RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.GJok8v/RM_2594161.TueApr222247322025 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: 1745387252 Database = /dev/shm/rModeler.GJok8v/GCA_048126745.1_DamDam1_v1.mat - Sequences = 1304 - Bases = 2723325442 - N50 = 78532571 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 136987182-146771910 | [ 1 ] 127202455-136987182 | [ 1 ] 117417728-127202455 | [ ] 107633000-117417727 | [ 2 ] 97848273-107633000 | [ 3 ] 88063546-97848273 | [ 2 ] 78278818-88063545 | [ 4 ] 68494091-78278818 | [ 2 ] 58709364-68494091 | [ 9 ] 48924636-58709363 | [ 5 ] 39139909-48924636 | [ 4 ] 29355182-39139909 | [ 1 ] 19570454-29355181 | [ ] 9785727-19570454 | [ ] 1000-9785727 |************************************************** [ 1270 ] Storage Throughput = excellent ( 1901.91 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40018880 bp ( 40018580 non ambiguous ) - Num Contigs Represented = 95 - Sequence extraction : 00:00:41 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:43 (hh:mm:ss) Elapsed Time Round Time: 00:12:48 (hh:mm:ss) Elapsed Time : 239 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13679 repeats masked totaling 3030427 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10004046 bp Num Contigs Represented = 45 Non ambiguous bp: Initial: 10003946 bp After Masking: 6696225 bp Masked: 33.06 % -- Input Database Coverage: 10004046 bp out of 2723325442 bp ( 0.37 % ) Sampling Time: 00:00:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:02:43 (hh:mm:ss) Elapsed Time, 7744 HSPs Collected Number of families returned by RECON: 694 Round Time: 00:03:30 (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 : 00:00:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 42524 repeats masked totaling 9404314 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30014754 bp Num Contigs Represented = 84 Non ambiguous bp: Initial: 30014554 bp After Masking: 19657380 bp Masked: 34.51 % -- Input Database Coverage: 40018800 bp out of 2723325442 bp ( 1.47 % ) Sampling Time: 00:02:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286903 Comparison Time: 00:12:16 (hh:mm:ss) Elapsed Time, 53783 HSPs Collected Number of families returned by RECON: 2121 Round Time: 00:16:02 (hh:mm:ss) Elapsed Time : 67 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 132750 repeats masked totaling 30245586 bp(s). - TE Masking time 00:00:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90028419 bp Num Contigs Represented = 188 Non ambiguous bp: Initial: 90028019 bp After Masking: 55899181 bp Masked: 37.91 % -- Input Database Coverage: 130047219 bp out of 2723325442 bp ( 4.78 % ) Sampling Time: 00:06:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2579856 Comparison Time: 01:17:48 (hh:mm:ss) Elapsed Time, 815438 HSPs Collected Number of families returned by RECON: 7629 Round Time: 01:26:05 (hh:mm:ss) Elapsed Time : 153 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 432917 repeats masked totaling 96424368 bp(s). - TE Masking time 00:02:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270010975 bp Num Contigs Represented = 429 Non ambiguous bp: Initial: 270008875 bp After Masking: 161906885 bp Masked: 40.04 % -- Input Database Coverage: 400058194 bp out of 2723325442 bp ( 14.69 % ) Sampling Time: 00:20:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23239153 Comparison Time: 08:55:45 (hh:mm:ss) Elapsed Time, 6472149 HSPs Collected Number of families returned by RECON: 32088 Round Time: 09:25:55 (hh:mm:ss) Elapsed Time : 356 families discovered. RepeatScout/RECON discovery complete: 834 families found Classification Time: 00:17:39 (hh:mm:ss) Elapsed Time Program Time: 11:41:59 (hh:mm:ss) Elapsed Time