RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Fp1YhN/RM_2109391.SunApr200541092025 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: 1745152868 Database = /dev/shm/rModeler.Fp1YhN/GCF_047511675.1_mMarFla1.hap1 - Sequences = 813 - Bases = 2704651887 - N50 = 145453728 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 206120711-220842399 | [ 1 ] 191399024-206120711 | [ 1 ] 176677336-191399023 | [ 1 ] 161955649-176677336 | [ 2 ] 147233962-161955649 | [ 1 ] 132512274-147233961 | [ 3 ] 117790587-132512274 | [ 3 ] 103068899-117790586 | [ 2 ] 88347212-103068899 | [ 1 ] 73625525-88347212 | [ 3 ] 58903837-73625524 | [ 1 ] 44182150-58903837 | [ ] 29460462-44182149 | [ 1 ] 14738775-29460462 | [ 2 ] 17088-14738775 |************************************************** [ 791 ] Storage Throughput = excellent ( 1690.99 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40026333 bp ( 40025433 non ambiguous ) - Num Contigs Represented = 60 - Sequence extraction : 00:01:24 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:39 (hh:mm:ss) Elapsed Time Round Time: 00:13:35 (hh:mm:ss) Elapsed Time : 220 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12162 repeats masked totaling 2343338 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10019215 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 10019215 bp After Masking: 7433630 bp Masked: 25.81 % -- Input Database Coverage: 10019215 bp out of 2704651887 bp ( 0.37 % ) Sampling Time: 00:00:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:02:54 (hh:mm:ss) Elapsed Time, 5850 HSPs Collected Number of families returned by RECON: 829 Round Time: 00:03:49 (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 : 00:01:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 41573 repeats masked totaling 8002389 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30007038 bp Num Contigs Represented = 52 Non ambiguous bp: Initial: 30006138 bp After Masking: 21219915 bp Masked: 29.28 % -- Input Database Coverage: 40026253 bp out of 2704651887 bp ( 1.48 % ) Sampling Time: 00:02:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:12:46 (hh:mm:ss) Elapsed Time, 26933 HSPs Collected Number of families returned by RECON: 2489 Round Time: 00:15:30 (hh:mm:ss) Elapsed Time : 60 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 134682 repeats masked totaling 26376584 bp(s). - TE Masking time 00:00:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90039563 bp Num Contigs Represented = 101 Non ambiguous bp: Initial: 90036363 bp After Masking: 61699883 bp Masked: 31.47 % -- Input Database Coverage: 130065816 bp out of 2704651887 bp ( 4.81 % ) Sampling Time: 00:06:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2552670 Comparison Time: 01:14:06 (hh:mm:ss) Elapsed Time, 100541 HSPs Collected Number of families returned by RECON: 8549 Round Time: 01:22:13 (hh:mm:ss) Elapsed Time : 165 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 459082 repeats masked totaling 89805944 bp(s). - TE Masking time 00:02:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270014724 bp Num Contigs Represented = 241 Non ambiguous bp: Initial: 270010362 bp After Masking: 174660552 bp Masked: 35.31 % -- Input Database Coverage: 400080540 bp out of 2704651887 bp ( 14.79 % ) Sampling Time: 00:20:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23028291 Comparison Time: 08:32:30 (hh:mm:ss) Elapsed Time, 282930 HSPs Collected Number of families returned by RECON: 35117 Round Time: 09:07:55 (hh:mm:ss) Elapsed Time : 417 families discovered. RepeatScout/RECON discovery complete: 881 families found Classification Time: 00:25:32 (hh:mm:ss) Elapsed Time Program Time: 11:28:34 (hh:mm:ss) Elapsed Time