RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.LD3xB5/RM_267207.SatJan71710022023 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: 1673140202 Database = /dev/shm/rModeler.LD3xB5/GCF_020740685.1_mJacJac1.mat.Y.cur - Sequences = 160 - Bases = 2863865261 - N50 = 167301369 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 321134580-344072713 | [ 1 ] 298196447-321134579 | [ ] 275258315-298196447 | [ ] 252320182-275258314 | [ ] 229382050-252320182 | [ ] 206443917-229382049 | [ 1 ] 183505784-206443916 | [ 1 ] 160567652-183505784 |* [ 3 ] 137629519-160567651 |* [ 4 ] 114691387-137629519 | [ 1 ] 91753254-114691386 |* [ 3 ] 68815121-91753253 |* [ 4 ] 45876989-68815121 | [ 2 ] 22938856-45876988 | [ 1 ] 724-22938856 |************************************************** [ 139 ] Storage Throughput = excellent ( 1284.94 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40165627 bp ( 40003755 non ambiguous ) - Num Contigs Represented = 36 - Sequence extraction : 00:03:14 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:09:35 (hh:mm:ss) Elapsed Time Round Time: 00:20:01 (hh:mm:ss) Elapsed Time : 278 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 20965 repeats masked totaling 4216855 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10080707 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 10000949 bp After Masking: 5616677 bp Masked: 43.84 % -- Input Database Coverage: 10080707 bp out of 2863865261 bp ( 0.35 % ) Sampling Time: 00:01:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:05:46 (hh:mm:ss) Elapsed Time, 2494 HSPs Collected Number of families returned by RECON: 479 Round Time: 00:07:22 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:56 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 61058 repeats masked totaling 12270519 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30084919 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 30002805 bp After Masking: 17286383 bp Masked: 42.38 % -- Input Database Coverage: 40165626 bp out of 2863865261 bp ( 1.40 % ) Sampling Time: 00:03:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:23:07 (hh:mm:ss) Elapsed Time, 15610 HSPs Collected Number of families returned by RECON: 1915 Round Time: 00:26:50 (hh:mm:ss) Elapsed Time : 39 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:38 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 188282 repeats masked totaling 37905490 bp(s). - TE Masking time 00:00:52 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90502519 bp Num Contigs Represented = 48 Non ambiguous bp: Initial: 90016142 bp After Masking: 50591114 bp Masked: 43.80 % -- Input Database Coverage: 130668145 bp out of 2863865261 bp ( 4.56 % ) Sampling Time: 00:10:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2559453 Comparison Time: 01:55:15 (hh:mm:ss) Elapsed Time, 86790 HSPs Collected Number of families returned by RECON: 6980 Round Time: 02:07:35 (hh:mm:ss) Elapsed Time : 154 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:16:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 605048 repeats masked totaling 120118189 bp(s). - TE Masking time 00:03:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271525127 bp Num Contigs Represented = 69 Non ambiguous bp: Initial: 270001301 bp After Masking: 145444974 bp Masked: 46.13 % -- Input Database Coverage: 402193272 bp out of 2863865261 bp ( 14.04 % ) Sampling Time: 00:31:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23089410 Comparison Time: 12:16:39 (hh:mm:ss) Elapsed Time, 997675 HSPs Collected Number of families returned by RECON: 26673 Round Time: 12:59:12 (hh:mm:ss) Elapsed Time : 340 families discovered. RepeatScout/RECON discovery complete: 820 families found Classification Time: 00:19:12 (hh:mm:ss) Elapsed Time Program Time: 16:20:12 (hh:mm:ss) Elapsed Time