RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.ExdhBJ/RM_325138.TueJan230052092024 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: 1705999926 Database = /dev/shm/rModeler.ExdhBJ/GCF_949774975.1_mLagAlb1.1 - Sequences = 410 - Bases = 2544835795 - N50 = 115079701 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 179702704-192538540 | [ 2 ] 166866868-179702704 | [ 1 ] 154031032-166866868 | [ ] 141195196-154031032 | [ 2 ] 128359360-141195196 | [ 1 ] 115523524-128359360 | [ 1 ] 102687688-115523524 | [ 5 ] 89851852-102687688 | [ 1 ] 77016016-89851852 | [ 6 ] 64180180-77016016 | [ ] 51344344-64180180 | [ 2 ] 38508508-51344344 | [ ] 25672672-38508508 | [ 1 ] 12836836-25672672 | [ ] 1000-12836836 |************************************************** [ 388 ] Storage Throughput = good ( 736.86 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40018794 bp ( 40013794 non ambiguous ) - Num Contigs Represented = 77 - Sequence extraction : 00:02:18 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:18 (hh:mm:ss) Elapsed Time Round Time: 00:32:36 (hh:mm:ss) Elapsed Time : 192 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9584 repeats masked totaling 3147915 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10032756 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 10031756 bp After Masking: 6709021 bp Masked: 33.12 % -- Input Database Coverage: 10032756 bp out of 2544835795 bp ( 0.39 % ) Sampling Time: 00:01:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:12:18 (hh:mm:ss) Elapsed Time, 14150 HSPs Collected Number of families returned by RECON: 862 Round Time: 00:14:31 (hh:mm:ss) Elapsed Time : 22 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 00:01:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 32783 repeats masked totaling 9881240 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30025958 bp Num Contigs Represented = 68 Non ambiguous bp: Initial: 30021958 bp After Masking: 19604546 bp Masked: 34.70 % -- Input Database Coverage: 40058714 bp out of 2544835795 bp ( 1.57 % ) Sampling Time: 00:03:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:40:41 (hh:mm:ss) Elapsed Time, 116573 HSPs Collected Number of families returned by RECON: 2441 Round Time: 00:45:36 (hh:mm:ss) Elapsed Time : 59 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:06:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 105292 repeats masked totaling 32006351 bp(s). - TE Masking time 00:00:57 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90017014 bp Num Contigs Represented = 119 Non ambiguous bp: Initial: 90009703 bp After Masking: 56615852 bp Masked: 37.10 % -- Input Database Coverage: 130075728 bp out of 2544835795 bp ( 5.11 % ) Sampling Time: 00:11:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2545896 Comparison Time: 03:01:44 (hh:mm:ss) Elapsed Time, 349417 HSPs Collected Number of families returned by RECON: 8275 Round Time: 03:16:44 (hh:mm:ss) Elapsed Time : 171 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:16:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 350252 repeats masked totaling 103237883 bp(s). - TE Masking time 00:04:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270037569 bp Num Contigs Represented = 210 Non ambiguous bp: Initial: 270014187 bp After Masking: 161865463 bp Masked: 40.05 % -- Input Database Coverage: 400113297 bp out of 2544835795 bp ( 15.72 % ) Sampling Time: 00:35:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22980810 Comparison Time: 19:37:37 (hh:mm:ss) Elapsed Time, 3232633 HSPs Collected Number of families returned by RECON: 33369 Round Time: 20:32:59 (hh:mm:ss) Elapsed Time : 333 families discovered. RepeatScout/RECON discovery complete: 777 families found Classification Time: 00:26:38 (hh:mm:ss) Elapsed Time Program Time: 25:49:04 (hh:mm:ss) Elapsed Time