RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.QIQtrw/RM_8302.TueJan160700502024 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: 1705417248 Database = /dev/shm/rModeler.QIQtrw/GCA_963514005.1_sRajBra1.1 - Sequences = 1647 - Bases = 2700467673 - N50 = 69067428 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 174943426-187439314 | [ 1 ] 162447538-174943425 | [ ] 149951651-162447538 | [ 1 ] 137455763-149951650 | [ ] 124959876-137455763 | [ 1 ] 112463988-124959875 | [ 3 ] 99968100-112463987 | [ ] 87472213-99968100 | [ 2 ] 74976325-87472212 | [ 2 ] 62480438-74976325 | [ 4 ] 49984550-62480437 | [ 4 ] 37488662-49984549 | [ 11 ] 24992775-37488662 | [ 9 ] 12496887-24992774 | [ 5 ] 1000-12496887 |************************************************** [ 1604 ] Storage Throughput = excellent ( 1114.63 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40014465 bp ( 40006665 non ambiguous ) - Num Contigs Represented = 90 - Sequence extraction : 00:01:40 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:17 (hh:mm:ss) Elapsed Time Round Time: 00:31:44 (hh:mm:ss) Elapsed Time : 648 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 26541 repeats masked totaling 5768477 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10039244 bp Num Contigs Represented = 54 Non ambiguous bp: Initial: 10036644 bp After Masking: 3680368 bp Masked: 63.33 % -- Input Database Coverage: 10039244 bp out of 2700467673 bp ( 0.37 % ) Sampling Time: 00:03:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:05:14 (hh:mm:ss) Elapsed Time, 3746 HSPs Collected Number of families returned by RECON: 601 Round Time: 00:08:36 (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 : 00:01:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 79665 repeats masked totaling 17213783 bp(s). - TE Masking time 00:01:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30015141 bp Num Contigs Represented = 78 Non ambiguous bp: Initial: 30009941 bp After Masking: 10639737 bp Masked: 64.55 % -- Input Database Coverage: 40054385 bp out of 2700467673 bp ( 1.48 % ) Sampling Time: 00:10:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 00:32:16 (hh:mm:ss) Elapsed Time, 18304 HSPs Collected Number of families returned by RECON: 1772 Round Time: 00:44:14 (hh:mm:ss) Elapsed Time : 36 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:25:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 241989 repeats masked totaling 52532008 bp(s). - TE Masking time 00:03:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90018592 bp Num Contigs Represented = 154 Non ambiguous bp: Initial: 90003392 bp After Masking: 30760299 bp Masked: 65.82 % -- Input Database Coverage: 130072977 bp out of 2700467673 bp ( 4.82 % ) Sampling Time: 00:33:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2609470 Comparison Time: 03:17:32 (hh:mm:ss) Elapsed Time, 203670 HSPs Collected Number of families returned by RECON: 4885 Round Time: 04:06:01 (hh:mm:ss) Elapsed Time : 269 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:16:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 784903 repeats masked totaling 166992199 bp(s). - TE Masking time 00:13:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270066641 bp Num Contigs Represented = 391 Non ambiguous bp: Initial: 270027083 bp After Masking: 83581984 bp Masked: 69.05 % -- Input Database Coverage: 400139618 bp out of 2700467673 bp ( 14.82 % ) Sampling Time: 01:41:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23389380 Comparison Time: 14:36:55 (hh:mm:ss) Elapsed Time, 482187 HSPs Collected Number of families returned by RECON: 14152 Round Time: 16:32:40 (hh:mm:ss) Elapsed Time : 530 families discovered. RepeatScout/RECON discovery complete: 1491 families found Classification Time: 01:03:17 (hh:mm:ss) Elapsed Time Program Time: 23:06:32 (hh:mm:ss) Elapsed Time