RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.NZNN7o/RM_4654.WedJan101935522024 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: 1704944152 Database = /dev/shm/rModeler.NZNN7o/GCA_016700455.2_mHomSap3.pat - Sequences = 994 - Bases = 2744463177 - N50 = 154437844 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 220838893-236613053 | [ 2 ] 205064733-220838892 | [ ] 189290573-205064732 | [ 1 ] 173516413-189290572 | [ 2 ] 157742253-173516412 | [ 1 ] 141968093-157742252 | [ 2 ] 126193933-141968092 | [ 3 ] 110419774-126193933 | [ 1 ] 94645614-110419773 | [ 1 ] 78871454-94645613 | [ 3 ] 63097294-78871453 | [ 2 ] 47323134-63097293 | [ 2 ] 31548974-47323133 | [ 2 ] 15774814-31548973 | [ 1 ] 655-15774814 |************************************************* [ 971 ] Storage Throughput = excellent ( 1125.72 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40149373 bp ( 40035151 non ambiguous ) - Num Contigs Represented = 52 - Sequence extraction : 00:03:04 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:11 (hh:mm:ss) Elapsed Time Round Time: 00:30:59 (hh:mm:ss) Elapsed Time : 263 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14405 repeats masked totaling 3180626 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001408 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 10000680 bp After Masking: 6589567 bp Masked: 34.11 % -- Input Database Coverage: 10001408 bp out of 2744463177 bp ( 0.36 % ) Sampling Time: 00:01:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:21 (hh:mm:ss) Elapsed Time, 6133 HSPs Collected Number of families returned by RECON: 880 Round Time: 00:07:33 (hh:mm:ss) Elapsed Time : 16 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 44166 repeats masked totaling 9808821 bp(s). - TE Masking time 00:00:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30147961 bp Num Contigs Represented = 46 Non ambiguous bp: Initial: 30034467 bp After Masking: 19413853 bp Masked: 35.36 % -- Input Database Coverage: 40149369 bp out of 2744463177 bp ( 1.46 % ) Sampling Time: 00:04:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 289180 Comparison Time: 00:28:19 (hh:mm:ss) Elapsed Time, 25261 HSPs Collected Number of families returned by RECON: 2378 Round Time: 00:34:19 (hh:mm:ss) Elapsed Time : 63 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:06:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 141080 repeats masked totaling 31447315 bp(s). - TE Masking time 00:01:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90201445 bp Num Contigs Represented = 68 Non ambiguous bp: Initial: 90001414 bp After Masking: 56514522 bp Masked: 37.21 % -- Input Database Coverage: 130350814 bp out of 2744463177 bp ( 4.75 % ) Sampling Time: 00:15:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2582128 Comparison Time: 03:11:35 (hh:mm:ss) Elapsed Time, 99235 HSPs Collected Number of families returned by RECON: 8342 Round Time: 03:31:17 (hh:mm:ss) Elapsed Time : 202 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:20:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:20:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 468421 repeats masked totaling 103226143 bp(s). - TE Masking time 00:07:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271075862 bp Num Contigs Represented = 182 Non ambiguous bp: Initial: 270022442 bp After Masking: 159789220 bp Masked: 40.82 % -- Input Database Coverage: 401426676 bp out of 2744463177 bp ( 14.63 % ) Sampling Time: 00:48:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23403061 Comparison Time: 24:56:07 (hh:mm:ss) Elapsed Time, 273356 HSPs Collected Number of families returned by RECON: 32873 Round Time: 26:14:54 (hh:mm:ss) Elapsed Time : 390 families discovered. RepeatScout/RECON discovery complete: 934 families found Classification Time: 00:40:54 (hh:mm:ss) Elapsed Time Program Time: 31:39:56 (hh:mm:ss) Elapsed Time