RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.nD4xaL/RM_12830.SatDec20344462023 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: 1701517485 Database = /dev/shm/rModeler.nD4xaL/GCA_030035685.1_sMobBir1.hap2 - Sequences = 1558 - Bases = 3634101053 - N50 = 169512688 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 237227765-254171768 | [ 2 ] 220283763-237227765 | [ 1 ] 203339761-220283763 | [ ] 186395758-203339760 | [ 4 ] 169451756-186395758 | [ 1 ] 152507754-169451756 | [ ] 135563751-152507753 | [ 2 ] 118619749-135563751 | [ ] 101675747-118619749 | [ 2 ] 84731744-101675746 | [ 1 ] 67787742-84731744 | [ 7 ] 50843740-67787742 | [ 7 ] 33899737-50843739 | [ 4 ] 16955735-33899737 | [ 2 ] 11733-16955735 |************************************************** [ 1525 ] Storage Throughput = excellent ( 1138.39 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40699520 bp ( 40018196 non ambiguous ) - Num Contigs Represented = 78 - Sequence extraction : 00:03:02 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:48 (hh:mm:ss) Elapsed Time Round Time: 00:29:30 (hh:mm:ss) Elapsed Time : 632 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 20656 repeats masked totaling 5640110 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10214744 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 10027839 bp After Masking: 3663954 bp Masked: 63.46 % -- Input Database Coverage: 10214744 bp out of 3634101053 bp ( 0.28 % ) Sampling Time: 00:02:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32640 Comparison Time: 00:04:25 (hh:mm:ss) Elapsed Time, 3067 HSPs Collected Number of families returned by RECON: 563 Round Time: 00:07:22 (hh:mm:ss) Elapsed Time : 5 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 62856 repeats masked totaling 17172081 bp(s). - TE Masking time 00:00:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30524619 bp Num Contigs Represented = 69 Non ambiguous bp: Initial: 30030200 bp After Masking: 10732641 bp Masked: 64.26 % -- Input Database Coverage: 40739363 bp out of 3634101053 bp ( 1.12 % ) Sampling Time: 00:08:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 295296 Comparison Time: 00:19:23 (hh:mm:ss) Elapsed Time, 25184 HSPs Collected Number of families returned by RECON: 1947 Round Time: 00:29:01 (hh:mm:ss) Elapsed Time : 73 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:07:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:18:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 196876 repeats masked totaling 53252731 bp(s). - TE Masking time 00:02:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91422898 bp Num Contigs Represented = 140 Non ambiguous bp: Initial: 90007494 bp After Masking: 30424978 bp Masked: 66.20 % -- Input Database Coverage: 132162261 bp out of 3634101053 bp ( 3.64 % ) Sampling Time: 00:28:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2664586 Comparison Time: 01:54:00 (hh:mm:ss) Elapsed Time, 112178 HSPs Collected Number of families returned by RECON: 4503 Round Time: 02:29:40 (hh:mm:ss) Elapsed Time : 219 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:20:55 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:52:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 619684 repeats masked totaling 166848092 bp(s). - TE Masking time 00:09:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 274050844 bp Num Contigs Represented = 313 Non ambiguous bp: Initial: 270004611 bp After Masking: 83939383 bp Masked: 68.91 % -- Input Database Coverage: 406213105 bp out of 3634101053 bp ( 11.18 % ) Sampling Time: 01:24:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23829156 Comparison Time: 12:41:15 (hh:mm:ss) Elapsed Time, 321163 HSPs Collected Number of families returned by RECON: 14106 Round Time: 14:23:18 (hh:mm:ss) Elapsed Time : 513 families discovered. RepeatScout/RECON discovery complete: 1442 families found Classification Time: 01:06:57 (hh:mm:ss) Elapsed Time Program Time: 19:05:48 (hh:mm:ss) Elapsed Time