RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.3swcKS/RM_3936.SunMay71025172023 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: 1683480315 Database = /dev/shm/rModeler.3swcKS/GCA_016128335.2_ZJU2.0 - Sequences = 767 - Bases = 1247435561 - N50 = 129385059 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 201841340-216258376 | [ 1 ] 187424305-201841340 | [ ] 173007270-187424305 | [ ] 158590235-173007270 | [ 1 ] 144173200-158590235 | [ ] 129756164-144173199 | [ ] 115339129-129756164 | [ 1 ] 100922094-115339129 | [ ] 86505059-100922094 | [ ] 72088024-86505059 | [ 3 ] 57670988-72088023 | [ ] 43253953-57670988 | [ 1 ] 28836918-43253953 | [ 3 ] 14419883-28836918 | [ 9 ] 2848-14419883 |************************************************** [ 748 ] Storage Throughput = excellent ( 1164.32 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40006150 bp ( 40004282 non ambiguous ) - Num Contigs Represented = 61 - Sequence extraction : 00:02:00 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:22:38 (hh:mm:ss) Elapsed Time Round Time: 00:33:46 (hh:mm:ss) Elapsed Time : 44 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 807 repeats masked totaling 299559 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10019550 bp Num Contigs Represented = 42 Non ambiguous bp: Initial: 10019120 bp After Masking: 9472353 bp Masked: 5.46 % -- Input Database Coverage: 10019550 bp out of 1247435561 bp ( 0.80 % ) Sampling Time: 00:01:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:11:04 (hh:mm:ss) Elapsed Time, 1428 HSPs Collected Number of families returned by RECON: 338 Round Time: 00:12:46 (hh:mm:ss) Elapsed Time : 4 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2590 repeats masked totaling 834502 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30026523 bp Num Contigs Represented = 48 Non ambiguous bp: Initial: 30025085 bp After Masking: 28887891 bp Masked: 3.79 % -- Input Database Coverage: 40046073 bp out of 1247435561 bp ( 3.21 % ) Sampling Time: 00:02:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:54:48 (hh:mm:ss) Elapsed Time, 8045 HSPs Collected Number of families returned by RECON: 1854 Round Time: 00:58:26 (hh:mm:ss) Elapsed Time : 19 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10268 repeats masked totaling 2920670 bp(s). - TE Masking time 00:00:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90040871 bp Num Contigs Represented = 112 Non ambiguous bp: Initial: 90034121 bp After Masking: 85691277 bp Masked: 4.82 % -- Input Database Coverage: 130086944 bp out of 1247435561 bp ( 10.43 % ) Sampling Time: 00:09:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2579856 Comparison Time: 05:39:00 (hh:mm:ss) Elapsed Time, 52950 HSPs Collected Number of families returned by RECON: 10329 Round Time: 05:52:00 (hh:mm:ss) Elapsed Time : 93 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:13:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:17:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 50038 repeats masked totaling 13785356 bp(s). - TE Masking time 00:02:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270054342 bp Num Contigs Represented = 278 Non ambiguous bp: Initial: 270039785 bp After Masking: 250038412 bp Masked: 7.41 % -- Input Database Coverage: 400141286 bp out of 1247435561 bp ( 32.08 % ) Sampling Time: 00:34:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23368866 Comparison Time: 41:28:28 (hh:mm:ss) Elapsed Time, 201046 HSPs Collected Number of families returned by RECON: 60853 Round Time: 43:08:01 (hh:mm:ss) Elapsed Time : 256 families discovered. RepeatScout/RECON discovery complete: 416 families found Classification Time: 00:32:05 (hh:mm:ss) Elapsed Time Program Time: 51:17:04 (hh:mm:ss) Elapsed Time