RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.i4Cjer/RM_2673117.SunFeb92111032025 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: 1739164261 Database = /data/tmp/rModeler.i4Cjer/GCA_965113325.1_fLeuLeu2.hap2.1 - Sequences = 530 - Bases = 1179019172 - N50 = 44970170 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 78195265-83780570 | [ 1 ] 72609960-78195264 | [ ] 67024656-72609960 | [ 1 ] 61439351-67024655 | [ 1 ] 55854046-61439350 | [ ] 50268742-55854046 | [ 2 ] 44683437-50268741 | [ 5 ] 39098132-44683436 | [ 8 ] 33512828-39098132 | [ 5 ] 27927523-33512827 | [ 2 ] 22342218-27927522 | [ ] 16756914-22342218 | [ ] 11171609-16756913 | [ ] 5586304-11171608 | [ ] 1000-5586304 |************************************************** [ 505 ] Storage Throughput = excellent ( 1520.56 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40038499 bp ( 40029699 non ambiguous ) - Num Contigs Represented = 61 - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:56 (hh:mm:ss) Elapsed Time Round Time: 00:18:00 (hh:mm:ss) Elapsed Time : 1256 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16109 repeats masked totaling 3649206 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10010810 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 10008410 bp After Masking: 5749775 bp Masked: 42.55 % -- Input Database Coverage: 10010810 bp out of 1179019172 bp ( 0.85 % ) Sampling Time: 00:01:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:04:27 (hh:mm:ss) Elapsed Time, 7584 HSPs Collected Number of families returned by RECON: 1806 Round Time: 00:05:58 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 48833 repeats masked totaling 10913481 bp(s). - TE Masking time 00:00:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30027609 bp Num Contigs Represented = 53 Non ambiguous bp: Initial: 30021209 bp After Masking: 17529404 bp Masked: 41.61 % -- Input Database Coverage: 40038419 bp out of 1179019172 bp ( 3.40 % ) Sampling Time: 00:03:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:18:15 (hh:mm:ss) Elapsed Time, 87782 HSPs Collected Number of families returned by RECON: 5633 Round Time: 00:23:25 (hh:mm:ss) Elapsed Time : 140 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 157490 repeats masked totaling 34154936 bp(s). - TE Masking time 00:02:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90049248 bp Num Contigs Represented = 111 Non ambiguous bp: Initial: 90034248 bp After Masking: 51029590 bp Masked: 43.32 % -- Input Database Coverage: 130087667 bp out of 1179019172 bp ( 11.03 % ) Sampling Time: 00:11:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2582128 Comparison Time: 01:49:24 (hh:mm:ss) Elapsed Time, 879719 HSPs Collected Number of families returned by RECON: 16200 Round Time: 02:10:13 (hh:mm:ss) Elapsed Time : 746 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:25:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 561236 repeats masked totaling 124163369 bp(s). - TE Masking time 00:14:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270059300 bp Num Contigs Represented = 244 Non ambiguous bp: Initial: 270008196 bp After Masking: 131138278 bp Masked: 51.43 % -- Input Database Coverage: 400146967 bp out of 1179019172 bp ( 33.94 % ) Sampling Time: 00:43:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23259610 Comparison Time: 11:49:41 (hh:mm:ss) Elapsed Time, 3728031 HSPs Collected Number of families returned by RECON: 41895 Round Time: 13:17:19 (hh:mm:ss) Elapsed Time : 1696 families discovered. RepeatScout/RECON discovery complete: 3849 families found Classification Time: 01:50:38 (hh:mm:ss) Elapsed Time Program Time: 18:05:33 (hh:mm:ss) Elapsed Time