477 HSPs Collected Number of families returned by RECON: 12382 Round Time: 03:42:37 (hh:mm:ss) Elapsed Time : 438 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:34:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 461015 repeats masked totaling 106846528 bp(s). - TE Masking time 00:12:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270067697 bp Num Contigs Represented = 56 Non ambiguous bp: Initial: 270025459 bp After Masking: 160357322 bp Masked: 40.61 % -- Input Database Coverage: 400149340 bp out of 2328538659 bp ( 17.18 % ) Sampling Time: 01:00:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22885995 Comparison Time: 23:43:40 (hh:mm:ss) Elapsed Time, 652685 HSPs Collected Number of families returned by RECON: 38295 Round Time: 25:47:11 (hh:mm:ss) Elapsed Time : 928 families discovered. RepeatScout/RECON discovery complete: 2066 families found Classification Time: 01:26:54 (hh:mm:ss) Elapsed Time Program Time: 32:25:22 (hh:mm:ss) Elapsed Time