RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.7Tmml5/RM_2409656.SatMay272052252023 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: 1685245942 Database = /dev/shm/rModeler.7Tmml5/GCF_023897955.1_iqSchGreg1.2 - Sequences = 1475 - Bases = 8742434016 - N50 = 874623940 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 1128931461-1209568729 | [ 1 ] 1048294193-1128931460 | [ 1 ] 967656925-1048294192 | [ ] 887019657-967656924 | [ 1 ] 806382390-887019657 | [ 1 ] 725745122-806382389 | [ 1 ] 645107854-725745121 | [ 1 ] 564470586-645107853 | [ 2 ] 483833318-564470585 | [ 1 ] 403196051-483833318 | [ ] 322558783-403196050 | [ ] 241921515-322558782 | [ 1 ] 161284247-241921514 | [ 1 ] 80646979-161284246 | [ 1 ] 9712-80646979 |************************************************** [ 1463 ] Storage Throughput = fair ( 674.61 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40001660 bp ( 40001560 non ambiguous ) - Num Contigs Represented = 82 - Sequence extraction : 00:13:11 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:12:34 (hh:mm:ss) Elapsed Time Round Time: 00:33:46 (hh:mm:ss) Elapsed Time : 736 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:03:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13952 repeats masked totaling 4421727 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001920 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 10001920 bp After Masking: 4480971 bp Masked: 55.20 % -- Input Database Coverage: 10001920 bp out of 8742434016 bp ( 0.11 % ) Sampling Time: 00:04:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:59 (hh:mm:ss) Elapsed Time, 23148 HSPs Collected Number of families returned by RECON: 1467 Round Time: 00:10:54 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:09:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 40757 repeats masked totaling 12694677 bp(s). - TE Masking time 00:00:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30039660 bp Num Contigs Represented = 70 Non ambiguous bp: Initial: 30039560 bp After Masking: 13860985 bp Masked: 53.86 % -- Input Database Coverage: 40041580 bp out of 8742434016 bp ( 0.46 % ) Sampling Time: 00:11:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:25:35 (hh:mm:ss) Elapsed Time, 66353 HSPs Collected Number of families returned by RECON: 4859 Round Time: 00:39:42 (hh:mm:ss) Elapsed Time : 129 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:29:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 128604 repeats masked totaling 41304723 bp(s). - TE Masking time 00:01:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90011292 bp Num Contigs Represented = 155 Non ambiguous bp: Initial: 90011092 bp After Masking: 36242961 bp Masked: 59.74 % -- Input Database Coverage: 130052872 bp out of 8742434016 bp ( 1.49 % ) Sampling Time: 00:35:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2550411 Comparison Time: 01:59:18 (hh:mm:ss) Elapsed Time, 316026 HSPs Collected Number of families returned by RECON: 12520 Round Time: 02:52:57 (hh:mm:ss) Elapsed Time : 569 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 01:31:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 459490 repeats masked totaling 147181597 bp(s). - TE Masking time 00:09:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270001204 bp Num Contigs Represented = 260 Non ambiguous bp: Initial: 270000504 bp After Masking: 91338812 bp Masked: 66.17 % -- Input Database Coverage: 400054076 bp out of 8742434016 bp ( 4.58 % ) Sampling Time: 01:53:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22960476 Comparison Time: 11:04:54 (hh:mm:ss) Elapsed Time, 906054 HSPs Collected Number of families returned by RECON: 30849 Round Time: 13:45:21 (hh:mm:ss) Elapsed Time : 1610 families discovered. RepeatScout/RECON discovery complete: 3052 families found Classification Time: 02:25:54 (hh:mm:ss) Elapsed Time Program Time: 20:28:34 (hh:mm:ss) Elapsed Time