RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.qZRWsp/RM_1259821.SunFeb92246382025 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: 1739169998 Database = /data/tmp/rModeler.qZRWsp/GCA_045843765.1_mUroPar1.hap2 - Sequences = 2307 - Bases = 2750197790 - N50 = 195712597 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 265112472-284047837 | [ 1 ] 246177107-265112471 | [ ] 227241742-246177106 | [ ] 208306377-227241741 | [ 1 ] 189371012-208306376 | [ 4 ] 170435647-189371011 | [ ] 151500282-170435646 | [ 1 ] 132564917-151500281 | [ 4 ] 113629552-132564916 | [ ] 94694187-113629551 | [ 1 ] 75758822-94694186 | [ ] 56823457-75758821 | [ 3 ] 37888092-56823456 | [ ] 18952727-37888091 | [ ] 17363-18952727 |************************************************* [ 2292 ] Storage Throughput = good ( 758.85 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40028895 bp ( 40027995 non ambiguous ) - Num Contigs Represented = 136 - Sequence extraction : 00:01:49 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:10:13 (hh:mm:ss) Elapsed Time Round Time: 00:17:52 (hh:mm:ss) Elapsed Time : 225 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10099 repeats masked totaling 1996887 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10020240 bp Num Contigs Represented = 49 Non ambiguous bp: Initial: 10020240 bp After Masking: 7723494 bp Masked: 22.92 % -- Input Database Coverage: 10020240 bp out of 2750197790 bp ( 0.36 % ) Sampling Time: 00:00:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:04:14 (hh:mm:ss) Elapsed Time, 8975 HSPs Collected Number of families returned by RECON: 827 Round Time: 00:20:43 (hh:mm:ss) Elapsed Time : 23 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 34486 repeats masked totaling 7484124 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30008575 bp Num Contigs Represented = 112 Non ambiguous bp: Initial: 30007675 bp After Masking: 21039777 bp Masked: 29.89 % -- Input Database Coverage: 40028815 bp out of 2750197790 bp ( 1.46 % ) Sampling Time: 00:03:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 291466 Comparison Time: 00:22:18 (hh:mm:ss) Elapsed Time, 25758 HSPs Collected Number of families returned by RECON: 2285 Round Time: 00:26:44 (hh:mm:ss) Elapsed Time : 54 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 113025 repeats masked totaling 23519435 bp(s). - TE Masking time 00:00:58 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90009304 bp Num Contigs Represented = 242 Non ambiguous bp: Initial: 90005604 bp After Masking: 61757851 bp Masked: 31.38 % -- Input Database Coverage: 130038119 bp out of 2750197790 bp ( 4.73 % ) Sampling Time: 00:12:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2636956 Comparison Time: 02:32:23 (hh:mm:ss) Elapsed Time, 223654 HSPs Collected Number of families returned by RECON: 8586 Round Time: 02:49:33 (hh:mm:ss) Elapsed Time : 186 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:13:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:21:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 381052 repeats masked totaling 78578687 bp(s). - TE Masking time 00:04:52 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270022644 bp Num Contigs Represented = 598 Non ambiguous bp: Initial: 270013044 bp After Masking: 176197905 bp Masked: 34.74 % -- Input Database Coverage: 400060763 bp out of 2750197790 bp ( 14.55 % ) Sampling Time: 00:40:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23533230 Comparison Time: 15:00:14 (hh:mm:ss) Elapsed Time, 1018089 HSPs Collected Number of families returned by RECON: 34712 Round Time: 15:52:52 (hh:mm:ss) Elapsed Time : 397 families discovered. RepeatScout/RECON discovery complete: 885 families found Classification Time: 00:28:43 (hh:mm:ss) Elapsed Time Program Time: 20:16:27 (hh:mm:ss) Elapsed Time