RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.CBil7E/RM_3362880.SunDec82352102024 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: 1733730730 Database = /scratch/tmp/rModeler.CBil7E/GCA_044704965.1_sPriJap1.hap2 - Sequences = 5626 - Bases = 6365258383 - N50 = 224395528 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 502380892-538264952 | [ 1 ] 466496832-502380891 | [ ] 430612773-466496832 | [ ] 394728713-430612772 | [ ] 358844654-394728713 | [ 1 ] 322960594-358844653 | [ ] 287076534-322960593 | [ 3 ] 251192475-287076534 | [ 1 ] 215308415-251192474 | [ 5 ] 179424356-215308415 | [ 4 ] 143540296-179424355 | [ ] 107656236-143540295 | [ 3 ] 71772177-107656236 | [ 3 ] 35888117-71772176 | [ 3 ] 4058-35888117 |************************************************** [ 5602 ] Storage Throughput = excellent ( 1460.18 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40034016 bp ( 40026216 non ambiguous ) - Num Contigs Represented = 227 - Sequence extraction : 00:02:11 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:10:12 (hh:mm:ss) Elapsed Time Round Time: 00:18:46 (hh:mm:ss) Elapsed Time : 588 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14833 repeats masked totaling 5636924 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10012896 bp Num Contigs Represented = 78 Non ambiguous bp: Initial: 10010296 bp After Masking: 2219422 bp Masked: 77.83 % -- Input Database Coverage: 10012896 bp out of 6365258383 bp ( 0.16 % ) Sampling Time: 00:07:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33153 Comparison Time: 00:02:34 (hh:mm:ss) Elapsed Time, 2522 HSPs Collected Number of families returned by RECON: 547 Round Time: 00:09:46 (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 : 00:01:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 45124 repeats masked totaling 17510743 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30021118 bp Num Contigs Represented = 186 Non ambiguous bp: Initial: 30015918 bp After Masking: 6618736 bp Masked: 77.95 % -- Input Database Coverage: 40034014 bp out of 6365258383 bp ( 0.63 % ) Sampling Time: 00:16:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 291466 Comparison Time: 00:08:56 (hh:mm:ss) Elapsed Time, 21699 HSPs Collected Number of families returned by RECON: 2061 Round Time: 00:25:45 (hh:mm:ss) Elapsed Time : 55 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:50:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 139675 repeats masked totaling 52582349 bp(s). - TE Masking time 00:00:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90051723 bp Num Contigs Represented = 416 Non ambiguous bp: Initial: 90035123 bp After Masking: 19363613 bp Masked: 78.49 % -- Input Database Coverage: 130085737 bp out of 6365258383 bp ( 2.04 % ) Sampling Time: 00:55:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2625486 Comparison Time: 00:37:47 (hh:mm:ss) Elapsed Time, 140718 HSPs Collected Number of families returned by RECON: 5190 Round Time: 01:35:26 (hh:mm:ss) Elapsed Time : 273 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:14:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 02:40:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 446348 repeats masked totaling 163831142 bp(s). - TE Masking time 00:02:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270062172 bp Num Contigs Represented = 977 Non ambiguous bp: Initial: 270008041 bp After Masking: 48786961 bp Masked: 81.93 % -- Input Database Coverage: 400147909 bp out of 6365258383 bp ( 6.29 % ) Sampling Time: 02:57:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23670640 Comparison Time: 02:57:25 (hh:mm:ss) Elapsed Time, 378815 HSPs Collected Number of families returned by RECON: 13172 Round Time: 06:02:45 (hh:mm:ss) Elapsed Time : 573 families discovered. RepeatScout/RECON discovery complete: 1494 families found Classification Time: 00:27:17 (hh:mm:ss) Elapsed Time Program Time: 08:59:45 (hh:mm:ss) Elapsed Time